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Using LaTeX to Write a PhD Thesis

1. documentclass oneside scrbook title A Sample Thesis author A N Other date July 2013 T Input titlehead A Thesis submitted for the degree of Doctor of Philosophy publishers School of Something University of Somewhere begin document maketitle frontmatter tableofcontents listoffigures Llistoftables Chapter 2 Getting Started 15 chapter Acknowledgements I would like to thank my supervisor Professor Someone This research was funded by the Imaginary Research Council chapter Abstract A brief summary of the project goes here A glossary and list of acronyms may go here or may go in the back matter mainmatter chapter Introduction label ch intro chapter Technical Introduction label ch techintro chapter Method label ch method chapter Results label ch results chapter Conclusions lLabel ch conc backmatter A glossary and list of acronyms may go here or may go in the front matter after the abstract The bibliography will go here end document 4 Input If you do this it will help ensure that your document has the correct structure before you begin with the actual contents of the document Note that the chapter titles will naturally vary depending on your subject or in stitution and you may need a different paper size if you are not in Europe I have based the above on my own PhD thesis which I wrote in the early to mid
2. Used in the argument of index to separate the sort key from the term being indexed 6 1 106 Symbols NE KSA CHM DOVDOAZZORAHH THOT SAeD Summary of Commands and Environments 107 Defined in PTEX Kernel Open delimiter of an optional argument See Volume 1 15 2 8 2 51 0 Defined in ETEX Kernel Escape character indicating a command See Volume 1 15 2 6 6 1 c Defined in TEX Kernel Umlaut over c Example 0 produces 6 See Volume 1 15 4 3 5 1 Vie Defined in PTEX Kernel Acute accent over c Example 0 produces See Volume 1 15 4 3 6 1 t Defined in tabbing environment Shifts the left border by one tab stop to the right 4 6 Defined in TEX Kernel 1 Outside tabbing environment inserts a discretionary hyphen 4 6 2 Inside tabbing environment shifts the left border by one tab stop 4 6 Defined in algorithm2e package When used in the body of one of the environments defined by algorithm2e such as algorithm marks the end of the line Outside those environments this is a math spacing command 4 8 lt Defined in tabbing environment Jumps to the next tab stop 4 6 Defined in ETEX Kernel 1 Outside tabbing environment puts a macron accent over the following character 4 6 2 Inside tabbing environment sets a tab stop 4 6 gt Defined in
3. If you prefer to use texindy instead of makeindex you will need to re place the above lines with change the language as appropriate add_cus_dep idx ind 0 texindy sub texindy system texindy L english _ 0 idx Now select LaTeXmk from the drop down menu next to the green Typeset button in TeXworks Figure 1 6 and you re ready to build your documents 1 1 2 Arara As mentioned in Section 1 1 arara is a Java application that automates the process of building a PTEX document In order to use arara you must have the Java Runtime Environment installed The latest TeX Live distribution includes arara so you can install it via the TeX Live package manager Alternative you can install arara manually as follows fetch the installer arara 3 0 installer jar or arara 3 0 installer exe from https github com cereda arara tree master releases On Windows run arara 3 0 installer exe On other operating systems run arara 3 0 installer jar in privileged mode For example on a Unix based system sudo java jar arara 3 0 installer jar Chapter 1 Introduction 8 thesisl tex TeXworks 0x File Edit Search Format Typeset Scripts Window Help LaTexmk H Oe gt db l a amp documentclass oneside scrbook title A Sample PhD Thesis author A N Other date July 2013 titlehead A Thesis submitted for the degree of Doctor of Philosophy publishers School of S
4. A1T gather this is not the case in some other countries where the viva is more informal and the decision to pass or fail you has already been made before your viva Appendix A General Advice 101 10 11 dated by the time they reach the book shelves Journal and conference papers are likely to be more up to date Always explain acronyms technical terms and symbols It is a good idea to include a glossary of terms list of notation or list of acronyms to avoid confusion see Chapter 6 Generating Indexes and Glossaries If you have equations make sure you explain the variables used and how you go from one equation to the next Depending on your field you might also consider clarifying the mathematics by providing graph ical representations of the equations If you include any graphs bar charts pie charts or any other form of data plot make sure it is clearly labelled and no distortion is introduced such as using three dimensional bar charts or pie charts If you have used a computer application to generate numerical results make sure you have some understanding of the underlying process and what the results mean This doesn t necessarily mean that you need to understand complex computer code or complex algorithms but what you shouldn t do is say something along the lines of well I clicked on this button and it said m 0 678 What is the purpose of the button What does m repre
5. Chapter 5 Generating a Bibliography 56 JabRef home eznObedu Documents nontiction latex thesis examples thesis rer bip File Edit Search View BibTeX Tools Plugins Options Help Da St Sohne se 4 BEX 4 Of B rl thesis ref bib Entry Journal Owner Timesta Article Cawley and Talbot Efficient approximate leave one out 2008 Machin ezn06edu 2012 1 Cawley Inpro Cawley et al Book Turabian A manual for writers of term papers 1996 ezn06edu 2012 1 turabia x I Required fields J Optional fields n General n Abstract il Review BibTex source Bernhard Sch lkopf and John Platt and Thomas Hofmann 209 216 Cambridge MA USA Organization Publisher MIT Press Note Status Added new inp Figure 5 10 JabRef Adding Editor List Chapter 5 Generating a Bibliography 57 It s also possible to import entries from other formats such as Copac or ISI using File Import into new database or file lmport into current database Alternatively you can copy and paste a plain text reference using BiblexX New entry from plain text This again opens the dialog box where you need to click on the entry type but then it opens the Plain text import window EXAMPLE Suppose I want to add an entry for an article whose DOI is 10 1007 s10994 008 5055 9 First I direct my browser to http dx doi org 10 1007
6. 6 1 Symbols NK KSA CHW DRODVOAZZORAHH THOM SAeD Summary of Commands and Environments 109 Acrlong options label insert Defined in glossaries package Displays the long form of the given acronym the first letter converted to uppercase 6 1 acrlong options label insert Defined in glossaries package Displays the long form of the given acronym 6 1 acronymfont text Defined in glossaries and datagidx packages Font used to display acronyms 6 2 Acrpl format label Defined in datagidx package As acrp1 but the first letter is converted to uppercase 6 2 acrpl format label Defined in datagidx package Displays the plural of an acronym On first use the full form is displayed On subsequent use only the short form is displayed 6 2 Acrshort options label insert Defined in glossaries package Displays the short form of the given acronym the first letter converted to uppercase 6 1 acrshort options label insert Defined in glossaries package Displays the short form of the given acronym 6 1 acs options label insert Defined in glossaries package A synonym for acrshort This command is only available if the package option shortcuts is used 6 1 addbibresource options resource Defined in biblatex package Adds a resource such as a bib file 5 3
7. Year Volume 71 E Pages 243 264 7 Bibtexkey Cawley2008 Status Preferences recorded Figure 5 8 JabRef Adding an Article BibTeX uses the European assumption that names are composed of fore FAQ B sT X names an optional von part which starts with a lower case letter a sur sorting and name and an optional jr part In order to enable BibTeX to correctly name prefixes identify these components names in the author or editor fields must be entered in one of the formats listed in Table 5 1 Table 5 1 Name Formats for Bibliographic Data forenames von surname von surname forenames von surname jr forenames Chapter 5 Generating a Bibliography 54 EXAMPLES Entry Abbreviated as A T von Neumann J C Smith Jones M J van de Klee F J Smith Jr M De La Cruz Alex Thomas von Neumann John Chris Smith Jones van de Klee Mary Jane Smith Jr Fred John Maria MakeUppercase d e La Cruz Compare the last example with Maria De La Cruz which would be ab breviated to M D L Cruz which is incorrect Let s analyse this last example in more detail BibTeX always expects the von part to start with a lower case letter but De and La both start with an upper case letter so BibTeX will assume that these form part of the forenames However BibTeX will ig nore any ETEX commands such as MakeUppercase
8. addtokomafont element name commands Defined in scrartcl scrreprt and scrbook classes Sets the font characteristics for the given KOMA Script element See Volume 1 15 5 3 4 1 AE Defined in ETEX Kernel ligature 6 1 afterpage code Defined in afterpage package Indicates code that should be implemented at the next page break A 1 begin algorithm placement Defined in algorithm2e package A floating environment for typesetting algorithms 4 8 begin falgorithm2e placement Defined in algorithm2e package Replacement for algorithm when used with the algo2e package option 4 8 ang angle Defined in siunitx package Typesets angle where angle is a single number or three semi colon separated values 4 9 Symbols NE KSA CHM DOVDOAZZORAHH THOT SAeD Summary of Commands and Environments 110 author name Defined in Most classes that have the concept of a title page Specifies the document author or authors This command doesn t display any text so may be used in the preamble but if it s not in the preamble it must be placed before maketitle 2 0 B backmatter Defined in Most book style classes such as scrbook Suppresses chapter and section numbering but still adds unstarred sectional units to the table of contents See also frontmatter and mainmatter 2 0 begin env name env option env ar
9. raggedsection This can be redefined as required For example suppose you are required to have centred headings then you can do renewcommand raggedsection centering 4 2 Changing the Page Style Volume 1 15 5 7 described the command pagestyle style which can be used to set the page style The scrbook class defaults to the headings page style but if this isn t appropriate you can use the scrpage2 21 Input Definition Input Definition Chapter 4 Formatting 22 package which comes with the KOMA Script bundle This package pro vides its own versions of the plain and headings page styles called scrplain and scrheadings For simplicity I m assuming that your thesis is a one sided document If this isn t the case and your odd and even page styles need to be different youll need to consult the KOMA Script documentation 8 With the scrheadings page style the page header and footer are both divided into three areas Figure 4 1 the inner left head foot the centre head foot and the outer right head foot Figure 4 1 Page Header and Footer Elements These elements can be set using ihead scrplain inner head scrheadings inner head chead scrplain centre head scrheadings centre head ohead scrplain outer head scrheadings outer head arene ifoot scrplain inner foot scrheadings inner foot cfoot scrplain centre foot scrheadings centre foot ofoot scrplai
10. arara pdflatex synctex on arara bibtex arara pdflatex synctex on arara pdflatex synctex on If you are using latexmk see Section 1 1 1 make sure you are using the bibtex argument Figure 1 5 If you are not using either latexmk or arara you will need to run PDFETEX then run BibT EX then run PDFETEX twice more see Section 1 1 If your citations appear as two question marks in your PDF then the citation key you used hasn t been recognised This could be that you ve forgotten the BibTeX and subsequent two PDFFTpx calls or it could be that the key hasn t been defined or you have misspelt it Recall from Volume 1 15 5 6 that the bibliography doesn t usually get added to the table of contents for most class files but the KOMA Script classes provide the options bibliography totocnumbered and bibliography totoc that add a numbered or unnumbered bibliography to the table of contents You can add backlinks from your bibliography back to the section or page where the entries were cited using the backref option of the hyperref package The hyperref package should usually be loaded last For example to have backreferences to the pages on which the citation occurs usepackage backref hyperref The hyperref package is covered in more detail in Volume 4 14 5 2 1 Author Year Citations The default behaviour of citations with bibliography styles such as plain is to produce a numeric
11. lt arara gt texindy german language codepage G modules input f options getBasename file idx arguments identifier german flag lt arara gt isTrue parameters german g identifier language flag lt arara gt L parameters language identifier codepage flag lt arara gt C parameters codepage identifier module flag lt arara gt M parameters module identifier input flag lt arara gt I parameters input identifier options flag lt arara gt parameters options The symbol gt above indicates a line wrap Don t insert a line break at that point This file should be saved in the rules subdirectory of the arara in stallation directory For example on Unix like systems usr local arara rules texindy yaml So if you d rather use texindy instead of makeindex you can replace the arara makeindex directive with arara texindy language english codepage latinl Change the language and encoding as appropriate CHAPTER 2 GETTING STARTED There are many different thesis designs varying according to university or discipline 5 If you have been told to use a particular class file use that one If not there are a selection of thesis class files available on CTAN 2 and listed in the OnLine TEX Catalogue s Topic Index 3 Since there are so many to choose from I m just going to follow on from Volume 1 of this series and use one of the KOMA Script
12. options This should go in the document where you want the bibliography to be displayed Like the natbib commands described in Section 5 2 1 the biblatex com mands generally have two optional arguments indicating the prenote and Input Input Input Definition Input 4 Input T Input 4 Input Definition Chapter 5 Generating a Bibliography 71 postnote and a mandatory argument specifying the key or a comma separated list of keys If you want a prenote but not a postnote you need to give an empty second optional argument The basic commands are cite prenote postnote key Cite prenote postnote key Definition These are bare citation commands The latter is provided if the citation occurs at the start of a sentence parencite prenote postnote key Parencite prenote postnote key Definition These commands are like cite and Cite but enclose the citation in paren theses square if the numeric style is used textcite prenote postnote key Textcite prenote postnote key Definition These commands are used for citations in the flow of text The latter is provided if the citation occurs at the start of a sentence For other citation commands see the biblatex documentation 9 So the example document from Listing 1 can now be edited so that the preamble looks like isting 17 Listing T PeP arara pd
13. tire aggregate the Document s Cover Texts may be placed on covers that bracket the Document within the aggregate or the electronic equivalent of covers if the Document is in electronic form Otherwise they must appear on printed covers that bracket the whole aggregate 8 TRANSLATION Translation is considered a kind of modification so you may distribute translations of the Document under the terms of section 4 Replacing In variant Sections with translations requires special permission from their copyright holders but you may include translations of some or all Invariant Sections in addition to the original versions of these Invariant Sections You may include a translation of this License and all the license notices in the Document and any Warranty Disclaimers provided that you also include the original English version of this License and the original versions of those notices and disclaimers In case of a disagreement between the trans lation and the original version of this License or a notice or disclaimer the original version will prevail If a section in the Document is Entitled Acknowledgements Dedica tions or History the requirement section 4 to Preserve its Title sec tion 1 will typically require changing the actual title 9 TERMINATION You may not copy modify sublicense or distribute the Document except as expressly provided for under this License Any other attempt to copy modify sublice
14. too many unprocessed floats error This is usually caused by having too many figures and tables in the results chapter and not enough surrounding text If this happens there are a number of things you can try doing 1 Make sure you haven t been too restrictive in where you want your floats to go If you use a placement specifier give LaTeX as many options as possible For example begin figure htbp which indicates that the figure can be placed here h at the top of a page t at the bottom of the page b or on a page solely consisting of floats p If you just use the h placement specifier then you are stating I want it here and nowhere else If TEX can t put it exactly here then you have given no alternative place to put it and it won t get placed anywhere unless a clearpage command is issued at which point all remaining unprocessed floats will be dumped at that point If you are determined that an image must be placed exactly here then it should not be placed in a floating environment 2 Try increasing the amount of text in the chapter Remember that you should never simply print all the figures and tables in a results chapter without discussing them to some extent 3 If all else fails try using the clearpage command This forces all unprocessed floats to be processed immediately and start a new page This may result in the page ending prematurely if you wish to avoid this you can use the afterpage
15. 4 3 These two commands take on differ ent meanings when they are used in the tabbing environment If you want accents in your tabbing environment either use the inputenc package see Volume 1 15 4 3 1 or use a accent symbol c for example a u instead of u Output Input A FAQ Why doesn t verbatim work within A FAQ Accents misbehave in tabbing Chapter 4 Formatting EXAMPLE 51 begin tabbing Zero 0ne Two Three gt First tab stop gt A gt gt B gt gt Second tab stop end tabbing This produces the following output Zero One Two Three First tab stop A B Second tab stop ANOTHER EXAMPLE This example sets up four tab stops but ignores the first line begin tabbing AAA BBBB XX YYYYYY Z kill gt gt gt Third tab stop Wa gt b gt gt c end tabbing This produces the following output Third tab stop a b c T Input 4 Input T Output Output T Input 4 Input T Output Output Chapter 4 Formatting 32 4 1 Theorems A PhD thesis can often contain theorems lemmas definitions etc The PTEX kernel comes with the command newtheorem name counter title outer counter Definition which can be used to create an environment called name that has an optional argument Each instance of the environment starts with title followed by the associated counter value
16. 4 6 begin table placement Defined in Most classes that define sectioning commands Floats the contents to the nearest location according to the preferred placement options if possible Within the environment caption may be used one or more times as required See Volume 1 15 7 2 4 8 tableofcontents Defined in Most classes that have the concept of document structure Inserts the table of contents A second possibly third run is required to ensure the page numbering is correct 2 0 textbf fext Defined in ETEX Kernel Renders fext with a bold weight in the current font family if it exists See Volume 1 15 4 5 1 1 0 Textcite prenote postnote Rey Defined in biblatex package Like textcite but for use at the start of a sentence 5 3 textcite prenote postnote key Defined in biblatex package Like cite but designed for use in the flow of text 5 3 texttt fext Defined in TEX Kernel Renders fext in the predefined monospaced font See Volume 1 15 4 5 1 6 1 begin thebibliography widest entry label Defined in Most classes that define sectioning commands Bibliographic list See Volume 1 15 5 6 5 0 Symbols NE KSA CHM DOVDOAZZORAHH THOT SAeD Summary of Commands and Environments 121 theorembody font declarations Defined in ntheorem package Changes the current theor
17. 89 leftarrow 43 115 listings package 25 listoffigures 14 18 115 listoftables 14 19 115 location list T4 76 lstinline 27 30 78 115 lstinputlisting 28 30 115 basicstyle 28 29 caption 28 label 28 mathescape 28 numbers 28 title 28 Istlisting environment 25 30 116 lstlistoflistings 28 116 lstset 25 116 basicstyle 30 lvert 41 116 M mainmatter 13 15 19 110 112 116 makeglossaries 80 87 89 116 makeglossaries 4 7 87 90 98 makeglossariesgui 89 makeidx package T4 T9 makeindex 74 78 79 114 116 118 makeindex 3 7 73 79 88 90 98 106 114 MakeTextUppercase 94 116 maketitle 13 14 18 24 110 111 116 121 MakeUppercase 54 116 mathbf 43 116 mathcal 82 87 90 97 116 memoir class 21 metre 45 116 120 mfirstuc package 94 N natbib package 64 68 70 126 authoryear 64 numbers 64 round 64 sort amp compress 64 70 square 64 super 64 newacro 93 116 newacronym 82 86 117 newcommand 23 117 newgidx 91 117 newglossary 86 117 newglossaryentry 80 82 84 86 87 89 93 112 117 description 81 first 81 83 84 86 firstplural 81 84 hyper 88 name 81 plural 81 84 sort 81 symbol 81 85 text 81 83 84 86 type 81 87 newline 37 1147 newterm 91 117 database 91 description 92 label 92 long 92 longplural 92 parent 92 plural 92 see 92 seealso 93 short 92 94 shortplural 92 sort 92 symbol 92 text 92 94 newtheorem 32 34 38 41 44 117 newt
18. F Output include lt stdio h gt needed for printf int main printf Hello World n return 1 l Output A more sophisticated approach is to use the listings package With this package you first need to specify the programming language For example the above code is in C so I need to specify this using lstset language C Input Now I can use the Istlisting environment to typeset my C code Chapter 4 Formatting 26 A Sample PhD Thesis A N Other A Thesis submitted for the degree of Doctor of Philosophy School of Something University of Somewhere July 2013 Figure 4 2 Sample Title Page Chapter 4 Formatting 27 T Input begin 1stlisting include lt stdio h gt needed for printf int main printf Hello World n return 1 end lstlisting 4 Input The resulting output looks like F Output include lt stdio h gt x needed for printf int main printf Hello World n return 1 l Output I can also have inline code snippets using lstinline options char code char Definition This is different syntax to the usual forms of command argument You can chose any character char that isn t the open square bracket and that doesn t occur in code to delimit the code but the start and end char must match The optional argument is discussed below So the following are all equivalent 1 char is the
19. Include an unaltered copy of this License GNU Free Documentation License 133 I Preserve the section Entitled History Preserve its Title and add to it an item stating at least the title year new authors and publisher of the Modified Version as given on the Title Page If there is no section Entitled History in the Document create one stating the title year authors and publisher of the Document as given on its Title Page then add an item describing the Modified Version as stated in the previous sentence J Preserve the network location if any given in the Document for pub lic access to a Transparent copy of the Document and likewise the network locations given in the Document for previous versions it was based on These may be placed in the History section You may omit a network location for a work that was published at least four years before the Document itself or if the original publisher of the version it refers to gives permission K For any section Entitled Acknowledgements or Dedications Pre serve the Title of the section and preserve in the section all the sub stance and tone of each of the contributor acknowledgements and or dedications given therein L Preserve all the Invariant Sections of the Document unaltered in their text and in their titles Section numbers or the equivalent are not considered part of the section titles M Delete any section Entitled Endorsements
20. JabRef untitled File Edit Search View BibTeX Tools Plugins Options Help Dah Sotaa 22 AREAN 27 of Bris untitled authors O Title Year journal owner Tmesta bibtexke rj I Required fields J Optional fields n General n Abstract il Review BibTex source Ay Edition E Month status Added new book entry Figure 5 7 JabRef Entering Optional Fields Chapter 5 Generating a Bibliography 55 Key button to generate the key to save me typing See Figure 5 8 I ve also used the General tab to enter the DOI for this article The entry now has an icon amp next to it I can click on this button to direct my web browser to the article s entry on the Internet JabRef untitled File Edit Search View BibTeX Tools Plugins Options Help DanH Sorina a gt ABEX 47 of Bris untitled Entry Author 4 Title Year Journal Owner Timesta Bibtexke Article Cawley and Talbot Efficient approximate leave one out 2008 Machin eznO6edu 2012 1 Cawley Book Turabian A manual for writers of term papers 1996 ezn06edu 2012 1 turabia I Required fields n Optional fields n General a Abstract n Review BibTex source Manage Efficient approximate leave one out cross validation for kernel logistic regression Journal Machine Learning Manage Toggle abbreviation
21. N newacro options short long Defined in datagidx package Defines a new acronym 6 2 Symbols NE KSA CHM DOVDOAZZORAHH THOT SAeD Summary of Commands and Environments 117 newacronym key val list label abbrv long Defined in glossaries package Shortcut that uses newglossaryentry to define an acronym 6 1 newcommand cmd n args default fext Defined in PTEX Kernel Defines a new command See Volume 1 15 8 4 2 newgidx label title Defined in datagidx package Defines a new index or glossary database 6 2 newglossary log ext name in ext out ext title counter Defined in glossaries package Defines a new glossary 6 1 newglossaryentry label Rey val list Defined in glossaries package Defines a new glossary entry or term 6 1 newline Defined in TEX Kernel Forces a line break 4 7 newterm opftions name Defined in datagidx package Defines a new index or glossary term 6 2 newtheorem name counter title outer counter Defined in TEX Kernel Defines a new theorem like environment The optional arguments are mutually exclusive Some packages such as ntheorem and amsthm redefine this command to have a starred variant that defines unnumbered theorem like environments 4 7 newtheoremstyle name space above space below
22. SI number unit This combines the functionality of num and si so that you can typeset both a number and a unit EXAMPLE The acceleration was approximately SI 9 78 metre per square second l Result The acceleration was approximately 9 78 m s T Output Output Definition Input Output Definition Input 4 Input T Output Output Definition Input 4 Input Output CHAPTER 5 GENERATING A BIBLIOGRAPHY Volume 1 15 5 6 introduced the thebibliography environment While it is possible to write this environment yourself as was done in Volume 1 it s not practical with a large number of citations Instead the preferred method is to create an external database of bibli ographic data and use an application that fetches the relevant information from that database and writes a file containing the thebibliography environ ment which can then be input into your document This means that 1 Only the references that you cite are included in the bibliography Examiners tend to fault uncited references 2 References are displayed in a consistent manner 5 Entries can be sorted in order of citation or alphabetically Traditionally the bibtex application is used to generate the thebibliography environment It comes with TeX distributions and most books on FTpx cover bibtex Unfortunately bibtex has some drawbacks most notably the complexity of creating your own custo
23. body font indent head font post head punctuation post head space head spec Defined in amsthm package Defines a new theorem style called name 4 7 normal font Defined in PTEX Kernel Switches to the default font style See Volume 1 15 4 5 1 4 2 num number Defined in siunitx package Typesets number with appropriate spacing 4 9 O ofoot scrplain scrheadings Defined in scrpage2 package Indicates what to put in the outer footer area for the scrplain and scrheadings page styles 4 2 ohead scrplain scrheadings Defined in scrpage2 package Indicates what to put in the outer heading area for the scrplain and scrheadings page styles 4 2 onehalfspacing Defined in setspace package Symbols NE MSA CGCHMNDRODPOAZZORASHH THOS AeD Summary of Commands and Environments 118 Switches to one half line spacing 4 5 P pagemark Defined in scrpage2 package Used in commands like ihead to insert the current page number 4 2 pagenumbering style Defined in ETEX Kernel Sets the style of the page numbers 2 0 pagestyle style Defined in TEX Kernel Sets the style of the headers and footers 4 2 par Defined in PTEX Kernel Insert a paragraph break 1 0 Parencite prenofe postnote key Defined in biblatex package Like parencite but for use at the start
24. font See Volume 1 15 4 5 1 4 1 rvert Defined in amsmath Math Mode Right vertical bar delimiter See Volume 1 45 9 4 9 4 8 S scshape Defined in TEX Kernel Switches to the small caps form of the current font family if it exists See Volume 1 15 4 5 1 4 7 second Defined in siunitx package Indicates the second unit for use in commands like si 4 9 SI number unit Defined in siunitx package Typesets a number and unit combining the functionality of num and si 4 9 si unit Defined in siunitx package Symbols NE KSA CHM DROVOAZZORASH TOTS ACeD Summary of Commands and Environments 120 Typesets the given unit 4 9 sim Defined in BTFX Kernel Math Mode Relational symbol 4 7 singlespacing Defined in setspace package Switches to single line spacing 4 3 sqrt order operand Defined in ETX Kernel Math Mode Displays a root See Volume 1 15 9 4 6 4 5 square unif Defined in siunitx package Indicates a squared unit in commands like si 4 9 squared Defined in siunitx package Indicates a squared term in commands like si after a unit command such as metre 4 9 sum Defined in BTFX Kernel Math Mode Summation symbol See Volume 1 15 9 4 7 4 8 T begin tabbing Defined in BTEX Kernel Allows you to define tab stops from the left margin
25. is a specified stopping criteria stop end tabbing end algorithm Output T Input j 4 Input Result Chapter 4 Formatting 42 Algorithm 1 Gauss Seidel Algorithm 1 For k 1 to maximum number of iterations 2 Fori iton i 1 k n k bi Daja ayx V j i WI Set x T 3 If x lt e where e is a specified stopping criteria stop k 1 See Volume 1 15 9 4 11 to find out how to redefine vec to display its argument in bold If you want a more sophisticated approach there are some packages available on CTAN 2 such as alg algorithm2e algorithms and algorithmicx I m going to briefly introduce the algorithm2e package here This provides the al gorithm floating environment Like the figure and table environments described in Volume 1 15 7 the algorithm environment has an optional argument that specifies the placement begin algorithm placement If you are using a class or package that already defines an algorithm environ ment you can use the algo2e package option usepackage algo2e algorithm2e This will define an environment called algorithm2e instead of algorithm to avoid conflict Within the body of the environment you must mark the end of each line with regardless of whether you want a semi colon to appear To suppress the default end of line semi colon use DontPrintSemicolon To switch it back on again use PrintSemicolon There are a v
26. list Then click on the Insert button For example in Figure 5 12 I have selected an author s name then I selected the author field in the Work options list Next I clicked on the Insert button Now the author s name is high lighted in red and the author field has a tick next to it see Figure 5 13 I can repeat this process for the next author Just make sure the Append rather than Override radio button is selected I can repeat this for all the different fields Each time I select the text in the raw source panel then select the appropriate field from the Work options list and then click Insert Once I have finished I then need to click Accept Chapter 5 Generating a Bibliography 58 Plain text import for Article Raw source BibTeX source Hints and Warnings O lefel Reference bine Journal Article Author Talbot Nicola Primary Title Efficient approximate leave one out cross validation for kernel logistic regression Journal Name Machine Learning Cover Date 2008 06 01 Publisher Springer Netherlands Issn 0885 6125 Subject Computer Science Start Page 243 End Page 264 Volume 71 Issue 2 Url http dx doi org 10 1007 s10994 008 5055 9 Doi 10 1007 s10994 008 5055 9 Plain text import Work options Allowed BibTex fields title journaltitle Append Override This is a simple copy and paste dialog First load or paste
27. printglossary options where options is a comma separated list of Rey value options Avail able keys e type The glossary to print If omitted the main default glossary is assumed Input T Input 4 Input Input Definition Definition Chapter 6 Generating Indexes and Glossaries 8 amp 8 e style The glossary style to use There are a lot of predefined styles to choose from such as list long or tree See the glossaries user manual 16 for further details e title Overrides the default title for this glossary e toctitle Overrides the default title for the table of contents e numberedsection Put this glossary in a numbered section instead of an unnumbered section e nonumberlist Suppress the location lists for this glossary NOTE By default the glossaries aren t added to the table of contents If you want them added to the table of contents use the package option toc usepackage toc glossaries Only those entries that have been used in the document via commands like gls are displayed in the glossary If you want to add an entry without displaying it in the document use glsadd options label where label is the unique label identifying the entry The optional argu ment options is the same as for commands like gls except there is no hyper key Alternatively you can add all defined entries using glsaddal1 options where options is the same as for
28. 120 T tabbing environment 30 41 107 108 114 120 table environment 42 120 tableofcontents 13 14 18 120 texindy 7 10 75 76 88 textbf 1 94 120 textcase package 94 Textcite 71 120 textcite 71 120 120 texttt 76 77 120 thebibliography environment 46 59 65 110 120 theorembody font 38 41 121 theoremheader font 38 121 theoremnumbering 38 121 Symbols NK KSSGHMNDOTDOAZZHMAS H TODOS Index theoremstyle 34 37 38 41 121 title 13 14 18 121 titlehead 14 18 121 titlepage environment 24 121 ttfamily 28 121 U uElseIf 43 121 ul 43 121 UK FAQ 1 105 usepackage 16 33 34 64 121 V vec 41 45 1241 vee 36 40 121 verbatim environment 25 30 121 vfill 24 121 vspace 24 122 W wedge 36 40 122 While 43 122 X xindy 3 73 TT 88 90 Z zoterordfxm 70 128 Symbols NKA Z lt CHAaADOVOZZn Rman 0mm GNU FREE DOCUMENTATION LICENSE Version 1 2 November 2002 Copyright 2000 2001 2002 Free Software Foundation Inc 51 Franklin St Fifth Floor Boston MA 02110 1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document but changing it is not allowed Preamble The purpose of this License is to make a manual textbook or other functional and useful document free in the sense of freedom to assure everyone the effective freedom to copy and redistribute it with or without modifying it either commerci
29. 3 The required and optional fields for the standard entry types are listed in Table 5 4 If an entry has a field that is neither required nor optional BibTeX will ignore it This means that you can have a field called say abstract which will be ignored by the standard bibliography styles but will be included if you use a bibliography style that has an abstract field So you FAQ Creating a BibTeX bibliography FAQ URLS in BibTeX bibliographies Chapter 5 Generating a Bibliography 60 Table 5 3 Standard BiBTeX fields address Publisher Institution s address author Author names booktitle Title of book where only a part of the book is being cited chapter Chapter or section number edition The edition of the book howpublished How a non standard work was published institution The institute sponsoring the work journal The name of the journal month The month the work was published note Any additional information number The number of the journal technical report etc organization Organization sponsoring conference or manual pages Page number or page range publisher Publisher s name school Academic institution where thesis was written series Name of a series title The title of the work type The type of technical report volume The volume number can store additional information in the database that won t appear in the bibliography The author and editor fields have the same format as described in Sec tion 5 1
30. 8 usepackage opftion list package list Defined in PTEX Kernel Loads the listed package s See Volume 1 15 4 2 2 0 v vec c Defined in BTFX Kernel Math Mode Typesets its argument as a vector See Volume 1 15 9 4 11 4 8 vee Defined in 2TEX Kernel Math Mode Operator V symbol See Volume 1 15 9 4 7 4 7 begin verbatim Defined in PTEX Kernel Typesets the contents of the environment as is Can t be used in the argument of a command 4 5 vfill Defined in ETEX Kernel Symbols NE KSA CHM DOVDOAZZORAHH THOT SAeD Summary of Commands and Environments Inserts a vertical space that will expand to fit the available height 4 4 vspace length Defined in TEX Kernel Inserts a vertical gap of the given height 4 4 W wedge Defined in BTFX Kernel Math Mode Operator A symbol See Volume 1 15 9 4 7 4 7 While condition body Defined in algorithm2e package For use in algorithm like environ ments to indicate a while loop 4 8 122 Symbols NKXZ lt SCHVAVDODVOZZoau Rmn 0mmoAaAw a Symbols A B INDEX c Page numbers in bold indicate the entry definition in the summary D E F G H I Symbols abstract environment 13 108 J 77 79 106 69 106 K 2 106 acf 85 108 L F 70 106 8 85 108 95106 Act 94 108 M 28 106 acr 94 95 98 108 N 15 106 Acrfull 85 108
31. Else 43 111 ElseIf So 114 121 emph 36 40 144 end 13 110 142 endnotexml 70 ensuremath 82 97 112 epsilon 41 112 equiv 36 40 112 ex 38 excludeonly 18 112 F figure environment 42 112 first use flag 85 For 45 112 frac 41 112 frontmatter 13 14 18 110 112 116 G geometry package 16 glossaries package 80 84 88 90 94 acronym 86 counter 87 description 83 footnote 83 shortcuts 85 toc 88 xindy 88 Gls 84 86 90 94 95 112 gls 83 85 88 90 94 95 98 108 113 counter 84 format 84 125 hyper 84 glsadd 88 94 98 113 glsaddall 88 95 113 types 88 glsentryfirst 86 113 glsentrytext 86 113 Glspl 84 85 90 94 113 glspl 83 94 95 113 glsreset 83 95 113 glssymbol 85 113 glsunset 83 95 113 gram 45 113 headfont 23 114 headmark 23 114 hfill 24 114 hspace 24 114 hyperref package 64 80 84 backref 64 If 43 114 121 ifoot 22 114 ihead 22 114 include 17 112 114 includeonly 18 112 114 index 74 76 79 81 84 106 108 114 116 118 input 17 114 inputenc package 30 47 54 68 86 interface 5 itshape 23 114 JabRef 47 66 kill 30 114 kilo 45 115 KOMA Script class options bibliography 64 parskip 16 KwData 42 115 KwIn 42 115 KwOut 42 115 KwResult 42 115 Symbols NK KSSCGHMNDPOTDOAZZOAHH TO TMSOOeD Index KwRet 42 115 KwTo 42 115 L label 15 19 20 43 47 115 large 21 115 latex 5 latexmk 5 9 16 64 72 75 79
32. If counter is present the new environment uses that counter instead of having a new counter defined for it If outer counter is present the environment counter is reset every time outer counter is incremented The optional arguments are mutually exclusive In the example below I ve use newtheorem to define a new environment called theorem which has an associated counter also called theorem that is dependant on the chapter counter in the preamble newtheorem theorem Theorem chapter T Input later in the document begin theorem If proposition P is a tautology then sim P is a contradiction and conversely end theorem i j 4 Input Resulting output l F Output Theorem 4 1 If proposition P is a tautology then P is a contradiction and conversely Output The optional argument to the new environment can be used to add a caption Modifying the above example changes shown like this in the preamble newtheorem theorem Theorem chapter T Input later in the document begin theorem Tautologies and Contradictions If proposition P is a tautology then sim P is a contradiction and conversely end theorem 4 Input Chapter 4 Formatting 55 Resulting output l F Output Theorem 4 2 Tautologies and Contradictions If proposition P is a tau tology then P is a contradiction and conversely l Output Here s
33. O arara 9 12 16 64 72 75 79 acrfull 85 90 108 p 89 106 Acrlong 85 86 109 i 36 106 acrlong 85 90 109 Q um 36 106 acronym package 80 R 62 106 acronymfont 93 109 S 75 77 79 81 1406 Acrpl 94 109 T 2 27 407 acrpl 94 109 76 107 Acrshort 85 109 U 54 107 acrshort 85 90 109 y Y 86 107 acs 35 109 wW 30 107 addbibresource 70 109 X 30 107 datatype 70 42 107 location 70 Y lt 30 107 addtokomafont 21 109 Z 30 44 107 ME 76 109 gt 30 44 107 afterpage 99 109 85 90 95 107 afterpage package 99 14 18 30 41 107 alg package 49 2 107 algorithm environment 42 45 109 A 41 43 107 algorithm2e environment 42 44 109 41 85 90 107 algorithm2e package 42 a 36 108 algo2e 49 43 2 28 108 algorithmicx package 42 76 79 84 94 108 algorithms package 49 2 28 108 amsmath package 33 36 40 78 108 amsthm package 33 34 39 ang 45 109 A arara 5 7 16 64 72 75 79 89 a 30 108 author 13 14 18 110 123 Index B backmatter 13 15 19 110 112 116 begin 13 110 112 bfseries 21 110 bib entry fields abstract 59 address 60 61 author 59 61 booktitle 60 61 chapter 60 61 date 66 edition 60 61 editor 60 61 howpublished 60 61 institution 60 61 journal 60 61 month 60 61 66 note 60 61 number 60 61 organization 60 61 pages 60 61 publisher 60 61 school 60 61 series 60 61 title 59 61 type 60 61 volum
34. Such a section may not be included in the Modified Version N Do not retitle any existing section to be Entitled Endorsements or to conflict in title with any Invariant Section O Preserve any Warranty Disclaimers If the Modified Version includes new front matter sections or appendices that qualify as Secondary Sections and contain no material copied from the Document you may at your option designate some or all of these sections as invariant To do this add their titles to the list of Invariant Sections in the Modified Version s license notice These titles must be distinct from any other section titles You may add a section Entitled Endorsements provided it contains nothing but endorsements of your Modified Version by various parties for example statements of peer review or that the text has been approved by an organization as the authoritative definition of a standard You may add a passage of up to five words as a Front Cover Text and a passage of up to 25 words as a Back Cover Text to the end of the list of Cover Texts in the Modified Version Only one passage of Front Cover Text and one of Back Cover Text may be added by or through arrangements made by any one entity If the Document already includes a cover text for the same cover previously added by you or by arrangement made by the same entity you are acting on behalf of you may not add another but you GNU Free Documentation License 154 may replace th
35. This time I ve used the Generate BibTeX Chapter 5 Generating a Bibliography 48 JabRef untitled File Edit Search View BibTeX Tools Plugins Options Help Daug binas se AA 42 of untitled Author Journal Owner Timesta Status New database created Figure 5 1 JabRef BREF p x General General ie dita Display imported entries in an inspection window before they are added Groups v Use inspection window also when a single entry is imported Appearance v Warn about unresolved duplicates when closing inspection window sober Ai Open right click menu with Ctrl left button Entry table columns v Show confirmation dialog when deleting entries ae v Show warning dialog when a duplicate BibTeX key is entered Name formatter v Show warning dialog when an empty BibTeX key is entered Import v Enforce legal characters in BibTeX keys ea a Load and Save preferences from to jabref xml on start up memory stick mode Mark new entries with owner name ezn06edu Overwrite a Mark new entries with addition date Date for yyyy MM dd Overwrite Field name timestamp a v Mark entries imported into an existing database v Unmark all entries before importing new entries into an existing database Language English v Default encoding UTF8 Import preferences Export
36. a Bibliography 47 to make syntactic mistakes It can also be hard to keep track of entries in a large database To make life easier there are a number of bibliography reference managers available that provide a convenient graphical interface One such application is JabRef and is described next 5 1 1 JabRef I ve chosen to describe JabRef here because it s an open source Java ap plication that can run on any operating system that has the Java Runtime Environment installed at least version 1 5 You can download JabRef from http jabref sourceforge net download php Linux users may also be able to install it via their Add Remove Software tool If you have success fully been using arara you already have Java installed Once you have installed it run JabRef and select File New database to create a new database see Figure 5 1 When you save your data it s saved as a BibTeX bib file Note that if you use the inputenc package in your thesis see Volume 1 15 4 3 1 you ll have to make sure JabRef is using the same encoding as your document You can do this by selecting Options Preferences to open the Pref erences dialog box and set the default encoding as appropriate For example I use UTF 8 so I ve set that as the default encoding see Figure 5 2 I also need to change the database encoding in the Database properties dialog Figure 5 3 which can be opened using File Database properties To create a ne
37. an example that uses the first optional argument of newtheorem Input in the preamble newtheorem exercise Exercise newtheorem suppexercise exercise Supplementary Exercise later in the document begin fexercise This is an example of how to create a theorem like environment end exercise begin suppexercise This is another example of how to create a theorem like environment end suppexercise 4 Input Result T Output Exercise 1 This is an example of how to create a theorem like environ ment Supplementary Exercise 2 This is another example of how to create a theorem like environment Output Unfortunately there isn t a great deal of flexibility with the environment appearance However there are various packages available that provide en FAQ Theorem hancements to this basic command allowing you to adjust the appearance bodies printed in to suit your requirements There seem to be two main contenders amsthm a roman font and ntheorem Both have advantages and disadvantages For example nthe orem is more flexible but amsthm is more robust Therefore I m going to describe both and you will have to decide which one you prefer NOTE If you are using either packages with amsmath you must load amsmath first T Input usepackage amsmath usepackage ntheorem 4 Input or Chapter 4 Formatting 354 T Input usepackage amsmath usepackage ams thm l j
38. as isbn url or doi For example usepackage isbn url doi biblatex The style can be set using the style option The default is numeric which produces a numeric citation such as 1 There is also numeric comp which is like natbib s sort amp compress option described in Section 5 2 1 or authoryear which displays author year citations There are many other citation styles For these and for other package options see the biblatex documentation 9 With BibLaTeX you don t use the bibliography command described in Section 5 2 Instead you add the bib file as a resource in the preamble using addbibresource options resource where resource is the name of the bib file including the file extension However the resource doesn t have to be a bib file You can only add one resource at a time addbibresource bibfile1 bib addbibresource bibfile2 bib l The resource can be a remote one in which case you need to use the location option with the value remote and specify the URL addbibresource location remote http www somewhere com bibfile2 bib l This is only available if you use biber as the backend Another option is datatype which specifies the format of the resource The default is bibtex but it can also be ris zoterordfxm or endnotexml See the biblatex and biber documentation 7 for further details The bibliography itself is displayed using printbibliography
39. defined the indexing database you can now define terms associated with that database using newterm options name where name is the term and options is a list of Rey value options The following keys are available e database Identifies the database in which to store this term For example newterm database index eigenvalue It can be somewhat cumbersome having to type the database for each new term Instead you can define the default database using DTLgidxSetDefaultDB label For example newgidx index Index DTLgidxSetDefaultDB index Definition Input Definition Definition Definition Input Chapter 6 Generating Indexes and Glossaries 92 newterm eigenvalue newterm eigenvector l 4 Input e label A label uniquely identifying this term If omitted the label is extracted from name e sort The sort key If omitted this is extracted from name e parent The parent entry if this is a sub term The value should be the label identifying the parent which must already be defined e text How the entry should appear in the document text If omitted name is used If present name indicates how the term should appear in the index glossary e description An optional associated description e plural The plural form of this term If omitted this value is obtained by an appending s to name or the value of text if supplied e symbol An o
40. entered without quotes For example inproceedings talbot97 author Talbot Nicola and Cawley Gavin title A fast index assignment algorithm for robust vector quantisation of image data booktitle Proceedings of the I E E E International Conference on Image Processing address Santa Barbara California USA month oct year 1997 5 2 BibTeX Now that we ve created a bib file as described above we next need to look at how to incorporate the information in the database into a BTEX document As mentioned in Volume 1 15 5 6 entries are cited in the document using cite text Rey list where key list is a comma separated list of keys Each key uniquely iden tifies an entry in the database If you used JabRef Section 5 1 1 this is the key you entered in the Bibtexkey field If you wrote the bib file in a text Input Input T Input 4 Input Definition Chapter 5 Generating a Bibliography 635 editor Section 5 1 2 it s the keyword bit at the start of the list of fields for the entry Next you need to specify what type of bibliography style you want to use There are many available but the basic ones are abbrv Entries sorted alphabetically with abbreviated first names months and journal names alpha Entries sorted alphabetically with the citation represented by abbrevi ated author surname and year instead of a number plain Entries sorted alphabetically with
41. exclamation mark character lstinline include lt stdio h gt Input 2 char is the vertical bar character lstinline include lt stdio h gt Input 3 char is the double quote character lstinline include lt stdio h gt Input 4 char is the plus symbol lstinline include lt stdio h gt Input And so on but char can t be say as that occurs in code Example Chapter 4 Formatting 28 The stdio header file required for the lstinline printf function is loaded using the directive lstinline include lt stdio h gt on the first line Result The stdio header file required for the printf function is loaded using the directive include lt stdio h gt on the first line Another alternative is to input the code from an external file For ex ample suppose my C code is contained in the file helloworld c then I can input it using lstinputlisting options helloworld c Remember to use a forward slash as the directory divider even if you are using Windows All the above lstinline lstinputlisting and the Istlisting environ ment have an optional argument options that can be used to override the default settings These are Rey value options There are a lot of options available but I m only going to cover a few If you want more detail have a look at the listings documentation 6 title fext is used to set an unnumbered and unlabelled tit
42. files be opened or imported into an already running instance of JabRef instead of opening a new instance For instance this is useful when you open a file in JabRef from your web browser Note that this will prevent you from running more than one instance of JabRef at a time Listen for remote operation on port 6050 File dialog Use native file dialog v Disable file renaming in non native file dialog Search IEEEXplore v Use IEEE LaTeX abbreviations BibLaTeX mode v BibLaTex mode OK Cancel Figure 5 14 JabRef Advanced Preferences File Edit Search View BibTeX Tools Plugins Options Help Clea earch All Fields Search All Fields _ 2 npr Cawley etal Sparse multinomial logistic 2007 Book Turabian A manual for writers of ter 1996 ezn06 2012 turabi Incremental Float Filter Global search Show results in dialog BibTeX source settings J 1 Hl Required fields fj Optional fields n Optional fields 2 E General E Abstract E Review Editor Volume Eid Date June Year 243 264 Note Doi 10 1007 s10994 008 5055 9 Eprintclass Eprinttype Url Urldate Figure 5 15 JabRef in BibLaTeX Mode Chapter 5 Generati
43. form word format where format is the name of a text block command without the leading backslash For example Input Input Input Input T Input 4 Input Input Definition Chapter 6 Generating Indexes and Glossaries 77 index eigenvector textbf You can combine and For example index sqrtQO texttt sqrt textbf NOTE Make sure the format you use is the name of a command that takes an argument While it won t cause an error to use say bfseries instead of textbf it will cause the unexpected side effect of rendering the rest of your index in that font instead of just that particular location You can also use format to cross reference another entry If you have an entry that s just a synonym for another entry you can use word see name where name is the other entry If you want to direct the reader to a similar topic you can use word seealso ftopic where fopic is the other entry For example index eigenvector seealso eigenvalue Sub Levels An entry in the index may have sub items With makeindex you can have a maximum of three levels With xindy you can have an arbitrary number of levels However it s a good idea to consider the advice in the Oxford Style Manual 12 In all but the most complex indexes subentries within subentries sub subentries should be avoided In other words just because it s possible to do something doesn t mean you
44. form The optional argument options is the same as for newterm This is equivalent to newterm description capitalisewords long short acronymfont short long long text DTLgidxAcrStyle long acronymfont short plural DTLgidxAcrStyle long s acronymfont short s sort short options 1 MakeTextUppercase short where DTLgidxAcrStyle long short Definition formats the full version of the acronym This defaults to long short and acronymfont fext Definition Chapter 6 Generating Indexes and Glossaries 94 is the font used to format acronyms By default this just displays its argu ment but can be redefined if you want the acronyms formatted in a par ticular style or font such as small caps The other commands used above are MakeTextUppercase text This is defined by the textcase package and converts fext to uppercase capitalisewords fext This is defined by the mfirstuc package and capitalises the first letter of each word in text EXAMPLE newacro svm support vector machine Once you have defined the terms in the preamble you can later use them in the document gls format label glspl format label Gls format label Glspl format label These are similar to those described in Section 6 1 2 but they have a dif ferent syntax Here format is the name of a text block commands such as tex
45. in MakeUppercase d e since it assumes that the command is an accent command So when it parses MakeUppercase d e it will skip MakeUppercase and look at the fol lowing letter In this case it is d which is lower case so from BibTeX s point of view the word MakeUppercase d e starts with a lower case letter d so it is therefore the von part You can either do the same with the La part or as in the above example you can place it in the same group as MakeUppercase d e Multiple authors should be separated by the keyword and Don t use a comma to separate the authors Here is an example with three authors Gavin C Cawley and Nicola L C Talbot and Mark Girolami If the author is an institution or company that happens to have the word and in its name such as Smith and Jones Inc then you need to group the and to indicate that you mean the word and rather than the keyword Smith and Jones Inc Figure 5 9 shows the entry for a paper in a conference proceedings so for that one I used BibTeX New entry and clicked on the Inproceedings button Notice the way I ve written the title for this entry Sparse multinomial logistic regression via Bayesian L1 regularisation l BibTeX automatically converts the title to lower case apart from the ini tial letter but here both Bayesian and L1 should begin with a capital I therefore need to enclos
46. later in the document 97 Chapter 6 Generating Indexes and Glossaries 98 Glspl matrix are usually denoted by a bold capital letter such as mathbf A The gls matrix s i j th element is usually denoted a_ ij Gls matrix mathbf I is the identity gls matrix First use acr svm Next use acr svm Full gls svm A gls not set is a collection of objects Some sample code is shown in Listing ref lst sample This uses the function gls fn sqrt glsadd sqrt begin Definition Tautology A emph gls textbf tautology is a proposition that is always true for any value of its variables end Definition begin Definition Contradiction A emph gls textbf contradiction is a proposition that is always false for any value of its variables end Definition At the end of the document backmatter printterms database glossary printterms database acronym printterms database notation printbibliography printterms database index l j 4 Input Note that there is now no need to call either makeindex or makeglossaries The only external application being called is biber for the bibliography APPENDIX A GENERAL ADVICE If you encounter any ETEX problems check Appendix B Common Errors and Appendix C Need More Help in BTFX for Complete Novices 15 A 1 Too Many Unprocessed Floats A common problem PhD student s encounter when writing a thesis is the
47. listing If you are using latexmk to build your document remember to include the idx custom dependency to your RC file as described in Section 1 1 1 If you aren t using an automated method to build your document you will need to run PDFBTEX then run makeindex and then run PDFETEX again see Section 1 1 If you prefer to use xindy instead of makeindex you need to run texindy a xindy wrapper customised for BTfX documents If you are using arara change the line arara makeindex to change the language as required arara texindy language english Make sure you have added the texindy rule as described in Section 1 1 2 If you are using latexmk to build your document you will need to change the custom dependency for idx files as described in Section 1 1 1 Overriding the Default Sort By default the index entry will be sorted according to the word being in dexed However you can override this by writing the argument of index in the form sort word Definition where sort is how to sort the term and word is how the term should appear in the index Chapter 6 Generating Indexes and Glossaries 76 The makeindex application doesn t understand BTEX commands It simply sorts the term as is So for example if you do index AE olian then makeindex will sort it according to the characters A E space o l i a n Since makeindex sorts symbols such as before letters it will put AE uoli
48. main topic about cesophagi T npu The gls textbf oesophagus connects the throat and the stomach ue l Input This produces The cesophagus connects the throat and the stomach Output and the associated location will be typeset in bold Here s an example using the svm example defined on the previous page j l a ipu First use acr svm Subsequent use acr svm Full form a SE iip This produces l ae utpu First use support vector machine SVM Subsequent use SVM Full To form support vector machine SVM l Output You can unset and reset acronyms using glsunset label Definition and glsreset label Definition To display the index or glossary or list of acronyms use printterms options Definition where options is a comma separated key value list Common options are Chapter 6 Generating Indexes and Glossaries 96 e database The label uniquely identifying the database containing the relevant terms e postdesc This may have the value dot put a full stop after the description if there is a description or none don t put a full stop after the description e columns This value must be an integer greater than or equal to 1 indicating the number of columns for the page layout e style The style to use There are a number of predefined styles such as index or gloss See the user guide 17 for further details e namecase Indicates whether any case change should be ap
49. of a sentence 5 3 parencite prenofe postnote key Defined in biblatex package Like cite but the citation is enclosed in parentheses 5 3 parindent Defined in PTEX Kernel A length register that stores the indentation at the start of paragraphs See Volume 1 15 2 17 4 7 per Defined in siunitx package Indicates a divider in commands like si 4 9 pnumfont Defined in scrpage2 package Determines the font used by pagemark with the scrplain and scrheadings page styles 4 2 printbibliography options Defined in biblatex package Prints the bibliography 5 3 printglossaries Defined in glossaries package Prints all of the defined glossaries 6 1 printglossary key val option list Defined in glossaries package Prints the glossary identified in the optional argument or the default glossary if none identified 6 1 print index Defined in makeidx package Prints the index Must be used with makeindex and index The external index file must first be processed by an indexing application 6 1 PrintSemicolon Defined in algorithm2e package Switches on the end of line semi colon See also DontPrintSemicolon 4 8 printterms options Defined in datagidx package Displays the index or glossary or list of acronyms 6 2 begin Proof title Defined in ntheorem package with standard package option Symbols NE
50. preferences OK Cancel Figure 5 2 JabRef Preferences Chapter 5 Generating a Bibliography 49 Database properties Database encoding UTF8 Override default file directories General file directory User specific file directory Database protection LI Refuse to save the database before external changes have been reviewed Figure 5 3 JabRef Database Properties Select entry type Entry types Figure 5 4 JabRef Select Entry Type Chapter 5 Generating a Bibliography 50 JabRef untitled File Edit Search View BibTeX Tools Plugins Options Help Da Sh Sohne se 4 BEX 4 Off Bria untitled Author Title Year Joumal Owner Timesta Bibtexkey l Ml Required fields n Optional fields m General m Abstract il Review BibTeX source Publisher Status Added new book entry Figure 5 5 JabRef New Entry Chapter 5 Generating a Bibliography 51 JabRef untitled File Edit Search View BibTeX Tools Plugins Options Help Da Se Sohne 22 4 BEX 4 Off Bria untitled A manual for writers of term papers theses and dissertations Publisher The University of Chicago Press Ls v Kate L Turabian 7 Bibtexkey turabian96 Status Added new book entry Figure 5 6 JabRef Entering the Required Fields Chapter 5 Generating a Bibliography 52
51. should do it To indicate a subentry the argument of index should be in the form main entry subentry For example index reptile caiman If you really must have a sub subentry index reptile crocodylian caiman You can combine and For example index methods sqrtO texttt sqrtQ textbf Listing 17 can now be modified as follows download the document for the complete code Input Input Definition Definition Input Definition Input Input Input Chapter 6 Generating Indexes and Glossaries 78 Listing 19 ro z Input In the preamble arara pdflatex synctex on arara biber arara makeindex arara pdflatex synctex on arara pdflatex synctex on documentclass oneside 12pt scrbook usepackage makeidx makeindex Later in the document Some sample code is shown in Listing ref lst sample This uses the function lstinline sqrtQ index sqrtQO texttt sqrt index functions sqrt texttt sqrt QC index square root see texttt sqrtQ begin Definition Tautology A emph tautology index tautology textbf is a proposition that is always true for any value of its variables end Definition begin Definition Contradiction A emph contradiction index contradiction textbf is a proposition that is always false for any value of its variables end Definition At the end of the document printbibliography pr
52. some text into the text input area After that you can mark text and assign it to a BibTex field Figure 5 12 Importing a Plain Text Reference Selecting a Field Plain text import for Article Raw source BibTeX source Hints and Warnings O ee Reference Type Journal Article Author Cawley Gavin Author Talbot Nicola Primary Title Efficient approximate leave one out cross validation for kernel logistic regression Journal Name Machine Learning Cover Date 2008 06 01 Publisher Springer Netherlands Issn 0885 6125 Subject Computer Science Start Page 243 End Page 264 Volume 71 Issue 2 Url http dx doi org 10 1007 s10994 008 5055 9 Doi 10 1007 s10994 008 5055 9 Plain text import After that you can mark text and assign it to a BibTex field Work options Allowed BibTeX fields commentator subtitle titleaddon Append Override This is a simple copy and paste dialog First load or paste some text into the text input area Figure 5 13 Importing a Plain Text Reference Field Selected Chapter 5 Generating a Bibliography 59 5 1 2 Writing the bib File Manually It may be that you don t want to or can t use a bibliography management application such as JabRef In which case you can create the bib file in an ordinary text editor such as the one you use to write your PTEX documents When you save the file make sure you give it the extension bib E
53. tabbing environment Jumps to the previous tab stop 4 6 Defined in Tex Kernel Used when a sentence ends with a capital letter This command should be placed after the letter and before the punctuation mark See Volume 1 15 2 13 6 4 Defined in ETEX Kernel Starts a new row in tabbing or tabular style environments See Volume 1 15 4 6 1 2 0 Defined in TEX Kernel Closing delimiter of an optional argument See Volume 1 15 2 8 2 51 0 4 maths Defined in PTEX Kernel Math Mode Displays its argument as a superscript See Volume 1 15 9 4 3 4 8 _ maths Defined in BTpX Kernel Math Mode Symbols NE KSA CHM DOVDOAZZORAHH THOT SAeD Summary of Commands and Environments 108 Displays its argument as a subscript See Volume 1 15 9 4 3 4 8 Defined in TEX Kernel Open double quote symbol See Volume 1 15 4 3 4 7 Defined in PTEX Kernel Marks the beginning of a group See Volume 1 45 2 7 4 0 When used in index this symbol indicates that the rest of the argument list is to be used as the encapsulating command for the page number 6 1 Defined in PTEX Kernel Marks the end of a group See Volume 1 15 2 7 1 0 Defined in BTEX Kernel Unbreakable space See Volume 1 15 4 3 4 7 A a accent symbol character Defined in PTEX Kernel Used
54. the citation represented by a num ber unsrt Entries sorted according to citation with the citation represented by a number The style is specified in your BTEX document with the command bibliographystyle style where style is the name of the style Some people put this command in the document s preamble and some people put it near their bibliography but wherever you choose to put it this command should only be used once The actual bibliography itself is input into the document using bibliography database where database is the name of the database without the bib extension In fact this argument can be a comma separated list of databases if your entries are stored across multiple files Recall the example thesis in Listing 1 ended with The bibliography will go here end document If my references are stored in the file thesis ref bib then I can replace the above comment as follows Listing 15 bibliographystyle plain bibliography thesis ref end document Elsewhere in my document I need some citations For example FAQ Choosing a bibliography style Definition Definition Input 4 Input Input 4 Input Chapter 5 Generating a Bibliography 64 See Turabian cite turabian96 for a comprehensive guide on preparing a thesis l If you are using arara see Section 1 1 2 you need the following lines in your source code
55. this was a drawback of being a mathematician doing a PhD in an electronics department A4The sole purpose of 3D pie charts or bar charts appears to be to look pretty and impress people who have no understanding of mathematics A5Sbut don t expect your supervisor to actually write your thesis Appendix A General Advice 102 at the eager anticipation that my algorithm would prove superior to all others and oh joy my experiments proved me right 12 Don t decorate your thesis with irrelevant clip art It is unprofessional and highly inappropriate in the sciences 13 Make regular backups of your work Be prepared for any of the following accidentally deleting your thesis accidentally overwriting your thesis with another file software failure hardware failure viruses fire and theft Consider using at least a two tier system where you keep one backup in a safe place where you live and ask a close relative or friend to take care of another backup Items 9 and 10 above were supplied by Dr Gavin Cawley who has been both a PhD supervisor and examiner A School of Computing Sciences University of East Anglia BIBLIOGRAPHY 1 John Collins Evan McLean and David J Musliner latexmk generate ETEX document 2012 http mirror ctan org support latexmk latexmk pdf or texdoc latexmk 2 The comprehensive TFX archive network http mirror ctan org 3 Jurgen Fenn The TeX catalogue online topic index http mirro
56. to the proof title Recall from earlier that amsthm s proof environment uses its optional argument as a replacement for the default proof title T Input 4 Input T Output Output A Chapter 4 Formatting 40 EXAMPLE Listing 13 rT Input in the preamble usepackage standard ntheorem later in the document begin Definition Tautology label def tautology A emph tautology is a proposition that is always true for any value of its variables end Definition begin Definition Contradiction label def contradiction A emph contradiction is a proposition that is always false for any value of its variables end Definition begin Theorem If proposition P is a tautology then sim P is a contradiction and conversely begin Proof If P is a tautology then all elements of its truth table are true by Definition ref def tautology so all elements of the truth table for sim P are false therefore sim P is a contradiction by Definition ref def contradiction end Proof end Theorem begin Example label ex rain It is raining or it is not raining is a tautology but it is not raining and it is raining is a contradiction end Example begin Remark Example ref ex rain used De Morgan s Law sim p vee q equiv sim p wedge sim q end Remark j 4 Input Result T Output Definition 3 Tautolo
57. treat the following entries differently T Input index identity_matrix index identity__matrix Chapter 6 Generating Indexes and Glossaries 80 j 4 Input ETEX however treats multiple spaces the same as a single space so the text will appear the same in the index e TeX says that the command printindex is undefined You have forgotten to load the makeidx package 6 1 2 Creating Glossaries Lists of Symbols or Acronyms glossaries package There are a number of packages available to assist producing a list of acronyms such as the acronym package or a glossary such as the nomencl package You can see a list of available packages in the OnLine T X Cat alogue s Topic Index 3 Here I ve chosen to describe the glossaries pack age Firstly it encompasses the functionality of both acronym and nomencl as glossaries allows you to define multiple lists of acronyms lists of symbols or glossaries Secondly I wrote the glossaries package so it s the one with which I am most familiar The glossaries package is very flexible but the downside to that is that it has too many features to cover briefly I m therefore only going to intro duce the basics here If you want more detail you ll have to read the user manual 16 I will use the term glossary to mean a list of terms or a list of notation or a list of symbols or a list of acronyms NOTE If you want to use both glossaries and hyperref you must load
58. your computer Use the button to add basename to the list of arguments as shown in Figure 1 8 Unlike latexmk arara doesn t read the log file to determine what appli cations need to be run Instead you tell arara how to build your document by placing special comments in your source code For example if your document contains the following dL arara pdflatex synctex on arara bibtex arara pdflatex synctex on arara pdflatex synctex on documentclass scrbook DL se Be 4There are some example RC files available at http mirror ctan org support latexmk example_rcfiles Input 4 Input Chapter 1 Introduction 10 Tool Configuration x Name Arara Program __ usr local bin arara Browse Arguments ty View PDF after running Cancel OK Figure 1 8 Adding Arara in the TeXWorks Tool Configuration Dialog Then running arara on the document will run pdflatex bibtex pdflatex and pdflatex on your document Arara knows the rules pdflatex and bibtex It also knows the rules biber makeglossaries and makeindex So if your document has a bibliography an index and glossaries you need to put the following comments in your source code replace bibtex with biber if required l T Input arara pdflatex synctex on arara bibtex arara makeglossaries arara makeindex arara pdflatex synctex on arara pdflate
59. 1 That is each name should be in one of the forms listed in Ta ble 5 1 and multiple authors or editors must be separated with the keyword and EXAMPLE MULTIPLE AUTHORS This example uses the book entry book goossens97 author Goossens Michel and Rahtz Sebastian and Mittelbach Frank title The LaTeX graphics companion illustrating documents with TeX and PostScript publisher Addison Wesley Longman Inc year 1997 T Input 4 Input In this example the keyword is goossens97 That is the identifying key used in cite described below The standard bibliography styles usually convert titles to lower case so the name PostScript is enclosed in curly braces to prevent this from happening Note that curly braces can be used instead of double quotes The above example can just as easily be written Chapter 5 Generating a Bibliography Entry Type article book booklet inbook incollection inproceedings manual mastersthesis misc phdthesis proceedings techreport unpublished 61 Table 5 4 Required and Optional Fields Required Fields author title journal year author or editor title publisher year title author or editor chapter or pages title publisher year author title booktitle publisher year author title booktitle year title author title school year author title school year title year author title instituti
60. 1990s in the Department of Electronic Systems Engineering at the University of Essex and it may well not fit your own requirements If you haven t started your thesis yet go ahead and try this Creating a skeletal document can have an amazing psychological effect on some people for very little effort it can produce a document several pages long Chapter 2 Getting Started 16 which can give you a sense of achievement that can help give you sufficient momentum to get started but of course it s not guaranteed to work with everyone Remember that if you want to use arara see Section 1 1 2 you must add the build rules to the document arara pdflatex synctex on arara pdflatex synctex on documentclass oneside scrbook TIl add the arara rules to sample listings in the event that you want to use arara Since they are comments they will be ignored if you use pdflatex explicitly or if you use another automation method such as latexmk Now think about other requirements What font size have you been told to use 10pt Use the 10pt class option documentclass oneside 10pt scrbook Ilpt Use the 11pt class option documentclass oneside 11pt scrbook I2pt Use the 12pt class option documentclass oneside 12pt scrbook Have you been told to have a blank line between paragraphs and no para graph indentation If so use the parskip full class option documentclass oneside 12pt parskip ful
61. 4 Input With both amsthm and ntheorem you can still define new theorem like en vironments using newtheorem but there is also a starred version of that command which can be used to define unnumbered theorem like environ ments EXAMPLE Suppose I want to have an unnumbered remark environment I can define the environment like this Input in the preamble newtheorem note Note later in the document begin note This is a note about something end note l j 4 Input Result F Output Note This is a note about something Output 4 7 1 The amsthm Package The amsthm package provides three predefined theorem styles plain definition and remark When you define a new theorem like environment with newtheorem it is given the style currently in effect You can change the current style with theoremstyle style name Definition where style name is the name of the theorem style EXAMPLE This example defines six theorem like environments theorem lemma defn conj note and remark The note environment is unnumbered as it s defined us ing the starred version of newtheorem The definitions have been arranged according to the required theorem style Chapter 4 Formatting 55 l T Input theoremstyle plain newtheorem theorem Theorem newtheorem lemma Lemma theoremstyle definition newtheorem defn Definition newtheorem conj Conjecture theoremsty
62. EX Kernel Loads the document class file which sets up the type of document you wish to write See Volume 1 15 4 2 0 DontPrintSemicolon Defined in algorithm2e package Switches off the end of line semi colon See also PrintSemicolon 4 8 doublespacing Defined in setspace package Switches to double line spacing 4 5 DTLgidxAcrStyle long short Defined in datagidx package Formats the long and short form of an acronym 6 2 DTLgidxSetDefaultDB database label Defined in datagidx package Sets the default indexing database 6 2 E Else block Defined in algorithm2e package For use in algorithm like environments to indicate an else block 4 8 ElseIf block Defined in algorithm2e package For use in algorithm like environments to indicate an elseif block 4 8 emph text Defined in ETEX Kernel Symbols NE KSA CHM DOVDOAZZORAHH THOT SAeD Summary of Commands and Environments 112 Toggles the upright and italic slanted rendering of text See Volume 1 15 4 5 1 4 7 end env name Defined in PTEX Kernel Ends an environment Must have a matching begin See Volume 1 15 2 15 2 0 ensuremath maths Defined in PTEX Kernel Ensures that its argument is displayed in maths mode If it s already in maths mode it just displays its argument but if it s not already in maths mode it will typeset its argument in in li
63. K FAQ These are displayed in the margin in square brackets as illustrated on the right You may find FAQ What is these resources useful in answering related questions that are not covered LaTeX in this book On line versions of this book along with associated files are available at http www dickimaw books com latex thesis The links in this docu ment are colour coded internal links are blue external links are magenta To refresh your memory or for those who haven t read Volume 1 through out this book source code is illustrated in a typewriter font with the word input placed in the margin and the corresponding output how it will appear in the PDF document is typeset with the word outpu in the margin EXAMPLE A single line of code is displayed like this This is an textbff example Input The corresponding output is illustrated like this This is an example Output Segments of code that are longer than one line are bounded above and below illustrated as follows thttp www tex ac uk faq Chapter 1 Introduction 2 Line one par Line two par Line three with corresponding output Line one Line two Line three Commands typeset in blue such as par indicate a hyperlink to the com mand definition in the summary Command definitions are shown in a typewriter font in the form documentclass options class file In this case the command being defined is called documentclas
64. KSA CHM DOVDOAZZORAHH THOT SAeD Summary of Commands and Environments 119 Typesets its contents as a proof 4 7 begin proof title Defined in amsthm package Typesets its contents as a proof 4 7 publishers text Defined in scrartcl scrreprt scrbook classes Specifies the publisher set after all the other titling information 2 0 Q qedhere Defined in amsthm package Overrides default location of QED marker in proof environment 4 7 qedsymbol Defined in amsthm package QED symbol used at the end of the proof environment 4 7 R raggedright Defined in TEX Kernel Ragged right paragraph justification See Volume 1 45 2 12 4 4 raggedsection Defined in KOMA Script classes such as scrbook and scrreprt Governs the justification of headings Defaults to raggedright 4 1 ref string Defined in TEX Kernel References the value of the counter linked to the given label A second possibly third run of BTEX is required to ensure the cross references are up to date See Volume 1 45 5 5 4 5 renewcommand cmd n args default text Defined in BTEX Kernel Redefines an existing command See Volume 1 15 8 2 4 1 Return value Defined in algorithm2e package For use in algorithm like environments to indicate a value returned 4 8 rmfamily Defined in PTEX Kernel Switches to the predefined serif
65. M support vector machine pigi l npu Another package option is footnote which will modify the behaviour of newacronym so that the long form is displayed as a footnote on first use For a full list of available options see the glossaries documentation 16 Displaying Terms in the Document Any glossary term that has been defined using newglossaryentry or newacronym as described above can be displayed in the document using one of the commands described in this section There are other less com monly used commands available as well see the glossaries documentation 16 for details of them Each term has an associated first use flag This is a boolean true false switch that determines whether or not the entry has been used This is how the glossaries package determines whether to display the value of the first key or to display the value of the text key You can reset this flag using glsreset label Definition Conversely you can unset it using glsunset label Definition To display a term that has previously been defined using either newglossaryentry or newacronym you can use one of the following com mands gls options label insert Definition glsp1 options label insert Definition Chapter 6 Generating Indexes and Glossaries 84 Gls options label insert Definition Glsp1 options label insert Definition These commands all have the same syntax label is
66. Output Definition T Input Chapter 4 Formatting 58 l j 4 Input Once you have defined the style you can now use it For example in the preamble l T Input theoremstyle note newtheorem scnote Note l j 4 Input This defines a theorem like environment called scnote You can now use it later in the document l T Input begin scnote This is an example of a theorem like environment end scnote l j 4 Input This produces F Output NOTE 4 This is an example of a theorem like environment l pow Output 4 7 2 The ntheorem Package The ntheorem package provides nine predefined theorem styles listed in Ta ble 4 1 The default is plain When you define a new theorem like envi ronment with newtheoren it is given the style currently in effect You can change the current style with theoremstyle style name Definition where style name is the name of the theorem style In addition to these styles you can also use theoremheader font declarations Definition to set the header font to declarations which should consist of font decla ration commands such as normal font theorembody font declarations Definition to set the body font to declarations and theoremnumbering style Definition Recall the ex unit from Volume 1 15 2 17 4 1 Chapter 4 Formatting 59 Table 4 1 Predefined Theorem Styles Provided by ntheorem plain Like th
67. TeX m Default pdfLaTeX v Hide console output Automatically v Restore Defaults Cancel OK Figure 1 4 TeXwork s Preferences Dialog Box Tool Configuration Name LaTeXmk Program live default bin x86_64 linux latexmk Browse Arguments 7 pdflatex q pdflatex synctexop pdf bibtex 7 View PDF after running Figure 1 5 Adding LaTeXmk in the TeXWorks Tool Configuration Dialog Chapter 1 Introduction 7 Unfortunately adding makeindex texindy or makeglossaries to LaTeXmk s set of rules is more complicated For this you need to create a configura tion initialisation RC file The name and location of this file depends on your operating system For example on a Unix like operating system this may be HOME latexmkrc You will need to consult the latexmk manual 1 for further details Once you ve found out the name and location of the RC file for your operating system you can use the text editor of your choice to create this file To add makeglossaries you need to type the following in the RC file add_cus_dep glo gls 0 makeglossaries add_cus_dep acn acr 9 makeglossaries sub makeglossaries system makeglossaries _ 0 To add makeindex you need to type the following add_cus_dep idx ind 0 makeindex sub makeindex system makeindex _ 0 idx
68. TeX to Sort and Collate Indexes or Glossaries datagidx package roce ned ww ew dw awdw dR ED Sew HA 96 ABSTRACT This book is aimed at PhD students who want to use ETE X to typeset their PhD thesis If you are unfamiliar with ETpX I recommend that you first read Volume 1 PTX for Complete Novices 15 vi CHAPTER 4 INTRODUCTION Many PhD students in the sciences are encouraged to produce their PhD thesis in FTpx particularly if their work involves a lot of mathematics In addition these days ET X is no longer the sole province of mathematicians and computer scientists and is now starting to be used in the arts and so cial sciences see for example some of the topics listed in the TEX online catalogue 3 This book is intended as a brief guide on how to typeset the various components that are usually required for a thesis If you have never used ETEX before I recommend that you first read Volume 1 BTFX for Complete Novices 15 as this book assumes you have a basic knowl edge of BPTEX As with Volume 1 I ll be using PDFETEX and TeXWorks If you are creating a DVI file or you are using a different editor you ll have to adapt the instructions A N If you are unfamiliar with terms such as preamble read Volume 1 15 2 If you don t know how to find package documentation read Volume 1 15 1 1 Throughout this document there are pointers to related topics in the UK List of TEX Frequently Asked Questions U
69. Using Tex to Write a PhD Thesis Version 1 3 Nicola L C Talbot Dickimaw Books www dickimaw books com 16t March 2013 Copyright 2007 Nicola L C Talbot Permission is granted to copy distribute and or modify this document under the terms of the GNU Free Documentation License Version 1 2 or any later version published by the Free Software Foundation with no In variant Sections no Front Cover Texts and one Back Cover Text If you choose to buy a copy of this book Dickimaw Books asks for your support through buying the Dickimaw Books edition to help cover costs A copy of the license is included in the section entitled GNU Free Documentation License The base URL for this document is http www dickimaw books com latex thesis CONTENTS ABSTRACT 4 INTRODUCTION 1 1 Building Your Document e e eae Boke os e e e a LILL bale mR eae ua aa s a e A re er a d LIS Ara o socion s ai oe e a ae Boe eae a a ee aS a 2 GETTING STARTED 3 SPLITTING A LARGE DOCUMENT INTO SEVERAL FILES 4 FORMATTING 4 1 Changing the Document Style 4 4 4 26 see 8s bu ees 4 2 Changing the Page Style 4 24464 b Re Re ewe eed 4 0 Double Spacing lt 4 5 4 ee oa Oo OG Ra ee teas 44 MI the Title PANE 6 ek che we te SESE Oe ee ee Sas 4 5 Listings and Other Verbatim Text S0 TaDDNG sale Sle csar eh ek xe ok Bh oR oe ek we aoe ote 5 of MOPS hoe kM BAe EC EEE SEE ee eee es SSS 4 7 1 The amsthm Package ik ce e
70. Xt LuaTeX er dat ConTeXt pdfTeX title s submitted for the degree of Doctor of Phil ConTeXt XeTeX m see O of Something University of Somewhere Makelndex Figure 1 2 Selecting BibTeX from the Drop Down Menu If the tool you require isn t listed in the drop down box you will have to add it For example to add makeglossaries to the list of available tools in TeXworks you need to select Edit Preferences which will open the TeX works Preferences dialog Make sure the Typesetting tab is selected and click on the lower button next to the Processing tools list This will open the Tool Configuration dialog Set the Name field to the name of the application as you want it to appear in the tool list for example MakeGlos saries Then click on the Browse button to find the application on your computer Next you need to click on the button next to the Arguments list Set the argument to basename Since makeglossaries doesn t modify the PDF uncheck the View PDF after running box see Figure 1 3 Tool Configuration x Name MakeGlossaries Program _ dist scripts glossaries makeglossaries Browse Arguments Jk View PDF after running Cancel OK Figure 1 3 Adding Makeglossaries to the list of tools in TeXworks This is a bit of a hassle if not downright confusing for a beginner and Chapter 1 Introduction 5 even more so when you have glossaries and an i
71. a directive in your source code arara makeglossaries Input If you are using latexmk then make sure you have added the custom depen dencies for gls as described in Section 1 1 1 If you are not using any auto mated tool to build your document you will have to invoke makeglossaries between PDF BTEX runs see Section 1 1 Adding to Listing 19 Listing 20 C T Input In the preamble arara pdflatex synctex on arara biber arara makeglossaries arara makeindex arara pdflatex synctex on arara pdflatex synctex on documentclass oneside 12pt scrbook usepackage toc acronym glossaries newglossary nlg notation not ntn Notation makeglossaries newglossaryentry matrix the label name matrix the term description a rectangular table of elements brief description plural matrices the plural newacronym svm SVM support vector machine newglossaryentry not set label type notation glossary type tor a lot of other useful Perl scripts such as epstopdf Chapter 6 Generating Indexes and Glossaries 90 name mathcal S description A set sort S Later in the document Glspl matrix are usually denoted by a bold capital letter such as mathbf A The gls matrix s i j th element is usually denoted a_ ij Gls matrix mathbf I is the identity gls matrix First use gls svm Next
72. abel insert Acrlong options label insert acrfull options label insert Acrfull options label insert These commands don t affect the first use flag The first two acrshort and Acrshort will display the abbreviation only the middle two acrlong and Acrlong will display the long form only and the last two acrfull and Acrfull display both the long and short form These commands have the same syntax as gls and Gls If you find these commands a little long winded to type you can use the package option shortcuts which will provide shorter synonyms such as acs acl and acf This option also defines ac which is equivalent to gls See the glossaries user guide 16 for further details ANOTHER EXAMPLE Suppose I have defined an acronym as follows newacronym svm SVM support vector machine Then later in the document First use gls svm Next use gls svm Short acrshort svm Long acrlong svm Full acrfull svm l T Input 4 Input T Output Output Definition Definition Definition Definition Input T Input 4 Input Chapter 6 Generating Indexes and Glossaries 86 produces First use support vector machine SVM Next use SVM Short SVM Long support vector machine Full support vector machine SVM l Recall from Volume 1 15 2 13 NOTE Avoid using commands like gls in section heading
73. ainmatter and backmatter 2 0 G Gls options label insert Defined in glossaries package Displays a glossary term according to its first use flag The first letter of the term is converted to uppercase 6 1 Gls format label Defined in datagidx package Displays a glossary or index term with the first letter converted to uppercase 6 2 Symbols NE KSA CHM DROVOAZZORASH TOTS ACeD Summary of Commands and Environments 113 gls format label Defined in datagidx package Displays a glossary or index term 6 2 gls options label insert Defined in glossaries package Displays a glossary term according to its first use flag 6 1 glsadd label Defined in datagidx package Adds the given entry to the glossary or index without displaying any text 6 2 glsadd options label Defined in glossaries package Adds the given entry to the glossary without displaying any text 6 1 glsaddall database name Defined in datagidx package Adds all the defined entries in the named database without displaying any text 6 2 glsaddall1 options Defined in glossaries package Adds all the defined entries without displaying any text 6 1 glsentryfirst label Defined in glossaries package Displays the value of the first key for a glossary entry 6 1 glsentrytext label Defined in glossaries package Displays the value
74. al reference in square brackets If you re using bibtex rather than biblatex described below you can override this using a number of packages One such package is natbib This comes with some drop in replacements for the standard bibliography styles plainnat unsrtnat and abbrvnat The natbib package comes with a variety of package options but I m just going to mention a few of them authoryear for author year citations default numbers for numerical citations super for superscripted numerical citations round for round parentheses square for square parentheses and sort amp compress which sorts multiple citations and compresses consecutive numbers into a range For example 4 2 8 3 will become 2 4 8 Input 4 Input T Input 4 Input Input Chapter 5 Generating a Bibliography 65 So for citations that give the author and year rather than a number you need to load natbib in the preamble usepackage round natbib Input and specify one of the natbib bibliography styles bibliographystyle plainnat Input There are two main replacements for cite citet pre post Rey Definition for textual citations and citep pre post Rey Definition for parenthetical citations Unlike cite these commands have two optional arguments The sec ond post is a suffix the same as cite s only optional argument The first optional argument pre is a prefix If only one optional argument is present it i
75. ally or noncommercially Secondarily this License preserves for the author and publisher a way to get credit for their work while not being considered responsible for modifications made by others This License is a kind of copyleft which means that derivative works of the document must themselves be free in the same sense It complements the GNU General Public License which is a copyleft license designed for free software We have designed this License in order to use it for manuals for free software because free software needs free documentation a free program should come with manuals providing the same freedoms that the software does But this License is not limited to software manuals it can be used for any textual work regardless of subject matter or whether it is published as a printed book We recommend this License principally for works whose purpose is instruction or reference 1 APPLICABILITY AND DEFINITIONS This License applies to any manual or other work in any medium that contains a notice placed by the copyright holder saying it can be distributed under the terms of this License Such a notice grants a world wide royalty free license unlimited in duration to use that work under the conditions stated herein The Document below refers to any such manual or work Any member of the public is a licensee and is addressed as you You ac cept the license if you copy modify or distribute the work in a way r
76. an before say adze since comes before a To get around this you need to specify the sort key index AEolian AE olian Now makeindex will put olian after adze Here s another example that indexes a function or method index sqrtQ texttt sqrt You will also need to do something similar if you are entering the char acter directly via the inputenc package indexfelite lite Note however that you don t need to do this if you are using xindy You just need to make sure you match the input encoding For example arara pdflatex synctex on arara texindy language english codepage latin1 arara pdflatex synctex on documentclass 12pt oneside scrbook usepackage latin1 inputenc usepackage makeidx Later in the document index lite Setting the Location Format Each index entry has an associated location list that directs the reader to the pages in the document associated with that entry For example if you look up index in this book s index the entry s location list will include this page If the location list is long it s helpful to highlight a particular location to direct the reader to the principle definition or discussion related to that term This is usually done by formatting the relevant location in a different font for example bold or italic You can specify the format for the location by writing the argument of index in the
77. and the machine generated HTML PostScript or PDF produced by some word processors for output purposes only The Title Page means for a printed book the title page itself plus such following pages as are needed to hold legibly the material this License requires to appear in the title page For works in formats which do not have any title page as such Title Page means the text near the most prominent appearance of the work s title preceding the beginning of the body of the text GNU Free Documentation License 131 A section Entitled XYZ means a named subunit of the Document whose title either is precisely XYZ or contains XYZ in parentheses follow ing text that translates XYZ in another language Here XYZ stands for a specific section name mentioned below such as Acknowledgements Dedications Endorsements or History To Preserve the Title of such a section when you modify the Document means that it remains a section Entitled XYZ according to this definition The Document may include Warranty Disclaimers next to the notice which states that this License applies to the Document These Warranty Disclaimers are considered to be included by reference in this License but only as regards disclaiming warranties any other implication that these Warranty Disclaimers may have is void and has no effect on the meaning of this License 2 VERBATIM COPYING You may copy and distribute the Doc
78. any typographical corrections Whilst they could write these comments on a separate piece of paper cross referencing the page in the thesis it is more efficient for the comments to actually be on the relevant page of the thesis That way as they go through the manuscript during your viva they can easily see the comments questions or criticisms they wish to raise alongside the corresponding text If you present them with a single spaced document with narrow margins you are effectively telling them that you don t want them to criticise your work 2 Don t try to pad your thesis with irrelevant information This includes adding items in your bibliography that are not referenced in the text adding figures or tables that are not explained in the text and supplying all the source code you have written The outcome of your viva will not depend on the physical size of your thesis but on the clarity of your writing and on the quality of your work 3 Clearly delineate your thesis through the use of chapters and sections outlining your original aims and objectives an overview of the subject matter including references to other people s work in the area the methods you employed to extend or innovate the field your results and conclusions 4 Make sure your references include some recent journal or conference papers to illustrate that you are aware of new developments in your field Remember that due to the nature of publishing most books are
79. ariety of commands that may be used within the algorithm envi ronment Some of the commands are described below but for a complete list you should consult the algorithm2e documentation 4 First there are the commands for the algorithm input output and data KwiIn input KwOut output KwData input KwResult oufput Next there are commands for basic keywords KwTo KwRet value Return value T Output Output Definition Input Definition Definition Definition Definition Chapter 4 Formatting 45 There are a lot of conditionals but here s a selection I condition then block ulf condition then block without end ElseIf else if block Definition uElseIf else if block without end Else else block Similarly there are a lot of loops but here s a selection For condition body While condition body hii EXAMPLE The above algorithm can be written using the algorithm2e environment as follows this document has used the algo2e package option Listing 14 ete begin falgorithm2e caption Gauss Seidel Algorithm label alg gauss seidel KwiIn scalar epsilon matrix mathbf A a_ ij vector vec b and initial vector vec x 0 For k leftarrow 1 KwTo maximum iterations For i leftarrow 1 KwTo n x_i k frac b_i sum_ j 1 i 1 a_ ij x_j k sum_ j i 1 n a_ ij x_
80. at the Document is released under this License A Front Cover Text may be at most 5 words and a Back Cover Text may be at most 25 words A Transparent copy of the Document means a machine readable copy represented in a format whose specification is available to the general public that is suitable for revising the document straightforwardly with generic text editors or for images composed of pixels generic paint programs or for drawings some widely available drawing editor and that is suitable for input to text formatters or for automatic translation to a variety of formats suitable for input to text formatters A copy made in an otherwise Transparent file format whose markup or absence of markup has been arranged to thwart or discourage subsequent modification by readers is not Transparent An image format is not Transparent if used for any substantial amount of text A copy that is not Transparent is called Opaque Examples of suitable formats for Transparent copies include plain ASCII without markup Texinfo input format LaTeX input format SGML or XML using a publicly available DTD and standard conforming simple HTML PostScript or PDF designed for human modification Examples of trans parent image formats include PNG XCF and JPG Opaque formats include proprietary formats that can be read and edited only by proprietary word processors SGML or XML for which the DTD and or processing tools are not generally available
81. autology then sim P is a contradiction and conversely begin proof If P is a tautology then all elements of its truth table are true by Definition ref def tautology so all elements of the truth table for sim P are false therefore sim P is a contradiction by Definition ref def contradiction end proof end theorem begin xmp 1 label ex rain It is raining or it is not raining is a tautology but it is not raining and it is raining is a contradiction end xmp1 begin remark Example ref ex rain used De Morgan s Law sim p vee q equiv sim p wedge sim q end remark l 4 Input Result f i amp Definition 1 Tautology A tautology is a proposition that is always true awe for any of its variables Definition 2 Contradiction A contradiction is a proposition that is always false for any value of its variables Theorem 4 5 If proposition P is a tautology then P is a contradiction and conversely Proof If P is a tautology then all elements of its true table are true by Definition 1 so all elements of the truth table for P are false therefore P is a contradiction by Definition 2 Example 1 It is raining or it is not raining is a tautology but it is not raining and it is raining is a contradiction Chapter 4 Formatting 37 Remark 1 Example 1 used De Morgan s Law p Vq pA q A new theore
82. class files But which one The scrreprt class is the one usually recommended for a report or thesis It defaults to one sided and has an abstract environment but it doesn t define frontmatter mainmatter or backmatter The scrbook class does define those commands but it doesn t provide an abstract environment and defaults to two sided layout So you can either do T Input documentclass scrreprt title A Sample Thesis author A N Other begin document maketitle pagenumbering roman tableofcontents chapter Acknowledgements begin abstract This is the abstract end abstract pagenumbering arabic chapter Introduction end document l j 4 Input or you can do 15 Chapter 2 Getting Started 14 documentclass oneside scrbook title A Sample Thesis author A N Other begin document maketitle frontmatter tableofcontents chapter Acknowledgements chapter Abstract This is the abstract mainmatter chapter Introduction end document T Input j 4 Input I m going to use the second approach simply out of personal preference The KOMA Script options mentioned in this book are available for both scrreprt and scrbook so choose whichever class file you feel best suits your thesis Unless you have been told otherwise I recommend that you start out with a skeletal document that looks something like the following Listing 1
83. crpage2 package Used in commands like ihead to insert the current running header 4 2 hfill Defined in PTEX Kernel Inserts a horizontal space that will expand to fit the available width 4 4 hspace length Defined in PTEX Kernel Inserts a horizontal gap of the given width 4 4 I If condition block Defined in algorithm2e package For use in algorithm like environments to indicate an if statement 4 8 ifoot scrplain scrheadings Defined in scrpage2 package Indicates what to put in the inner footer area for the scrplain and scrheadings page styles 4 2 ihead scrplain scrheadings Defined in scrpage2 package Indicates what to put in the inner heading area for the scrplain and scrheadings page styles 4 2 include file name Defined in TEX Kernel Issues a clearpage creates an associated auxiliary file inputs file name and issues another clearpage See also input 5 0 includeonly file list Defined in TeX Kernel Preamble Only Lists which of the files that are included using include should be read in Any files not in the list won t be included 3 0 index text Defined in PTEX Kernel Adds indexing information to an external index file The command makeindex must be used in the preamble to enable this command The external index file must be post processed with an indexing application such as makeinde
84. d while reading file thesis biblatex aux I found no bibstyle command while reading file thesis biblatex aux then you have inadvertently used bibtex instead of biber If you actually want to use bibtex with the biblatex package remember that you have to specify bibtex using usepackage backend bibtex biblatex Input CHAPTER 6 GENERATING INDEXES AND GLOSSARIES Most theses will need a glossary of terms or a list of acronyms or notation It s less likely that you ll need an index in your thesis but since the same mechanism is used to generate glossaries and indexes both topics are cov ered in this chapter There are two basic methods of generating a glossary or index 1 The glossary or indexing information is written to a temporary file by ETEX while the document is being built An external application is then used to collate and sort the entries defined in that temporary file and ETEX code to display the result is written to another file You then need to run PDF ETEX on your document to ensure the sorted and collated glossary or index is displayed You may then need an additional BT X run to ensure the table of contents is up to date This is similar to the way you had to use bibtex or biber between LaTeX runs in the previous chapter 2 The glossary or indexing information is collated and sorted by FTpxX during the document build At least two runs are required but no external indexing application is needed T
85. distribute and or modify this document under the terms of the GNU Free Documentation License Version 1 2 or any later ver sion published by the Free Software Foundation with no Invariant Sections no Front Cover Texts and no Back Cover Texts A copy of the license is included in the section entitled GNU Free Docu mentation License If you have Invariant Sections Front Cover Texts and Back Cover Texts replace the with Texts line with this with the Invariant Sections being LIST THEIR TITLES with the Front Cover Texts being LIST and with the Back Cover Texts being LIST If you have Invariant Sections without Cover Texts or some other com bination of the three merge those two alternatives to suit the situation If your document contains nontrivial examples of program code we recommend releasing these examples in parallel under your choice of free software license such as the GNU General Public License to permit their use in free software HISTORY 16 March 2013 Version 1 3 e Added recap on building the document e Added sections on latexmk and arara e Changed examples to use KOMA e Added sections on jabref natbib and biblatex e Added information about the listings siunitx amsthm ntheorem and algo rithm2e packages e Added section on datagidx to the chapter on indexes and glossaries e Added summary section e Some sections have been reordered e Removed section on modifying textual tags s
86. e bib file but it doesn t appear in the bibliography check to make sure that the field is required or optional for that type of entry and check the spelling You can avoid this problem by using a bibliography management system such as JabRef e Check the BIBTEX log file blg for messages e If you get an error that looks something like ERROR Cannot find control file thesis ref bcf did you pass the backend biber option to BibLaTeX then you have inadvertently used biber see below instead of bibtex e If you get an error that looks something like I found no citation commands while reading file thesis1 aux I found no bibdata command while reading file thesis1 aux I found no bibstyle command while reading file thesis1l aux then you probably forgot to use the bibliography and bibliographystyle commands in your document 5 5 Biblatex The biblatex package is a reimplementation of PTEX s bibliographic facilities The formatting of the bibliography is governed by ETEX commands instead of selecting a BibTeX style as was done with bibliographystyle described above This package uses biber instead of BibTeX to process the biblio graphic database and sort the entries Legacy BibTeX is also supported but with a reduced feature set The biblatex package also supports multiple bib liographies for example a bibliography for each chapter in the document The biblatex package requires e T X so make sure y
87. e 60 61 year 61 66 bib entry types article 59 61 book 59 61 booklet 59 61 conference 59 inbook 59 61 incollection 59 61 inproceedings 59 64 manual 59 61 mastersthesis 59 61 misc 59 61 phdthesis 59 64 proceedings 59 64 techreport 59 61 unpublished 59 61 biber 3 46 66 70 72 98 bibitem 47 59 110 biblatex package 46 64 66 72 118 backend 70 124 backref 70 doi 70 isbn 70 sorting 68 style 70 url 70 bibliography 63 65 66 70 110 bibliographystyle 63 65 66 110 bibtex 3 46 64 66 70 72 bibtex styles bst abbrv 63 abbrvnat 64 alpha 63 plain 63 plainnat 64 unsrt 63 unsrtnat 64 book class 21 C capitalisewords 94 96 110 caption 43 110 112 120 centering 21 24 110 cfoot 22 110 chapter 13 15 19 20 110 chead 22 110 Cite 71 144 cite 47 59 60 62 65 71 1414 118 120 citep 65 68 1114 citet 65 68 111 class file options 10pt 16 11pt 16 12pt 16 bibliography KOMA 64 letterpaper 2 parskip KOMA 16 class files cls book 21 memoir 21 report 21 scrbook 2 13 14 21 scrreprt 13 14 clearpage 18 99 111 114 counters algocf 44 page 87 Symbols NK KS lt SCGHNDPOTDOAZZOAHH TOT OOSD Index CTAN 2 3 Or 40 4a 89 105 D datagidx package 90 94 datatool package 90 date 14 18 111 documentclass 13 14 16 18 111 DontPrintSemicolon 42 111 118 doublespacing 24 111 DTLgidxAcrStyle 93 111 DTLgidxSetDefaultDB 91 111 E
88. e eznObedu Documents nontiction latex thesis examples thesis rer bip oOx File Edit Search View BibTeX Tools Plugins Options Help Daut Stina 25 AARNEN 4 oF thesis ref bib Journal Owner Tim Bibtex Search All Fields ne j Clear Incremental Float Filter Show results in dialog Global search settings xa BibTex source re I Required fields n Optional fields E Optional fields 2 E General E Abstract E Review me Author Gavin C Cawley and Nicola L C Talbot Inpr Cawley et al Sparse multinomial logistic 2007 ezn06 2012 Cawle Book Turabian A manual for writers of ter 1996 ezn06 2012 turabi Efficient approximate leave one out cross validation for kernel logistic regression 2008 06 Cawley2008 Figure 5 17 JabRef in BibLaTeX Mode Setting the Publication Date Chapter 5 Generating a Bibliography 70 If you want a list of back references in the bibliography referring to the pages on which the entries were cited you can use the backref option usepackage backref biblatex The default database backend is biber which is recommended but if for some reason you want to stick to using bibtex you can use the backend option to switch to bibtex usepackage backend bibtex biblatex There are also options that govern whether certain fields are printed in the bibliography such
89. e old one on explicit permission from the previous publisher that added the old one The author s and publisher s of the Document do not by this License give permission to use their names for publicity for or to assert or imply endorsement of any Modified Version 5 COMBINING DOCUMENTS You may combine the Document with other documents released un der this License under the terms defined in section 4 above for modified versions provided that you include in the combination all of the Invariant Sections of all of the original documents unmodified and list them all as Invariant Sections of your combined work in its license notice and that you preserve all their Warranty Disclaimers The combined work need only contain one copy of this License and multiple identical Invariant Sections may be replaced with a single copy If there are multiple Invariant Sections with the same name but different contents make the title of each such section unique by adding at the end of it in parentheses the name of the original author or publisher of that section if known or else a unique number Make the same adjustment to the section titles in the list of Invariant Sections in the license notice of the combined work In the combination you must combine any sections Entitled History in the various original documents forming one section Entitled History like wise combine any sections Entitled Acknowledgements and any sections Entitl
90. e original BTEX style break Header is followed by a line break change Like plain but header and number interchanged changebreak Combination of change and break margin Number is set in the margin marginbreak Like margin but header followed by a line break nonumberplain Like plain but without the number nonumberbreak Like break but without the number empty No number and no name Only the optional argu ment is used in the header to set the appearance of the theorem number where style may be one of arabic roman Roman alph Alph greek Greek or fnsymbol Remember that the above commands all need to be used before the new theorem like environment is defined For additional commands that affect the style of the theorems see the ntheorem documentation 10 EXAMPLE in the preamble theoremstyle marginbreak theorembody font normal font newtheorem note Note chapter later in the document begin note This is a sample note The number is in the margin end note Result Note This is a sample note The number is in the margin If you use the standard package option to ntheorem it will automatically define the following environments Theorem Lemma Proposition Corollary Satz Korollar Definition Example Beispiel Anmerkung Bemerkung Remark Proof and Be weis Unlike amsthm s proof environment ntheorem s Proof environment appends its optional argument in parentheses if present
91. e those words in braces to instruct BibTeX not to convert their case Multiple editors must also be separated by the and keyword as shown in Figure 5 10 For that entry the editors are listed as Bernhard Sch lkopf and John Platt and Thomas Hofmann Note that if I don t use the inputenc package I need to change this to Bernhard Sch o lkopf and John Platt and Thomas Hofmann FAQ Case changing oddities FAQ Accents in bibliographies Input Input T Input 4 Input Input Input Chapter 5 Generating a Bibliography 55 JabRef home eznObedu Documents nontiction latex thesis examples thesis rer bip File Edit Search View BibTeX Tools Plugins Options Help Dash Sohne se 4BEN 4 AUO oF thesis ref bib i Journal Owner Timesta Article Cawley and Talbot Efficient approximate leave one out 2008 Machin ezn06edu 2012 1 Cawley Book Turabian A manual for writers of term papers 1996 ezn06edu 2012 1 turabia X I Required fields Em Optional fields E General m Abstract E Review BibTex source Gavin C Cawley and Nicola L C Talbot and Mark Girolami Sparse multinomial logistic regression via Bayesian L1 regularisation z a Q 8 a S A Booktitle Advances in Neural Information Processing Systems 19 G Cawley2007 Status Added new inproceedings entry Figure 5 9 JabRef Adding a Conference Paper
92. e word matrix is matrices not matrixs so the term needs the plural form set explicitly newglossaryentry matrix the label name matrix the term description a rectangular table of elements brief description plural matrices the plural The glossaries package also provides the shortcut command newacronym key val list label abbrv long The default behaviour of this command is equivalent to newglossaryentry label name abbrv description long text abbrv first long abbrv plural abbrv s firstplural long s abbrv s key val list EXAMPLE newacronym svm SVM support vector machine is equivalent to 4 Input T Input 4 Input T Input 4 Input Definition Input 4 Input Input Input Chapter 6 Generating Indexes and Glossaries 85 newglossaryentry svm the label name SVM description support vector machine first support vector machine SVM firstplural support vector machines SVMs text SVM plural SVMs l j 4 Input There are some package options that modify the behaviour of newacronym For example the package option description changes newacronym so that you need to explicitly set the description in the optional argument For example l F usepackage description glossaries ee newacronym description a statistical pattern recognition technique svm SV
93. eX Archive Network CTAN s obsolete tree http mirror ctan org obsolete Stefan Kottwitz also has a list of obsolete classes and packages in his TeXblog The other thing 12nttp mirror ctan org Input 4 Input T Output Output Definition Input Input Chapter 1 Introduction 5 to do is check the package s entry on CTAN 2 to see if it has been depre cated For example suppose someone tells you to use the glossary package If you go to http ctan org pkg glossary it will tell you that the glossary package is no longer supported and that it s been replaced by the glossaries package Similarly if you go to http ctan org pkg epsfig it will tell you that the epsfig package is obsolete and you should use graphicx instead 1 1 Building Your Document To typeset build compile or LaTeX your document means to run the pdflatex or latex executable on your document source code If you are using a front end such as TeXworks WinEdt TeXstudio or TeXnicCenter this usually just means clicking on the appropriate button or selecting the appropriate menu item See Volume 1 15 3 for further details It s important to remember that a front end is an interface It s not for example TeXworks that is creating your PDF When you click on the typeset button TeXworks tells the operating system to run the required executable This is usually pdflatex but there are other executables t
94. ed Dedications You must delete all sections Entitled Endorsements 6 COLLECTIONS OF DOCUMENTS You may make a collection consisting of the Document and other docu ments released under this License and replace the individual copies of this License in the various documents with a single copy that is included in the collection provided that you follow the rules of this License for verbatim copying of each of the documents in all other respects You may extract a single document from such a collection and distribute it individually under this License provided you insert a copy of this License into the extracted document and follow this License in all other respects regarding verbatim copying of that document 7 AGGREGATION WITH INDEPENDENT WORKS A compilation of the Document or its derivatives with other separate and independent documents or works in or on a volume of a storage or distribution medium is called an aggregate if the copyright resulting from the compilation is not used to limit the legal rights of the compilation s users beyond what the individual works permit When the Document is GNU Free Documentation License 135 included in an aggregate this License does not apply to the other works in the aggregate which are not themselves derivative works of the Document If the Cover Text requirement of section 3 is applicable to these copies of the Document then if the Document is less than one half of the en
95. ed to the most recently incremented cross referencing counter in the current scope See Volume 1 15 5 5 2 0 large Defined in Most document classes Switches to large sized text See Volume 1 15 4 5 2 4 1 leftarrow Defined in BTEX Kernel Math Mode Left arrow See Volume 1 15 9 4 7 4 8 listoffigures Defined in Most classes that have the concept of document structure Inserts the list of figures A second possibly third run is required to ensure the page numbering is correct 2 0 listoftables Defined in Most classes that have the concept of document structure Inserts the list of tables A second possibly third run is required to ensure the page numbering is correct 2 0 lstinline opts char code char Defined in listings package Typesets code as an inline code snippet 4 5 lstinputlisting options filename Defined in listings package Symbols NE KSA CHM DOVDOAZZORAHH THOT SAeD Summary of Commands and Environments 116 Reads in filename and typesets the contents as displayed code 4 5 begin 1stlisting options Defined in listings package Typesets the contents of the environment as displayed code 4 5 Istlistoflistings Defined in listings package Prints a list of listings for those listings with the caption set 4 5 lstset options Defined in listings package Sets optio
96. em body fonts to declarations 4 7 theoremheader font declarations Defined in ntheorem package Changes the current theorem header fonts to declarations 4 7 theoremnumbering style Defined in ntheorem package Changes the current theorem numbering style to style 4 7 theoremstyle style name Defined in ntheorem and amsthm packages Changes the current theorem style to style name 4 7 title text Defined in Most classes that have the concept of a title page Specifies the document title This command doesn t display any text so may be used in the preamble but if it s not in the preamble it must be placed before maketitle 2 0 titlehead ftext Defined in scrartcl scrreprt scrbook classes Specifies the title header typeset at the top of the title page 2 0 begin titlepage Defined in Most classes that have the concept of a title page The contents of this environment are displayed on a single column page with no header or footer and the page counter is set to 1 4 4 ttfamily Defined in PTEX Kernel Switches to the predefined monospaced font See Volume 1 15 4 5 1 4 5 U uElseIf condition block Defined in algorithm2e package Like ElseIf but doesn t put end after block 4 8 ul condition block Defined in algorithm2e package Like If but doesn t put end after block 4
97. ending on whether or not the entry has already been used Similarly glspl and Glsp1 will display the value of the firstplural or plural key depending on whether or not the entry has already been used The upper case forms Gls and Glspl will capitalise the first letter EXAMPLE Suppose I have defined the following entry newglossaryentry matrix the label name matrix the term description a rectangular table of elements brief description plural matrices the plural l 4 Input Input Then later in the document Chapter 6 Generating Indexes and Glossaries 85 Gispl matrix are usually denoted by a bold capital letter such as mathbf A The gls matrix s i j th element is usually denoted a_ ij Gls matrix mathbf I is the identity gls matrix l J will display Matrices are usually denoted by a bold capital letter such as A The matrix s i j th element is usually denoted aj Matrix I is the identity matrix If you have used the symbol key when you defined a term you can access its value with glssymbol options label insert This has the same syntax as commands like gls but it doesn t affect or query the first use flag Terms that have been defined using newacronym can also be referenced using the commands acrshort options label insert Acrshort options label insert acrlong options l
98. equiring permission under copyright law 129 GNU Free Documentation License 130 A Modified Version of the Document means any work containing the Document or a portion of it either copied verbatim or with modifications and or translated into another language A Secondary Section is a named appendix or a front matter section of the Document that deals exclusively with the relationship of the publishers or authors of the Document to the Document s overall subject or to related matters and contains nothing that could fall directly within that overall subject Thus if the Document is in part a textbook of mathematics a Secondary Section may not explain any mathematics The relationship could be a matter of historical connection with the subject or with related matters or of legal commercial philosophical ethical or political position regarding them The Invariant Sections are certain Secondary Sections whose titles are designated as being those of Invariant Sections in the notice that says that the Document is released under this License If a section does not fit the above definition of Secondary then it is not allowed to be designated as Invariant The Document may contain zero Invariant Sections If the Document does not identify any Invariant Sections then there are none The Cover Texts are certain short passages of text that are listed as Front Cover Texts or Back Cover Texts in the notice that says th
99. es l J 4 5 Double Spacing Whilst double spacing is usually frowned upon in the world of modern type setting it is usually a requirement for anything that may need hand written annotations which can include theses This extra space gives the examiners room to write comments I Despite the current digital age many people still use hand written annotations on manuscripts It s unlikely that your examiners have pens that are incompatible with your paper Definition Definition Input 4 Input Input 4 Input Chapter 4 Formatting 24 Double spacing can be achieved via the setspace package You can either set the spacing using the package options singlespacing onehalfspacing or doublespacing or you can switch via the declarations singlespacing onehalfspacing doublespacing So if your thesis has to be double spaced you can do Listing 9 usepackage doublespacing setspace Definition T Input l j 4 Input 4 4 Changing the Title Page Volume 1 15 5 1 described how to lay out the title page using maketitle If this layout isn t appropriate for your school or department s specifications you can lay out the title page manually using the titlepage environment instead of maketitle Within this environment you can use hspace length and vspace length to insert horizontal and vertical spacing The unstarred versions are ignored if they occur at the sta
100. flatex synctex on arara biber arara pdflatex synctex on arara pdflatex synctex on documentclass oneside scrbook usepackage backend biber biblatex addbibresource thesis refs bib l j 4 Input where thesis refs bib is the name of my bibliography database see Sec tion 5 1 and the end of the document looks like l T Input printbibliography end document l j 4 Input Elsewhere in the document I need to cite some of the entries in my bibli ography database Chapter 5 Generating a Bibliography 72 First of all let s cite a book parencite wainwright93 now let s cite a journal paper and a conference proceedings parencite cawley96 talbot97 Finally let s cite a chapter in a book parencite Chapter 9 goossens97 If you want to build the document using arara Section 1 1 2 remember to include the arara comments as shown above If you are using latexmk Section 1 1 1 remember to use the bibtex option as illustrated in Figure 1 5 If you re not using an automated method such as arara or latexmk you need a PDFETEX run a biber run or bibtex if you ve chosen that as your backend followed by two more PDFBTEX runs 5 5 1 Troubleshooting Most of the comments from the BIBTEX troubleshooting section also apply here If you get an error that looks like Input 4 Input I found no citation commands while reading file thesis biblatex aux I found no bibdata comman
101. g 1 env arg n Defined in Tex Kernel Starts an environment Must have a matching end See Volume 1 15 2 15 2 0 bfseries Defined in PTEX Kernel Switches to the bold weight in the current font family See Volume 1 15 4 5 1 4 1 bibitem tag Rey Defined in PTEX Kernel Indicates the start of a new reference in the bibliography May only be used inside the contents of thebibliography environment See Volume 1 15 5 6 5 1 bibliography bib list Defined in ETEX Kernel Inputs the bb1 file if it exists and identifies the name s of the bibliography database files where the citations are defined 5 2 bibliographystyle style name Defined in TEX Kernel Specifies the bibliography style to be used by bibtex 5 2 C capitalisewords text Defined in mfirstuc package Converts the initial letter of each word in fext to uppercase 6 2 caption short caption caption text Defined in TEX Kernel Inserts the caption for a float such as a figure or table See Volume 1 15 7 4 8 centering Defined in PTEX Kernel Switches the paragraph alignment to centred See Volume 1 15 2 12 4 1 cfoot scrplain scrheadings Defined in scrpage2 package Indicates what to put in the centre footer area for the scrplain and scrheadings page styles 4 2 chapter short title title Defined in Boo
102. ge allows you to define databases that you can access in your document The datagidx package has a special interface to this facil ity that allows you to define databases for the purposes of indexing These databases and their definitions must be defined in the preamble In this sec tion the term indexing will be used to refer to either indexes or glossaries as the same mechanism is used for both tasks A new indexing database is defined using newgidx label title where label is a label that uniquely identifies this database and title is the title to be used when the index or glossary is displayed For example newgidx index Index creates a new database labelled index When the index is displayed it will have the section heading Index As in Section 6 1 each term in the index or glossary database has an associated location list This list is initially null The locations are added to terms used in the document on the second TEX run When you display the index only those entries with a non null location list or a cross reference will be shown The default location is the page number on which the entry was referenced The datagidx package knows about the following page num bering styles arabic roman Roman alph and Alph If your document has another type of numbering style or if you want to use a different counter for the location consult the datagidx section of the datatool manual 17 Once you have
103. glsadd except that there is also a types key where the value should be a comma separated list of all the glossaries to iterate over For example to add all entries defined in the acronym glossary and the notation glossary but not the main glossary glsaddall types acronym notation NOTE As with printindex the glossaries won t be displayed until the relevant files have been created either by makeindex or by xindy Unlike in Sec tion 6 1 1 if you want to use xindy to create your glossary files you can t use the texindy wrapper but must either use xindy directly or use the makeglossaries wrapper described below If you want to use xindy with the glossaries package you must use the xindy package option Input Definition Definition Input A Chapter 6 Generating Indexes and Glossaries 89 usepackage xindy glossaries Input If omitted makeindex will be assumed If you have Perl installed you can use the makeglossaries application that comes with the glossaries package If you have been using latexmk or xindy then you already have Perl installed If you don t want to install Perl for some reason there s a Java alternative to makeglossaries called makeglossariesgui that s available from CTAN 2 However if you don t install Perl you are restricting your options as you won t be able to use xindy If you are using arara see Section 1 1 2 then all you need to do is add another arar
104. gy A tautology is a proposition that is always true for any value of its variables Definition 4 Contradiction A contradiction is a proposition that is al ways false for any value of its variables Chapter 4 Formatting 41 Theorem 4 4 If proposition P is a tautology then P is a contradiction and conversely ProoF If P is a tautology then all elements of its truth table are true by Definition 3 so all elements of the truth table for P are false therefore P is a contradiction by Definition 4 Example 2 It is raining or it is not raining is a tautology but it is not raining and it is raining is a contradiction Remark 2 Example 2 used De Morgan s Law p V q PA q 4 8 Algorithms If you want to display an algorithm such as pseudo code you can use a com bination of the tabbing environment described in Section 4 6 and a theorem like environment described above in Section 4 7 EXAMPLE in the preamble theoremstyle break theorembody font normal font newtheorem algorithm Algorithm later in the document begin algorithm Gauss Seidel Algorithm begin tabbing 1 For k 1 to maximum number of iterations gt 2 For i 1 to n gt gt Set begin math x_i4 k frac b_i sum_ j 1 i 1l a_ ij x_j Ck sum_ j i 1 n a_ ij x_j k 1 a_ ii end math gt 3 If lvert vec x 4 k vec x 4 k 1 rvert lt epsilon where epsilon
105. hat may need to be used to help create your document such as bibtex or biber discussed in Chapter 5 Generating a Bibliography and makeindex or xindy discussed in Chapter 6 Generating Indexes and Glossaries For example if your document has a bibliography and you are using TeXworks you first need to make sure the drop down menu is set to pdfLa TeX see Figure 1 1 and click on the green Typeset button Then you need to select BibTeX from the drop down menu see Figure 1 2 and click on the green Typeset button Then again select pdfLaTeX Figure 1 1 and click the Typeset button Finally to ensure your cross references are all up to date you need to click on the Typeset button again If you are using biber instead of bibtex see Section 5 3 then you have to replace the above BibTeX step with Biber instead E ex 0X File pdfLatex U Typeset Scripts Window Help Luatex UG ot ag doc Lualatex neside scrbook i XeTeX title xeLaTex 1D Thesis a ut ConTeXt LuaTeX er dat ConTeXt pdfTeX title ee s submitted for the degree of Doctor of Phil 97 9A ee e puk BibTex of Something University of Somewhere Makelndex Figure 1 1 Selecting pdfLaTeX from the Drop Down Menu Chapter 1 Introduction 4 E oro ox File pdfLaTeX at Typeset Scripts Window Help LuaTeX ry ab o lal A doc LvalaTex neside scrbook a XeTeX title xeLatex 1D Thesis a ut ConTe
106. he first approach see Section 6 1 is more efficient but a lot of users especially beginners have difficulty with the intermediate step where the external indexing application is run The second approach see Section 6 2 is slower but you don t need to worry about running an indexing applica tion If you re not writing in English in particular if you are not using the Latin alphabet you re better off using the first approach with xindy In this chapter I ll describe both approaches and you can choose which you prefer 6 1 Using an External Indexing Application This section describes how to create indexes Section 6 1 1 or glossaries Section 6 1 2 using an external indexing application There are two popular indexing applications makeindex and xindy All T X distributions should come with makeindex The Tpx Live distribution also comes with xindy but if you have a different TeX distribution such as MikTeX you may need to fetch xindy from http www xindy org 75 Chapter 6 Generating Indexes and Glossaries 74 NOTE You must have Perl installed in order to use xindy as it s a Perl script See 2 20 from Volume 1 If you have successfully been using latexmk you already have Perl installed 6 1 14 Creating an Index makeidx package Volume 1 15 8 introduced the command index text to index the word given in text For example if index circuit occurs on page 42 then 42 will be added to the loca
107. heoremstyle 3 117 nomencl package 80 normal font 23 38 117 ntheorem package 33 99 39 standard 39 num 44 117 119 Symbols NK KSSCGHNDPOTDOAZZOAHH THO TMOOeD Index ofoot ohead onehalfspacing P page style headings plain scrheadings scrplain pagemark pagenumbering pagestyle par Parencite parencite parindent pdflatex per pnumfont printbibliography 22 117 22 117 24 117 21 22 22 22 23 118 13 118 21 23 118 2 118 T1 118 T1 118 57 118 5 16 45 118 23 118 70 118 printglossaries 86 87 116 118 printglossary 86 87 116 118 nonumberlist 88 numberedsection 88 style 88 title 88 toctitle 88 type 87 printindex 74 79 80 88 118 PrintSemicolon 42 111 118 printterms 95 118 columns 96 database 96 namecase 96 postdesc 96 style 96 Proof environment 39 118 proof environment 535 39 119 publishers 14 18 119 Q qedhere 35 119 qedsymbol 35 119 127 R raggedright 21 119 raggedsection 21 119 ref 28 47 78 119 renewcommand 21 119 report class 21 Return 42 119 ris 70 rmfamily 21 119 rvert 41 119 S scrbook class 2 13 14 21 scrpage2 package 21 scrreprt class 13 14 scshape 37 119 second 45 119 setspace package 24 doublespacing 24 onehalfspacing 24 singlespacing 24 SI 45 119 si 45 119 sim 52 36 40 120 singlespacing 24 30 120 siunitx package 44 sqrt 29 120 square 45 120 squared 45 120 sum 41
108. hould be double or single spaced NOTE It is not usually appropriate to have reams of listings in your thesis It can annoy an examiner if you have included every single piece of code you have written during your PhD as it comes across as padding to make it look as though your thesis is a lot larger than it really is Examiners are not easily fooled and it s best not to irritate them as it is likely to make them less sympathetic towards you If you want to include listings in your thesis check with your supervisor first to find out whether or not it is appropriate Be careful when you use verbatim like environments or commands such as verbatim Istlisting lstinline and lstinputlisting In general they can t be used in the argument of another command 4 6 Tabbing The tabbing environment lets you create tab stops so that you can tab to a particular distance from the left margin Within the tabbing environment you can use the command to set a tab stop gt to jump to the next tab stop lt to go back a tab stop to shift the left border by one tab stop to the right to shift the left border by one tab stop to the left In addition will start a new line and kill will set any tabs stops defined in that line but will not typeset the line itself NOTE You may recall two of the above commands from Volume 1 was de scribed as a discretionary hyphen in 2 14 and was described as the macron accent command in
109. hyperref before glossaries This is an exception to the usual advice of loading hyperref last Defining Glossary Entries Firstly in order to make the glossary or glossaries if you have more than one appear you must use the command makeglossaries in the preamble This is analogous to the makeindex command described in Section 6 1 1 Next you need to define the terms you want to appear in the glossary This is done using the command newglossaryentry label Rey val list The first argument label is a unique label so that you can refer to this entry in your document text The entry will only appear in the glossary if you have referenced it in the document using one of the commands listed later The second argument is a comma separated list of key value options Common keys are A Definition Definition Chapter 6 Generating Indexes and Glossaries 81 e name The name of the entry as it will appear in the glossary e description A brief description of this entry to appear in the glossary e text How this entry will appear in the document text where the singular form is required If this key is omitted the value of name will be used e first How this entry will appear in the document text the first time it is used where the first use requires the singular form If this key is omitted the value of text is used e plural How this entry will appear in the document text where the plural form i
110. in the tabbing environment to create accented characters 4 6 begin abstract Defined in Most article or report style classes such as scrartcl or scrreprt Not usually defined in book style classes such as scrbook but is defined in memoir Displays its contents as an abstract 2 0 ac options label insert Defined in glossaries package A synonym for gls This command is only available if the package option shortcuts is used 6 1 ac options label insert Defined in glossaries package A synonym for acrfull This command is only available if the package option shortcuts is used 6 1 acl options label insert Defined in glossaries package A synonym for acrlong This command is only available if the package option shortcuts is used 6 1 Acr format label Defined in datagidx package As acr but the first letter is converted to uppercase 6 2 acr format label Defined in datagidx package Displays an acronym On first use the full form is displayed On subsequent use only the short form is displayed 6 2 Acrfull options label insert Defined in glossaries package Displays the long and short form of the given acronym the first letter converted to uppercase 6 1 acrfull options label insert Defined in glossaries package Displays the long and short form of the given acronym
111. intindex end document 4 Input The index for the above document looks like oz contradiction 2 Tees functions sqrt 2 sqrt 2 Chapter 6 Generating Indexes and Glossaries 79 square root see sqrtQ tautology 2 l Output Troubleshooting e My index hasn t appeared 1 Make sure you have the command printindex at the place where you want the index to appear this com mand is defined in the makeidx package 2 Make sure you have the command makeindex in the preamble 5 If you are building the document using arara make sure you included all the arara directives as shown in Listing 19 If you are using latexmk make sure you have included the idx dependency as described in Section 1 1 1 If you re not using an automated tool make sure you run PDF PTpx then makeindex and then PDF BTpx again see Section 1 1 4 Check makeindex s log file which has the extension ilg by default for error messages e want to index the character or but it s not working If you want any of these symbols in your index you will need to prefix the character with the double quote symbol For example to index the symbol index Input e have multiple entries of the same item For example identity matrix 10 22 30 identity matrix 4 Check to make sure the sort argument to each of the corresponding index commands is the same Pay particular attention to spaces as makeindex will
112. j k 1 3 a_ ii If lvert vec x k vec x k 1 rvert lt epsilon Stop end algorithm2e l j 4 Input The result is shown in Algorithm 2 The algorithm environment as defined by algorithm2e without the algo2e option or algorithm2e environment as defined with the algo2e option uses Chapter 4 Formatting 44 Input Scalar e matrix A aij vector b and initial vector 7 for k 1 to maximum iterations do fori lt 1tondo k 1 i 1 k x bi Vojat ayax U j i1 WA i aii end if 2 lt e then Stop end end Algorithm 2 Gauss Seidel Algorithm the algocf counter So in this document to ensure that the algorithm environ ment defined with newtheorem used the same counter as algorithm2e I had the following in my preamble usepackage ntheorem usepackage algo2e algorithm2e theoremstyle break theorembody font normal font newtheorem algorithm algocf Algorithm 4 9 Formatting SI Units If you need to typeset numbers and units then I strongly recommend that you use the siunitx package This section just provides a brief introduction to that package You will need to read the siunitx package documentation 20 if you want further details num number This command typesets number adding appropriate spacing between number groups where necessary It also adds a leading zero if omitted before the decimal point and identifies ex
113. k style classes such as scrbook or scrreprt that have the concept of chapters Inserts a chapter heading 2 0 chead scrplain scrheadings Defined in scrpage2 package Symbols NE KSA CHM DOVDOAZZORAHH THOT SAeD Summary of Commands and Environments 111 Indicates what to put in the centre heading area for the scrplain and scrheadings page styles 4 2 Cite prenofe postnote key Defined in biblatex package Like cite but for use at the start of a sentence 5 3 cite text key list Defined in PTEX Kernel Inserts the citation markers of each reference identified in the key list A second run is required to ensure the reference is correct When used with biblatex this command has two optional arguments 5 2 citep pre post key Defined in natbib package Parenthetical citation 5 2 citet pre post key Defined in natbib package Textual citation 5 2 clearpage Defined in PTEX Kernel Inserts a page break and processes any unprocessed floats 3 0 D date text Defined in Most classes that have the concept of a title page Specifies the document date This command doesn t display any text so may be used in the preamble but if it s not in the preamble it must be placed before maketitle If omitted most classes assume the current date 2 0 documentclass option list class name Defined in ET
114. l scrbook Have you been told to have certain sized margins If so you can use the geometry package For example if you have been told you must have 1 inch margins you can do usepackage margin 1lin geometry Changing the default fonts is covered in Volume 1 15 4 5 3 Other possible formatting requirements such as double spacing are covered in Chapter 4 Formatting T Input 4 Input Input Input Input Input FAQ Changing the margins in ETEX Input CHAPTER 3 SPLITTING A LARGE DOCUMENT INTO SEVERAL FILES Some people prefer to place each chapter of a large document in a separate file and then input the file into the main document There are two basic ways of including the contents of an external file input filename and include filename where filename is the name of the file The tex extension may be omitted in both cases The differences between the two commands are as follows input acts as though the contents of the file were typed where the input command was For example suppose my main file contained the fol lowing Here is a short paragraph input myfile and suppose the file myfile tex contained the following lines Here is some sample text then the input command behaves as though you had simply typed the following in your main document file 17 Definition Definition T Input 4 Input Input 4 Input T Input Chapte
115. le If text contains a comma or equal sign make sure you enclose text in curly braces and caption short fext is used to set a numbered caption The optional part short is an alternative short caption for the list of listings which can be produced using Istlistoflistings As above if the caption contains a comma or equal sign make sure you enclose it in curly braces and label fext is used to assign a label to this listing so the number can be referenced via ref numbers sefting The value setting may be one of none no line num bers left line numbers on the left or right line numbers on the right mathescape This is a boolean key that can either be true dollar charac ter acts as the usual math mode shift or false deactivates the usual behaviour of basicstyle declaration The value one or more declarations is used at the start of the listing to set the basic font style For example declaration could be ttfamily which actually makes more sense for a listing Input 4 Input T Output Output Input Definition Chapter 4 Formatting 29 NOTE A If you set basicstyle to ttfamily and you want bold keywords make sure you are using a typewriter font that supports bold as not all of them do Recall from Volume 1 15 4 5 3 how to change the font family This book uses txtt see Volume 1 15 8 2 Other possibilities include beramono tgcur sor co
116. le remark newtheorem note Note newtheorem remark Remark 4 Input The amsthm package also provides the proof environment which can be used for typesetting proofs begin proof title Definition The optional argument title is a replacement for the default title This environment automatically inserts a QED symbol at the end of it but if the default location isn t appropriate which can happen if the proof ends with an equation then use qedhere Definition where you want the QED symbol to appear The symbol is given by qedsymbol Definition This defaults to an unfilled square LJ but you can redefine qedsymbol to something else if you prefer Recall redefining commands from Vol ume 1 15 8 2 Listing 12 T Input in the preamble usepackage ams thm theoremstyle plain newtheorem theorem Theorem theoremstyle definition newtheorem defn Definition newtheorem xmp1 Example chapter theoremstyle remark newtheorem remark Remark later in the document Chapter 4 Formatting 56 begin defn Tautology label def tautology A emph tautology is a proposition that is always true for any value of its variables end defn begin defn Contradiction label def contradiction A emph contradiction is a proposition that is always false for any value of its variables end defn begin theorem If proposition P is a t
117. m style UTF 8 has also been a problem although newer versions of bibtex apparently fix this In 2006 Philipp Lehman brought out the biblatex package to provide a more flexible way of typesetting bibliographies This originally used bibtex to just sort the entries and used ETEX macros to deal with the actual formatting but it is now moving over to using biber instead of bibtex Since some journals conferences or other types of scientific publishers require you to use bibtex Section 5 2 provides a brief introduction to bibtex and then Section 5 3 discusses biblatex and biber But first Section 5 1 covers creating the actual database which is required for both methods 5 1 Creating a Bibliography Database This section covers creating a bib file that contains the bibliographic in formation you want to cite in your documents You can use an ordinary text editor to create a bibliographic database as described in Section 5 1 2 but it can be difficult to remember the names of the required fields and it s easy 51When your examiners read through your thesis they can check off each citation they encounter against your bibliography When they reached the end of the thesis they can then look through the bibliography for unchecked entries One or two may appear the result of carelessness whereas a large quantity will look like padding and may lead the examiners to suspect a certain amount of duplicity on your part 46 Chapter 5 Generating
118. m style can be created using newtheoremstyle name space above space below body font indent head font post head punctuation post head space head spec This defines a new theorem style called name which can later be set using theoremstyle The other arguments are as follows space above the amount of space above the theorem like en vironment space below the amount of space below the theorem like en vironment body font the font to be used in the main theorem body indent the amount of indentation empty means no in dent or use parindent for normal paragraph in dentation head font the font to be used in the theorem header post head punctuation the punctuation to be inserted after the theorem head post head space the space to put after the theorem head use u for a normal interword space or newline for a linebreak head spec the theorem head spec EXAMPLE This example creates a new style called note that inserts a space of 2ex above the theorem and 2ex below The body font is just the normal font There is no indent the theorem header is in small caps a full stop is put after the theorem head and a line break is inserted between the theorem head and body newtheoremstyle note style name 2ex above space 2ex below space 3 body font indent amount scshape head font post head punctuation newline post head punctuation 3 head spec
119. n Date 69 iii 4 1 o i she 5 9 5 4 LIST OF TABLES Theorem Styles sasunaru 39 Name Formats for Bibliographic Data 53 Standard BibTeX entry types essas 566d be ee ees 59 Standard BiBTeX fields 2 226 844 be PRR REL Oe edo 60 Required and Optional Fields 868444040444 61 OWANDOKWNHE LISTINGS Getting Started co eci ea ba a ae a a 14 Splitting a Large Document into Several Files thesis tex 18 Splitting a Large Document into Several Files intro tex 19 Splitting a Large Document into Several Files techintro tex 19 Splitting a Large Document into Several Files method tex 19 Splitting a Large Document into Several Files results tex 19 Splitting a Large Document into Several Files conc tex 20 Changing the Page Style 0 cc eee eee 23 Double Spa ing os isan ae ae ee a a oe ee a 24 Changing the Title Page oi he a ok ee ee aa 24 Listings and Other Verbatim Text 0 000 29 The msthm Package o ora ae aw doa ed ee ee aR 35 The ntheorem Package ca jie ie aw ok oe a a uo 40 PUPS s a hs he ee ee we Re eee Be 43 ee eh Coke hee eee Cee ee eee 63 Author Year Citations ee ew eee ee 65 PAET o hee es bs Bowe te de twee eee Se ee ees 71 Creating an Index makeidx package 4 T4 Creating an Index makeidx package naonnana nannaa 78 Creating Glossaries Lists of Symbols or Acronyms glossaries packagej 64 65 062 Hee ee eed rau RERE Ea 89 Using
120. n outer foot scrheadings outer foot In each case the optional argument indicates what to do if the scrplain page style is in use and the mandatory argument indicates what to do if the scrheadings page style is in use If the optional argument is missing no Chapter 4 Formatting 25 modification is made to the scrplain style Within both types of argument you can use pagemark to insert the current page number and headmark to insert the running heading For example suppose you are required to put your registration number on the bottom left of each page and the page number on the bottom right and you are also required to put the current chapter or section heading at the top left of each page unless it s the first page of a chapter Then you can do Listing 8 a l usepackage scrpage2 pagestyle scrheadings newcommand myregnum 123456789 registration number ihead chead ohead headmark i foot myregnum myregnum registration number cfoot o foot pagemark pagemark Note that the above don t use any font changing commands If you want to change the font for the header and footer you need to redefine headfont The page number style is given by pnumfont So for italic headers and footers with bold page numbers you can redefine these com mands as follows renewcommand headfont normal font itshape renewcommand pnumfont normalfont bfseri
121. n place the following command in the preamble includeonly method results Input CHAPTER 4 FORMATTING It used to be that in order to change the format of chapter and section headings you needed to have some understanding of the internal workings of classes such as report or book Modern classes such as memoir and the KOMA Script classes provide a much easier interface However I recom mend that you first write your thesis and then worry about changing the document style The ability to separate content from style is one of the ad vantages of using PTEX over a word processor Remember that writing your thesis is more important than the layout Whilst it may be that your school or department insists on a certain style it should not take precedence over the actual task of writing 4 1 Changing the Document Style If you are using a custom thesis class file provided by your department or school then you should stick to the styles set up in that class If not you may need to change the default style of your chosen class to fit the requirements Volume 1 15 5 3 described how to change the fonts used by chapter and section headings for the KOMA Script classes For example if the chapter headings must be set in a large bold serif font you can do addtokomafont large bfseries rmfamily The headings in the KOMA Script classes default to ragged right justification recall raggedright from 2 12 of Volume 1 which is done via
122. ndex in your document as well as a bibliography Fortunately there are ways of automating this process so that you only need one button press to perform all those dif ferent steps There are several applications available to do this for you and I strongly recommend you try one of them if possible to reduce the complexity involved in building a document Volume 1 15 5 5 mentioned latexmk which is available on CTAN 2 This is a Perl script so it will run on any operating system that has Perl installed see Volume 1 15 2 20 Since Volume 1 was published a Java alternative called arara has arrived on CTAN 2 Java applications will run on any operating system that has the Java Runtime Environment installed so both latexmk and arara are multi platform solutions to automated doc ument compilation Section 1 1 1 gives a brief introduction to latexmk and Section 1 1 2 gives a brief introduction to arara 1 1 1 LaTeXmk As mentioned above latexmk is a Perl script that automates the process of building a PTEX document In order to use latexmk you must have Perl installed see Volume 1 15 2 20 Both TeX Live and MikTeX come with latexmk but if for some reason you don t have it installed you can use the TeX Live or MikTeX update manager to install it Alternatively you can download http mirror ctan org support latexmk zip and install it manually Once latexmk is installed you then need to add it to the list of available
123. ne maths mode This command is usually only used in definitions such as in newglossaryentry where it may be used in either text or math mode 6 1 epsilon Defined in BTEX Kernel Math Mode Greek lower case epsilon See Volume 1 15 9 4 2 4 8 equiv Defined in PTEX Kernel Math Mode Relational symbol See Volume 1 15 9 4 7 4 7 excludeonly file list Defined in excludeonly Package Lists which of the files that are not to be included using include Only those files not in the list will be included The opposite effect of includeonly 3 0 F begin figure placement Defined in Most classes that define sectioning commands Floats the contents to the nearest location according to the preferred placement options if possible Within the environment caption may be used one or more times as required See Volume 1 15 7 1 4 8 For condition body Defined in algorithm2e package For use in algorithm like environments to indicate a for loop 4 8 frac numerator denominator Defined in ETEX Kernel Math Mode Displays a fraction See Volume 1 15 9 4 5 4 8 frontmatter Defined in Most book style classes such as scrbook Switches to lower case Roman numeral page numbering Also suppresses chapter and section numbering but still adds unstarred sectional units to the table of contents See also m
124. ng a Bibliography 68 select entry type Entry types Inproceedings Inreference Manual Mastersthesis Misc Online Patent Periodical Phdthesis Proceedings Reference Report Figure 5 16 JabRef in BibLaTeX Mode Select Entry Type new date field Note that the date should be specified as year month day where day or month day maybe omitted A slash should be used to indicate a range for example 2002 01 2002 02 Recall from Figure 5 2 and Figure 5 3 that I set the default encoding to UTF 8 With BibLaTeX and biber my UTF 8 bibliography can be correctly sorted but I need to make sure that I load the inputenc package before biblatex in my document usepackage utf 8 inputenc T Input usepackage biblatex input l ji ee RU Section 5 2 1 described the natbib package BibLaTeX has a compatibility module usepackage natbib biblatex Input This provides the same commands such as citet and citep that natbib provides The default sorting order is name title and year This can be changed using the sorting package option For example to sort by name year and title usepackage sorting nyt biblatex Input Or you can suppress the sorting so that all entries are in citation order usepackage sorting none biblatex Input For other possible values see the biblatex documentation 9 Chapter 5 Generating a Bibliography 69 JabRef hom
125. nition A T Input 4 Input Definition Chapter 6 Generating Indexes and Glossaries 87 the input and output files for this new glossary The first optional argument log ext is the extension for the log file This information is provided for the benefit of the makeglossaries application The final optional argument counter is the name of the counter used by default in the location lists for this new glossary If omitted the page counter is used unless overridden by the counter package option NOTE All glossaries must be defined before makeglossaries to ensure that the relevant output files are opened EXAMPLE The following defines a new glossary called notation newglossary nlg notation not ntn Notation When it gets displayed using printglossary or printglossaries the title will default to Notation I now need to use the type key if I want to define an entry to go in this new glossary newglossaryentry not set label type notation glossary type name mathcal S description A set sort S F Later in the document I can use this entry A gls not set is a collection of objects Displaying Glossaries Now that you know how to define entries and how to use them in the document text let s now look at the more complicated task of displaying the glossaries To display all the defined glossaries use printglossaries To only display a particular glossary use
126. ns used by the listings package 4 5 lvert Defined in amsmath Math Mode Left vertical bar delimiter See Volume 1 15 9 4 9 4 8 M mainmatter Defined in Most book style classes such as scrbook Switches to Arabic page numbering and enables chapter and section numbering See also frontmatter and backmatter 2 0 makeglossaries Defined in glossaries package Activates printglossaries and printglossary 6 1 makeindex Defined in PTEX Kernel Preamble Only Enables index 6 1 MakeTextUppercase text Defined in textcase package Converts fext to uppercase 6 2 maketitle Defined in Most classes that have the concept of a title page Generates the title page or title block This command is usually placed at the beginning of the document environment 2 0 MakeUppercase text Defined in TEX Kernel Converts its argument to upper case 5 1 mathbf maths Defined in BTFX Kernel Math Mode Renders maths in the predefined maths bold font Doesn t work with numbers and nonalphabetical symbols See Volume 1 15 9 4 1 4 8 mathcal maths Defined in BTEX Kernel Math Mode Typesets its argument in the maths calligraphic font Example mathcal S produces S See Volume 1 15 9 4 1 6 1 metre Defined in siunitx package Indicates the metre unit for use in commands like si 4 9
127. nse or distribute the Document is void and will automati cally terminate your rights under this License However parties who have received copies or rights from you under this License will not have their licenses terminated so long as such parties remain in full compliance 10 FUTURE REVISIONS OF THIS LICENSE The Free Software Foundation may publish new revised versions of the GNU Free Documentation License from time to time Such new versions will be similar in spirit to the present version but may differ in detail to address new problems or concerns See http www gnu org copyleft Each version of the License is given a distinguishing version number If the Document specifies that a particular numbered version of this License or any later version applies to it you have the option of following the terms and conditions either of that specified version or of any later version that has been published not as a draft by the Free Software Foundation If the Document does not specify a version number of this License you may choose any version ever published not as a draft by the Free Software Foundation GNU Free Documentation License 136 ADDENDUM How to use this License for your documents To use this License in a document you have written include a copy of the License in the document and put the following copyright and license notices just after the title page Copyright YEAR YOUR NAME Permission is granted to copy
128. ntclass oneside scrbook title A Sample Thesis author A N Other date July 2013 titlehead A Thesis submitted for the degree of Doctor of Philosophy publishers School of Something University of Somewhere begin document maketitle frontmatter tableofcontents listoffigures Chapter 3 Splitting a Large Document into Several Files 19 Llistoftables chapter Acknowledgements I would like to thank my supervisor Professor Someone This research was funded by the Imaginary Research Council chapter Abstract A brief summary of the project goes here mainmatter include intro include techintro include method include results include conc backmatter end document Input Listing 3 intro tex chapter Introduction label ch intro Input Input I lt Listing 4 techintro tex E chapter Technical Introduction label ch techintro Input Input I4 Listing 5 method tex chapter Method label ch method Input Input __ Listing 6 results tex chapter Results label ch results I Input Input Chapter 3 Splitting a Large Document into Several Files 20 Listing 7 conc tex ro Input chapter Conclusions lLabel ch conc j 4 Input If you only want to work on say the Method and Results chapters you ca
129. ntries in this file should have the following form entry type keyword field name text field name i text where entry type indicates the type of entry e g book or article Standard entry types are listed in Table 5 2 Table 5 2 Standard BiBTeX entry types Entry Name Description article Article from a journal book Published book booklet Printed work without a publisher conference Identical to inproceedings inbook Part chapter section etc of a book incollection A chapter of a book with its own author and title inproceedings An article in a conference proceedings manual Technical documentation mastersthesis A master s thesis misc Non standard work phdthesis PhD thesis proceedings Conference proceedings techreport Report published by an institution unpublished Unpublished work with an author and title Within an entry keyword is a short label that is used to cite this work with the cite command If you have written bibliographies with the the bibliography environment it s the same as the argument to bibitem There then follows a comma separated list of fields of the form field name value The field name indicates what kind of field it is e g title or author Table 5 3 lists the standard fields Note that some bibliography styles may define additional non standard fields such as email or url See the BibTeX documentation 11 for information about other fields not listed in Table 5
130. o oe RR Hw ea ed 4 7 2 The ntheorem Package 24 cs eevee evas AS ARONNE ek eh ek ee he we we A a 49 Formatting SI Units s e somre wow e Boh e a a 5 GENERATING A BIBLIOGRAPHY 5 1 Creating a Bibliography Database let JBR eea oe ee e ee Ee E 5 1 2 Writing the bib File Manually ee a ee es E oe SR E E ne 5 2 1 Author Year Citations 2 0 0 6 2b ee ee ee 5 2 2 Troubleshooting 2 2 6 es eS ORR eee be eed S9 PMONMCS eaaa nce we Seo ews G4 SRE HEY SEE Oe EG 5 5 1 Troubleshooting ek ee 6 GENERATING INDEXES AND GLOSSARIES 6 1 Using an External Indexing Application 6 1 1 Creating an Index makeidx package vi Naw 13 17 21 21 21 23 24 25 50 52 54 58 41 44 46 46 47 59 62 64 65 66 72 73 13 Th 6 1 2 Creating Glossaries Lists of Symbols or Acronyms glossaries package bed ees ko es ee Ghee Ee eS 6 2 Using TeX to Sort and Collate Indexes or Glossaries datagidx package oe Ge ee Se ee ED ore So we ee a a 80 Contents A GENERAL ADVICE A 1 Too Many Unprocessed Floats AZ General Thesis Writing Advice 545465404 BIBLIOGRAPHY ACRONYMS SUMMARY OF COMMANDS AND ENVIRONMENTS INDEX GNU FREE DOCUMENTATION LICENSE HISTORY LIST OF FIGURES 1 1 Selecting pdfLaTeX from the Drop Down Menu 5 1 2 Selecting BibTeX from the Drop Down Menu 4 1 5 Adding Makeglossaries to the list of tools in TeXw
131. odified Version filling the role of the Document thus licensing distribution and modification of the Modified Version to whoever possesses a copy of it In addition you must do these things in the Modified Version A Use in the Title Page and on the covers if any a title distinct from that of the Document and from those of previous versions which should if there were any be listed in the History section of the Document You may use the same title as a previous version if the original publisher of that version gives permission B List on the Title Page as authors one or more persons or entities responsible for authorship of the modifications in the Modified Version together with at least five of the principal authors of the Document all of its principal authors if it has fewer than five unless they release you from this requirement C State on the Title page the name of the publisher of the Modified Ver sion as the publisher D Preserve all the copyright notices of the Document E Add an appropriate copyright notice for your modifications adjacent to the other copyright notices F Include immediately after the copyright notices a license notice giving the public permission to use the Modified Version under the terms of this License in the form shown in the Addendum below G Preserve in that license notice the full lists of Invariant Sections and required Cover Texts given in the Document s license notice H
132. of the text key for a glossary entry 6 1 Glsp1 options label insert Defined in glossaries package Displays the plural form of a glossary term according to its first use flag The first letter of the plural text is converted to uppercase 6 1 Glsp1 format label Defined in datagidx package Displays the plural form of a glossary or index term with the first letter converted to uppercase 6 2 glspl format label Defined in datagidx package Displays the plural form of a glossary or index term 6 2 glsp1 options label insert Defined in glossaries package Displays the plural form of a glossary term according to its first use flag 6 1 glsreset label Defined in glossaries and datagidx packages Resets a glossary term s first use flag 6 1 glssymbol options label insert Defined in glossaries package Displays the symbol element of a glossary entry 6 1 glsunset label Defined in glossaries and datagidx packages Unsets a glossary term s first use flag 6 1 gram Defined in siunitx package Symbols NE KSA CHM DOVDOAZZORAHH THOT SAeD Summary of Commands and Environments 114 Indicates a gram in commands like si 4 9 H headfont Defined in scrpage2 package Determines the font used by the header and footer with the scrplain and scrheadings page styles 4 2 headmark Defined in s
133. omenclature lists of symbols and acronyms The LaTeX Community s Know How Section March 2009 http www latex community org know how latex 55 latex general 263 glossaries nomenclature 1lists of symbols and acronyms 103 Bibliography 104 14 Nicola L C Talbot Creating a PDF Document Using PDFPT gx volume 4 of Dickimaw PTITFX Series Dickmaw Books 2004 http www dickimaw books com latex pdfdoc 15 Nicola L C Talbot BTFX for Complete Novices volume 1 of Dickimaw BTFX Series Dickmaw Books 2012 http www dickimaw books com latex novices 16 Nicola L C Talbot User manual for glossaries sty 2012 http mirror ctan org macros latex contrib glossaries glossaries user pdf or texdoc glossaries user 17 Nicola L C Talbot User manual for datatool bundle 2013 http mirror ctan org macros latex contrib datatool datatool user pdf or texdoc datatool user 18 Mark Trettin and J rgen Fenn An essential guide to ATEX 2 usage ob solete commands and packages 2007 http mirror ctan org info 12tabu english or texdoc 12tabu en 19 UK list of TEX frequently asked questions http www tex ac uk faq or texdoc faq 20 Joseph Wright siunitx a comprehensive SI units pack age 2013 http mirror ctan org macros latex contrib siunitx Siunitx pdf or texdoc siunitx ACRONYMS CTAN The Comprehensive TEX Archive Network http mirror ctan org UK FAQ UK List of TEX Frequently Asked Questi
134. omething University of Somewhere begin document maketitle frontmatter tableofcontents listoffigures listoftables chapter Acknowledgements would like to thank my supervisor Professor Someone This reacasarch wimae fundar hu the Imaainarn Dacasarceh LF UTF 8 Line 1 of 52 col O Figure 1 6 LaTeXmk Tool Selected in TeXworks Chapter 1 Introduction 9 IzPack Installation of arara Select the packs you want to install Q Note Grayed packs are required M Main application 2 59 MB Vv Include the arara user manual 1 56 MB V Include predefined rules 11 13 KB Add a symbolic link to arara in usr local bin 0 bytes Description Total space Required 4 16 MB Available space 37 5 GB Made with IzPack http izpack org Previous Quit Figure 1 7 Arara Installer If you are doing a manual install make sure you check the box to add the predefined rules as shown in Figure 1 7 Once arara has been installed you can add it to the list of tools in TeX works As before open the TeXwork s Preferences dialog box using Edit Preferences and select the Typesetting tab Figure 1 4 To add a new tool click on the lower button next to the list of process ing tools This opens the tool configuration dialog box Figure 1 8 Type Arara in the Name box and use the Browse button to find the arara application on
135. on year author title note Optional Fields volume month note number pages address edition volume or number month note pages series author address howpublished month note year address edition volume or number month note series type address chapter editor edition volume or number month note pages series type address editor volume or number month note organization pages publisher series type author address edition month note organization year address month note type author howpublished month note title year address month note type editor organization address volume or number series month publisher note type number address month note month year Chapter 5 Generating a Bibliography 62 book goossens97 author Goossens Michel and Rahtz Sebastian and Mittelbach Frank title The LaTeX graphics companion illustrating documents with TeX and PostScript publisher Addison Wesley Longman Inc year 1997 T Input 4 Input Numbers such as the year 1997 don t need to be delimited with quotes or braces So you can have pages 10 but a page range would need to be delimited pages 10 45 Bibliography styles always have three letter abbreviations for months jan feb mar etc These should be used instead of typing them in explicitly as their format depends on the bibliography style These abbreviations should be
136. ons http www tex ac uk faq 105 SUMMARY OF COMMANDS AND ENVIRONMENTS Commands or environments defined in the BTFX kernel are always avail able Symbols l makeindex sublevel special character 6 1 u A visual indication of a space in the code When you type up the code replace all instances of this symbol with a space via the space bar on your keyboard 1 0 makeindex escape special character 6 1 digit Defined in PTEX Kernel Replacement text for argument digit See Volume 1 15 8 4 5 Defined in TEX Kernel Switches in and out of in line math mode See Volume 1 15 9 1 4 5 Defined in PTEX Kernel Comment character used to ignore everything up to and including the newline character in the source code Sometimes comments are used to provide information to applications that build your document such as arara 2 0 arara Instruction to arara indicating how to build the document This is ignored if you are not using arara 1 1 Defined in ETEX Kernel Closing quote or apostrophe symbol in text mode or prime symbol in math mode See Volume 1 15 4 3 4 7 Defined in PTEX Kernel Closing double quote symbol in text mode or double prime in math mode See Volume 1 15 4 3 4 7 Defined in ETEX Kernel En dash symbol Normally used for number ranges See Volume 1 15 4 3 5 1
137. orks A 1 4 TeXwork s Preferences Dialog Box 5 see soe nanea 6 1 5 Adding LaTeXmk in the TeXWorks Tool Configuration Dialog 6 1 6 LaTeXmk Tool Selected in TeXworks 2 42 se ce ess 8 1 7 Arara installer nk ck eee Hee ede HERES EES ee 9 1 8 Adding Arara in the TeXWorks Tool Configuration Dialog 10 1 1 9 Using Arara in TeXworks ssi aw ee eee eee ee 1 4 1 Page Header and Footer Elements 006 22 G Sample Tille Page lt s os ee ee hee oe OE OE See Sarees 26 el AOL enee Ke 6 Oh HD ee ee eB Oe 48 5 2 JabRef Preferences ns ce kee ee ERS ee ee ee wo 48 oo JabRef Database Properties 2c 2062 s de eed ad een od 49 5 4 JabRef Select Entry Type 2 002 ee eee 49 5 5 JabRef New Entry 2 454 400 004 eet eeee cb ve eee 50 5 6 JabRef Entering the Required Fields 51 5 7 JabRef Entering Optional Fields 52 5 8 JabRef Adding an Article nasen aeaaea 553 5 9 JabRef Adding a Conference Paper 55 5 10 JabRef Adding Editor List sssaaa aaaeeeaa 56 5 11 Importing a Plain Text Reference nsns anana 57 5 12 Importing a Plain Text Reference Selecting a Field 58 5 13 Importing a Plain Text Reference Field Selected 58 5 14 JabRef Advanced Preferences nnana aaa 67 5 15 JabRef in BibLaTeX Mode 4482e522048 8008 67 5 16 JabRef in BibLaTeX Mode Select Entry Type 68 5 17 JabRef in BibLaTeX Mode Setting the Publicatio
138. other respects If the required texts for either cover are too voluminous to fit legibly you should put the first ones listed as many as fit reasonably on the actual cover and continue the rest onto adjacent pages If you publish or distribute Opaque copies of the Document numbering more than 100 you must either include a machine readable Transparent copy along with each Opaque copy or state in or with each Opaque copy a computer network location from which the general network using public GNU Free Documentation License 1352 has access to download using public standard network protocols a complete Transparent copy of the Document free of added material If you use the latter option you must take reasonably prudent steps when you begin distribution of Opaque copies in quantity to ensure that this Transparent copy will remain thus accessible at the stated location until at least one year after the last time you distribute an Opaque copy directly or through your agents or retailers of that edition to the public It is requested but not required that you contact the authors of the Document well before redistributing any large number of copies to give them a chance to provide you with an updated version of the Document 4 MODIFICATIONS You may copy and distribute a Modified Version of the Document under the conditions of sections 2 and 3 above provided that you release the Mod ified Version under precisely this License with the M
139. ou have a recent TEX distribution Biber comes with the latest version of TEX Live If you are using JabRef described in Section 5 1 1 there is a BibLaTeX mode option in the Advanced tab of the JabRef preferences dialog illus trated in Figure 5 14 Use Options Preferences to open the dialog You will have to quit and restart JabRef after enabling this option When you restart you should find extra fields when you edit an entry or create a new entry as illustrated in Figure 5 15 You should also find that there are more entry types available see Figure 5 16 With BibTeX there was a month and year field BibLaTeX provides a re placement date field although if this field is missing it will fall back on the month and year fields In Figure 5 17 I ve edited my earlier example to use the Chapter 5 Generating a Bibliography 67 General File Entry editor Groups Appearance External programs Entry table Entry table columns BibTeX key generator Entry preview Name formatter Import XMP metadata Import preferences Export preferences Look and feel Default look and feel com jgoodies looks plastic Plastic3DLookAndFeel Use other look and feel Class name oodies plaf plastic Plastic3DLookAndFee Note that you must specify the fully qualified class name for the look and feel and the class must be available in your classpath next time you start JabRef Remote operation This feature lets new
140. package and use the command afterpage clearpage For other problems check the FAQ 19 99 FAQ Too many unprocessed floats Input Input Appendix A General Advice 100 A 2 General Thesis Writing Advice This section is not specific to ETEX Some of the points have already been mentioned in asides or footnotes Remember that each college or university or even school within a university may have different requirements and requirements will also vary according to country so some of this advice may not apply to you I am writing from the point of view of an English scientist and am basing it on my own experience and on the comments of English science based PhD examiners and supervisors I cannot guarantee that your own department or university will agree with them If in doubt check with your supervisor 1 Find out the thesis style requirements from your supervisor or your department s website Many universities still require double spaced single sided documents with wide margins Double spacing is by and large looked down on in the world of typesetting but this requirement for a PhD thesis has nothing to do with esthetics or readability In England the purpose of the PhD viva is to defend your work Before your viva paper copies of your thesis are sent to your examiners The double spacing and wide margins provide the examiners room to write the comments and criticisms they wish to raise during the viva as well as
141. plied to the entry s name Available values are nochange no change uc convert to uppercase 1c convert to lower case firstuc convert the first let ter to uppercase and capitalise capitalise each initial letter using capitalisewords For a full list of options see the datagidx section of the datatool user guide 17 Listing 20 can now be rewritten as follows Listing 21 T Input arara pdflatex synctex on arara biber arara pdflatex synctex on arara pdflatex synctex on documentclass oneside 12pt scrbook usepackage datagidx newgidx index Index newgidx glossary Glossary newgidx acronym Acronyms newgidx notation Notation DTLgidxSetDefaultDB glossary newterm description a rectangular table of elements brief description plural matrices the plural 1 matrix the name Chapter 6 Generating Indexes and Glossaries DTLgidxSetDefaultDB acronym newacro svm support vector machine DTLgidxSetDefaultDB notation newterm label not set label description A set sort S 1 ensuremath mathcal S DTLgidxSetDefaultDB index newterm label function text function 1 functions newterm see sqrt 1 square root newterm label fn sqrt parent function 1 texttt sqrtQ newterm label sqrt 1 sqrtQ newterm tautology newterm contradiction
142. ponents Note that the command recognises both and as the decimal marker If you want one of these characters between number groups instead of the default space you can change the settings but it s best to stick to the default settings unless instructed to do otherwise EXAMPLE Out of num 12890 experiments num 1289 of them had a mean squared error of num 346 and num 128 of them had a mean squared error of num 1 23e 6 l J T Input 4 Input Definition Input 4 Input Chapter 4 Formatting 45 Result Out of 12890 experiments 1289 of them had a mean squared error of 0 346 and 128 of them had a mean squared error of 1 23 x 107 ang angle This command typesets an angle The argument angle may be a single number or three some possibly empty values separated by semi colons EXAMPLE The result formed an arc from ang 45 to ang 60 2 3 Result The result formed an arc from 45 to 60 2 3 si unit This command typesets a unit The unit can be formed from commands like metre gram second or kilo See the siunitx documentation 20 for the full list EXAMPLE The distance was measured in si kilo metre and the area in si kilo metre squared The acceleration was given in si metre per square second l Result The distance was measured in km and the area in km The acceleration was given in m s
143. ptional associated symbol e short An associated short form if required Defaults to name if omitted e long An associated long form if required Defaults to name if omitted e shortplural The plural of the associated short form If omitted the value is obtained by appending s to the short form e longplural The plural of the associated long form If omitted the value is obtained by appending s to the long form e see A cross reference to a synonym The value should be the label of another entry This entry will not have a location list just the reference to the other term Chapter 6 Generating Indexes and Glossaries 95 e seealso A cross reference to a closely related term Both this term and the cross referenced term should have a location list It s also possible to add your own custom keys See the datagidx section of the datatool user guide 17 for further details As with newglossaryentry discussed in Section 6 1 2 if the term starts with an accented letter or a ligature the letter must be grouped EXAMPLE T Input newterm label elite sort elite lite newterm plural e sophagi label oesophagus sort oesophagus description tube connecting throat and stomach e sophagus 4 Input There is a shortcut command for defining acronyms newacro options short long Definition where short is the abbreviation and long is the long
144. r ctan org help Catalogue bytopic html 4 Christophe Fiorio algorithm2e sty package for algorithms 2013 http mirror ctan org macros latex contrib algorithm2e doc algorithm2e pdf or texdoc algorithm2e 5 TeX for Humans Thesis and dissertation templates for BT X 2011 http latexforhumans wordpress com 2011 03 10 thesis templates for latex 6 Carsten Heinz and Brooks Moses The listings package 2007 http mirror ctan org macros latex contrib listings listings pdf or texdoc listings 7 Philip Kime and Fran ois Charette biber A backend bibliography processor for biblatex 2012 http mirror ctan org biblio biber documentation biber pdf or texdoc biber 8 Markus Kohm and Jens Uwe Morawski KOMA Script a versa tile ETEX2 bundle 2012 http mirror ctan org macros latex contrib koma script doc scrguien pdf or texdoc koma 9 Philipp Lehman Audrey Boruvka Philip Kime and Joseph Wright The biblatex package 2013 http mirror ctan org macros latex contrib biblatex doc biblatex pdf or texdoc biblatex 10 Wolfgang May and Andreas Schedler An extension of the BT X theorem environment 2011 http mirror ctan org macros latex contrib ntheorem ntheorem pdf or texdoc ntheorem 11 Oren Patashnik BibTeXing 1988 http mirror ctan org biblio bibtex base btxhak pdf or texdoc bibtex 12 R M Ritter Oxford Style Manual Oxford University Press 2003 13 Nicola Talbot Glossaries n
145. r 3 Splitting a Large Document into Several Files 18 Here is a short paragraph Here is some sample text 4 Input include does more than just input the contents of the file It also starts a new page using clearpage and creates an auxiliary file associated with the included file It also issues another clearpage once the file has been read in Using this approach you can also govern which files to include using includeonly file list Definition in the preamble where file list is a comma separated list of files you want included This way if you only want to work on one or two chapters you can only include those chapters which will speed up the document build ET X will still read in all the cross referencing information for the missing chapters but won t include those chapters in the PDF file There is a definite advantage to this if you have say a large number of images in your results chapter which you don t need when you re working on say the technical introduction You can still reference all the figures in the omitted chapter as long as you have previously ETpXed the document without the includeonly command The excludeonly package provides the logically opposite command excludeonly file list Definition The previous example can now be split into various files Listing 2 thesis tex T Input arara pdflatex synctex on arara pdflatex synctex on docume
146. rt of a line or page respectively The starred versions will insert the given spacing regardless of their lo cation You can also use hfill and vfill which will expand to fill the available space horizontally or vertically respectively EXAMPLE Listing 10 begin titlepage centering vspace 1in begin Large bfseries A Sample PhD Thesis par end Large vspace 1 5in begin large bfseries A N Other par end large vfill A Thesis submitted for the degree of Doctor of Philosophy par vspace Q 5in School of Something par University of Somewhere par vspace Q 5in Input Chapter 4 Formatting 25 July 2013 par end titlepage l 4 Input The result is shown in Figure 4 2 If you require double spacing you may need to wait until after the title page before switching to double spacing 4 5 Listings and Other Verbatim Text FAQ Code There may be times when you want to include text exactly as you have listings in BIFX typed it into your source code For example you may want to include a short segment of computer code This can be done using the verbatim environment EXAMPLE Note how I don t need to worry about special characters such as within the verbatim environment l T Input begin verbatim include lt stdio h gt needed for printf int main printf Hello World n return 1 end verbatim l 4 Input This just produces
147. s and text typed like this such as options and class file indicates the type of thing you need to substitute Don t type the angle brackets For example if you want the scrbook class file you would substitute class file with scrbook and if you want the letterpaper option you would substitute options with letterpaper like this documentclass letterpaper scrbook When it s important to indicate a space the visible space symbol is used For example A sentence consisting of six_words When you type up the code replace any occurrences of with a space NOTE Be careful of the dangers of obsolete code propagation It often happens that students pass on their ETEX code to new students who in their turn pass it on to the next lot of students and so on You re told use this magic bit of code to format your thesis without knowing what it does Ancient buggy code that s 20 years out of date festers in university departments refusing to die But if it worked for previous students what s the problem The problem is that it may stop working a week before your submission date and when you go for help you may be told you re using obsolete packages and there s nothing for it but to rewrite your thesis using the modern alternatives How do you know if a package is obsolete Some of the obsolete pack ages and commands are listed in l2tabu 18 or you can check to see if a package is listed in the Comprehensive T
148. s assumed to be post so if you only want a prefix and no suffix you have to specify an empty argument for post EXAMPLE Using the same thesis ref bib database as earlier Listing 16 rl 9 T Input A textual citation citet turabian96 and a parenthetical citation citep see Chapter 9 goossens97 vine npu Result z A textual citation Turabian 1996 and a parenthetical citation see Goossens P et al 1997 Chapter 9 Output 5 2 2 Troubleshooting e BIBTEX writes the thebibliography environment to a bb1 file which is then input into the document by bibliography If you have made a ETpX error in the bib file this error will be copied to the bbl file If you have corrected the error in the bib file but you are still getting an error when you FTEX your document try deleting the bb1 file In TeXworks you can use the menu item File Remove Aux Files e Remember to use double quotes or braces to delimit the field names in your bib file e Remember to put a comma at the end of each field entry except the last Chapter 5 Generating a Bibliography 66 e It is better to only use alphanumerical characters in the keywords Some punctuation characters such as full stop should be fine unless you re using a package such as babel that makes them active but spaces are not recommended and commas should definitely be avoided e If you have entered a field in th
149. s or captions Instead use commands like glsentrytext label displays the value of the text key without a hyperlink or glsentryfirst label displays the value of the first key without a hyperlink These commands don t affect the first use flag For related commands see the glossaries user guide 16 Take care if you want to use the uppercase variants such as Gls or Acrlong If the first letter is an accent either entered using accents com mands such as e or entered directly such as with the inputenc package then you must group that letter when you define the term EXAMPLE newglossaryentry felite label name lite description select group or class i Defining New Glossaries If you want the list of acronyms to be separate from the main glossary you need to use the package option acronym This will change the effect of newacronym so that it adds the term to the list of acronyms instead of to the main glossary You can also define your own custom glossaries using newglossary log ext name in ext out ext title counter where name is a label that uniquely defines this new glossary and title is the title to be used when the glossary is displayed in the document via printglossary or printglossaries see Section 6 1 2 The other manda tory arguments in ext and out ext specify the file extensions to give to T Output Output Definition Defi
150. s required If this key is omitted the value is obtained by appending the letter s to the value of the text key e firstplural How this entry will appear in the document text the first time it is used where the first use requires the plural form If this field is omitted the value is obtained by appending the letter s to the value of the first key e symbol This key is provided to allow the user to specify an associated symbol but most glossary styles ignore this value e sort This value indicates how to sort this entry analogous to using the character in the argument of index as described in Section 6 1 1 If this key is omitted the value of name is used e type This is the glossary type to which this entry belongs see Section 6 1 2 If omitted the main default glossary is assumed EXAMPLES The following defines the term set and assigns a brief description The term is given the label set This is the minimum amount of information you must give Input Chapter 6 Generating Indexes and Glossaries 82 newglossaryentry set the label name set the term description a collection of objects a brief description The following entry also has an associated symbol newglossaryentry U the label name universal set the term description the set of all things a brief description symbol ensuremath mathcal U the associate symbol The plural of th
151. s10994 008 5055 9 which takes me to the article s web page In this case it s in a journal published by Springer so my browser is redirected to the SpringerLink cite There I can use the export as text only option then copy and paste the reference into JabRef s import window as shown in Figure 5 11 Plain text import for Article Raw source BibTeX source Hints and Warnings a rWork options O EE E wl FE Allowed BibTeX fields Reference Type Journal Article ow Author Cawley Gavin X author Author Talbot Nicola title Primary Title Efficient approximate leave one out cross validation for kernel 3 journaltitle logistic regression X year Journal Name Machine Learning x date Cover Date 2008 06 01 Publisher Springer Netherlands x translator Issn 0885 6125 3 annotator Subject Computer Science X commentator Start Page 243 subtitle End Page 264 OP Volama 71 x titleaddon Issue 2 E 5 Url http dx doi org 10 1007 s10994 008 5055 9 Appen Doi 10 1007 s10994 008 5055 9 Override insert Plain text import This is a simple copy and paste dialog First load or paste some text into the text input area After that you can mark text and assign it to a BibTeX field Accept Cancel Figure 5 11 Importing a Plain Text Reference Next I need to select text for example an author s name and select the appropriate field in the Work options
152. sent What does the result m 0 678 signify What value were you expecting or hoping to get Numbers on their own are meaningless If I ran into a room shouting I ve got 42 What does that mean Forty two what Forty two brilliant reviews Great Forty two percent in an exam Not good Forty two spots on my face Very bad Don t waste time worrying about the best way to word your thesis in your first draft Write first then edit it later or you will never get started If your supervisor offers to critique chapters of your thesis don t say no Such offers are not made out of politeness but a desire to en sure that you pass Don t be embarrassed and worry that it s not good enough that s the whole point in your supervisor helping you improve ita Write in a clear concise manner A thesis is a technical document not a novel so don t be tempted to write something along the lines of I awaited with bated breath my whole body quivering with excitement A 2Having said that I know someone who submitted an article to a journal and it took three and a half years before the reviewers came back with comments In the end the author withdrew the manuscript because by that time the topic was out of date A3When I was a PhD student I was once rendered speechless when asked to provide a graphical illustration of an equation involving a quadruple summation that had no graphical meaning from my point of view Perhaps
153. tbf without the initial backslash that should be used to format the location for this reference This is analogous to the special character described in Section 6 1 1 There are also commands associated with acronyms acr format label acrpl format label Acr format label Acrpl format label Unlike the glossaries package described in Section 6 1 2 there is a difference between datagidx s gls and acr Here gls will always display the value of the text field whereas acr will display the full form on first use the text field and the abbreviation on subsequent use the short field You can also add terms to the index without creating any link text glsadd label Definition Definition Input Definition Definition Definition Definition Definition Definition Definition Definition A Definition Chapter 6 Generating Indexes and Glossaries 95 This adds the term uniquely identified by label glsaddall database name Definition This adds all the terms defined in the database uniquely identified by database name NOTE A Unlike most commands the optional part of the above commands occurs inside the mandatory argument EXAMPLES Given the elite and oesophagus examples defined on page 93 I can refer ence those entries in the text as follows Glsfelite and glspl oesophagus Input This produces Elite and cesophagi Output Elsewhere I might have the
154. the label that uniquely identifies the term as supplied in newglossaryentry or newacronym insert is additional text to insert after the term but inside the hyperlink if used with the hyperref package and options is a key value list of options Available options are e format This specifies how to format the associated location for this entry It is analogous to the special character used in index see Section 6 1 1 As with index the format must not include the initial backslash For example format textbf indicates that the location should be displayed in bold If you are using the hyperref package you should use the hyper xx formats instead such as hyperbf see the glossaries docu mentation 16 for further detail e counter This specifies which counter to use for the associated location in the glossary This is usually the page number but can be changed to say the section in which the term is used e hyper This is a boolean key which can be used to enable disable the hyperlink to the relevant entry in the glossary Note that setting hyper true will only have an effect if hyperlinks are supported through loading the hyperref package before loading the glossaries package The above com mands all have starred versions that are a shortcut for hyper false For example gls svm is equivalent to gls hyper false svm The above commands gls and Gls will display the value of the first or text key dep
155. tion list for the term circuit NOTE index doesn t display any text It just adds a line to the index file with the information required by makeindex or xindy to sort and collate the information The default action of index simply ignores its argument To ensure the indexing mechanism works you must activate it by placing makeindex in the document preamble Finally you need to use printindex defined in the makeidx package to display the index NOTE printindex won t produce any text until you have run the external indexing application Here s an example document Listing 18 arara pdflatex synctex on arara makeindex arara pdflatex synctex on documentclass 12pt oneside scrbook usepackage makeidx makeindex title Sample Document author Me begin document maketitle Definition A Definition Definition A T Input Chapter 6 Generating Indexes and Glossaries 75 chapter Sample Stuff about eigenvectors index eigenvector and eigenvalues index eigenvalue chapter Another Sample Some more stuff about eigenvectors index eigenvector and eigenvalues index eigenvalue Something about eigen decomposition index eigen decomposition backmatter printindex end document l j 4 Input If you are using arara to build your document see Section 1 1 2 re member to include the arara comments as shown in the above
156. tools in TeXworks This is done via the Edit Preferences menu item This opens TeXwork s Preferences dialog box Make sure the Typesetting tab is selected Figure 1 4 To add a new tool click on the lower button next to the list of pro cessing tools This opens the tool configuration dialog box Figure 1 5 Type LaTeXmk in the Name box then use the Browse button to locate latexmk on your computer Next you need to click on the button to add each argument The argument list should consist of the following in the order listed e pdflatex q pdflatex synctexoption 0 S pdf bibtex fullname Once you ve done this click Okay to close the tool configuration dialog and click Okay to close the Preferences dialog box LaTeXmk should now be listed in the drop down menu next to the green Typeset button Now if you have LaTeXmk selected and you click on the Typeset button pdflatex and bibtex biber will be run as necessary to create an up to date PDF 3If you are using a different front end you will have to consult your front end s manual Chapter 1 Introduction 6 TeXworks Preferences x General Editor Preview Typesetting Scripts Paths for TeX and related programs home nict bin usr Local texlive default bin x86_64 Linux M Processing tools go pdfLaTeX LuaTeX Edit LuaLaTeX XeTeX XeLaTeX ConTeXt LuaTeX CanTeXt ndf
157. uch as contentsname now in Volume 1 137 BACK COVER TEXT See http www gnu org licenses fdl howto opt html SEC2 If you choose to buy a copy of this book Dickimaw Books asks for your support through buying the Dickimaw Books edition to help cover costs 138
158. ument in any medium either com mercially or noncommercially provided that this License the copyright no tices and the license notice saying this License applies to the Document are reproduced in all copies and that you add no other conditions whatsoever to those of this License You may not use technical measures to obstruct or control the reading or further copying of the copies you make or dis tribute However you may accept compensation in exchange for copies If you distribute a large enough number of copies you must also follow the conditions in section 3 You may also lend copies under the same conditions stated above and you may publicly display copies 3 COPYING IN QUANTITY If you publish printed copies or copies in media that commonly have printed covers of the Document numbering more than 100 and the Doc ument s license notice requires Cover Texts you must enclose the copies in covers that carry clearly and legibly all these Cover Texts Front Cover Texts on the front cover and Back Cover Texts on the back cover Both covers must also clearly and legibly identify you as the publisher of these copies The front cover must present the full title with all words of the title equally prominent and visible You may add other material on the covers in addition Copying with changes limited to the covers as long as they pre serve the title of the Document and satisfy these conditions can be treated as verbatim copying in
159. urier DejaVuSansMono or dejavu to load the serif and sans serif DejaVu fonts as well Imodern and luximono KOMA anp listings A N If you want to use the listings package with one of the KOMA Script classes you need to load scrhack before listings otherwise you will get a warning that looks like Class scrbook Warning Usage of deprecated float listhead Cscrbook You should use the features of package tocbasic Cscrbook instead of float listhead Cscrbook Definition of float listhead my be removed from Cscrbook scrbook soon so it should not be used on input line 57 EXAMPLE Listing 11 rl z F Input begin lstlisting language C basicstyle ttfamily mathescape true include lt stdio h gt needed for printf include lt math h gt needed for sqrt int main double x sqrt 2 0 x sqrt 2 printf x f n x return 1 ven let listing 4 Input Result F Output include lt stdio h gt needed for printf include lt math h gt needed for sqrt int main double x sqrt 2 0 x V2 Chapter 4 Formatting 50 printf x f n x return 1 If you are using double spacing you may need to temporarily switch it off in the listings You can do this by adding singlespacing to the basicstyle setting lstset basicstyle ttfamily singlespacing Check with your supervisor to find out if listings s
160. use gls svm Short acrshort svm Long acrlong svm Full acrfull svm A gls not set is a collection of objects At the end of the document backmatter printglossaries l j 4 Input Troubleshooting If you run into difficulties with the glossaries package first consult the glos saries FAQ You can also check my bug tracker if you think you ve stumbled on a bug If you are using TeXnicCenter instead of TeXworks there are in structions on how to get TeXnicCenter to run makeglossaries in an article I wrote on the PTEX Community s Know How section 13 If you re completely confused about how to generate the glossary files you might want to consider using datagidx instead described next 6 2 Using PTEX to Sort and Collate Indexes or Glossaries datagidx package Section 6 1 described how to create an index or glossaries using an ex ternal indexing application Some users stumble when it comes to invok ing the indexing application There is an alternative where TeX does the sorting and collating This by passes the need to use makeindex xindy or makeglossaries but it s less efficient and takes longer to build your doc ument This section describes how to do this using the datagidx package This package comes with my datatool bundle at least version 2 13 The documentation for datagidx is included in the datatool user manual 17 Chapter 6 Generating Indexes and Glossaries 91 The datatool packa
161. w entry you can select BibTeX New entry which will open the dialog box shown in Figure 5 4 Now you need to click on the button appropriate to the entry For example click on Article for an article in a journal or click on Inproceedings for a paper in a conference proceed ings EXAMPLE Book Suppose I want to enter information about a book I need to select BibTeX New entry and then click on the button labelled Book This now displays fields in which I can enter the relevant information see Figure 5 5 Next I need to enter information in the Required fields tab This will usually include the title and the author I also need to specify a key that uniquely identifies this entry If you have read Volume 1 15 5 6 this key corresponds to the mandatory argument of bibitem and is also used in cite Figure 5 6 shows the details for my new entry I ve set the key to the author s surname followed by the year to make it easy to remember This key won t appear anywhere in the document it s just used to identify the entry just like the label ref mechanism Alternatively I can click on the Generate BibTeX Key button N to automatically insert a unique key There are also optional fields you can specify as well In Figure 5 7 I ve added the book s edition EXAMPLE JOURNAL ARTICLE Now I want to enter an article in a journal So I need to go back to BibTeX New entry and click on Article
162. x 6 1 input file name Defined in TEX Kernel Reads in the contents of file name See also include 3 0 itshape Defined in PTEX Kernel Switches to the italic form of the current font family if it exists See Volume 1 15 4 5 1 4 2 K kill Defined in tabbing environment Symbols NE KSA CHM DOVDOAZZORAHH THOT SAeD Summary of Commands and Environments 115 Sets the tab stops defined in the line but won t typeset the actual line 4 6 kilo Defined in siunitx package Indicates a kilo multiplier in commands like si 4 9 KwData text Defined in algorithm2e package For use in algorithm like environments to indicate the algorithm input data 4 8 KwIn fext Defined in algorithm2e package For use in algorithm like environments to indicate the algorithm input 4 8 KwOut text Defined in algorithm2e package For use in algorithm like environments to indicate the algorithm output 4 8 KwResult text Defined in algorithm2e package For use in algorithm like environments to indicate the algorithm output 4 8 KwRet value Defined in algorithm2e package For use in algorithm like environments to indicate a value returned 4 8 KwTo Defined in algorithm2e package For use in algorithm like environments to indicate to keyword 4 8 L label string Defined in TEX Kernel Assigns a unique textual label link
163. x synctex on documentclass scrbook I j 4 Input Now you just need to select Arara from the drop down list in TeXworks Figure 1 9 and click the green Typeset button and arara will do all the work for you NOTE If you don t add these arara comments to your source code nothing will happen when you run arara on your document You must remember to provide arara with the rules to build your document Unfortunately arara v3 0 doesn t have a rule for texindy but you can add one by creating a file called texindy yaml that contains the following config TeXindy rule for arara 5Thanks to Paulo Cereda for supply this Chapter 1 Introduction 11 P O OO thesis bibliotex Texworks x File Edit Search Format Typeset Scripts Window Help Arara O EA gt A 00E amp arara pdflatex synctex on arara bibtex arara pdflatex synctex on arara pdflatex synctex on documentclass oneside 12pt scrbook usepackage lipsum usepackage scrhack usepackage amsmath usepackage standard ntheorem usepackage algo2e algorithm2e set up document fonts usepackage T1 fontenc usepackage dejavu theoremstyle break theorembodyfont normalfont newtheorem algorithm algocf Algorithm usepackage setspace Figure 1 9 Using Arara in TeXworks Chapter 1 Introduction 12 requires arara 3 0 identifier texindy name TeXindy command

Using LaTeX to Write a PhD Thesis

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