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Package `runjags`

1. for i in 1 10000000 hold lt exp 100 PROCESS TO TIME post time lt Sys time timestring pre time post time Convert 4687 seconds into hours timestring 4687 units hours show units FALSE xgrid run Remote execution of user specified R functions on Apple Xgrid dis tributed computing clusters Description Allows arbitrary R code to be executed on Apple Xgrid distributed computing clusters and the results returned to the R session of the user Jobs can either be run synchronously the process will wait for the model to complete before returning the results or asynchronously the process will terminate on submission of the job and results are retrieved at a later time Access to an Xgrid cluster with R along with all packages required by the function installed is required Due to the dependance on Xgrid software to perform the underlying submission and retrieval of jobs these functions can only be used on machines running Mac OS X The two utility functions xgrid jobs and xgrid delete allow the currently running jobs to be examined and deleted from inside R Note Apple has discontinued Xgrid from Mac OS 10 8 onwards so future development and testing of these functions will be extremely limited 34 xgrid run Usage xgrid run f function iteration niters 1 object list list file list character 0 max threads 100 arguments as list 1 niters Rversion packages list artfun function writeL
2. And back to a named list namedlist2 lt list format chardata These should be the same stopifnot identical namedlist1 namedlist2 findjags Attempt to Locate a JAGS Install Description Search the most likely locations for JAGS to be installed on the users system based on the operating system and return the most likely path to try Where multiple installs exist findjags will attempt to return the path to the install with the highest version number For Unix systems calling jags using jags requires the jags binary to be in the search path which may be specified in your user Profile if necessary the JAGS executable is also looked for in the default install location of usr local bin jags if popen support is enabled Usage findjags ostype Platform 0S type look in if ostype windows c Program Files Windows Program Files C Program Files from variable jagspath Arguments ostype the operating system type There is probably no reason to want to change this look_in for Windows only the path to a folder or vector of folders which contains another folder with name containing JAGS where the JAGS executable s are to be found findjags will attempt to find the highest version assuming that the version number is somewhere in the file path to the executable as per default installation from variable a global variable that may contain the path to JAGS This pr
3. www fis iarc fr martyn software jags for more information The R package rjags is a native R interface to the JAGS library and allows a greater level of control for compiled models which may be more useful for model development This package was intended to provide additional functions to help automate the process of running models including interpretation of WinBUGS type text files including data and initial values automated convergence diagnostics automated collation and plotting of results and convinience wrappers for running models either individually or for multiple data sets over dis tributed computing cluster such as those provided by snow and Apple s now discontinued Xgrid The package also includes functions for running any other user specified R code over Xgrid dis tributed computing clusters from within R requires Mac OS X and access to an Xgrid system Author s Matthew Denwood lt matthew denwood glasgow ac uk gt See Also run jags and extend jags for basic model runs autorun jags and autoextend jags for automated running of models to convergence and auto mated calculation of necessary sample sizes runjags class for S3 methods relating to runjags objects incluing conversion to from jags objects for compatibility with the rjags package read winbugs for translation of WinBUGS text files into JAGS compatible model data and initial values files combine mcmc and dump format for MCMC related tools
4. JAGS using paral lel and distributed computing 28 runjags Description This package provides high level interface utilities for JAGS either running locally via the rjags package or using multiple cores in parallel or via distributed computing clusters such as those pro vided by snow a Simple Network Of Workstations Apple Xgrid distributied computing clusters Mac OS X 10 5 10 7 only and possibly others via user specified functions The primary moti vation is to facilitate running relatively simple JAGS models to convergence including evaluating the performance of a model against simulated data and compatibility with the WinBUGS syntax of model files with data and initial values lists Runjags interface functions also provide convenience wrappers for automatic control of model convergence assessment and run length diagnostics cal culation of relevant summary statistics generation of trace and density plots calculation of DIC and automatic retrieval of R objects as data and initial values Running of arbitrary R commands not involving JAGS over Xgrid is also supported Requires Just Another Gibbs Sampler JAGS for most functions see http www fis iarc fr martyn software jags Details JAGS is a program which allows analysis of Bayesian models using Markov chain Monte Carlo MCMC simulation and was developed by Martyn Plummer to be an alternative to BUGS that ran on UNIX systems as well as Windows systems see http
5. The return may also be a list including the named element complete which refers to the same thing as well as other elements that are returned to the top level If you are interested in developing another method please feel free to contact the package author method options an optional named list of argument to be passed to the method function includ ing a user specified method function Of the default arguments only nsims indicating the number of separate simulations for parallel snow and bgparallel methods and cl specifying an existing snow cluster and or remote jags spec ifying the path to JAGS on the remote machines for the snow method only can be used Others are ignored with a warning Value an object of class runjags see runjags class Author s Matthew Denwood lt matthew denwood glasgow ac uk gt See Also run jags read winbugs combine mcmc 9 xgrid autoextend jags runjags class Examples run a model to calculate the intercept and slope of the expression y m x c assuming normal observation errors for y Not run Simulate the data N lt 100 X lt 1 N Y lt rnorm N 2 X 10 1 Model in the JAGS format model lt model for i in 1 N Y i dnorm true y il precision true yLi lt m X i c m dunif 1000 1000 c dunif 1000 1000 precision dexp 1 data N X Y Fe Run the model results
6. hence the ability to set fewer threads than iterations Functions that return objects of a very large size should use a large number of threads and use the xgrid method separatejobs to minimise the total size of objects returned by each xgrid job additional arguments to be passed to the function provided by f jobinfo the output of a call to xgrid submit wait option to wait for the Xgrid job to complete if it has not done so already partial retrieve for xgrid results option to retrieve results of partially completed jobs By default makes cleanup FALSE Default TRUE comment option to display any comments relevant to the Xgrid jobs running user option to display information on the user that submitted each Xgrid job jobs the number of most recent jobs to display information for X for xapply a vector atomic or list over which to apply the function provided Equivalent to arguments for xgrid run with niters length X FUN for xapply the function to be passed to xgrid run as f method options for xapply any arguments with the exception of f niters and arguments which are ignored to be passed to xgrid run Details These functions allow JAGS models to be run on Xgrid distributed computing clusters from within R using the same syntax as required to run the models locally All the functionality could be replicated by saving all necessary objects to files and using the Xgrid command line ut
7. RE CALLED WITHIN THE FUNCTION BEFORE USE In order to use functions within an R library it is therefore necessary for the required library to be installed on the Xgrid nodes on which the job will be run If not all nodes have the required libraries installed you can use an ART script to en sure the job is sent only to machines that do see the example provided below or you can use mgrid to manually request certain nodes using the f h lt node name gt options Alternatively text files containing R code can be included in the file list argument and source d within the function Default blank list no objects copied a vector of filenames representing files in the current working directory that will be copied to the working directory of the executed function This allows R code to be source d datasets to be loaded and compiled code to be dynamically linked within the function among other things Default none the maximum number of tasks or jobs to split into a list of values to be passed as the first argument to the function with each element of the list specifying the value at that iteration Default is as list 1 niters which passes only the iteration number to the function the required R version for worker nodes to be given tasks may include or gt to signify exact or minimum version requirements a list of R packages that must be installed on host nodes for them to be used an optional user speci
8. before calculating summary statistics and returning the chains Thinning very long chains allows summary statistics to be calculated more quickly If TRUE the chain is thinned to as close to a minimum of startsample iterations as possible i e using a thinning interval of floor chain length thin sample since the value must be an integer and any autorun jags jags silent jags interactive max time adaptive thin excess iterations discarded to ensure the chain length matches thin sample If FALSE the chains are not thinned A positive integer can also be specified as the desired chain length after thinning the chains will be thinned to as close to this minimum value as possible Default TRUE thinned chains of length startsample returned This option does NOT carry out thinning in JAGS therefore R must have enough available memory to hold the chains BEFORE thinning To avoid this problem use the thin option instead the system call or path for activating JAGS Default calls findjags to attempt to locate JAGS on your system should the JAGS output be suppressed logical If TRUE no indication of the progress of individual models is supplied Default FALSE option to allow the simulation to be interactive in which case the user is asked if the simulation should be extended when run length and convergence calculations are performed and the extended simulation will take more than 1 minute The function will wait for a re
9. mcmc runjags runjags class 29 as runjags runjags class 29 ask 2 14 28 autoextend JAGS autorun jags 3 autoextend jags 28 autoextend jags autorun jags 3 autorun JAGS autorun jags 3 autorun jags 3 22 25 27 28 30 31 43 autorun JAGSfile run jagsfile 27 autorun jagsfile run jagsfile 27 combine MCMC combine mcmc 9 combine mcmc 9 23 28 31 dump 11 dump format 11 23 28 extend JAGS run jags 17 extend jags 28 41 45 extend jags run jags 17 failedjags runjags class 29 findJAGS findjags 12 findjags 12 32 jags model 29 30 lapply 25 list format dump format 11 mclapply 25 38 menu 3 new_unique 13 28 parLapply 25 38 plot runjags runjags class 29 print crosscorr stats runjags class 29 print dic stats runjags class 29 print gelman with target runjags class 29 print mcse stats runjags class 29 print runjags runjags class 29 raftery diag 6 read WinBUGS read winbugs 14 read winbugs 4 8 14 18 27 28 readline 3 results JAGS run jags 17 results jags 22 results jags run jags 17 run JAGS run jags 17 run jags 3 8 10 11 13 15 17 25 28 30 32 38 41 43 run JAGS study run jags study 24 run jags study 24 run JAGSfile run jagsfile 27 run jagsfile 15 27 runJAGS runjags 27 46 runjags 27 runJAGS class runjags class 29 runjags class 29 runJA
10. ples for a model with no autocorrelation and good convergence Default 10000 iterations datalist an optional named list containing variables used as data or alternatively a func tion with no arguments that returns a named list If any variables are specified in the model block using data lt variable gt the value for the corresponding named variable is taken from datalist if present or the result of datalist if spec ified as a function which is useful for specifying randomly generated data or the parent environment or finally the global environment if not found anywhere else Ignored if data lt variable gt is not used in the model block Default NA initlist an optional named list containing variables used as initial values or alternatively a function with a single argument representing the chain number that returns a named list If any variables are specified in the model block using inits lt vari able gt the value for the corresponding named variable is taken from initlist if present or the result of datalist chain no if specified as a function which allows both randomly generated initial values and different values for each chain or the parent environment or finally the global environment if not found anywhere else Ignored if inits lt variable gt is not used in the model block Note dif ferent chains are all given the same starting values if specified as a named list or taken from any
11. showprofiles FALSE jagspath usr local bin jags mgridpath system file xgrid mgrid sh package runjags hostname Sys getenv XGRID_CONTROLLER_HOSTNAME password Sys getenv XGRID_CONTROLLER_PASSWORD xgrid autoextend jags runjags object stop The output of a runjags function with class runjags max threads Inf JAGSversion gt 2 0 0 email NA profiling TRUE cpuarch NA minosversion NA queueforserver FALSE hostnode NA forcehost FALSE ramrequired 10 jobname NA cleanup TRUE showprofiles FALSE jagspath usr local bin jags mgridpath system file xgrid mgrid sh package runjags hostname Sys getenv XGRID_CONTROLLER_HOSTNAME password Sys getenv XGRID_CONTROLLER_PASSWORD xgrid submit jags model stop No model supplied max threads Inf JAGSversion gt 2 0 0 email NA profiling TRUE cpuarch NA minosversion NA queueforserver FALSE hostnode NA forcehost FALSE ramrequired 10 jobname NA jagspath usr local bin jags mgridpath system file xgrid mgrid sh package runjags hostname Sys getenv XGRID_CONTROLLER_HOSTNAME password Sys getenv XGRID_CONTROLLER_PASSWORD xgrid results jags background runjags object stop An object produced by an xgrid submit call must wait TRUE cleanup TRUE Arguments model a JAGS model as would be provided to the run jags function runjags object an object of class runjags as w
12. the function over all iterations is returned as a list with each element of the list representing the results at each iteration If the function returned an error then the error will be held in the list as the return value at the iteration that returned the error If the function returns an object that exceeds the max filesize when combined with the results for other iterations in that job or greater than max filesize threads for multi task jobs the results for that thread are replaced with an error message this is to prevent the xgrid controller crashing due to transferring large files The xapply function returns as xgrid run or xgrid submit if xgrid options list submitandstop TRUE in which case the results can be retrieved using xgrid results Author s Matthew Denwood lt matthew denwood glasgow ac uk gt See Also xgrid run jags for functions to run JAGS models on Xgrid or run jags to do so locally mclapply and parLapply in the parallel package for parallel execution of code over multiple local or remote cores Examples A basic example of synchronous running of code over 100 iterations split up between 10 tasks Not run The function to evaluate f lt function iteration All objects supplied to object list will be visible here but remember to call all necessary libraries within the function cat Running iteration iteration n Some lengthy code evaluation output lt rpoi
13. the sensitivity of the convergence diagnostic but will cause the simulation to run more slowly although this may be improved by using a method such as parallel or snow The minimum and default number of chains is 2 inits either a character vector with length equal to the number of chains the model will be run using or a list of named lists representing names and corresponding values of inits for each chain If a vector each element of the vector must be a Character string in the R dump format representing the initial values for that chain or NA If not all initialising variables are specified the unspecified vari ables are sampled from the prior distribution by JAGS Values left as NA result in all initial values for that chain being sampled from the prior distribution The special variables RNG seed RNG name and RNG state are allowed for explicit control over random number generators in JAGS Default NA runjags object the model to be extended the output of a run jags or autorun jags or extend jags etc function with class runjags No default background runjags object the output of a run jags or extend jags function call using a background JAGS method with class runjags bginfo No default add monitor a character vector of variables to add to the monitored variable list All previ ously monitored variables are automatically included although see the drop monitor argument De
14. to be read by JAGS as either data or initial values using the run jags function Usage dump format namedlist list checkvalid TRUE list format data character checkvalid TRUE Arguments namedlist a named list of numeric or integer or something that can be coerced to numeric vectors matrices or arrays The name of each list item will be used as the name of the resulting dump format variables data a character string in the R dump format such as that produced by dump format checkvalid option to ensure that the object returned from the function does not contain any values that would be invalid for import into JAGS such as Inf Inf character or factor values etc Details The dump format function creates a character string of the supplied variables in the same way that dump would except that the result is returned as a character string rather than written to file Additionally dump format will look for any variable with the name RNG name and double quote the value if not already double quoted to ensure compatibility with JAGS Value Either a character string in the R dump format for dump format or a named list for list format Author s Matthew Denwood lt matthew denwood glasgow ac uk gt See Also run jags dump 12 findjags Examples A named list namedlist1 lt list N 10 Count c 4 2 7 0 6 9 1 4 12 1 Conver to a character vector chardata lt dump format namedlist1
15. ALSE Analyse the results results summary End Not run Submit a job to xgrid and later retrieve the results Use an ART script to ensure the job is only sent to nodes with JAGS installed Not run Ensure the required environmental variables are set Sys setenv XGRID_CONTROLLER_HOSTNAME lt hostname gt Sys setenv XGRID_CONTROLLER_PASSWORD lt password gt Simulate the data X lt 1 100 Y lt rnorm length X 2 X 10 1 Model in the JAGS format model lt model for i in 1 NX Y il dnorm true yLil precision true yLi lt m XLi c m dunif 1000 1000 c dunif 1000 1000 precision dexp 1 y Run the model asynchronously name lt xgrid submit jags model model monitor c m data list N length X X X Y Y n chains 2 plots inits list list RNG name base Wichmann Hill list RNG name base Marsaglia Multicarry Retrieve the results results lt xgrid results jags name End Not run nan c precision FALSE Xgrid run jags Index Topic methods ask 2 combine mcmc 9 dump format 11 findjags 12 new_unique 13 read winbugs 14 run jags study 24 runjags 27 testjags 31 timestring 32 xgrid run 33 xgrid run jags 40 Topic models autorun jags 3 run jags 17 run jagsfile 27 runjags class 29 as jags runjags class 29 as mcmc list runjags runjags class 29 as
16. Default none factories a character vector of factory modules to be loaded into JAGS More than 1 fac tory can be used Factories should be provided in the format lt facname gt lt factype gt for example factories mix TemperedMix sampler Also ensure that any re quired modules are also specified in this case mix for example Default none raftery options a named list which is passed as additional arguments to raftery diag Default none default arguments to raftery diag are used crash retry the number of times to re attempt a simulation if the model returns an error Default 1 retry simulation will be aborted after the second crash summarise should summary statistics be automatically calculated for the output chains Default TRUE confidence the prob argument to be passed to HPDinterval for calculation of confidence intervals Default 0 95 95 confidence intervals plots should traceplots and density plots be produced for each monitored variable If TRUE the object of class runjags returned will include elements trace and density which consist of a list of lattice objects with a specific print func tion that can also be accessed using plot results The alternative is to use plot as mcmc list results to look at the density and traceplots for each vari able using the traditional graphics system See also runjags class Default TRUE thin sample option to thin the final MCMC chain s
17. GS package runjags 27 runjags package runjags 27 runJAGS bginfo class runjags class 29 runjags bginfo class runjags class 29 runJAGS bginfoclass runjags class 29 runjags bginfoclass runjags class 29 runJAGS data class runjags class 29 runjags data class runjags class 29 runJAGS dataclass runjags class 29 runjags dataclass runjags class 29 runJAGS model class runjags class 29 runjags model class runjags class 29 runJAGS modelclass runjags class 29 runjags modelclass runjags class 29 runJAGS plots class runjags class 29 runjags plots class runjags class 29 runJAGS plotsclass runjags class 29 runjags plotsclass runjags class 29 runJAGS study class runjags class 29 runjags study class runjags class 29 runJAGS studyclass runjags class 29 runjags studyclass runjags class 29 runJAGSclass runjags class 29 runjagsclass runjags class 29 runJAGSpackage runjags 27 runjagspackage runjags 27 summary mcmc 31 summary runjags runjags class 29 Sys time 33 test JAGS testjags 31 testjags 13 23 31 timestring 28 32 xapply xgrid run 33 xgrid autoextend JAGS xgrid run jags 40 xgrid autoextend jags 5 9 21 xgrid autoextend jags xgrid run jags 40 xgrid autorun JAGS xgrid run jags 40 xgrid autorun jags xgrid run jags 40 xgrid autorun JAGSfile run jagsfile 27 xgrid xgrid xgrid xgrid xgrid xgrid xgrid xgrid xgrid xgrid
18. ONTROLLER_PASSWORD xgrid delete jobinfo keep files FALSE xapply X FUN method options list Arguments f the function to be iterated over on Xgrid This must take at least 1 argument the first of which represents the value of the arguments list to be passed to the function for that iteration which is the iteration number unless arguments or X for xapply is specified Any other arguments to be passed to the function can be supplied as additional arguments to xgrid run xgrid submit xapply The value s of interest should be returned by this function an object of any class is xgrid run niters object list file list max threads arguments Rversion packages artfun email profiling cpuarch minosversion queueforserver hostnode forcehost ramrequired 35 permissable No default the total number of iterations over which to evaluate the function f This can be less than the number of threads in which case multiple iterations are evaluated serially as part of the same task No default a named list of objects that will be copied to the global environment on Xgrid and so will be visible inside the function Alternatively this can be a character vector of objects that will be looked for in the global environment rather than a named list All other objects in the current working directory will not be vis ible when the function is evaluated THIS INCLUDES LIBRARIES WHICH MUST BE
19. Package runjags March 26 2013 Version 1 0 0 6 Date 2013 03 26 Title Interface utilities for MCMC models in Just Another Gibbs Sampler JAGS using parallel and distributed computing methods Author Matthew Denwood lt mat thew denwood glasgow ac uk gt Maintainer Matthew Denwood lt mat thew denwood glasgow ac uk Depends R gt 2 14 coda gt 0 16 1 lattice gt 0 20 10 parallel Imports coda lattice parallel stats utils Suggests rjags SystemRequirements jags see http mcmc jags sourceforge net Description This package provides high level interface utilities for JAGS either running locally via the rjags package or using multiple cores in parallel or via distributed computing clusters such as those provided by snow a Simple Network Of Workstations Apple Xgrid distributed computing clusters Mac OS X 10 5 10 7 only and possibly others via user specified functions The primary motivation is to facilitate running relatively simple JAGS models to convergence including evaluating the performance of a model against simulated data and compatibility with the Win BUGS syntax of model files with data and initial values lists Runjags interface functions also provide convenience wrappers for automatic control of model convergence assess ment and run length diagnostics calculation of relevant summary statistics generation of trace and density plots calculation of DIC and automatic retrieval of R objects as data
20. Rinst packagesinst Or to get more details about a particular package g lt function i p lt library help bayescount 40 xgrid run jags return p info J Get the information back from 2 specific machines called newnode1 and newnode2 results lt xgrid run f niters 2 threads 2 hostnode newnode1 newnode2 See the installed packages on the two nodes results End Not run xgrid run jags Run a JAGS Model using an Apple Xgrid distributed computing cluster from Within R Description Extends the functionality of the run jags family of functions to use with Apple Xgrid distributed computing clusters Jobs can either be run synchronously using xgrid auto run jags in which case the process will wait for the model to complete before returning the results or asynchronously using xgrid submit jags in which case the process will terminate on submission of the job and results are retrieved at a later time using xgrid results jags The latter function can also be used to check the progress of incomplete simulations without stopping or retrieving the full job Access to an Xgrid cluster with JAGS although not necessarily R installed is required Due to the dependance on Xgrid software to perform the underlying submission and retrieval of jobs these functions can only be used on machines running Mac OS X Further details of required environmental variables and the optional mgrid script to enable mult
21. able simple runs JAGS as a foreground process the default behaviour for runjags lt 0 9 6 interruptible allows the JAGS pro cess to be terminated immediately using the interrupt signal parallel runs each chain as a separate process on a separate core snow uses a simple network of workstations which may be passed into the method options list as cl and background amp bgparallel starts JAGS as one or more background processes 22 method options Value run jags and returns the information needed to be passed to results jags to retrieve the simulations when they have finished The default for run jags is to use rjags if the rjags package is load Qed or the interactive method otherwise The default for the extend jags function is to use the same method as used for the previous JAGS call Note that the parallel snow and bgparallel methods all use separate JAGS in stances to speed up execution of models with multiple chains at the expense of using more RAM but cannot be used to monitor pd popt pd i and there fore DIC Each chain is specified using a different random number genera tor RNG name for up to 4 chains the number of different RNG available in JAGS unless RNG name is specified in the initial values Because each chain uses a separate JAGS instance JAGS has no way of ensuring independence between multiple chains using the same random number generator as would nor
22. al values or a character string of the same No default The model must be started with the string model and ended with on new lines Data must be similarly started with data monitored variables with moni tor and initial values as inits and all ended with If multiple models are found all but the first one are ignored with a warning Multiple data blocks and monitor blocks are combined multiple inits blocks are used for different chains The model block may also contain automatically generated data and initial val ues variables using data variable and inits variable and more monitored variables using monitor variable See read winbugs for more information No default run jags 19 monitor a character vector of the names of variables to monitor The special node names deviance pd pd i popt and dic are used to monitor these model fit diag nostics see the JAGS user manual for more information but with the exception of deviance these monitored nodes won t appear as variables in the summary statistics or plots Note multiple chains are required for calculation of pd i pd popt and dic No default data a character string in the R dump format or a named list containing the data If left as NA no external data is used in the model Default NA n chains the number of chains to use with the simulation More chains will improve
23. and initial values Running of arbitrary R commands not involving JAGS over Xgrid is also supported License GPL URL http cran r project org web packages runjags NeedsCompilation no 2 ask Repository CRAN Date Publication 2013 03 26 14 43 36 R topics documented ASK sk Gea BORREGO Sao a BG whe Bo So Se gag hl Goa gh a ago a 2 Gen o e eA SEES ee A EGA ewe 3 combine memc s s sos sose k RRR RS RU AR ee Sl 9 dump format 220428344 2 44 2 344 SS ae Sena ERO De OHSS BOs 11 UIMOAES ma woe ee dd Scere Ge bh ee dd o Boe ek fos 12 DEW UNIQUE 254 6k a SPEAR eS ELMER Oe RAS AE Ea eA IN 13 read Winbugs e e bed ek eo ee A A 14 TUN AGS chee A Bes BG Ba pe ge Deo Ba ae RE ca colby Ge BRS Re pede 17 TUN Jagsistudy ur 80 bbe Ste date Peed e eRe SELES 24 mangan no e g Xe ah ee Se ee Se OE ER A ee 27 TUMAGS A eerie a hs Rh a A AS Ra ees Be A ce a 21 r njags class iia e A di 29 TOSUALS eric a e e a a Gd KERA 31 TESIS hd brat Gee RS e e KAK Pan 32 RUIDO Se Me ee wk eA AAA Pee ps 33 XSvid TUN JAS sk a ee be ESS A AAA ee RS SR ae Ee ee eek 40 Index 45 ask Obtain Input from User With Error Handling Description A simple function to detect input from the user and keep prompting until a response matching the class of input required is given Usage ask prompt type logical bounds c Inf Inf na allow FALSE Arguments prompt what text string should be used to prompt the user character string type the class of object
24. assessing convergence and Monte Carlo error when parameter estimates are being made from real data For more complex models the use of run jags directly with manual assessment of necessary run length may be preferable Requires Just Another Gibbs Sampler JAGS see http www fis iarc fr martyn software jags Usage autorun jags model stop No model supplied monitor NA data NA n chains NA inits NA startburnin 5000 startsample 10000 datalist NA initlist NA psrf target 1 05 normalise mcmc TRUE check stochastic TRUE modules c factories c raftery options list crash retry 1 summarise TRUE confidence 0 95 plots summarise thin sample FALSE jags findjags silent jags FALSE interactive FALSE max time Inf adaptive list type burnin length 200 thin 1 monitor deviance 4 autorun jags FALSE monitor pd FALSE tempdir TRUE jags refresh 0 1 batch jags silent jags method if rjags in packages rjags else interruptible method options list autoextend jags runjags object stop The output of a runjags function with class runjags must b add monitor character 0 drop monitor character 0 drop chain numeric 0 combine length c add monitor drop monitor drop chain 0 startburnin 0 startsample 10000 psrf target 1 05 normalise mcmc TRUE check stochastic TRUE raftery options listQ crash retry 1 summarise TRUE co
25. cord chains option to return the full runjags objects returned from each simulation as a list item named runjags Default FALSE runjags options a named list of options to be passed to the underlying autorun jags function used to run the models cat progress option to print a message when individual simulations have finished running This is available for use with lapply but messages will not be printed for some parallel methods such as the default parLapply Default FALSE test option to test the model compilation on a single randomly chosen dataset to ensure that the model compiles before calling the parallel method Default TRUE parallel method a function that will be used to call the repeated simulations This must take the first two arguments X and FUN as for lapply with other optional argu ments passed through from the parent function call Default uses parLapply but lapply or mclapply could also be used optional arguments to be passed directly to the parallel method function such as cl in the case of parLapply 26 run jags study Value An object of class runjags study class containing a summary of the performance of the model with regards to the target variables specified If record chains TRUE an element named runjags containing a list of all the runjags objects returned will also be present Author s Matthew Denwood lt matthew denwood glasgow ac uk gt See Also run jags runja
26. e summary statistics print results Extract only the coefficient as an mcmc list object coeff lt as mcmc list results vars m End Not run 24 run jags study The same model but using embedded shortcuts to specify data inits and monitors Not run Model in the JAGS format model lt model for i in 1 N data N Y il dnorm true yLi precision data Y true ylil lt m XLi c data X m dunif 1000 1000 inits m c dunif 1000 1000 precision dexp 1 monitor m c precision y Simulate the data X lt 1 100 Y lt rnorm length X 2 X 10 1 N lt length X initfunction lt function chain return switch chain 1 list m 10 2 list m 10 results lt run jags model n chains 2 initlist initfunction Look at a traceplot of the intercept and slope on a 2x1 grid plot results type trace vars c m c layout c 2 1 End Not run run jags study Run an MCMC Model in JAGS Using Multiple Simulated Datasets Description This function can be used to fit a user specified JAGS model to multiple datasets with automatic control of run length and convergence over a distributed computing cluster such as that provided by snow The results for monitored variables are compared to the target values provided and a summary of the model performance is returned This may be used to facilitate model validation using simulated data or to asse
27. e user Usage S3 method for class runjags print x vars NA digits 5 S3 method for class runjags plot x vars NA layout NA newwindows NA file type all S3 method for class runjags model print x linenumbers TRUE S3 method for class runjags data print x linenumbers TRUE S3 method for class runjags inits print x linenumbers TRUE S3 method for class runjags study print x S3 method for class runjags bginfo print x S3 method for class runjags as mcmc x S3 method for class runjags as mcmc list x vars NA 30 runjags class S3 method for class runjags as jags x al S3 method for class jags as runjags x monitor modules c factories c check TRUE jags Arguments Xx vars digits layout newwindows file type linenumbers monitor modules factories check jags stop No monitored variables supplied findjags an object of class runjags as returned by the run jags or autorun jags func tions or for the as runjags method an object of class jags as returned by the jags model function in the rjags package an optional character vector of variable names to extract If supplied only vari able names in the object supplied with a partial match to anything in vars will be summarised plo
28. ensity plots be produced for each monitored variable If TRUE the returned list will include elements trace and density which consist of a list of lattice objects accessible using the plot method for the runjags class The alternative is to use for example plot as mcmc list results to look at the density and traceplots for each variable using the traditional graphics system Default follows the summarise argument which is required to be TRUE for plots to be produced the value of the point estimate for the potential scale reduction factor of the Gelman Rubin statistic below which the chains are deemed to have converged must be greater than 1 Ignored if check conv FALSE Default 1 05 the Gelman Rubin statistic is based on the assumption that the posterior dis tribution of monitored variables is roughly normal For very skewed posterior distributions it may help to log logit transform the posterior before calculat ing the Gelman Rubin statistic If normalise mcmc TRUE the normality of the untransformed and log logit transformed posteriors are compared for each monitored variable and the least skewed is used to calculate the Gelman Rubin statistic If FALSE the data are left untransformed this may give problems cal culating the statistic in extreme cases Ignored if check conv FALSE Default TRUE check stochastic non stochastic monitored variables will cause errors when calculating the Gelman Rubin statist
29. envirnoment if different values are desired for each chain initlist should be specified as a function Default NA autorun jags psrf target the value of the point estimate for the potential scale reduction factor of the Gelman Rubin statistic below which the chains are deemed to have converged must be greater than 1 Default 1 05 normalise mcmc the Gelman Rubin statistic is based on the assumption that the posterior dis tribution of monitored variables is roughly normal For very skewed posterior distributions it may help to log logit transform the posterior before calculat ing the Gelman Rubin statistic If normalise mcmc TRUE the normality of the untransformed and log logit transformed posteriors are compared for each monitored variable and the least skewed is used to calculate the Gelman Rubin statistic this may take some time for large numbers of monitored variables If FALSE the data are left untransformed this may give problems calculating the statistic in extreme cases Default TRUE check stochastic non stochastic monitored variables will cause errors when calculating the Gelman Rubin statistic if check stochastic TRUE then all monitored variables will be checked to ensure they are stochastic beforehand This has a small compu tational cost which can be avoided by specifying check stochastic FALSE Default TRUE modules a character vector of external modules to be loaded into JAGS More than 1 module can be used
30. er specified WinBUGS type textfile or character variable and extract any models data monitored variables or initial values as character vectors Used by auto run jags to interpret the input file s or strings Usage read winbugs path Arguments path either a relative or absolute path to a textfile including the file extension con taining a model in the JAGS language and possibly monitored variable names data and or initial values or a character string of the same May also be a vector of paths to different text files possibly separately containing the model data and intitial values No default The model must be started with the string model and ended with on new lines Data must be similarly started with data read winbugs 15 monitored variables with monitor and initial values as inits and all ended with Y Seperate variables in such blocks must be separated by a line break If multiple models are found all but the first one are ignored with a warning Multiple data blocks and monitor blocks are combined multiple inits blocks are used for different chains Monitors may also be given using the phrase moni tor variable within the model block in which case variable is added to the list of monitored variables found in the monitor block s The use of automatically generated data and initial values is also supported using similar syntax with data variable for automaticall
31. expected to be returned logical numeric integer character If the user input does not match this return the prompt is repeated bounds the lower and upper bounds of number to be returned Ignored if type is logical or character na allow if TRUE allows the user to input NA for any type which is returned as NA autorun jags 3 Author s Matthew Denwood lt matthew denwood glasgow ac uk gt See Also readline menu Examples Ask the user if they want to proceed Not run ask Do you want to start the program now type logical End Not run autorun jags Run or Extend a User Specified Bayesian MCMC Model in JAGS with Automatically Calculated Run Length and Convergence Diagnostics Description Runs or extends a user specified JAGS similar to WinBUGS model from within R returning an object of class runjags class Chain convergence over the first run of the simulation is assessed using the Gelman and Rubin s convergence diagnostic If necessary the simulation is extended to improve chain convergence up to a user specified maximum time limit before the required sample size of the Markov chain is calculated using Raftery and Lewis s diagnostic The simulation is extended to the required sample size dependant on autocorrelation and the number of chains This function is provided primarily for automated running of large simulated data studies and is not a replacement for manually
32. fault no additional monitors drop monitor a character vector of previously monitored variables to remove from the moni tored variable list for the extended model Default none drop chain a numeric vector of chains to remove from the extended model Default none combine a logical flag indicating if results from the new JAGS run should be combined with the previous chains Default TRUE if not adding or removing variables or chains and FALSE otherwise burnin the number of burnin iterations not sampled to use numeric Default 5000 iterations sample the number of sampling iterations to use numeric Default 10000 iterations adapt advanced option to control the length of the adaptive phase directly which is otherwise half the length of the burnin period Default is 0 unless burnin is less than 200 in which case 100 adapitve iterations are used datalist an optional named list containing variables used as data or alternatively a func tion with no arguments that returns a named list If any variables are speci fied in the model block using data variable the value for the corresponding 20 initlist jags silent jags summarise confidence plots psrf target normalise mcmc run jags named variable is taken from datalist if present or the result of datalist 1f spec ified as a function which is useful for specifying randomly generated data or the parent environment or finally the global environ
33. fied R function to determine the suitability of nodes in an ART script must either cat 1 indicating suitable or 0 indicating unsuitable to stdout an email address to be used to notify of job status option to use ART ranking to select the most suitable host nodes preferentially option to restrict the job to ppe or intel nodes option to restrict the job to nodes running a minimum Mac OS version option to restrict the job to nodes considered to be Server machines option to prefer or restrict to if forcehost TRUE running the job on the speci fied nodes must be provided as a single character string with the colon character separating node names option to restrict the job to only nodes specified by hostnode the minimum amount of free RAM obtained using an approximation for each node to be assigned a task 36 jobname cleanup showprofiles Rpath Rbuild max filesize mgridpath hostname password tempdir keep files show output separate jobs threads xgrid run the name to give the job on Xgrid optional option to remove the job from Xgrid after completion option to show the node scores based on the ART ranking used the path to the R executable on the xgrid machines If not all machines on the xgrid cluster have R or a required package installed then it is possible to use an ART script to ensure the job is sent to only machines that do see the examples section f
34. gs study class Examples Not run Perform a drop 1 validation study for a simple model themodel lt model for i in 1 N Y i dnorm true y il precision true ylil lt m XLi c m dunif 1000 1000 c dunif 1000 1000 precision dexp 1 data N X inits m c precision y Simulate the data N lt 20 X lt 1 N Y lt rnorm length X 2 X 1 1 Some initial values to use for 2 chains m lt list 10 10 c lt list 10 10 precision lt list 0 01 100 A simple function that removes over writes with NA one datapoint at a time datafun lt function s simdata lt Y simdata s lt NA return list Y simdata run jagsfile 27 Set up a cluster to use with the parLapply method cl lt makeCluster 20 Call the 20 simulations over the snow cluster results lt run jags study simulations 20 model themodel datafunction datafun targets list Y Y m 2 c 1 r Examine the results results End Not run run jagsfile Deprecated functions Description These functions are deprecated and only remain for backwards compatibility Please use the run jags or autorun jags functions directly with the model argument replacing path Author s Matthew Denwood lt matthew denwood glasgow ac uk gt See Also autorun jags run jags xgrid run jags read winbugs runjags Interface utilities for Just Another Gibbs Sampler
35. i task jobs can be found in the details section Note Apple has discontinued Xgrid from Mac OS 10 8 onwards so future development and testing of these functions will be extremely limited Usage xgrid run jags model stop No model supplied max threads Inf JAGSversion gt 2 0 0 email NA profiling TRUE cpuarch NA minosversion NA queueforserver FALSE hostnode NA forcehost FALSE ramrequired 10 jobname NA cleanup TRUE showprofiles FALSE jagspath usr local bin jags mgridpath system file xgrid mgrid sh package runjags hostname Sys getenv XGRID_CONTROLLER_HOSTNAME password Sys getenv XGRID_CONTROLLER_PASSWORD xgrid run jags 41 xgrid autorun jags model stop No model supplied max threads Inf JAGSversion gt 2 0 0 email NA profiling TRUE cpuarch NA minosversion NA queueforserver FALSE hostnode NA forcehost FALSE ramrequired 10 jobname NA cleanup TRUE showprofiles FALSE jagspath usr local bin jags mgridpath system file xgrid mgrid sh package runjags hostname Sys getenv XGRID_CONTROLLER_HOSTNAME password Sys getenv XGRID_CONTROLLER_PASSWORD xgrid extend jags runjags object stop The output of a runjags function with class runjags must max threads Inf JAGSversion gt 2 0 0 email NA profiling TRUE cpuarch NA minosversion NA queueforserver FALSE hostnode NA forcehost FALSE ramrequired 10 jobname NA cleanup TRUE
36. ic if check stochastic TRUE then all monitored variables will be checked to ensure they are stochastic beforehand This has a computational cost and can be bypassed if check stochastic FALSE Default TRUE run jags 21 modules external modules to be loaded into JAGS More than 1 module can be used Default none factories factory modules to be loaded into JAGS More than 1 factory can be used Factories should be in the format lt facname gt lt factype gt for example fac tories mix TemperedMix sampler Default none thin the thinning interval to be used in JAGS Increasing the thinning interval may reduce autocorrelation and therefore reduce the number of samples required but will increase the time required to run the simulation Default 1 monitor deviance this argument is deprecated and remains for backwards compatibility only See the monitor variable monitor pd this argument is deprecated and remains for backwards compatibility only See the monitor variable monitor pd i this argument is deprecated and remains for backwards compatibility only See the monitor variable monitor popt this argument is deprecated and remains for backwards compatibility only See the monitor variable check conv this argument is deprecated and remains for backwards compatibility only See the summarise variable keep jags files option to keep the folder with files needed to call JAGS rather than dele
37. ility to submit and retrieve the job manually these functions merely provide the convenience of not having to do this manually Xgrid support is only available on Mac OS X machines running OS X 10 5 10 7 Xgrid support was discontinued in Mac OS X 10 8 The xgrid controller hostname and password can also be set as environmental variables The com mand line version of R knows about environmental variables set in the profile file but unfortunately the GUI version does not and requires them to be set from within R using Sys setenv XGRID_CONTROLLER_HOSTNAME lt hostname gt Sys setenv XGRID_CONTROLLER_PASSWORD lt password gt These lines could be copied into your Rprofile file for a set and forget solution Note that the runjags package also contains a utility shell script called mgrid that enhances the capabilities of Xgrid substantially to install this from the command line navigate to the folder given by system file xgrid package runjags and from the terminal type sudo cp mgrid sh usr local bin mgrid or similar to make the script visible in your search path Help on the mgrid script can then be obtained by typing mgrid with no arguments at the command line 38 Xgrid run Value For xgrid submit a list containing the jobname which will be required by xgrid results to re trieve the job and the job ID s for use with the xgrid command line facilities For xgrid run and xgrid results the output of
38. ines 1 email NA profiling TRUE cpuarch NA minosversion NA queueforserver FALSE hostnode NA forcehost FALSE ramrequired 10 jobname NA cleanup TRUE showprofiles FALSE Rpath usr bin R Rbuild 64 max filesize 1GB mgridpath system file xgrid mgrid sh package runjags hostname Sys getenv XGRID_CONTROLLER_HOSTNAME password Sys getenv XGRID_CONTROLLER_PASSWORD tempdir FALSE keep files FALSE show output TRUE threads min niters max threads io xgrid submit f function iteration niters 1 object list list file list character 0 max threads 100 arguments as list 1 niters Rversion packages list artfun function writeLines 1 email NA profiling TRUE cpuarch NA minosversion NA queueforserver FALSE hostnode NA forcehost FALSE ramrequired 10 jobname NA Rpath usr bin R Rbuild 64 max filesize 1GB mgridpath system file xgrid mgrid sh package runjags hostname Sys getenv XGRID_CONTROLLER_HOSTNAME password Sys getenv XGRID_CONTROLLER_PASSWORD show output TRUE separate jobs FALSE threads min niters max threads xgrid results jobinfo wait TRUE partial retrieve wait cleanup partial retrieve show output TRUE xgrid jobs comment FALSE user FALSE jobs 10 mgridpath system file xgrid mgrid sh package runjags hostname Sys getenv XGRID_CONTROLLER_HOSTNAME password Sys getenv XGRID_C
39. jags object so the usual options to lattice or plot functions are not available The as mcmc method combines the chains with a warning and returns an memc object and the as mcmc list method extracts the mcmc list from the runjags object or possibly a sub selection of variables given by vars See also combine mcmc which can be used directly on runjags objects The print methods for runjags model data and initial value strings simply provide the option for printing line numbers which may be useful for debugging The print methods for runjags study and runjags bginfo objects provide a basic overview of the objects Author s Matthew Denwood lt matthew denwood glasgow ac uk gt See Also combine mcmc run jags autorun jags summary mcmc testjags Analyse the System to Check That JAGS Is Installed Description Test the users system to determine the operating system version of R installed and version of JAGS installed Some information is collected from other functions such as platform and Sys info Used by the run jags function Usage testjags jags findjags silent FALSE 32 timestring Arguments jags the system call or path for activating JAGS Default calls findjags to attempt to locate JAGS on your system automatically In unix the system call should always be jags in Windows a path to the JAGS executable or the enclosing bin or JAGS folder is required silent should on screen feedback be
40. le 10000 adapt max 200 burnin 0 datalist NA initlist NA jags findjags silent jags FALSE summarise TRUE confidence 0 95 plots summarise psrf target 1 05 normalise mcmc TRUE check stochastic TRUE modules c factories c thin 1 monitor deviance FALSE monitor pd FALSE monitor pd i FALSE monitor popt FALSE check conv summarise keep jags files FALSE tempdir TRUE jags refresh 0 1 batch jags silent jags method if rjags Xing packages rjags else interruptible method options list extend jags runjags object stop The output of a runjags function with class runjags must be su add monitor character 0 drop monitor character 0 drop chain numeric 0 combine length c add monitor drop monitor drop chain 0 burnin 0 sample 10000 adapt max 200 burnin 0 jags findjags silent jags FALSE summarise TRUE confidence 0 95 plots summarise psrf target 1 05 normalise mcmc TRUE check stochastic TRUE thin runjags object thin keep jags files FALSE tempdir TRUE jags refresh 0 1 batch jags silent jags method NA method options NA results jags background runjags object stop An object produced by a background runjags method must Arguments model either a relative or absolute path to a textfile including the file extension con taining a model in the JAGS language and possibly monitored variable names data and or initi
41. lt autorun jags model model monitor c m c precision Analyse traceplots of the results to assess convergence plot results type trace layout c 3 1 Summary of monitored variables results End Not run combine mcmc Combine Two or More MCMC Objects Into One Longer MCMC Ob ject Description Allows an MCMC object with 1 or more chains to be combined with another or several other MCMC object s representing extensions of the same simulation to produce one MCMC object that contains the continuous combined Markov chains of the other MCMC objects Alternatively a single MCMC list object can be converted into an MCMC object with one chain by combining all chains from the MCMC list 10 Usage combine mcmc combine mcmc mcmc objects list thin 1 return samples NA collapse chains if length mcmc objects 1 TRUE else FALSE vars NA Arguments mcmc objects thin return samples collapse chains vars Value a list of MCMC or runjags objects all with the same number of chains and matching variable names or a single MCMC object list or runjags object No default an integer to use to thin the final MCMC object by in addition to any thinning already applied to the objects before being passed to combine mcmc Ignored if return samples is specified is na Default 1 no additional thinning is per formed the number of samples to return after thinning The chains will be
42. mally be done when calling a single JAGS instance with multiple chains Using more than 4 chains with one of these methods without the use of new RNG factories may therefore produce dependence between chains and is not recommended a warning is given if trying to do so Starting with runjags version 1 0 0 there has been an attempt to abstract the method used to call JAGS as a result a user specified function may also be passed as the method This function must call JAGS on a given batch script contained within sim folders in the working directory and either wait for JAGS to output simulation results to file then return TRUE or return FALSE which is assumed to mean that the JAGS processes are still running in which case the behaviour is as for background The return may also be a list including the named element complete which refers to the same thing as well as other elements that are returned to the top level If you are interested in developing another method please feel free to contact the package author an optional named list of argument to be passed to the method function includ ing a user specified method function Of the default arguments only nsims indicating the number of separate simulations for parallel snow and bgparallel methods and cl specifying an existing snow cluster and or remote jags spec ifying the path to JAGS on the remote machines for the snow method only can be used Others a
43. ment if not found anywhere else Ignored if data variable is not used in the model block Default NA an optional named list containing variables used as initial values or alternatively a function with a single argument representing the chain number that returns a named list If any variables are specified in the model block using inits variable the value for the corresponding named variable is taken from initlist if present or the result of datalist chain no if specified as a function which allows both randomly generated initial values and different values for each chain or the parent environment or finally the global environment if not found anywhere else Ignored if inits variable is not used in the model block Note differ ent chains are all given the same starting values if specified as a named list or taken from any envirnoment if different values are desired for each chain initlist should be specified as a function Default NA the system call or path for activating JAGS Default calls findjags to attempt to locate JAGS on your system should the JAGS output be suppressed logical If TRUE no indication of the progress of individual models is supplied Default FALSE should summary statistics be assessed after the model has completed Default TRUE the prob argument to be passed to HPDinterval for calculation of confidence intervals Default 0 95 95 confidence intervals should traceplots and d
44. nfidence 0 95 plots summarise thin sample FALSE jags findjags silent jags FALSE interactive FALSE max time Inf adaptive list type burnin length 200 thin runjags object thin tempdir TRUE jags refresh 0 1 batch jags silent jags method NA method options NA Arguments model either a relative or absolute path to a textfile including the file extension con taining a model in the JAGS language and possibly monitored variable names data and or initial values or a character string of the same No default The model must be started with the string model and ended with on new lines Data must be similarly started with data monitored variables with moni tor and initial values as inits and all ended with If multiple models are found all but the first one are ignored with a warning Multiple data blocks and monitor blocks are combined multiple inits blocks are used for different chains The model block may also contain automatically generated data and initial val ues variables using data variable and inits variable and more monitored variables using monitor variable See read winbugs for more details No default monitor a Character vector of the names of variables to monitor The special node names deviance pd pd 1 popt and dic are used to monitor these model fit diag nostics see the JAGS user manual for more info
45. nits list mean lt 100 F monitor mean end text file read winbugs pathtofile mymodel bug Use internal character variable define monitors in the model string lt use autodata and manual initial values n model for i in 1 N Count i dpois mean data Count N read winbugs run jags 17 mean dgamma 0 01 100 monitor mean inits mean lt 1 J inits mean lt 100 n read winbugs string Use autoinits and a mixture of manual and autodata string lt model for i in 1 N CountLi dpois mean data Count mean dgamma 0 01 100 monitor mean inits mean data N lt 10 read winbugs string End Not run run jags Run or Extend a User Specified Bayesian MCMC Model in JAGS from Within R Description Runs or extends a user specified JAGS model from within R returning an object of class runjags class Data and initial values can either be supplied in the R dump format see dump format for an easy 18 run jags way to do this or as a named list A character vector of variables to monitor must also be supplied either to the monitor argument or inside the model code Requires Just Another Gibbs Sampler JAGS see http www fis iarc fr martyn software jags Usage run jags model stop No model supplied monitor NA data NA n chains NA inits NA burnin 5000 samp
46. onitor pd tempdir jags refresh batch jags this argument is deprecated and remains for backwards compatibility only See the monitor variable this argument is deprecated and remains for backwards compatibility only See the monitor variable option to use the temporary directory as specified by the system rather than cre ating files in the working directory Any files created in the temporary directory are removed when the function exits for any reason Default TRUE the refresh interval in seconds for monitoring JAGS output using the interac tive and parallel methods see the method argument Longer refresh inter vals will use less processor time Default 0 1 seconds option to call JAGS in batch mode rather than using input redirection On JAGS gt 3 0 0 this suppresses output of the status which may be useful in some situ ations Default TRUE if silent jags is TRUE or FALSE otherwise 8 autorun jags method the method with which to call JAGS probably a character vector specifying one of rjags simple interruptible parallel or snow and see also xgrid autoextend jags The former runs JAGS using the rjags package whereas other options do not re quire the rjags package and call JAGS as an external executable simple runs JAGS as a foreground process the default behaviour for runjags lt 0 9 6 in terruptible allows the JAGS process to be terminated immedia
47. or details Default usr bin R this is the default install location for R the preferred binary of R to invoke 64 results in Rpath64 if it exists 32 in Rpath32 if it exists and or either of 32 or 64 if they are not found results in Rpath Notice that this indicates a preference not a certainty if the indicated build is not avalable then another will be used Also note that specifying 64 may be ignored for PPC nodes depending on what version of R they are running you can ensure only intel nodes are used with mgrid using sub options c intel Default the maximum total size of the objects produced by the function for each thread if xgrid method separatejobs or for the entire job if xgrid method separatetasks This is a failsafe designed to prevent attempted transfer of huge files bringing the xgrid controller down If the maximum size is exceeded for a thread or job then the results are erased for all iterations within that thread or job and the job will likely have to be re submitted If each chain is likely to return a large amount of information then separatejobs should be used because jobs are retrieved individually which reduces the chances of overloading the Xgrid controller The object list is also checked to ensure it complies with the maximum size but the file list and any objects saved to the working directory by the function are NOT automatically cheked Units can be pr
48. ould be provided to the extend jags function background runjags object an object of class runjags bginfo returned from the xgrid submit jags function max threads the maximum number of tasks to split the job into JAGSversion the required JAGS version for worker nodes to be given tasks may include or gt to signify exact or minimum version requirements 42 xgrid run jags email an email address to be used to notify of job status profiling option to use ART ranking to select the most suitable host nodes preferentially cpuarch option to restrict the job to ppc or intel nodes minosversion option to restrict the job to nodes running a minimum Mac OS version queueforserver option to restrict the job to nodes considered to be Server machines hostnode option to prefer or restrict to if forcehost TRUE running the job on the speci fied nodes must be provided as a single character string with the colon character separating node names forcehost option to restrict the job to only nodes specified by hostnode ramrequired the minimum amount of free RAM obtained using an approximation for each node to be assigned a task jobname the name to give the job on Xgrid optional cleanup option to remove the job from Xgrid after completion showprofiles option to show the node scores based on the ART ranking used jagspath the path to JAGS on the host nodes mgridpath the path to the local mgrid script defa
49. ovided as either MB or GB Default 1GB the path to the local mgrid script default uses the version installed with the runjags package the hostname of the Xgrid server to connect to the password for the Xgrid server given by hostname for xgrid run option to use the temporary directory as specified by the system rather than creating files in the working directory Any files created in the tem porary directory are removed when the function exits A temporary directory cannot be used for xgrid submit Default TRUE when running the job syn chronously option to keep the folder with files needed to run the job rather than deleting it when the job is deleted from Xgrid This may be useful for attempting to bug fix failing jobs Default FALSE option to print the output of the function obtained using cat writeLine or print for example at each iteration after retrieving the job s from xgrid If FALSE the output is suppressed Default TRUE option to submit multiple jobs to Xgrid to help with file size constraints see the entry for threads below the number of threads either jobs if separate jobs TRUE or tasks otherwise to generate for the job Each thread is sent to a separate node for execution so the Xgrid run 37 more threads there are the faster the job will finish unless the number of threads exceeds the number of available nodes A very large number of threads may cause problems with the Xgrid controller
50. ovides a set and for get solution if you have a non standard JAGS install by assigning the variable jagspath the default argument value to the path to JAGS in your R profile file this will be read every time R starts new_unique 13 Value A path or command for the most likely location of the desired JAGS executable on the system On unix this will always be jags on Windows for example C Program Files JAGS bin jags terminal exe or C Program Files JAGS JAGS 1 0 0 bin jags terminal exe Author s Matthew Denwood lt matthew denwoodeglasgow ac uk gt See Also testjags run jags new_unique Create a Unique Filename Description Search the current working directory for a file or directory matching the input name and if it exists suggest a new name by appending a counter to the input name Alternatively the function can ask the user if the existing file should be overwritten in which case the existing file will be erased if the answer is yes The function also checks for write access permissions at the current working directory Usage new_unique name NA suffix ask FALSE prompt A file or directory with this name already exists Overwrite touch FALSE type file Arguments name the filename to be used character string A vector of character strings is also permissible in which case they will be pasted together One or more missing NA values can also be used
51. racter vector of the names of variables to monitor No default external modules to be loaded into JAGS More than 1 module can be used Default none factory modules to be loaded into JAGS More than 1 factory can be used Factories should be in the format lt facname gt lt factype gt for example fac tories mix TemperedMix sampler Default none should the runjags object returned be checked to ensure that an external call to JAGS is able to run the model Default TRUE the system call or path for activating JAGS ignored if check FALSE Default calls findjags to attempt to locate JAGS on your system testjags 31 Details The runjags class contains the full model data modules factories etc required to run JAGS and is designed to encapsulate the model in a similar vein to the Im or mer class Most interaction with a runjags object should be done using the print plot as memc list methods but it may also be helpful to access some elements of the list directly the names of the elements can be access using names runjags object For example this is currently the only method of extracting the full pd popt pd i information Value The print method for runjags objects displays a range of summary statistics for the MCMC chains similar to that produced by summary mcmc but with additional details The plot method produces trace and density plots note that these are pre plotted and stored inside the run
52. re ignored with a warning Usually an object of class runjags or an object of class runjags bginfo for background methods see runjags class Author s Matthew Denwood lt matthew denwood glasgow ac uk gt See Also runjags class autorun jags xgrid run jags run jags combine mcmc testjags dump format Examples run a model to calculate the intercept and slope of the expression y mx c assuming normal observation errors for y Not run Simulate the data X lt 1 100 Y lt rnorm length X 2 X 10 1 Model in the JAGS format model lt model for i in 1 N Y i dnorm true y il precision true yLi lt m XLi c m dunif 1000 1000 c dunif 1000 1000 precision dexp 1 y Use dump format to convert the data and initial values files into the R dump format with explicit control over the random number generator used for each chain optional data lt dump format list X X Y Y N length X inits1 lt dump format list m 1 c 1 precision 1 RNG name base Super Duper RNG seed 1 inits2 lt dump format list m 0 1 c 10 precision 1 RNG name base Wichmann Hill RNG seed 2 Run the model and produce plots results lt run jags model model monitor c m c precision data data n chains 2 inits c inits1 inits2 plots TRUE Plot the monitored variables plot results Look at th
53. rmation but with the exception of deviance these monitored nodes won t appear as variables in the summary statistics or plots Note multiple chains are required for calculation of pd i pd popt and dic data either a named list or a character string in the R dump format containing the data If left as NA the model will be run without external data n chains the number of chains to use with the simulation More chains will improve the sensitivity of the convergence diagnostic but will cause the simulation to run more slowly although this may be improved by using a method such as parallel or snow The minimum and default number of chains is 2 inits either a character vector with length equal to the number of chains the model will be run using or a list of named lists representing names and corresponding values of inits for each chain If a vector each element of the vector must be a character string in the R dump format representing the initial values for that autorun jags 5 chain or NA If not all initialising variables are specified the unspecified vari ables are sampled from the prior distribution by JAGS Values left as NA result in all initial values for that chain being sampled from the prior distribution The special variables RNG seed RNG name and RNG state are allowed for explicit control over random number generators in JAGS Default NA runjags object the model to be ex
54. ructural assignments If none of these are found the data block is assumed to be a WinBugs type data block and is passed to JAGS as data This behaviour can be over ridden by inserting jagsdata or bugsdata into the data block as appropriate More than one data block is allowed and each will be differentiated independently Author s Matthew Denwood lt matthew denwood glasgow ac uk gt See Also run jags Examples Not run ALL SYNTAX GIVEN BELOW IS EQUIVALENT Use a modified WinBUGS text file with manual inits and manual data and 16 a seperate monitor block requires least modification from a WinBUGS file For compatibility with WinBUGS the use of list to enclose data and initial values is allowed and ignored however all seperate variables in the data and inits blocks must be seperated with a line break commas or semicolons before linebreaks are ignored dataf and inits must also be added to WinBUGS textfiles so that the function can seperate data from initial values Iterative loops are allowed in data blocks but not in init blocks See also the differences in JAGS versus WinBUGS syntax in the JAGS help file Contents of a textfile mymodel bug model for i in 1 N CountLi dpois mean mean dgamma 0 01 100 data list Count lt c 1 2 3 4 5 6 7 8 9 10 N lt 10 inits list mean lt 1 i
55. s 10 iteration return output Run the function on xgrid for 100 iterations split between 10 machines results lt xgrid run f niters 100 threads 10 End Not run xgrid run 39 A basic example of xapply to calculate the mean of a list of numbers Not run A list of 3 datasets from which to calculate the mean datasets lt list c 1 5 6 NA c 9 2 NA 0 c 1 4 10 20 Standard lapply syntax results1 lt lapply datasets mean na rm TRUE Equivalent xapply syntax results2 lt xapply datasets mean xgrid options list wait interval 15s na rm TRUE Or submit the job id lt xapply datasets mean xgrid options list submitandstop TRUE na rm TRUE And retrieve the results results3 lt xgrid results id End Not run Not run Subit an xgrid job just to see which packages are installed on a particular machine A function to harvest details of R version and installed packages f lt function i archavail lt any dimnames installed packages 2 Archs To deal with older versions of R if archavail packagesinst lt installed packages c Version Archs Built Jelsef packagesinst lt installed packages c Version OS_type Built Rinst lt unlist R version c version string arch platform names Rinst lt c Version Archs Built return rbind R
56. sponse before extending the simulations If FALSE the simulation will be run until the chains have converged or until the next extension would extend the simulation beyond max time Default FALSE the maximum time for which the function is allowed to extend the chains to im prove convergence as a character string including units or as an integer in which case units are taken as seconds Ignored if interactive TRUE If the function thinks that the next simulation extension to improve convergence will result in a total time of greater than max time the extension is aborted The time per iter ation is estimated from the first simulation Acceptable units include seconds minutes hours days weeks or the first letter s of each Default 1hr a list of advanced options controlling the length of the adaptive mode of each simulation Extended simulations do not require an adaptive phase but JAGS prints a warning if one is not performed Reduce the length of the adpative phase for very time consuming models type must be one of adaptive or burnin the thinning interval to be used in JAGS Increasing the thinning interval may reduce autocorrelation and therefore reduce the number of samples required but will increase the time required to run the simulation Using this option thinning is performed directly in JAGS rather than on an existing MCMC object as with thin sample Default 1 monitor deviance m
57. ss model fit using a drop k type cross validation study where one or more data points are removed in turn and the model s ability to predict that datapoint is assessed run jags study 25 Usage run jags study simulations model NULL datafunction NULL targets list confidence 0 95 record chains FALSE runjags options list cat progress FALSE test TRUE parallel method parLapply Arguments simulations the number of datasets to run the model on model the JAGS model to use in the same format as would be specified to run jags datafunction an optional function that will be used to specify the data If provided this must take exactly one argument representing the simulation number and return either a named list or character vector in the R dump format containing the data specific to that simulation It is possible to specify any data that does not change for each simulation using a data lt variable gt tag in the model code If a datafunction is not provided the data will be the same for all simulations and a warning will be printed targets a named list of variables which can include vectors arrays with values to which the model outputs are compared if stochastic The target variable names are also automatically included as monitored variables confidence a probability or vector of probabilities to use when calculating the proportion of credible intervals containing the true target value Default 95 CI re
58. suppressed Default FALSE Value A named list of values containing information about the JAGS installs found on the user s system Author s Matthew Denwood lt matthew denwood glasgow ac uk gt See Also run jags findjags Examples Run the function to determine if JAGS is installed results lt testjags timestring Calculate the Elapsed Time in Sensible Units Description Function to calculate the elapsed time between 2 time periods in seconds or to calculate a number of seconds into a time measurement in more sensible units Usage timestring timel time2 NA units NA show units TRUE Arguments timel either the time index from Sys time at the start of the time period a length of time in seconds or an object of class difftime time2 either the time index from Sys time at the end of the time period or missing data if converting a single length of time Default NA xgrid run 33 units either missing in which case a sensible time unit is chosen automatically or one of s m hk d w y to force a specific unit Default NA show units if TRUE then the time is returned with units if FALSE then just an integer is returned Default TRUE Value A time measurement with or without units Author s Matthew Denwood lt matthew denwoodeglasgow ac uk gt See Also Sys time Examples time how long it takes to complete a task pre time lt Sys time
59. tely using the interrupt signal parallel runs each chain as a separate process on a separate core and snow uses a simple network of workstations which may be passed into the method options list as cl The default for autorun jags is to use rjags if the rjags package is load ed or the interactive method otherwise The de fault for the autoextend jags function is to use the same method as used for the previous JAGS call Note that the parallel snow and bgparallel methods all use separate JAGS in stances to speed up execution of models with multiple chains at the expense of using more RAM but cannot be used to monitor pd popt pd i and therefore DIC If no RNG name is specified in the initial values each chain is assigned a different random number generator RNG name for up to 4 chains the number of different RNG available in JAGS or using the lecuyer module for 5 or more chains requires rjags to be installed Starting with runjags version 1 0 0 there has been an attempt to abstract the method used to call JAGS as a result a user specified function may also be passed as the method This function must call JAGS on a given batch script contained within sim folders in the working directory and either wait for JAGS to output simulation results to file then return TRUE or return FALSE which is assumed to mean that the JAGS processes are still running in which case the behaviour is as for background
60. tended the output of a run jags or autorun jags or extend jags etc function with class runjags No default add monitor a character vector of variables to add to the monitored variable list All previ ously monitored variables are automatically included although see the drop monitor argument Default no additional monitors drop monitor a character vector of previously monitored variables to remove from the moni tored variable list for the extended model Default none drop chain a numeric vector of chains to remove from the extended model Default none combine a logical flag indicating if results from the new JAGS run should be combined with the previous chains Default TRUE if not adding or removing variables or chains and FALSE otherwise startburnin the number of burnin iterations Default 0 startsample the total number of samples including the chains supplied in runjags object for autoextend jags on which to assess convergence If the runjags object already contains this number of samples then convergence will be assessed on this ob ject otherwise the required number of additional samples will be obtained be fore combining the chains with the old chains More samples will give a better chance of allowing the chain to converge but will take longer to achieve Also controls the length of the pilot chain used to assess the required sampling length The minimum is 4000 samples which is the minimum required number of sam
61. that enhances the capabilities of Xgrid substantially to install this from the command line navigate to the folder given by system file xgrid package runjags and from the terminal type sudo cp mgrid sh usr local bin mgrid or similar to make the script visible in your search path Help on the mgrid script can then be obtained by typing mgrid with no arguments at the command line xgrid run j ags 43 Value Equivalent to that of the run jags family of functions Author s Matthew Denwood lt matthew denwood glasgow ac uk gt See Also run jags autorun jags and runjags class for more information on JAGS models xgrid run for functions to execute user specified functions on Xgrid Examples run a simple model on Xgrid using a single job Not run Ensure the required environmental variables are set Sys setenv XGRID_CONTROLLER_HOSTNAME lt hostname gt Sys setenv XGRID_CONTROLLER_PASSWORD lt password gt Simulate the data X lt 1 100 Y lt rnorm length X 2 X 10 1 Model in the JAGS format model lt model for i in 1 N Y i dnorm true y il precision true ylil lt m XLi c m dunif 1000 1000 c dunif 1000 1000 precision dexp 1 y Run the model synchronously using the simple method results lt xgrid run jags model model monitor c m c precision data list N length X X X Y Y n chains 2 plots F
62. thinned to as close to this minimum value as possible and any excess iterations dis carded Supersedes thin if both are specified Ignored if niter mcmc objects lt return samples Default NA option to combine all MCMC chains into a single MCMC chain with more it erations Can be used for combining chains prior to calculating results in or der to reduce the Monte Carlo error of estimates Default TRUE if a single memc object is provided or FALSE otherwise an optional character vector of variable names to extract If supplied only vari able names in the MCMC object list supplied with a partial match to anything in vars will be summarised plotted extracted Note that regular expressions are not allowed but the caret token can be used to specify the match at the start of a variable name and a quoted vars will be matched exactly Default NA meaning all variables available are returned An MCMC object if collapse chains TRUE or a list of MCMC objects is supplied or an mcmc list object if given a list of or single mcmc list or runjags objects and collapse chains FALSE Author s Matthew Denwood lt matthew denwood glasgow ac uk See Also run jags runjags class dump format 11 dump format Conversion Between a Named List and a Character String in the R Dump Format Description Convert a named list of numeric vector s or array s of data or initial values to a character string in the correct format
63. timestring new_unique and ask for more general tools xgrid run jags and xgrid submit jags for use of Xgrid clusters to run JAGS models remotely xgrid run and xgrid submit for use of Xgrid clusters for remote execution of user specified R code runjags class 29 jags model in the rjags package for fine control over the JAGS libraries runjags class The runjags class and associated classes and available S3 methods Description Objects of class runjags are produced by the run jags extend jags autorun jags etc functions and can be passed to extend jags and autoextend jags to extend the simulation They also have a few specific S3 methods for print plot and extraction of the MCMC objects contained within the runjags object Objects of class runjags study are produced by the run jags study function and class runjags bginfo represents a JAGS model being run using a background method and can be passed to the results jags function to retrieve a copy of this object will also have been saved to jagsinfo Rsave in the work ing directory of the background JAGS call in case the returned object is not saved by the user These functions provide print and plot methods and conversion facilities to from MCMC objects and objects of class jags for compatibility with the rjags package The failedjags environment is used to store JAGS model data initial value files from failed simu lations for inspection by th
64. ting it May be useful for attempting to bug fix models A character string can also provided in which case this folder name will be used instead of the default existing folders will NOT be over written Default FALSE tempdir option to use the temporary directory as specified by the system rather than creating files in the working directory If keep jags files TRUE then the folder is copied to the working directory after the job has finished with a unique folder name based on runjagsfiles Any files created in the temporary directory are removed when the function exits for any reason Default TRUE jags refresh the refresh interval in seconds for monitoring JAGS output using the interac tive and parallel methods see the method argument Longer refresh inter vals will use less processor time Default 0 1 seconds batch jags option to call JAGS in batch mode rather than using input redirection On JAGS gt 3 0 0 this suppresses output of the status which may be useful in some situ ations Default TRUE if silent jags is TRUE or FALSE otherwise method the method with which to call JAGS probably a character vector specifying one of rjags simple interruptible parallel background bgparallel or snow and see also xgrid autoextend jags The former runs JAGS using the rjags package whereas other options do not require the rjags package and call JAGS as an external execut
65. tted extracted Note that regular expressions are not allowed but the caret token can be used to specify the match at the start of a vari able name and a quoted vars will be matched exactly Default NA meaning all variables available are returned the number of significant digits to display for tabulated statistics Default 5 a numeric vector of length 2 representing the number of rows and columns to produce plots in Default 1 plot per page for trace and density options or a single row of 2 plots if plotting both types 1f there are a greater number of variables than will fit on one page should new graphics windows be created for each plot or the exisiting device used for all plots Ignored if writing plots to file Default TRUE on Mac Windows GUI systems and FALSE otherwise an optional character string representing a filename to save plots to as a PDF rather than using the default graphics device Default ie don t write to file option to produce trace plots density plots a crosscorr plot or all Cases are ignored and partial matching is used the argument may also be of length gt 1 Default all option to prepend lines with line numbers for runjags model data initial value strings This may be helpful for debugging against the output of failed JAGS runs Default TRUE other options to be passed down to underlying methods where available ignored for plot runjags see below a cha
66. ult uses the version installed with the runjags package hostname the hostname of the Xgrid server to connect to password the password for the Xgrid server given by hostname wait option to wait for the Xgrid job to finish if it has not already done so other options to be passed to the underlying run jags family functions as if the model were being run locally Details These functions allow JAGS models to be run on Xgrid distributed computing clusters from within R using the same syntax as required to run the models locally All the functionality could be replicated by saving all necessary objects to files and using the Xgrid command line utility to submit and retrieve the job manually these functions merely provide the convenience of not having to do this manually Xgrid support is only available on Mac OS X machines running OS X 10 5 10 7 Xgrid support was discontinued in Mac OS X 10 8 The xgrid controller hostname and password can also be set as environmental variables The com mand line version of R knows about environmental variables set in the profile file but unfortunately the GUI version does not and requires them to be set from within R using Sys setenv XGRID_CONTROLLER_HOSTNAME lt hostname gt Sys setenv XGRID_CONTROLLER_PASSWORD lt password gt These lines could be copied into your Rprofile file for a set and forget solution Note that the runjags package also contains a utility shell script called mgrid
67. which will be replaced with a randomly generated 9 character alphanumeric string Default NA suffix the file extension including to use character string If this does not start with a one will be prepended automatically Default none ask if a file exists with the input name should the function ask to overwrite the file logical If FALSE a new filename is used instead and no files will be over written Default FALSE prompt what text string should be used to prompt the user character string Ignored is ask FALSE A generic default is supplied 14 read winbugs touch option to create touch the file folder after generating the unique name which prevents other processes from sneaking in and creating a file with the same name before the returned filename has had chance to be used Default FALSE type if touch TRUE then type controls if a file or directory is created One of file f directory or d Defult file Value A unique filename that is safe to use without fear of destroying existing files Author s Matthew Denwood lt matthew denwood glasgow ac uk gt See Also ask Examples Create a file name that is unlikely to exist already with a R extension new_unique c new_file NA R ask FALSE read winbugs Extract Any Models Data Monitored Variables or Initial Values As Character Vectors from a Winbugs Type Textfile Description Read a us
68. xgrid xgrid xgrid xgrid xgrid xgrid xgrid xgrid xgrid xgrid INDEX autorun jagsfile run jagsfile 27 delete xgrid run 33 extend JAGS xgrid run jags 40 extend jags xgrid run jags 40 jobs xgrid run 33 results xgrid run 33 results JAGS xgrid run jags 40 results jags xgrid run jags 40 run 28 33 43 run JAGS xgrid run jags 40 run jags 22 27 28 38 40 run JAGSfile run jagsfile 27 run jagsfile run jagsfile 27 submit 28 submit xgrid run 33 submit JAGS xgrid run jags 40 submit jags 28 submit jags xgrid run jags 40 submit JAGSfile run jagsfile 27 submit jagsfile run jagsfile 27
69. y generated data variables or inits variable for automatically generated initial value variables in which case variable is used as data or initial values with a value taken by run jagsfile from datalist initlist or R objects as appropriate inits data and monitor state ments can appear on the same line as model code but no more than one of these statements should be used on the same line Examples of acceptable model syn tax are given below Value A named list of model containing the model description data containing the data given in the data block s autodata containing data variables specified using data in the model block inits containing the initial values given in the initial value block s autoinits containing initial value variables specified using inits in the model block and monitor containing the moni tored variables specified in the monitor blocks and by using monitor within the model block This function is specified primarily for WinBugs compatibility so data blocks would normally con tain the data in a list format rather than the code format that is allowed in JAGS to perform data transformations see JAGS manual section 7 0 5 These JAGS format data blocks can be specified and the function will attempt to differentiate the two types of data from the presence of syntactical cues such as square brackets for loops list and Dim st

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