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APPENDIX A1 - TBEP Tech Calendar

1. JP Kw N wm Aw NSI i i i i i J Jd B OF HH DS n H R Column Format Tab delimited Hills binnarnes tt Space delimited r Periph binnames txt Reaches binnames tet Character delimited SouthCB binnames tat Fixed width space padded w Include Column Titles Empty Cell Text Cancel File Name 4 Openanew MS Excel file 5 Under the Data Tab select Get External Data From Text 6 Import the water quality load text file and save to xls format R CODE FOR POST PROCESSING Table 3 1 R Table 3 1 R Bridgette Froeschke Dec 1 2013 7 00 PM R Manual for Old Tampa Bay Integreated Model System Watershed Model Objective Calculate geometric means from table 3 1 in the calibration report using an open resource data analysis package Genearl information R stores functions as libraries We will be using the library doBy for calculating means The first time you use doBy you must download the library 1 select the cran mirror choose USA CA2 and then select install package S choose doBy all of this is under the Packages drop down menu afterwards you then need to tell R to open the library by using the following command library doBy Loading required package multcomp Loading required package mvtnorm Loading required package survival Loading required package splines Loading required package MASS Steps Data mport The primary functions
2. File Edit View Tools Help Organize Burn New folder 4 Gi Libraries b Documents b J Music gt Pictures gt Bf Videos a jE Computer gt fy 05 Ci gt a home TPASRV2 Hi bE gis data TPAGISOL k Digg Gis archive TPAMAINO4 L gt 2 projects Nignv projects M gt egg drafting TPASRV2 N gt bg HOME S4R HOME O b amp projects Gnvsrv07 Q gt Eg Projects WSAR PROJECTS Ri Network sarsnv04 m Name d Archived Modflow Output d Post ReVverification 20130923191 207 CellHistory csv EL CellStats csv GL HeadHistory csv IHM log EH IHMOutput_H mdb IHMOutput M mdb IHMParameters csv L IHMPostProcessing mdf _ IHMPostProcessing_log ldf EL ImpersiousHistory csy EL LandSegmentintegrationHistory csv ModelUpload 20130923191208 log j Qutputsummary mdb Eh PerviousHistory csv ReachHistory csv EL ReachIntegrationHistory csv RivercellHistory csv EL RivercellStats csv Mame ConstantHeadFlow IHM_COPY DiffuseBaseflow IHM_COPY EVT IHM_COPY FlowNextColumnJHM_COPY FlowMextLayer IHM_COPY _ FlowNetRow IHM_COPY _ GHBFlow IHM_COPY Head IHM_COPY D LowerZoneStorageTransfer IHM_COPY Recharge IHM_COPY SpecificYield IHM_COPY pE SpecificYieldCorrectionIHM COPY SpringFlow IHM COPY StorageChange IHM COPY WellFlow IHM COPY Date modified 10 7 2013 5 09 AM 10 22 2013 6 07 PM 9 23 2013 7
3. O NODO OR ON TN TKN NOx NH3 TP Ortho P TSS BOD Constituents D af 26 224 selected SJ Day Gi 51179 51179 51173 End ena eta 2009 124851 2000712221 2009 1251 55197 STES IMERESE 51179 51179 51179 SEE IE 99911 51179 a 151173 2009 1 2231 2009 124091 eNO ret USA i 23 3 Boa F 12 ROTA 201221 2008 12 31 2009 12 31 2009 12 31 2009 12 31 2009 1 2431 2009 12 31 2009 12 31 20091 2 31 2009 12 31 2009 1231 2 Within the Timeseries Data table select File gt Save to Text File File Edit Scenario SOUTHCB SOUTHCB SOUTHCB SOUTHCB SCUTHCB SOUTHCB SOUTHCB SOUTHCB SOUTHCB SOUTHCB SOUTHCB SOUTHCB SOUTHCB Location 60 60 60 60 to 60 60 60 63 63 63 63 63 63 Constituent l 2 3 4 5 6 7 8 1 2 3 4 5 6 2002 11 24 14 2002 11 25 2002 11 26 2002 11 27 2002 11 28 2002 11 29 2002 11 30 2002 12 01 2002 12 02 2002 12 03 2002 12 04 2002 12 05 2002 12 06 2002 12 07 2002 12 08 2002 12 09 2002 12 10 2002 12 11 2002 12 12 2002 12 13 2002 12 14 2002 12 15 2002 12 16 2002 12 17 2002 12 18 2002 12 19 2002 12 20 2002 12 21 2 2 2002 12 22 m lt m lt Go Oo ro 0 08 0 5 co co 070 is fe 11 40 ee 145 142 Te ee Be 0 10 0 10 80 0 0 010 10 0 OO D010 0D 2 00 00 Poca Cie E RI PO s Da Dinar RS T 1 JE Ds gt 0 NN NA 10101010 Bi gt 0 1070 0 0 01 01010 1 070 POSTO Lem ae Re be 17 o AE Ai AE Mi NE DE DE AE SE Ai Gs tse PATA eaaa Pe
4. NH3 0eomeanh NOK Geo mean ie ORTHOP geomean gione TSS Ge Ome dies BOD geomean head mod geomean County TKN geomean NH3 geomean NOX geomean TN geomean 1 Hillsborough 0 6713 0 06799 0 1526 0 8355 2 Pinellas 0 6959 0 05958 0 1287 0 8527 ORTHOP geomean TP geomean TSS geomean BOD geomean 1 0 07204 0 1319 4 956 2 048 2 0 08028 0 1253 di 32 2 292 Export data write csv mod geomean C Users john Documents old tampa bay water optimal model bf simulated county geomean csv row names FALSE Calculate the means of each varible overal all TKN mean lt mean na omit as numeric as character TKN P all NH3 mean lt mean na omit as numeric as character NH3 P all NOX mean lt mean na omit as numeric as character NOX P all TN mean lt mean na omit as numeric as character TNSP all ORTHOP mean lt mean na omit as numeric as character ORTHOPSP all TP mean lt mean na omit as numeric as character TP P all TSS mean lt mean na omit as numeric as character TSS P all BOD mean lt mean na omit as numeric as character BODSP all In TKN mean lt mean na omit as numeric as character TKN In all In NH3 mean lt mean na omit as numericas character NH3 In all In NOX mean lt mean na omit as numeric as character NOX In MN means mean na minta Ss numericas character TN i mn i all In ORTHOP mean lt mean na omt as numeric as character O
5. data frame cbind ambient conc county ORTHOP ambient conc county County obs TP na lt data frame cbind ambient conc county tp ambient conc county County obs TSS na lt data frame cbind ambient conc county tss ambient conc county County obs BOD na lt data frame cbind ambient conc county BOD ambient _ conc county County head obs TKN na X1 X2 1 1 8 Hillsborough 2 1 22 Hillsborough 3 1 31 Hillsborough 4 1 1 Hillsborough 5 1 2 Hillsborough 6 1 02 Hillsborough di m obs TKN na 1 683 2 Remove NAs from all the data sets obs TKN lt na omit obs TKN na obs NH3 lt na omt obs NH3 na obs NOX lt na omit obs NOX na obs TN lt na omt obs TN na file Cl Users johnf Downloads Table 203 1 html 12 1 2013 7 25 11 PM Table 3 1 R obs obs obs obs ORTHOP lt na omit obs ORTHOP na TPx na omit obs TP na TSSs na omit obs TSS na BOD lt na omit obs BOD na head obs TKN DD VI R WW NP Fo X1 X2 1 8 Hillsborough 1 22 Hillsborough 1 31 Hillsborough 1 1 Hillsborough 1 2 Hillsborough 1 02 Hillsborough di mi obs TKN 1 683 2 Calculate the natural log as a new column in each dataset Have to include as character to ensure that R recognizes the value as a number and not as a level a factor obs Obs Obs Obs Obs Obs Obs Obs of TKN In TKN MOD lt log as numeric as character obs TKN 1 NH3 In NH3 MOD lt log as numeri
6. 8516144000000E 002 6 70400572000000E 000 x 31876953000000E 002 34615266000000E 000 43915772000000E 000 394888 T 674998 7 815438 814486 185477 1 060521 9 Ss 7225 673007 025655 9 322880 897729 5 052954 722961 4 240123 31000000E 000 76000000E 000 75000000E 000 03000000E 000 64000000E 000 38000000E 001 67000000E 000 37000000E 4 000 27000000E 000 74000000E 000 49000000E 001 67000000E 000 43000000E 000 27000000E 000 l 6 Create a new query in Access 7 Open the query in SQL view and paste the following statement and save SELECT ReachHistory FROM ReachHistory WHERE ReachHistory ReachID lt 473 ORDER BY ReachHistory Date ReachHistory ReachlD Field ReachHistory Date ReachID Table ReachHistory ReachHistory ReachHistory Sort Ascending Ascending Show EJ F E Criteria lt 473 or 8 Right Click on the query and select export to text file 9 Browse to and save over the original ReachHistory csv 10 In the Export Text Wizard select Include Field Names on First Row then click Finish What delimiter separates your fields Select the appropriate delimiter and see how your text is affected in the preview below Choose the delimiter that separates your fields Other Text Qualifier Date ReachID DEP VOL STAGE AVDEP TWID HRAD SAREA RO IVOL PRSUPY 1 1 2000 0 00 00 1 7 99488831 95694 2031 7 99488831 2 964
7. Ca iaia ee ee pe PostProcessing Public Enum Transforms None ShiftedLogNormal End Enum Public Enum Calculationintervals Fixedinterval CalendarMonth CalendarWeek CalendarYear End Enum Date modified _ ee 6 19 2012 9 46 AM 6 19 2012 9 46 AM 6 19 2012 9 46 AM 6 5 2012 3 41 PM 6 19 2012 9 46 AM 6 19 2012 9 45 AM 6 19 2012 9 46 AM 6 19 2012 9 46 AM 4 2 2013 3 38 PM 4 2 2013 3 38 PM 6 6 2012 11 04 AM 6 19 2012 9 46 AM 6 19 2012 9 45 AM 12 1 2013 1 36 PM 12 1 2013 1 36 PM 4 gt m Computer OS C INTB ReVerification Bin Post Processing Plugins Standard Post Processing Application exte PDB File XML Document PLUGIN File Application CONFIG File PDB File XML Document Microsoft Acces Microsoft Acces PLUGIN File Application CONFIG File Microsoft Acces Microsoft Acces d Check the Grapher library that is consistent with the install version of Grapher You may find that a different version of Grapher is checkmarked with MISSING printed next to it Uncheck this version of the Grapher library first Then scroll through the list of references to find the installed version of Grapher and checkmark it Exit the database when finished References IHM Input Available References v Visual Basic For Applications Microsoft Access 14 0 Object Library v OLE Automation v Microsoft ActiveX Data Objects 2 8 Library W Mic
8. ambient concs read csv C Users john Documents old tampa bay water optimal model run dataset ambientdata 131022 csv header TRUE head ambient conc REACH name date tn tkn NOX NH3 tp ORTHOP tss BO 60 Bishop Mullet 20JAN00 0 545 0 54 0 01 0 11 0 14 0 085 1 1 5 2 60 Bishop Mullet 10FEBOO 0 460 0 45 0 01 0 05 0 12 0 080 5 1 0 3 60 Bishop Mullet 16FEB00 0 520 0 50 0 02 0 12 0 10 0 050 1 1 0 4 60 Bishop Mullet 27MAR00 0 615 0 58 0 04 0 13 0 12 0 060 17 2 0 5 60 Bishop Mullet O5APRO0 0 740 0 70 0 04 0 20 0 37 0 230 15 NA 6 60 Bishop Mullet 11APR00 0 650 0 64 0 01 0 30 0 14 0 080 13 1 0 oc 1 Pinellas 2 Pinellas 3 Pinellas 4 Pinellas 5 Pinellas 6 Pinellas di m ambient conc 1 1397 12 Subset data to only include reaches in OTB ambient conc OTB lt subset ambient conc ambient conc REACH 60 ambient conc REACH 63 ambient conc REACH 65 ambient conc REACH 68 ambient conc REACH 76 ambient conc REACH 77 ambient conc REACH 227 ambient conc REACH 229 file Cl Users johnf Downloads Table 203 1 html 12 1 2013 7 25 11 PM Table 3 1 R Create County column First line creates a column with only Pinellas ambient conc OTB County Pinellas Modify the column to include Hillsborough ambient conc OTB County ambient conc OTB REACH 68 lt Hillsborough ambient conc OTB County ambient conc OTB REACH 76 lt Hillsborough ambient conc OTB County ambient conc OTB REACH 77 lt Hil
9. 0 mgd 1991 2 2 CWUP_WellMitigation_90_90_Prescribed Consolidated WF scenario for well mitigation pumping at historical 1989 1990 then at 90 prescribed 1 CWUP_WellMitigation_90Prescribed_200 Consolidated WF scenario for well mitigation pumping at historical 1989 1990 then at 90 prescribed 1 HotStartCheck Confirm hot start heads match source run heads 1 week simulation PEST_Run 2 year run for PEST PEST_RunTest 1 week test run for PEST Pre Processing Test Short run to test pre processing ReachOnly Reaches Only INTB Calibration 1 day integration ReVerification INTB Verification 1 day integration 2000 to 2009 INTB Verification 1 day integration 2000 only INTB Verification 1 day integration 2000 and 2001 only INTB Verification 1 day integration 1999 to 2009 INTB Verification Plus three antecedent years 1 day integration 1996 to 2006 Frequency 73 integration Timesteps Total Archive Records 3653 End Date 12 31 2009 C EXECUTE THE MODEL 1 Save the simulation scenario Help Name Description da __ rr __ __ __ P _P mdmo0v o 00o0 0040 010 n10 0n 1 t24 CWUP Environmental 70 idated WF scenario for water body impact assessment pumping at historical 1929 1990 then at CWUP Of Environmental CWUP Of WellMitigation CWUP CWUP OtherWUPs At50PercPumping CWUP 1 CWUP Well
10. 05 22 AM L L L L L L BOD BOD BOD BOD BOD BOD Appendix D ts R 35793 NA NA NA NA NA 2002 4 Dry Nov May 38713 2 828 NA NA NA NA 2003 4 Dry Nov May 41641 fadd NA NA NA NA 2004 4 Dry Nov May 44561 3 154 NA NA NA NA 2005 4 Dry Nov May n a me 29953 Alligator Allens Long Branch 32873 Alligator Allens Long Branch 35793 Alligator Allens Long Branch 38713 Alligator Allens Long Branch 41641 Alligator Allens Long Branch 44561 Alligator Allens Long Branch Create new data set for each set observed and sti mulated bind the two sets together This prevents R from deleting an entire row when there is a missing value obs lt data frame REACH al REACH parameter all parameter dv all observed method observed label all X LABEL name all name year all year month all month head obs REACH parameter dv method label l 63 BOD NA observed Modeled Biological Oxygen Demand 5 mg L 2 63 BOD NA observed Modeled Biological Oxygen Demand 5 mg L 3 63 BOD NA observed Modeled Biological Oxygen Demand 5 mg L 4 63 BOD NA observed Biological Oxygen Demand 5 mg L 5 63 BOD NA observed Modeled Biological Oxygen Demand 5 mg L 6 63 BOD NA observed Modeled Biological Oxygen Demand 5 mg L name year month 1 Alligator Allens Long Branch 2000 4 2 Alligator Allens Long Branch 2001 4 3 Alligator Allens Long Branch 2002 4 4 Alligator Allens Long Branch 2003 4 5 Alligator Allens Long Branch 2004 4 6 A
11. 1 63 NA 0 11556 NA NA NA 2004 1 6 2005 1 63 NA 0 11444 NA NA NA 2005 1 dec year 1 2000 2 2001 3 2002 4 2003 5 2004 6 2005 Si mul ated aggdata sim dec year lt aggdata sim year aggdata sim month 12 1 12 head aggdata sim file CIUsers johnf Downloads Appendix 20D 20ts 20 4 html 12 2 2013 11 05 22 AM Appendix D ts R Group 1 Group 2 Group 3 Group 4 REACH parameter 2000 TP Alligator Allens Long Branch 6 3 NA 2 2001 TP Alligator Allens Long Branch 6 3 NA 3 2002 TP Alligator Allens Long Branch 6 3 NA 4 2003 il TP Alligator Allens Long Branch 63 NA 5 2004 TP Alligator Allens Long Branch 6 3 NA 6 2005 TP Alligator Allens Long Branch 6 3 NA dv method ts name year month dec year l NaN NA NA NA 2000 1 2000 2 NaN NA NA NA 2001 i 2001 3 0 1504 NA NA NA 2002 1 2002 4 0 1256 NA NA NA 2003 1 2003 5 0 1874 NA NA NA 2004 1 2004 6 0 1697 NA NA NA 2005 1 2005 Sort by decimal year Observed newdata lt aggdata order aggdatasdec year head newdata Group 1 Group 2 REACH parameter dv method label name year month 2000 63 NA 0 1083 NA NA NA 2000 1 l 2000 2 63 NA 0 1720 NA NA NA 2000 2 21 2000 3 6 3 NA 0 2583 NA NA NA 2000 3 31 2000 4 6 3 NA 0 1725 NA NA NA 2000 4 41 2000 5 6 3 NA 0 2250 NA NA NA 2000 5 51 2000 6 63 NA 0 3233 NA NA NA 2000 6 dec year l 2000 11 2000 Z1 2000 3l 2000 41 2000 5l 2000 Si mulated newdata sim lt aggdata simlorder aggdata si m dec year head n
12. 60 01SEP2004 Ammonia mg L NH3 0 0147 1306 60 02JUL2002 Ammonia mg L NH3 0 0196 6586 60 03APR2002 Ammonia mg L NH3 NA 0 560 ABSOP OP2 year month season name 4626 NA NA 2001 8 Wet Jun Oct Bishop Mullet 11442 NA NA 2003 12 Dry Nov May Bishop Mullet 19970 NA NA 2006 11 Dry Nov May Bishop Mullet 13642 0 0603 0 003636 2004 9 Wet Jun Oct Bishop Mullet 7306 0 0504 0 002540 2002 7 Wet Jun Oct Bishop Mullet 6586 NA NA 2002 4 Dry Nov May Bishop Mul et sort by name parameter date all lt data frame all order all name all parameter all date head all REACH date 29953 63 O1APR2000 Modeled Biological Oxygen Demand 5 mg 32873 63 O1APR2001 Modeled Biological Oxygen Demand 5 mg 35793 63 O1APR2002 Modeled Biological Oxygen Demand 5 mg 38713 63 O1APR2003 Biological Oxygen Demand 5 mg 41641 63 O1APR2004 Modeled Biological Oxygen Demand 5 mg L 44561 63 OLAPR2005 Modeled Biological Oxygen Demand 5 mg L Simulated observed OP ABSOP OP2 year month season 29953 NA NA NA NA NA 2000 4 Dry Nov May 32873 4 067 NA NA NA NA 2001 4 Dry Nov May Bi shop Mull et Simulated observed NA 0 100 NA 0 010 NA 0 100 0 0147 0 0196 NA 0 560 Alligator Allens Long Branch Roosevelt Double Branch Rocky Creek Lower Channel A Channel G Sweetwater Creek 0 075 0 070 0 075 0 070 X LABEL parameter file Cl Users johnf Downloads A ppendix 20D 20ts 20 4 html 12 2 2013 11
13. 9 71850014 2 62117076 1 00 00 12 6 05295467 531 876953 6 05295467 1 19094706 3684 44995 1 19017768 44 00 00 13 8 72296143 1 34615266 8 72296143 1 1203934 9 91237545 0 913816512 1 x 1 1 2000 11 2000 1 1 2000 1 1 2000 1 1 2000 0 0 O O D 0 16 Close MS Access and navigate back to the model run CINTB RevVerification ReVerification_YearMonthDayTime 17 Delete the IHMOutput H mdb IHMOutput_M mdb and OutputSummary mdb files B HYDROLOGY To complete the post processing results for the hydrology model 1 Navigate to the INTB model scenario working directory 2 Open the bin folder and execute IHM exe to open the IHM interface folder i e s IHM Post File Help Name I nua Calibration _ UFACoastalDischarge HotStart19990101 Calibration_NoGrph VerifAnnualET Verification NoGrph _ HeadsCalibr Verificati VerificationOROPWellsCalibrationSet VerificationOROPWells Verification EtendedWellSet INTBVenfAll INTBVerif Annual Overlays VerfAll Regions VenfAll Le KM KM Le le MY KMI KM KN KM KM KM Le KN KM KM KM KA le Register Plugin ZConfigure Step 33 Execute Step C3 Delete Step e 3 At the menu bar use File Open to open the model input database the file INTB mdb within the ReVerification scenario working directory On the left hand
14. 966 3 054 0 9518 0 3569 0 5155 0 3569 16 17 BOD MOD REACH name County NA 60 Bishop Mullet Pinellas 2 NA 63 Alligator Allens Long Branch Pinellas 3 NA 65 Roosevelt Pinellas 5 NA 6 8 Double Branch Hillsborough 7 NA 76 Rocky Creek Hillsborough 8 7 178 11 Lower Sweetwater Hillsborough Sort by county model conc county lt data frame model conc OTB order model conc OTB County head model conc county date TN MOD TKN MOD NOX MOD NH3 MOD TP MOD ORTHOP MOD TSS MOD 5 01 AN2000 NA NA NA NA NA NA NA 7 01 AN2000 NA NA NA NA NA NA NA 8 01 AN2000 3 966 3 054 0 9518 0 3569 0 5155 0 3569 16 695 14 01JAN2000 1 460 1 127 0 3485 0 1262 0 1943 0 1262 6 168 15 01JAN2000 2 478 1 921 0 5926 0 2155 0 3232 0 2155 10 469 26 02 AN2000 NA NA NA NA NA NA NA BOD MOD REACH name County 5 NA 68 Double Branch Hillsborough 1 NA 16 Rocky Creek Hillsborough file Cl Users johnf Downloads Table 203 1 html 12 1 2013 7 25 11 PM Table 3 1 R 8 1 178 77 Lower Sweetwater Hillsborough 14 2 644 221 Channel A Hillsborough 13 4 489 229 Channel G Hillsborough 2 6 NA 6 8 Double Branch Hillsborough change 0 to na model conc county model conc county 0 lt NA Subset data into seperate parameter data sets NAS are still present TKN na lt data frame cbind model conc county TKN MOD model conc county County NH3 na lt data frame cbind model conc county NH3 MOD model conc county County NOX na lt data frame cbind model conc coun
15. Integrated Model System e Provide instructions post processing steps to produce graphics and statistics Based on these objectives the manual provides specific descriptions and instructions for the time frame for the OTB Integrated Model System 2000 2009 and is not a general user s manual The first part of the training manual steps through setting up the model files running the model and post processing information for the hydrology portion of the model The second part of the training manual steps through the water quality model component development and post processing The instructions for the hydrology are presented in three primary steps these are e Step 1 Setting up the Watershed Model e Step 2 Running the Watershed Model e Step 3 Watershed Model post processing for calibration graphics and statistics STEP 1 SETTING UP THE WATERSHED MODEL Some of the coding that integrates the three components requires a specific file placement naming and setup Below are the preliminary steps to e Configuring the Software Environment e Installing the Model Files e Understanding the Modeling Components A CONFIGURING THE SOFTWARE ENVIRONMENT Before installing any model files set up the software environments as follows 1 Install Microsoft Components a NET Framework v4 5 b SQL Server 2012 Express LocalDB 2 Confirm Microsoft Access 2003 or later 32 bit version if 2010 or later Install ERA BASINS 4 0 or later 4 Install Golden
16. P obs all NOX mean lt mean na omit as numeric as character obs NOX P obs all TN mean lt mean na omit as numeric as character obs TN P obs all ORTHOP mean lt mean na omit as numeric as character obs ORTHOP P obs all TP mean lt mean na omit as numeric as character obs TP P obs all TSS mean lt mean na omit as numeric as character obs TSS P obs all BOD mean lt mean na omit as numeric as character obs BOD SP obs all In TKN mean lt mean na omit as numeric as character obs TKNSIn obs all In NH3 mean lt mean na omit as numeric as character obs NH3 In obs all In NOX mean x mean na omit as numeric as character obs NOxX In obs all In TN mean lt mean na omit as numeric as character obs TN In obs all In ORTHOP mean lt mean na omit as numeric as character obs ORTHOPS In obs all In TP means mean na omit as numeric as character obs TPSIn obs all In TSS means mean na omit as numeric as character obs TSS In obs all In BOD means mean na omit as numeric as character obs BOD In Merge the mean values into one data set using the function cbind all obs2 lt data frame cbind obs all TKN_ mean obs all NH3 mean obs all NOX mean obs all TN mean file Cl Users johnf Downloads Table 203 1 html 12 1 2013 7 25 11 PM Table 3 1 R obs all ORTHOP mean obs all TP mean 1090 ds ngan obs all BOD mean obs all In TKN
17. Ta on sh V v Flo I a D D I I I I 2000 2002 2005 2008 2010 dec vear specifiy the theme for the plot this theme removes the default gray background and adds axes lines ts p3 lt ts p2 theme legend title element blank theme legend justification c 1 1 legend position c 1 1 theme panel border element rect colour black fill NA theme axis text element Text coloun black size 12 theme panel background element rect fill NA colour black theme legend key element rect fill NA 3 Warning Removed 6 rows containing missing values geom path Warning Removed 10 rows containing missing values geom point file CI Users johnf Downloads Appendix 20D 20ts 20 4 html 12 2 2013 11 05 22 AM Appendix D ts R Observed Simulated 2000 2002 2005 2008 2010 dec vear add the x and y labels ts p4 lt ts p3 scale x continuous breaks c 2000 2001 2002 2003 2004 QUIET QI Lon ah aa ts p4 Warning Removed 6 rows containing missing values geom path Warning Removed 10 rows containing missing values geom point file Cl Users johnf Downloads A ppendix 20D 20ts 20 4 html 12 2 2013 11 05 22 AM Appendix D ts R Observed Simulated ol ge Poe na DATA gig x ea h 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 Year add title ts p5 lt ts p4 ggtitle paste OTB Waterhed Water Quality n ts s
18. data management wdm files o MODFLOW folder contains files necessary to run the MODFLOW application interfaced with IHM se INTB_PreProcessing bat automatically initializes predetermined processes needed to start the model IHM ctl control file IHM_Code mdb contains integration code for the interface between the 3 model components This file is not accessible to the user se INTB mdb contains modeling parameters reference tables look up tables and observed data for reverification 2 9 2 Post Processing Plugins a Navigate to the Bin Folder and open the Post Processing Plugin folder pe rr ___m 11 24 2013 2 38 PM File folder S AttribControls dll 6 20 2012 11 51 AM Application extens 164 KB _ AttribControls pdb 6 20 2012 11 51 AM PDB File 294 KB AttribControls 6 20 2012 11 51 AM XML Document 21 KB 8 AttribManager dil 6 20 2012 11 51 AM Application extens 58 KB _ AttribManager pdb 6 20 2012 11 51 AM PDB File 142 KB AttribManager 6 20 2012 11 51 AM XML Document 13 KB 8 C1 Win ClInput 2 dil 11 1 2008 3 27 PM Application extens 678 KB C1 Win ClInput 2 i z C1 Win C1TrueDBGrid 2 dll 20 4 IHM exe config 6 19 2012 9 37 AM CONFIG File kS C1 Win C1TrueDBGrid 2 p04 HM 7 5 2012 8 09 PM Text Document _ IHM pdb 6 20 2012 11 51 AM PDB File E IHM 6 20 2012 11 51 AM XML Document 18 ConnectionManager 8 IHMObjects dill 6 20 2012 11 51 AM App
19. et sort by name parameter date all lt data frame all order all name all parameter all date head all REACH date X LABEL parameter 29953 63 O1APR2000 Modeled Biological Oxygen Demand 5 mg L 32873 63 O1APR2001 Modeled Biological Oxygen Demand 5 mg L 35793 63 O1APR2002 Modeled Biological Oxygen Demand 5 mg L 38713 63 01APR2003 Biological Oxygen Demand 5 mg L 41641 63 01APR2004 Modeled Biological Oxygen Demand 5 mg L 44561 63 01APR2005 Modeled Biological Oxygen Demand 5 mg L Simulated observed OP ABSOP OP2 year month season 29953 NA NA NA NA NA 2000 4 Dry Nov May 32873 4 067 NA NA NA NA 2001 4 Dry Nov May 35793 NA NA NA NA NA 2002 4 Dry Nov May 38713 2 828 NA NA NA NA 2003 4 Dry Nov May 41641 Lig b 2 NA NA NA NA 2004 4 Dry Nov May 44561 Je 104 NA NA NA NA 2005 4 Dry Nov May file Cl Users johnt Downloads A ppendix 20C 20cdfts html 12 1 2013 7 22 32 PM Appendix C cdfs R name 29953 Alligator Allens Long Branch 32873 Alligator Allens Long Branch 35793 Alligator Allens Long Branch 38713 Alligator Allens Long Branch 41641 Alligator Allens Long Branch 44561 Alligator Allens Long Branch Variables to define PARAMETER TP Reach 60 Subset by Reach and Parameter cdf data lt subset all all REACH Reach amp all paramet er PARAMETER Create new data set for each set observed and stimulated bind the two sets together This prevents R from deleting an entire row when t he
20. exe 6 19 2012 4 46 AM Application 49 Computer uu III L OutputSummary exe config 6 19 2012 9745 AM CONFIG Fite P iy OS C ba home TPASRV2 HI 090397 ala OutputSummary Idb 12 1 20131 36 PM Microsoft Acces ome Wa CH m_m R E OutputSummary mdb 12 1 2013 1 36PM Microsoft Acces FFE aris data CATPAGISOTI EY b Double click on Post Processing to open any of the code scripts Home Create External Data Database a A Cut y gt Ascending Ga Copy Descending View Paste Filter N Y Format Painter 797 Remove Sort Views Clipboard Ta Sort amp Filt Modules H 2 MDB Utilities clsPostProcessingContext PostProcessing_INTB2 StatsFunctions c On the menu bar go to Tools Options 7 Microsoft Visual Basic for Applications OutputSummary File Edit View Insert Debug Run Add Ins Window Help A H Gad 90 Frs Aj Ln2 C0116 wi f References Project IH A Input Xx ha NS ud M as pen tas IHM Input Properties id Lu i i n TMPCLP 528541 3 A MDB Utilities c Digital Signature stabase 3 Hi dah died l dl R PostProcessing_JNTI Public Enum Transforms Log StatsFunctions None E Class Modules ShiftedLogNormal End Enum Public Enum CalculationIntervals FixedInterval CalendarMonth CalendarWeek CalendarYear End Enum dialog 4 Grapher Library a Inthe root of the ReVerification run folder open Bin Post Pro
21. mean 2 HOS Me ime e AMOS mesin OS in BOD meani 21 Add column names colnames obs2 lt c County TKN mean NH3 mean EO means I Meet SORA as STAR SS Meana BOD mean N TKN meani SIN NES means ln NOX mean S merana EIN ORTHOP mean Aa R mean AN Wess meani An RODT mess head obs2 i 2 i 2 l 2 County TKN mean NH3 mean NOX mean TN mean ORTHOP mean TP mean Hillsborough pes 10 37 21 79 182 4 46 27 13 21 Pinellas 54 21 10 34 18 16 ITF a 3144 15 66 TSS mean BOD mean In TKN mean In NH3 mean In NOX mean In TN mean 14 88 20 48 0 1388 2 544 2 024 0 06152 14 88 34 34 0 1142 2 855 2 250 0 06981 In ORTHOP mean In TP mean In TSS mean In BOD mean 2 896 2 195 La 234 0 2935 2 687 1 991 L234 0 7557 Final calculation using the function exp obs geom TKN lt data frame County c Hillsborough Pinellas geomean exp obs2 In TKN mean obs geom NH3 lt data frame County c Hillsborough Pinellas geomeanzexp obs2 In NH3 mean obs geom NOX lt data frame County c Hillsborough Pinellas geomean exp obs2 In NOX mean obs geom TN lt data frame County c Hillsborough Pinellas geomean exp obs2 In TN mean obs geom_ ORTHOP data frame County c Hillsborough Pinellas geamedn exn obs 2 in ORTHOP mean obs geom TP lt data frame County c HilIsborough Pinellas geomean exp obs2s sin_TP_mean obs geom TSS lt data frame County c
22. mean obs all In NH3 mean TOS ell ta iO mean 1996 ella WL mean obs all In_ ORTHOP mean obs TAP mean GUIS wail ina mean obs all In BOD mean Add column names colnames all obs2 lt c TKN mean ANAS Mea nie NOX mean ste Merete ORTHOP mean tro mean TSS e BOD mean h TKN mean SSN meant A NOX meani In TN mean AN ORTROR meani An TE meani ln TSS mean In BOD mean vas cll os TKN mean NH3 mean NOX mean TN mean ORTHOP mean TP mean TSS mean BOD mean l 0 9643 0 1184 0 2049 1 163 0 08519 0 1505 5 213 1 917 In TKN mean In NH3 mean In NOX mean In TN mean In ORTHOP mean In TP mean l 0 1239 2 735 2 164 0 06656 2 11 2 072 In TSS mean In BOD mean 1 12317 0 5126 Final calculation using the function exp all geom TKN obs lt data frame geomean exp all o0bs2 In TKN mean all geom NH3 obs lt data frame geomean exp all obs2 In NH3 mean all geom NOX obs lt data frame geomean exp all obs2 In NOX mean all geom TN obs lt data frame geomean exp all obs2 ln_TN_ mean all geom ORTHOP obs lt data frame geomean exp all obs2 ln_ ORTHOP mean all geom_TP_obs lt data frame geomean exp all obs2 In TP mean all geom TSS obs lt data frame geomean exp all obs2 In TSS mean all geom BOD obs lt data frame geomean expl all obs2 In BOD mean head all geom TKN obs geomean 1 0 8835 Merge the geometric mean values into one data set using the function cbind all obs geom
23. side of the interface click on the Post Processing button 4 Within the box at the top half of the interface select the name ReVerification from the list of possible post processing sequences if you wish to create plots with Grapher If you are NOT making plots with Grapher select ReVerification_NoGrph from the list 5 Click Execute Sequence 6 Browse to the Simulation Output Directory The output directory i e C INTB ReVerification ReVerification_ YearMonthDayTime and then click Start 7 When the post processing sequence completes there will be a new folder under the simulation output directory that is named Post ReVerification YearMonthDayTime that contains post processed Balances and OutputSummary folders ReVerification folder created during the Post Processing routine i File Edit View Tools Help Organize Burn New folder 4 Gi Libraries b Ei Documents be a Music b B Pictures gt Bf Videos a Computer r sC gt og home TPASRV2 H b Ga gis_data TPAGISO1 J b bag Gis archive ATPAMAINO4 L gt 8 projects gnyv projects M Sy drafting TPASRV2 N b G HOME SAR HOME b Ga projects Monvsnv r Q gt Gal Projects N SAR PROJECTS R gt Cal gis Sar projects S b Gg work MATPASRV2 T b common Sar common Vi Pig imagery TPAGISOL X ea 2 TE drive 2 Archived Modfow Output folder io
24. to read data into R are read table for text files and read csv for csv files To read in a data file l name the file if you do not name the file then R wil open up the data in the workspace 2 tell R what function to use read table or read csv 3 tell R where the file is 4 how the data are separated 5 and if there are column names header Note R is case sensitive A skeleton example x lt read table C tmpR example txt sep header FALSE since the file was named the file is now stored in R read table C tmpR example txt sep header FALSE V1 V2 1 4 2 2 6 3 5 8 4 10 10 the above command was not named therefore the file will appear in the workspace 4 Note R is case sensiti ve 4 4 4 4 4 4 4 4 4 Below is the code used to calculate the geometric means in Table 3 1 of the calibration report Data files used simulated model conc 131029 csv observed ambientdata 131022 csv Files are csv files with headers EEE EEEEETETETE TE TIZI ET EEE EEEE EEE EELEE EEEE EES Mul at COFFEE HARSH HEHEHE HHH HH HH EEE Data model concs read csv C Users john Documents old tampa bay water optimal model run dataset model conc 131029 csv header TRUE head model conc date TN MOD TKN MOD NOX MOD NH3 MOD TP MOD ORTHOP MOD TSS MOD 1 01 AN2000 NA NA NA NA NA NA NA 2 01 AN2000 NA NA NA NA NA NA NA 3 01 AN2000 NA NA NA NA NA NA NA 4 01JAN2000 1 775 1 312 0
25. you change or add a location make sure Trusted Documents that the new location is secure Description Date Modified v Add ins a t ActiveX Settings z Chum Files Migrosoft Office Office1MACCWIA Access default Warning This location will be treated as a trusted source for opening files If you g STIA change or add a location make sure that the new location is secure CAtemp INTBY Path KINTB_copy tb ri hin Macro Settings Message Bar Privacy Options Policy Locations C Subfdlders of this location are also trusted Date and Time Created 10 28 2013 10 26 AM Path Cirintb Description Date Modified 10 28 2013 10 26 AM Sub Folders Allowed V _ __N ca ewioraon Remove Note MS Access 2007 or 2010 Add the working directory as a trusted location in the Access Trust Center File Options Trust Center click on the Trust Center Settings button Be sure to checkmark the Subfolders of the location are also trusted box on the Trusted Location configuration form MS Access 2003 Set security to low under the Access menu Tools Macros Security STEP 2 RUNNING THE MODEL A GRAPHICAL INTERFACE 1 Navigate to the INTB model scenario working directory typically in the C drive Open the bin folder and double click on IHM exe to open the IHM interface 11 24 2013 2 38 PM File folder AttribControls dil 20 2012 11 51 AM Application extens 164 KB _ Attrib
26. 0 1 Dry Nov May 4 NA NA NA NA NA 2000 1 Dry Nov May 5 NA NA NA NA NA 2000 1 Dry Nov May 6 NA NA NA NA NA 2000 1 Dry Nov May file Cl Users johnf Downloads A ppendix 20D 20ts 20 4 html 12 2 2013 11 05 22 AM Appendix D ts R S Ort head all REACH 4626 60 11442 60 19970 60 13642 60 7306 60 6586 6 0 ABSOP 4626 NA 11442 NA 19970 NA 13642 0 0603 7306 0 0504 6586 NA add water by reach x label date all lt data frame all order all REACH all X LABEL all date date X LABEL parameter 01AUG2001 Ammonia mg L NH3 01DEC2003 Ammonia mg L NH3 01NOV2006 Ammonia mg L NH3 01SEP2004 Ammonia mg L NH3 02 UL2002 Ammonia mg L NH3 03APR2002 Ammonia mg L NH3 OP2 year month season NA 2001 8 Wet Jun Oct NA 2003 12 Dry Nov May NA 2006 11 Dry Nov May 0 003636 2004 9 Wet Jun Oct 0 002540 2002 7 Wet Jun Oct NA 2002 4 Dry Nov May body name column all name lt Bishop Mullet all name al all name al all name al all name al all name al all S name al all namef al all namel ali REACH 60 lt REACH 63 lt REACH 65 lt REACH 68 lt REACH 76 lt REACH 77 lt REACH 227 lt REACH 229 lt head al REACH date X LABEL parameter simulated observed 4626 60 01AUG2001 Ammonia mg L NH3 NA 0 100 11442 60 01DEC2003 Ammonia mg L NH3 NA 0 010 19970 60 O1NOV2006 Ammonia mg L NH3 NA 0 100 13642
27. 0 25 0 50 0 75 1 00 specifiy the theme for the plot this theme removes the default gray background and adds axes lines p2 lt pl theme legend title element blank 4 theme legena justification c 1 1 legend position c 1 1 theme panel border element rect colour black fill NA LNemel ax Ss text element Text coloun black size 12 theme panel background element rect fill NA colour black theme legend key element rect fill NA p 2 file CIUsers johnf Downloads Appendix 20C 20cdfs html 12 1 2013 7 22 32 PM Appendix C cdfs R observed simulated 0 00 0 25 0 50 0 75 1 00 add the x and y labels p3 lt p2 scale y continuous labels percent imts c 0 00001 1 ylab Percentile xlab both label 1 p3 Warning Removed 2 rows containing missing values geom path Warning Removed 2 rows containing missing values geom path file CIUsers johnf Downloads Appendix 20C 20cdfs html 12 1 2013 7 22 32 PM Appendix C cdfs R observed simulated PJ Total Nitrogen mg L 0 29 50 75 100 Percentile add title p4 lt p3 ggtitle paste OTB Waterhed Water Quality n both name 1 Reach Reach sep p 4 Warning Removed 2 rows containing missing values geom path Warning Removed 2 rows containing missing values geom path file CIUsers johnf Downloads Appendix 20C 20cdfs html 12 1 2013 7 22 32 PM
28. 0 I 63 NA 0 6567 NA NA NA 2000 1 11 2000 2 63 NA 0 8720 NA NA NA 2000 21 2000 3 63 NA 1 6200 NA NA NA 2000 3 31 2000 4 63 NA 0 8150 NA NA NA 2000 4 41 2000 5 6 3 NA 1 0775 NA NA NA 2000 5 51 2000 6 63 NA 1 5800 NA NA NA 2000 6 dec year l 2000 14 2000 21 2000 31 2000 4 2000 51 2000 S1 mul ated newdata sim lt aggdata sim order aggdata simS dec year head newdata sim Group 1 Group 2 Group 3 Group 4 REACH parameter l 2000 l TN Alligator Allens Long Branch 63 NA l 2000 2 TN Alligator Allens Long Branch 63 NA Zi 2000 3 TN Alligator Allens Long Branch 6 3 NA 31 2000 4 TN Alligator Allens Long Branch 6 3 NA 41 2000 5 TN Alligator Allens Long Branch 6 3 NA 51 2000 6 TN Alligator Allens Long Branch 6 3 NA dv method ts name year month dec year 1 NaN NA NA NA 2000 1 2000 11 NaN NA NA NA 2000 2 2000 21 NaN NA NA NA 2000 3 2000 31 NaN NA NA NA 2000 4 2000 41 NaN NA NA NA 2000 5 2000 51 NaN NA NA NA 2000 6 2000 Pl ot Si mualted YLAB ts obs data parameter 1 ts pl lt ggplot newdata sim aes x dec year y dv colour Simulated ts pl Warning Removed 6 rows containing missing values geom path file Cl Users johnf Downloads A ppendix 20D 20ts 20 4 html 12 2 2013 11 05 22 AM geom linefshape line Appendix D ts R rj HJ 7 Simulated Simulated dv 10 vi TE ul I I I I I 2000 2002 2005 2008 2010 dec year 0bserved ts p2 lt ts pl geom point aes x dec year y dv sha
29. 12 PM 9 23 2013 12 PM 9 23 2013 7 12 PM 9 24 2013 2 02 AM 9 23 2013 8 04 PM 9723 2013 7 50 PM 9 23 2013 4 17 PM 9 24 2013 2 09 AM Of24 2013 2 09 AM 9 23 2013 712 PM 9 23 2013 7 12 PM 9 23 2013 7 31 PM 9 23 2013 9 38 PM 9725 2013 7 12 PM 9 23 2013 712 PM 9 23 2013 712 PM 9 23 2013 7 12 PM 9 23 2013 712 PM Kaos gt Network p sarsn04 INTE gt Verification gt ReVerification 20130023161715 gt Archived Modflow Output Date modified 23 2013 7 12 PM 23 2013 7 12 PM 9 23 2013 7 12 PM 9 23 2013 7 12 PM 9 23 2013 7 12 PM 9 23 2013 7 2 PM 9 23 2013 7 12 PM 9 23 2015 7 12 PM 23 2013 712 PM 9 23 2013 7 12 PM 9 23 2013 7 12 PM 9 23 2015 12 PM 9 23 2013 7 12 PM 923 2013 712 PM 9 23 2013 7 12 PM Type File folder File folder Microsoft Excel Microsoft Excel C Microsoft Excel C Text Document Microsoft Access Microsoft Access Microsoft Excel C MDF File LDF File Microsoft Excel C Microsoft Excel C Text Document Microsoft Access Microsoft Excel C Microsoft Excel Ci Microsoft Excel C Microsoft Excel Microsoft Excel Type HM COPY File HM COPY File IHM COPY File HM COPY File IHM COPY File IHM COPY File IHM COPY File IHM COPY File HM COPY File HM COPY File THM_COPY File IHM_COPY File IHM COPY Fite IHM COPY File IHM COPY File Search ReV erifin Size 356 206 KE 13 964 KE 309 329 KE 14 890 KE 978 620 KE 1 415 156 KB 1 KB 1
30. 4 In ORTHOP mean In TP mean In TSS mean In BOD mean i 2 631 2 026 1 601 0 7167 2 2 522 2 077 1 670 0 8296 Final calculation using the function ni geom TKN MOD lt data frame County c Hillsborough Pinellas geomean exp mod2 n_ TKN mean geom NH3 MOD lt data frame County c hillsborough Pinellas geomean exp mod2 n NH3 mean geom NOX MOD lt data frame County c Hillsborough Pinellas geomean exp mod2 In NOX mean geom TN MOD lt data frame County c Hillsborough Pinellas geomean exp mod2 iIn TN mean geom ORTHOP MOD lt data frame County c hillsborough Pinell as geomean exp mod2 in ORTHOP mean w geom TP_MOD lt data frame County c Hillsborough Pinellas geomean exp mod2 In TP mean geom TSS MOD lt data frame County c Hillsborough Pinellas geomean exp mod2 In TSS mean geom BOD MOD lt data frame County c Hillsborough Pinellas geomean exp mod2 In BOD mean file Cl Users johnf Downloads Table 203 1 html 12 1 2013 7 25 11 PM Table 3 1 R head geom TKN MOD County geomean 1 Hillsborough 0 6713 2 Pinellas 0 6959 Merge the geometric mean values into one data set using the function cbind mod geomean lt chind geom TKN MOD geom NH3 MODI 2 geom NOX MODI 2 geom TN_MOD 2 geom ORTHOP MODI 2 geom TP_MOD 2 geom TSS_MOD 2 geom BOD MODI 21 Add column names colnames mod geomean lt c County NO RO meo
31. 414 400 KB 15 040 KB 76 595 KB 1 412 100 KB 5 KB 6 912 KB 1 591 600 KB 487 067 KE 331 841 KB 486 286 KB 17 687 KB x ea MN Search Archive z Size 2 094 634 KB 2 554 634 KB 1 297 505 KB 2 594 634 KB 2 594 634 KE 2 594 634 KE 2 994 634 KE 1 297 505 KB 2 554 634 KE 1 297 505 KB 432 502 KE 2 594 634 KE 2 594 634 KE 1 297 505 KB 2 994 634 KE Post Verification Folder K mi sarsv04 gt INTE Verif_Ext0009 Verifi 00 09 20130924093303 Post_Verif_ext 20130924131714 File Edit View Tools Help Organize v Burn New folder Mame Date modified 4 lt Libraries i all d Balances 10 7 2013 3 53 AM H Documents igi Rag ta J OutputSummary 10 7 2013 4 09 AM b al Music Balances folder Name J INTBVerifAll J INTBVerifAnnual J OverlaysVerifAll J RegionsVerifAll Output Summary folder Name de Verification VerificationExtendedWellSet VerificationOROPWells di Verification OROPWellsCalibrationSet Within the Balances and Output Summary folders are the post processing statistics graphical and tablular used to reverify water balance streamflow ET springflow surficial well data and aquifer water levels C WATER QUALITY 1 Double click the WDMUtil icon on the desktop From the file drop down navigate to the rein_ret wdm for the current simulation and open Select and highlight the reach or watershed data to export and click on the icon in the Tool
32. 4223 0 1516 1 2373 0 1518 1 522 file Cl Users johnf Downloads Table 203 1 htm1 12 1 2013 7 25 11 PM Table 3 1 R 5 01 AN2000 NA NA NA NA NA NA NA 6 01 AN2000 NA NA NA NA NA NA NA BOD MOD REACH name i NA 60 Bishop Mullet 2 NA 63 Alligator Allens Long Branch 3 NA 65 Roosevelt 4 3 013 6 6 St Pete 5 NA 6 8 Double Branch 6 NA 69 Safety Harbor Mobbly Bay di m model conc 1 76713 Li Subset data to only include reaches in OTB model conc OTB lt subset model conc model conc REACH 60 model conc REACH 63 model conc REACH 65 model conc REACH 68 model conc REACH 76 model conc REACH 77 model conc REACH 227 model conc REACH 229 Create County column First line creates a column with only Pinellas model conc OTB County Pinellas Modify the column to include Hillsborough model conc OTB County model conc OTB REACH 68 lt Hillsborough model conc OTB County model conc OTB REACH 76 lt Hillsborough model conc OTB County model conc OTB REACH 77 lt Hillsborough model conc OTB County model conc OTB SREACH 227 lt Hillsborough model conc OTB County model conc OTB REACH 229 lt Hillsborough head model conc OTB date TN MOD TKN MOD NOX MOD NH3 MOD TP MOD ORTHOP MOD TSS MOD 1 01 AN2000 NA NA NA NA NA NA NA 2 01 AN2000 NA NA NA NA NA NA NA 3 01 AN2000 NA NA NA NA NA NA NA 5 01 AN2000 NA NA NA NA NA NA NA 7 01 AN2000 NA NA NA NA NA NA NA 8 O01 AN2000 3
33. 50448 266310 2 96443844 32280 0 f1 2000 0 00 00 2 7 67499876 32526 7148 7 67499876 1 989645 134871 1 98958635 16348 9 6 1 1 2000 0 00 00 3 7 81543875 13464 9834 7 81543875 1 63889337 67781 1719 1 63881409 821 1 1 2000 0 00 00 4 7 81448603 3794 75122 7 81448603 2 38004971 13153 7998 2 37018878 159 1 1 2000 0 00 00 5 7 78547764 248 061859 7 78547764 1 25651848 1628 71497 1 25452276 197 00 00 6 10 6052198 7625 5625 10 6052198 1 51982367 41393 5469 1 51971209 5017 00 00 7 9 53732967 3241 62622 9 53732967 2 00956345 13308 0742 2 00895667 161 00 00 8 5 67300797 20267 6895 5 67300797 1 40728307 118816 5 1 40724969 14401 00100 9 7 02565527 4670 79443 7 02565527 1 70075893 22656 9766 1 70050359 274 00 00 10 9 32288074 298 516144 9 32288074 2 26165748 1088 91748 2 25230145 13 00 00 11 12 9772949 6 70400572 18 9772349 5 69100666 9 71850014 2 62117076 1 00 22 6 05295467 531 876953 6 05295467 1 19094706 3684 44995 1 19017768 44 00 13 8 72296143 1 34615266 8 72296143 1 1203934 9 91237545 0 913816512 1 17172000 1 1 2000 1 1 2000 1 1 2000 1 1 2000 0 0 D 0 0 D D Microsoft Access recommends that you define a primary key for your new table A primary key is used to uniquely identify each record in your table It allows you to retrieve data more quickly Cona ney Ann nan AAN AAN AAA AAN ANAN de Let Access add primary key sti sari narra Choose my own primar
34. 60 ABSOP OP2 year month season 4626 NA NA 2001 8 Wet Jun Oct 11442 NA NA 2003 12 Dry Nov May 19970 NA NA 2006 11 Dry Nov May 13642 0 0603 0 003636 2004 9 Wet Jun Oct 7306 0 0504 0 002540 2002 7 Wet Jun Oct 6586 NA NA 2002 4 Dry Nov May add water all name all REACH 60 lt all name all REACH 63 all name all REACH 65 all name all REACH 68 all name all REACH 76 NNN N N body name column Bishop Mullet Alligator Allens Long Branch Roosevelt Double Branch Rocky Creek BOD BOD BOD BOD BOD BOD all name all REACH 77 Lower Sweetwater Creek all name all REACH 223 lt Lake Tarpon all name all REACH 227 lt Channel A all name all REACH 229 lt Channel G head all REACH date X LABEL parameter simulated observed 4626 60 01AUG2001 Ammonia mg L NH3 NA 0 100 11442 60 01DEC2003 Ammonia mg L NH3 NA 0 010 19970 60 O1NOV2006 Ammonia mg L NH3 NA 0 100 13642 60 01SEP2004 Ammonia mg L NH3 0 0147 0 075 7306 60 02 UL2002 Ammonia mg L NH3 0 0196 0 070 6586 60 03APR2002 Ammonia mg L NH3 NA 0 560 ABSOP OP2 year month season name 4626 NA NA 2001 8 Wet Jun Oct Bishop Mull et 11442 NA NA 2003 12 Dry Nov May Bishop Mullet 19970 NA NA 2006 11 Dry Nov May Bishop Mullet 13642 0 0603 0 003636 2004 9 Wet Jun Oct Bishop Mull et 7306 0 0504 0 002540 2002 7 Wet Jun Oct Bishop Mullet 6586 NA NA 2002 4 Dry Nov May Bishop Mull
35. 996 to 2 On the Simulation Control tab at the bottom half of the interface click on Start Simulation which will begin the simulation and open a log screen Cup Environmental 70 Consolidated WF scenano for water body impact assessment pumping at historical 15 1985 1990 then at then at CWUP_ Off_Environmental Consolidated WF pumping off after 1990 1 day integration 1989 through 2006 2 day archiving for Modflo CWUP Of WellMitigation Consolidated WF pumping off after 1990 1 day integration 1989 through May 2001 1 day archiving for M CWUP _OtherwUPsAtSOPercPumping Consolidated WF scenano for other nearby WUPS at 50 pumping pumping at historical 1583 1990 the CWUP WellMitigation DOPrescribed 200 Consolidated WF scenario for well mitigation pumping at at historical 1929 1990 then at mgd 1991 2121 CUP _ wfellMitigation_ 30 90 Prescnbed Consolidated WF scenario for well mitigation pumping at at historical 1989 1990 then at 90 prescribed 1 t CWUP WellMitigation 90Prescribed _ 200 Consolidated WF scenario for well mitigation pumping z at historical 1989 1990 then at 90 prescribed fat HotStartCheck Confirm hot start heads match source run heads 1 week simulation 2 year run for PEST PEST_ _RunTest 11 week test run for PEST Pre Processing Test Short run to test pre processing ReachOnly aetas Only INTE Cali
36. APPENDIX A1 WATERSHED MODEL TRAINING MANUAL Sey i a MEALA N si TI i p a r rik Safety H baz 23 pmr F ag by ei iS A A Ng d mal 2 gt sr r r g tt tas 4x st gt PI erking Cu sel Da P j Soc senter m mutan mit 7 Pate uniri other nel i Kno M cans k amp we wht 2 ate ap r I s x 1 vs gt W sk i r s KY j PP nS ipa Pe i P Ens Ab 54 P gt Lr j Booth M ni 4 2 aon WATERSHED MODEL TRAINING MANUAL 1 Prepared for Tampa Bay Estuary Program Southwest Florida Water Management District Prepared by ha Jones Edmunds amp Associates Inc 5104 N Lockwood Ridge Road Suite 307 Sarasota FL 34234 BOR wry December 2013 of J i 7 Wi 1 i A i j R K a fe Ne LI Se 3 1 Le 1 FVE k 1 s rasi gt n at a j r pas j f n i i L n vp Tra t oS te ssi ja 1 LA ry bang i Q to te F i gt n OLD TAMPA BAY INTEGRATED MODEL SYSTEM INTRODUCTION This training manual has been prepared to support the first training session for the Old Tampa Bay Integrated Model System Watershed Model The objectives of the first training are e Provide instruction to the user group on the Watershed Model structure and how to set up and run the watershed model for the OTB
37. Appendix C cdfs R OTB Waterhed Water Quality Bishop Mullet Reach 60 observed 1 simulated P Total Nitrogen mg D 0 29 50 75 100 Percentile save and export plot plot filename lt pasteQ C Users john Documents old tampa bay water optimal model bf PARAMETER Reach pdf ggsave p4 filename plot filename height 8 wi dth 8 Warning Removed 2 rows containing missing values geom path Warning Removed 2 rows containing missing values geom path file Cl Users johnt Downloads A ppendix 20C 20cdfts html 12 1 2013 7 22 32 PM
38. Click on the query and select export to text file 14 Browse to and save over the original ReachIntegrationHistory csv 15 In the Export Text Wizard select Include Field Names on First Row then click Finish What delimiter separates your fields Select the appropriate delimiter and see how your text is affected in the preview below Choose the delimiter that separates vour fields Tab 3 Semicolon ia Comma em Other Text Qualifier Date ReachID DEP VOL STAGE AVDEP TWID HRAD SAREA RO IVOL PRSUPY 1 1 2000 0 00 00 1 7 99488831 95694 2031 7 99488831 2 96450448 266310 2 96443844 32220 0 f1 2000 0 00 00 2 7 67499876 32526 7148 7 67499876 1 989645 134871 1 08958635 16348 9 6 1 1 2000 0 00 00 3 7 81543875 13464 9834 7 81543875 1 638895337 67781 1719 1 63881409 821 1 1 2000 0 00 00 4 7 81448603 3794 75122 7 81448603 2 38004971 13153 7998 2 37918878 159 1 1 2000 0 00 00 5 7 78547764 248 061859 7 78547764 1 25651848 1628 71497 1 25458276 197 00 00 6 10 6052198 7625 5625 10 6052198 1 51982367 41393 5469 1 51971209 5017 00 00 7 9 53732967 3241 62622 9 53732967 2 00956345 13308 0742 2 00895667 161 00 00 8 5 67300797 20267 6895 5 67300797 1 40728307 118816 5 1 40724969 14401 00 00 5 7 02565527 4670 79443 7 02565527 1 70075893 22656 9766 1 70050359 274 00 00 10 9 32288074 298 516144 9 32288074 2 26165748 1088 91748 2 25230145 13 00 00 11 18 9772949 6 70400572 18 9772949 5 69100666
39. Controls pdb 20 2012 11 51 AM PDB File 294 KB 2 AttribControls 20 2012 11 51 AM XML Document 21 KB AttribManager dil 20 2012 11 51 AM Application extens 58 KB AttribManager pdb 20 2012 11 51 AM PDB File 142 KB AttribManager 20 2012 11 51 AM XML Document 13 KB 8 CL Win ClInput 2 dil 1 2008 3 27 PM Application extens 678 KB l Post Processing Plugins 2 C1 Win ClInput 2 28 C1 Win C1TrueDBGrid 2 dll 2 C1 Win C1TrueDBGrid 2 28 ConnectionManager dil ConnectionManager pdb ConnectionManager FPU Resetter dil FPU Resetter ilk __ FPU Resetter pdb hass ent dil T HspfEngine 2 21 6 AAA AAA 1 2008 3 27 PM 20 2008 2 27 AM 20 2008 2 26 AM 2012 11 51 AM 2012 11 51 AM 2012 11 51 AM 2012 11 51 AM 20 2012 11 51 AM 2012 11 51 AM 23 2009 1 27 PM 24 2004 5 22 PM 4 2010 12 38 PM 20 2012 11 51 AM XML Document Application extens XML Document Application extens PDB File XML Document Application extens ILK File PDB File Application extens Application WDM File Application 177 KB 1 454 KB 1 368 KB 52 KB 114 KB 9 KB 397 KB 909 KB 1 675 KB 4 264 KB 68 KB 1 320 KB 615 KB B LOADING THE SIMULATION 1 At the menu bar use File Open to open the modeling database On the left hand side of the interface click on the Scenarios button Within the box at the top half of the interface select the name ReVerification f
40. Hillsborough Pinellas geomean exp obs2 In TSS mean file Cl Users johnf Downloads Table 203 1 html 12 1 2013 7 25 11 PM In ORTHOP means summaryBy In County data obs ORTHOP FUN c mean na rm TRUE keep names TRUE Table 3 1 R obs geom BOD lt data frame County c Hillsborough Pinellas geomean exp obs2 ln_ BOD mean obs geom TKN County geomean 1 Hillsborough 0 8704 2 Pinellas 0 8920 Merge the geometric mean values into one data set using the function cbind obs geomean lt cbind obs geom TKN Obs geom NASTI ODore om NOX 2E obs geom TNI 21 obs geom ORTHOP 2 HOS Teo TE oos geom TSi obs geom BODI 21 Add column names colnames obs geomean lt c County TKN geomean NH3 geomean NOX geomean AIN geomeani ORTHOP geomean P eo mean TSS qeomean BOD geomean head obs geomean County TKN geomean NH3 geomean NOX geomean TN geomean 1 Hillsborough 0 8704 0 07858 0132 1 063 2 Pinellas 0 8920 0 05753 0 1054 1 072 ORTHOP geomean TP geomean TSS geomean BOD geomean 1 0 05523 0 1113 3 445 1 341 2 0 06807 0 1365 3 445 2 129 Export data write csv obs geomean C Users john Documents old tampa bay water optimal model bf observed county geomean csv row names T RUE Calculate the means of each varible overal obs all TKN mean lt mean na omit as numeric as character obs TKN P obs all NH3 mean lt mean na omit as numeric as character obs NH3
41. L Log Transformed Modeled Ammonia mg L Log Transformed Modeled Nitrate Nitrite si g L Log Transformed Modeled Total Nitrogen mg L Log Transformed Modeled Ortho Phosphorus a g L Log Transformed Modeled Total Phosphorus al Log Transformed Modeled Total Suspended Solids mg L Log Transformed Modeled Biological Oxygen Demand 5 mg L Reach Name Calculate the means of each variable by County using the function summaryBy in the library doBy TKN mean lt summaryBy P County data TKN FUN c mean na rm TRUE keep names TRUE NH3 mean lt summaryBy P County data NH3 FUN c mean na rm TRUE keep names T RUE NOX mean lt SummaryBy P County data NOX FUN c mean na rm TRUE keep names TRUE TN mean lt summaryBy P County data TN FUN c mean na rm TRUE keep names TRUE ORTHOP mean lt summaryBy P County data ORTHOP FUN c mean na rm TRUE keep names TRUE TP_mean lt summaryBy P County data TP FUN c mean na rm TRUE keep names TRUE TSS mean lt summaryBy P County data TSS FUN c mean na rm TRUE keep names T RUE BOD mean lt summaryBy P County data BOD FUN c mean na rm TRUE keep names TRUE In TKN mean lt summaryBy In County data TKN FUN c mean na rm TRUE keep names TRUE In NH3 mean lt summaryBy In County data NH3 FUN c mean na rm TRUE keep names TRUE file Cl Users johnf Downloads Table 203 1 html 12 1 2013 7 25 11 PM Table 3 1 R In NOX mean l
42. Ln TN Ln TP Ln TSS all lt subset sim obs sim obs parameter B0D sim obs parameter NH3 sim obs parameter NOX sim obs parameter ORTHOP sim obs parameter TKN sim obs parameter TN sim obs parameter TP sim obs parameter TSS head all REACH date X LABEL parameter l 60 01JAN2000 Modeled Biological Oxygen Demand 5 mg L BOD 2 60 01J AN2000 Modeled Ammonia mg L NH3 3 60 01J AN2000 Modeled Nitrate Nitrite mg L NOX 4 60 01 AN2000 Modeled Ortho Phosphorus mg L ORTHOP 5 60 01 AN2000 Modeled Total Kjeldahl Nitrogen mg L TKN 6 60 O01 AN2000 Modeled Total Nitrogen mg L TN simulated observed OP ABSOP OP2 year month season 1 NA NA NA NA NA 2000 1 Dry Nov May 2 NA NA NA NA NA 2000 1 Dry Nov May 3 NA NA NA NA NA 2000 1 Dry Nov May 4 NA NA NA NA NA 2000 1 Dry Nov May 5 NA NA NA NA NA 2000 1 Dry Nov May 6 NA NA NA NA NA 2000 1 Dry Nov May sort by reach x label date all lt data frame all order all REACH all X LABEL all date file Cl Users johnf Downloads A ppendix 20C 20cdfs html 12 1 2013 7 22 32 PM Appendix C cdfs R head all REACH date X LABEL parameter simulated observed 4626 60 01AUG2001 Ammonia mg L NH3 NA 0 100 11442 60 01DEC2003 Ammonia mg L NH3 NA 0 010 19970 60 O1NOV2006 Ammonia mg L NH3 NA 0 100 13642 60 01SEP2004 Ammonia mg L NH3 0 0147 0 075 1306 60 02 UL2002 Ammonia mg L NH3 0 0196 0 070 6586 60 03APR2002 Ammonia mg L NH3 NA 0 5
43. Mitigation OOPrescribed 200 WUP CWUF_WellMitigation_30 30 90 Prescribed CWUP WellMitigation 90 30Prescribed 200 Consolidated WF pumping off after 1990 1 day integration 1989 through 2006 2 day archiving for Modflo Consolidated WF pumping off after 1990 1 day integration 1989 through May 2001 1 d 2001 1 day archiving archiving for M Consolidated WF scenario for other nearby WUPS at 50 pumping pumping at at historical 1989 19 1989 1990 t Consolidated WF scenario for well mitigation pumping at historical 1989 1990 then at 0 mad 1981 202 Consolidated WF scenario for well mitigation pumping at historical 1989 1990 then at 20 prescribed is Consolidated WF scenario for well mitigation pumping at histoncal 1989 1950 then at 90 prescribed 1 HotStartCheck Confirm hot start heads match source run heads 1 week simulation PEST Run 2 year run for PEST PEST_RunTest 1 week test run for PEST Pre Processing Test Short run to test pre processing ReachOnly Reaches eae INTB Calibration 1 day IE ReVenfication INTBVenfication Today integration 2000 to 2009 Vierifi_2000 INTE Verification 1 day integration 2000 2000 only Verfh_2000_ 2001 INTE Verification 1 day integration integration 2000 and 2001 only Verification INTE Verification 1 day integration 1999 to 2009 VerificationPlus INTE Verification Plus three antecedent years 1 day integration 1
44. NA NA 2005 1 Change year to decimal year for plotting Observed aggdata dec year lt aggdata year aggdatasmonth 12 1 12 head aggdata Group 1 Group 2 REACH parameter dv method label name year month l 2000 1 63 NA 0 6567 NA NA NA 2000 1 2 2001 1 63 NA 1 1067 NA NA NA 2001 1 3 2002 l 63 NA 1 0575 NA NA NA 2002 1 4 2003 1 63 NA 1 3507 NA NA NA 2003 1 5 2004 1 63 NA 0 9172 NA NA NA 2004 1 6 2005 1 63 NA 0 8322 NA NA NA 2005 1 dec year 1 2000 2 2001 3 2002 4 2003 5 2004 6 2005 Si mul ated aggdata sim dec year lt aggdata sim year aggdata sim month 12 1 12 head aggdata sim Group 1 Group 2 Group 3 Group 4 REACH parameter 1 2000 1 TN Alligator Allens Long Branch 6 3 NA 2 2001 1 TN Alligator Allens Long Branch 6 3 NA 3 2002 1 TN Alligator Allens Long Branch 6 3 NA 4 2003 1 TN Alligator Allens Long Branch 6 3 NA 5 2004 1 TN Alligator Allens Long Branch 6 3 NA 6 2005 1 TN Alligator Allens Long Branch 6 3 NA dv method ts name year month dec year 1 NaN NA NA NA 2000 1 2000 2 Na N NA NA NA 2001 1 2001 3 1 1109 NA NA NA 2002 1 2002 4 0 7984 NA NA NA 2003 1 2003 5 1 3199 NA NA NA 2004 1 2004 6 1 1442 NA NA NA 2005 1 2005 file Cl Users johnf Downloads A ppendix 20D 20ts 20 4 html 12 2 2013 11 05 22 AM Appendix D ts R Sort by decimal year 0bserved newdata lt aggdata order aggdatasdec year head newdata Group 1 Group 2 REACH parameter dv method label name year month 1 200
45. PM Table 3 1 R NOX In NOX MOD lt log as numeric as character NOX 1 Warning NaNs produced TN On TN MOD lt log l as numeric as cian acler TNI 11 7 ORTHOP In ORTHOP MOD lt og as numeric as character ORTHOP 1 RES We AMOD Loos numer Cees ar a er Melly It TSS In TSS MOD lt loglas numeric as character TSS 1 BOD I n BOD MOD lt log as numeric as character BOD 1 head TKN X1 X2 In TKN MOD 3 3 0536 Hillsborough 1 11632 4 1 1275 Hillsborough 0 12000 5 1 9214 Hillsborough 0 65305 8 1 7354 Hillsborough 0 55124 9 1 0638 Hillsborough 0 06185 10 1 5501 Hillsborough 0 43832 Add column names to each data set Mame se a e ee colnames TKN lt names colnames NH3 lt names col names NOX lt names colnames TN lt names col names ORTHOP lt names colnames TP lt names col names TSS lt names col names BOD lt names k e y TKN MOD Modeled Total Kjeldahl Nitrogen mg L NH3_ MOD Modeled Ammonia mg L NOX MOD Modeled Nitrate Nitrite mg L TN MOD Modeled Total Nitrogen mg L ORTHOP MOD Modeled Ortho Phosphorus mg L TP MOD Modeled Total Phosphorus mg L TSS MOD Modeled Total Suspended Solids mg L BOD MOD Modeled Biological Oxygen Demand 5 mg L In TKN MOD In NH3 MOD In NOX MOD In TN MOD In ORTHOP MOD In TP MOD In TSS MOD In BOD MOD reach name Log Transformed Modeled Total Kjeldahl Nitrogen mg
46. RTHOPS In a n TP mean lt mean na omit as Men character TEPSIN aA ETRE na omt as numericas character ee all In BOD mean lt mean na omit as numeric as character BOD In Merge the mean values into one data set using the function cbind all mod2 lt data frame cbind all TKN mean all NH3 mean all NOX mean all TN mean all ORTHOP mean ella Ie e file Cl Users johnf Downloads Table 203 1 html 12 1 2013 7 25 11 PM Table 3 1 R Mf SS mean all BOD mean all In TKN mean all In NH3 mean all In NOX mean all In TN mean all In ORTHOP mean A oi ngan ii SS negli all In BOD mean Add column names colnames all mod2 lt c TKN mean NH3 mean NOX mean Nun ORTHOP mean erna Tso mean BO meali In TKN mean NM NAS mean iin NOX mean Sn TN mean n ORTHOP meani An TE meane Sme gn In BOD mean head all mod2 TKN mean NH3 mean NOX mean TN mean ORTHOP mean TP mean TSS mean BOD mean 1 0 7952 0 07705 0 1755 0 9867 0 0867 0 1512 5 922 2 46 In TKN mean In NH3 mean In NOX mean In TN mean In ORTHOP mean In TP mean l 0 3884 2 125 1 927 0 174 2 6 2 04 In TSS mean In BOD mean 1 1 62 0 7485 Final calculation using the function exp all geom TKN MOD lt data frame geomean exp all geom NH3 MOD lt data frame geomean exp all geom NOX MOD lt data frame geomean exp mod2 ln NOX mean all geom TN MOD lt data frame geomean exp mod2 SiIn
47. Software s Grapher v10 0 or later Using machine administrator login register Grapher B INSTALLING THE MODEL FILES 1 Model Files Directory To minimize model run time and minimize errors due to file path length limitations start by creating a working directory on the local drive C INTB In the electronic training materials is a folder 4 IHM InstalNReVerification Copy the ReVerification folder only to the local drive C INTB tle Edit View Tools Help Organize Include in library Share with w Burn New folder dir Favorites a Name Date modified EI Desktop Bin 11 24 2013 2 38 PM lp Downloads i HSPF 11 24 2013 2 38 PM Recent Places J MODFLOW 11 24 2013 2 38 PM J BASINS OOOO External G L Hotstart Builder 6 14 2013 4 13 PM EF BASINS 4 Help Internal 2TB 2 LINTB_PreProcessing 6 20 2012 2 32 PM l BASINS 4 Updates amp SAR Common Vj IHM ctl 11 4 2011 5 02 PM l BASINS 4 IHM_Code 6 14 2013 4 13 PM Wifi BASINS Home Page GI Libraries Aj INTE 10 30 2013 11 08 2 GenScn r MapWindow Home Page H WOMOutput F Documents a Music INI E Pictures WDMUtil Hi Videos l WinHSPF H l WinHSPFLt The necessary folders files included in the folder are Bin folder contains executable files for the three model components necessary processing files and the IHM interface executable file to start the model run s HSPF folder contains four user control input files uci and six water
48. TN mean all geom ORTHOP MOD lt data frame geomean exp all mod2 iIn ORTHOP mean all geom TP _MOD lt data frame geomeanz exp all mod2 n TP mean all geom TSS MOD lt data frame geomean exp all mod2 iIn TSS mean all geom BOD MOD lt data frame geomean exp all mod2 iIn BOD mean mod2 In TKN mean mod2 I n NH3 mean head all geom TKN MOD geomean 1 0 6781 Merge the geometric mean values into one data set using the function cbind all mod geomean lt data frame cbind all geom TKN MOD all geom NH3 MOD all geom NOX MOD all geom TN MOD all geom ORTHOP MOD all geom TP MOD all geom TSS MOD all geom BOD MOD Add column names colnames all mod geomean lt c TKN SNA file Cl Users johnf Downloads Table 203 1 html1 12 1 2013 7 25 11 PM Table 3 1 R NOX TN ORTHOP T E 515 54 BOD head all mod geomean TKN NH3 NOX TN ORTHOP TP TSS BOD 1 0 6781 0 06557 0 1456 0 8403 0 07424 0 13 5 054 2 114 transpose data set trans otb geomean lt data frame Geometric mean t all mod geomean head trans otb geomean Geometric mean TKN 0 67811 NH3 0 06557 NOX 0 14556 TN 0 84030 ORTHOP 0 07424 TP 0 13000 Export data write csv trans otb geomean C Users john Documents old tampa bay water opti mal model bf simulated otb geomean csv row names TRUE 444 44 44444 44 4 4 4 0bserved 4 4 4 4 4 4 4 4 4 4 4 4 4 Data
49. a obs ORTHOP FUN c mean na rm TRUE keep names T RUE TP_mean lt summaryBy P County data obs TP FUN c mean na rm TRUE keep names TRUE TSS_mean lt summaryBy P County data obs TSS FUN c mean na rm TRUE keep names TRUE BOD mean lt summaryBy P County data obs BOD FUN c mean na rm TRUE keep names T RUE In TKN mean lt summaryBy n County data obs TKN FUN c mean na rm TRUE keep names TRUE file Cl Users johnf Downloads Table 203 1 html 12 1 2013 7 25 11 PM Table 3 1 R obs ln NH3 mean lt summaryBy In County data obs NH3 FUN c mean na rm TRUE keep names TRUE obs ln NOX mean lt summaryBy In County data obs NOX FUN c mean na r Mm TRUE keep names TRUE obs ln TN means summaryBy In County data obs TN FUN c mean na rm TRUE keep names TRUE obs obs ln TP means summaryBy In County data obs TP FUN c mean na rm TRUE keep names TRUE obs ln TSS mean lt summaryBy In County data obs TSS FUN c mean na rm TRUE keep names TRUE obs ln BOD mean lt summaryBy In County data obs BOD FUN c mean na rm TRUE keep names TRUE Merge the mean values into one data set using the function cbind obs2 lt cbhind obs TKN mean obs NH3 mean 2 obs NOX mean 2 obs TN mean 2 HOS Oa OP ngan OMS Me nee obs Los meani 21 obs BOD mean 2 obs In TKN mean 2 OOS In NH3 meani 21 obs In NOX mean 2 obs In TN meani 2 obs In ORTHOP
50. ality n both name 1 Reach Reach sep p 4 Warning Removed 2 rows containing missing values geom path Warning Removed 2 rows containing missing values geom path file CIUsers johnf Downloads Appendix 20C 20cdfs html 12 1 2013 7 22 32 PM Appendix C cdfs R OTB Waterhed Water Quality Bishop Mullet Reach 60 DI in Total Phosphorus mg L 0 25 50 75 100 Percentile save and export plot plot filename lt paste0 C Users john Documents old tampa bay water optimal model bf PARAMETER Reach pdf ggsave p4 filename plot filename height 8 wi dth 8 Warning Removed 2 rows containing missing values geom path Warning Removed 2 rows containing missing values geom path HHEFHHHHHHHHAHHHHH RH HHHH HH ADE Tine new variables the remainder of the code remains the same Variables to define PARAMETER TN Reach 60 Subset by Reach and Parameter cdf data lt subset all all REACH Reach amp all parameter PARAMETER Create new data set for each set observed and stimulated bind the two sets together This prevents R from deleting an entire row when t here 1S a missing value obs lt na omit data frame REACH Reach parameter PARAMETER dv cdf data observed method observed label cdf data X LABEL name cdf data name SIM lt na omit data frame REACH Reach parameter PARAMETER dv cdf data si mul ated method si mulated label cdf data X LABEL
51. and Permissions 7 Recent Mew Set Database Password rr Use a password to restrict access to your database Files that use the 2007 Print Microsoft Access file format or later are encrypted Set Database 1 Password Save amp Publish Help Exit b Click on Trust Center then Trust Center Settings Access Options General Help keep your documents safe and your computer secure and healthy Current Database Datasheet Protecting your privacy Microsoft cares about your privacy For more information about how Microsoft Access helps to protect your privacy please see the privacy statements Object Designers Proofing Show the Microsoft Access privacy statement Office com privacy statement Customer Experience Improvement Program language Client Settings Customize Ribbon Security amp more Quick Access Toolbar Learn more about protecting your privacy and security from Office com Microsoft Trustworthy Computing Microsoft Access Trust Center The Trust Center contains security and privacy settings These settings help keep your computer secure We recommend that you do not change these settings Trust Center Settings k c Click on Trusted Locations and add a new location Once added check the Subfolders of this location area also trusted Trust Center 3 Ex Trusted Publishers Tee Trusted Locations Warning All these locations are treated as trusted sources for opening files If
52. ata lt subset obs obs REACH Reach amp obs paramet er PARAMETER ts sim datas subset sim si m REACH Reach amp si m paramet er PARAMETER Aggregrate and calculate means by year and month Observed aggdata suppressWarnings aggregate ts obs data by list ts obs data year ts obs data month FUN mean na rm TRUE head aggdata Group 1 Group 2 REACH parameter dv method label name year month 1 2000 l 63 NA 0 6567 NA NA NA 2000 1 2 2001 63 NA 1 1067 NA NA NA 2001 1 3 2002 i 6 3 NA 1 0575 NA NA NA 2002 1 4 2003 i 63 NA 1 3507 NA NA NA 2003 1 file Cl Users johnf Downloads Appendix 20D 20ts 20 4 htm1 12 2 2013 11 05 22 AM Appendix D ts R 5 2004 63 NA 0 9172 NA NA NA 2004 1 6 2005 63 NA 0 8322 NA NA NA 2005 1 Si mulated aggdata sim lt suppressWarnings aggregate ts sim data by list ts sim data year ts sim datasmonth ts sim data parameter ts sim data name FUN mean na rm TRUE head aggdata si m Group 1 Group 2 Group 3 Group 4 REACH parameter 2000 TN Alligator Allens Long Branch 6 3 NA 2 2001 l TN Alligator Allens Long Branch 63 NA 3 2002 i TN Alligator Allens Long Branch 6 3 NA 4 2003 TN Alligator Allens Long Branch 6 3 NA 5 2004 l TN Alligator Allens Long Branch 63 NA 6 2005 1 TN Alligator Allens Long Branch 63 NA dv method ts name year month 1 Na N NA NA NA 2000 1 2 NaN NA NA NA 2001 1 3 1 1109 NA NA NA 2002 1 4 0 7984 NA NA NA 2003 1 5 1 3199 NA NA NA 2004 1 6 1 1442 NA
53. bration 1 dh mo R j INTE Vertication 1 day integration 2000 t j INTE Veri cation 1 day integration rime INTE Verification 1 day integration 2000 and 2001 only Verification INTE Verification 1 day integration 1999 to 2009 VerificationPlus INTE Verification Plus three antecedent years 1 nt years 1 da 1 day inte integration ion 1996 to 2006 4 Description INTE Verification 1 day integration 2000 to 2009 Simulation Start Date 4 1 2000 M End Date 12 31 2009 ini Integration Time Step days fi Preprocessing Batch File C INTB ReVerfication _INTB_PreProcessing bat Browse ea V Timestamp Simulation Directory Run Reaches Only Note The simulation will create a number of temporary and output files in the working directory including a log file anda series of output files and databases The temporary and output files can occupy a very large amount of disk space depending on the input data set and the configuration options selected STEP 3 POST PROCESSING Once the model run is complete the IHM model will begin the Model Upload sequence This sequence will produce errors because the IHM program was not designed to handle the changes in the UCI files and model database necessary to run the water quality model Steps 1 17 provide a work around to reach the end of the Hydrology Post Processing A DATABASE REVISIONS 1 Navigate to the model run folder i e C INTB ReVerification ReVerificati
54. c as character obs NH3 1 NOX In NOX MOD lt log as numeric as character obs NOXI 11 TN In TN MOD s log as numericfas character obs TNI 1 ORTHOP In ORTHOP MODxs log as numeric as character obs ORTHOP 1 Pen WP Ms oh as ea GPS wos Mey II LSS SSS MOS oe Eder eso BOD I n_BOD MOD lt log as numeric as character obs BOD 1 head obs TKN X1 X2 In TKN MOD 1 8 Hillsborough 0 58779 22 Hillsborough 0 19885 31 Hillsborough 0 27003 1 1 Hillsborough 0 09531 1 2 Hillsborough 0 18232 02 Hillsborough 0 01980 Add column names to each data set Mames lt C Pe County in col names colnames colnames col names colnames col names colnames colnames obs TKN lt names obs NH3 lt names obs NOX lt names obs TN lt names obs ORTHOP lt names obs TP lt names obs TSS lt names obs BOD lt names LL OS Tr LL Calculate the means of each variable by County using the function summaryBy in the library doBy obs obs obs obs obs obs obs obs obs TKN mean lt summaryBy P County data obs TKN FUN c mean na rm TRUE keep names TRUE NH3_mean lt SummaryBy P County data obs Nh3 FUN c mean na rm TRUE keep names TRUE NOX mean lt summaryBy P County data obs NOX FUN c mean na rm TRUE keep names TRUE TN mean lt summaryBy P County data obs TN FUN c mean na rm TRUE keep names T RUE ORTHOP mean lt summaryBy P County dat
55. cessing Plugins Standard Post Processing OutputSummary mdb mimine Tools Help jae Aj Open Burn rganize v New folder HI Desktop SI Name x iB Downloads TE E Recent Places 5 ConnectionManager dil External G ConnectionManager pdb BJ Internal 2TB 2 2 ConnectionManager xml G SAR Common V Hotstart Builder plugin l HotstartBuilder exe lk HotstartBuilder exe config 4 lt Libraries x a HotstartBuilder pdb gt Documents b r E 8 HotstartBuilder xml usic gt l Pict IHMOutput_H mdb ictures gt amp vid IHMOutput_M mdb IdEOS Output Summary Database plugin OutputSummary exe 4 Computer El utp ry BE amp 0s C an yaa gt amp home TPASRV2 H gt ais data ANTPAGISO1 1 b Double click on Post Processing to open any of the code scripts Create External Data Database Home pa di Cut V 4 Ascending fom SI Ba Copy View Paste Filter F Format Painter z Descending z Remove Sort Views Clipboard Ta Sort amp Filti B clsPostProcessingContext MDB_Utilities PostProcessing_INTB2 A StatsFunctions c Onthe menu bar go to Tools References File Edit View Insert Debug Run Too Add Ins Window Help ca Ada DC pe Tx BS we A 1in2 Coll6 _ Options 9 5 Modules n IHM Input Properties i ba TMPCLP528541 RARE ab i 2 MDB_Utiliti c Digital Signature aa
56. e Gy EARANN OME NE HE E1 a e Er 10101000 O1DTO 0 D DJOC Pb o fo fo da Telan ler ie be fe 0 0 0 0 0 0 0 0 0 0 0 RT Ste o L s P Tara TEA RS 20 x ao 0000 No oO 0100 0600 a a 0 o 10 10 11 11 mal TI ORI RT 43501 Y ee ee O1DTO 0 D DJOJOTVDTIT TEMRE T r Jd JN rw wb amp h W K U e 0N boa W B a OF M To Peyton ee Lev 1 Pes Pedic P D NM ke Nb ON WW Ff DO H o o o r sooo O OAN 0 10 1 070 0 60 01 1017010 1 01r ae Oe se DRS TST Cb 65 de Lada he be Dn od F amp F Wh MBA amp W h FH oO eo oF io 6 OJ OIO Oo N ese foe fa Lee ROSSORE i ya e le TERIOS J nana ww oOo FP J A Hw ON Mm yoo mh oO eB WO oH no a 40 t 16 1447 A 1 LI IR et O 1 0 ypu ow a DH dp N00 DO NO vs bh A o aka R s w w u H J P M w n o co NN 000000000020 o o sela Ia PMM R nN m sa n n H o o b un obs D w o US wa J o N H n w n aq o wW wo mn D b P o H J 1 2 ese Kat be Pi Dio Pee lee ies fee fe 19 1 Ve TTG de Let 19 da Pe da TESTNE 119 1 Ta BE ES e AS GU e BE o an OC IP FP MIA FP OY UN NM Oo Oa 0on 0 0 01010110170 VO0000000U 4 FN WOOO wor rP Att oo oooaouonana ao GB u J o PE P D 01010107010 CWI NDNA K QO HIV NIN MA O 1DIDIO 6 D D10 10 107 D o D m w 2002 12 23 2002 12 24 No oOo o o 0 00 i i NO 01010 O ow DO NO OH Hh Nh
57. ean lt data frame cbina all geom TKN obs all geom NH3 obs all geom NOX obs all geom TN obs all geom ORTHOP obs all geom TP obs all geom TSS obs all geom BOD obs Add column names file CI Users johnf Downloads Table 203 1 html 12 1 2013 7 25 11 PM Table 3 1 R colnames all obs geomean lt c TKN NE ORTHOP D 7 31555 BOD head all obs geomean TKN NH3 NOX TN ORTHOP he TSS BOD 1 0 8835 0 06492 0 1149 1 069 0 06268 0 126 3 445 1 67 transpose data set trans otb geomean obs lt data frame Geometric_mean t all obs geomean head trans ot b geomean obs Geometric mean TKN 0 88349 NH3 0 06492 NOX 0 11491 TN 1 06883 ORTHOP 0 06268 TP 0 12599 Export data write csv trans otb geomean obs C Users john Documents old tampa bay water optimal model bf otb geomean observed csv row names TRUE file Cl Users johnf Downloads Table 203 1 html 12 1 2013 7 25 11 PM Appendix D ts R Appendix D ts R Bridgette Froeschke Dec 2 2013 10 57 AM R Manual for Old Tampa Bay Integreated Model System Watershed Model Objective Construct time series plots fromthe calibration report using an open resource data analysis package librari es Mugen una mport data sim obs lt read csv C Users john Documents old tampa bay water optimal model bf 5 Appendix D ti meserl es predicted s observed sim obs Tun20 bydate plot sv head sim obs REACH date X_LABEL_ parame
58. erved PARAMETER Reach pdf ggsave ts p6 filename plot filename height 8 width 8 Warning Removed 6 rows containing missing values geom path Warning Removed 10 rows containing missing values geom point file Cl Users johnf Downloads A ppendix 20D 20ts 20 4 html 12 2 2013 11 05 22 AM Appendix C cdfs R Appendix C cdfs R Bridgette Froeschke Dec 1 2013 7 02 PM R Manual for Old Tampa Bay Integreated Model System Watershed Model Objective Construct cdf plots fromthe calibration report using an open resource data analysis package mport data sim obs lt read csv C Users john Documents old tampa bay water optimal model bf 4 Appendix C COPS MOUS ON SN WWW dales head sim obs REACH date X LABEL parameter 1 60 01J AN2000 Modeled Biological Oxygen Demand 5 mg L BOD 2 60 01 AN2000 Modeled Ammonia mg L NH3 3 60 01 AN2000 Modeled Nitrate Nitrite mg L NOX 4 60 01 AN2000 Modeled Ortho Phosphorus mg L ORTHOP 5 60 01 AN2000 Modeled Total Kjeldahl Nitrogen mg L TKN 6 60 01 AN2000 Modeled Total Nitrogen mg L TN Simulated observed OP ABSOP OP2 year month season ji NA NA NA NA NA 2000 1 Dry Nov May 2 NA NA NA NA NA 2000 1 Dry Nov May 3 NA NA NA NA NA 2000 1 Dry Nov May 4 NA NA NA NA NA 2000 1 Dry Nov May 5 NA NA NA NA NA 2000 1 Dry Nov May 6 NA NA NA NA NA 2000 1 Dry Nov May di m sim obs 1 467584 12 Subset data remove Ln BOD Ln NH3 Ln NOX Ln ORTHOP Ln TKN
59. ewdata sim Group 1 Group 2 Group 3 Group 4 REACH parameter l 2000 TP Alligator Allens Long Branch 6 3 NA 11 2000 2 TP Alligator Allens Long Branch 6 3 NA 21 2000 3 TP Alli gator Allens Long Branch 6 3 NA Jl 2000 4 TP Alligator Allens Long Branch 63 NA 41 2000 5 TP Alligator Allens Long Branch 63 NA 51 2000 6 TP Alligator Allens Long Branch 6 3 NA dv method ts name year month dec year 1 NaN NA NA NA 2000 1 2000 11 NaN NA NA NA 2000 2 2000 21 NaN NA NA NA 2000 3 2000 31 NaN NA NA NA 2000 4 2000 41 NaN NA NA NA 2000 5 2000 51 NaN NA NA NA 2000 6 2000 PI ot Si mualted YLAB ts obs data parameter 1 ts pl lt ggplot newdata sim aes x dec year y dv colour Simulated geom line shape line ts pl Warning Removed 6 rows containing missing values geom path file Cl Users johnf Downloads Appendix 20D 20ts 20 4 html 12 2 2013 11 05 22 AM Appendix D ts R 0 9 ai Simulated Simulated 0 3 0 0 I 2000 2002 2005 2008 2010 dec year 0bserved ts p2 lt ts pl geom point aes x dec year y dv shape Observed data newdata size 3 colour black Se pz Warning Removed 6 rows containing missing values geom path Warning Removed 10 rows containing missing values geom point file Cl Users johnf Downloads A ppendix 20D 20ts 20 4 html 12 2 2013 11 05 22 AM Appendix D ts R 0 9 Observed JA Observed p Simulated Simulated ja U S ff K 1
60. imdata name 1 Reach Reach sep See Warning Removed 6 rows containing missing values geom path Warning Removed 10 rows containing missing values geom point file Cl Users johnf Downloads A ppendix 20D 20ts 20 4 html 12 2 2013 11 05 22 AM Appendix D ts R OTB Waterhed Water Quality Alligator Allens Long Branch Reach 63 Observed Simulated 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 Year clean up legend ts po lt ts p5 scale colour manual values c dodgerblue4 scale shape manual values 1 ts p Warning Removed 6 rows containing missing values geom path Warning Removed 10 rows containing missing values geom point file Cl Users johnf Downloads A ppendix 20D 20ts 20 4 html 12 2 2013 11 05 22 AM Appendix D ts R OTB Waterhed Water Quality Alligator Allens Long Branch Reach 63 Observed Simulated 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 Year save and export plot plot filename lt paste0 C Users john Documents old tampa bay water optimal model bf 5 Appendix D timeseries predicted amp observed PARAMETER Reach pdf ggsave ts p6 filename plot filename height 8 width 8 Warning Removed 6 rows containing missing values geom path Warning Removed 10 rows containing missing values geom point Redefine REACH and parameter PARAMETER TN Reach 63 Subset by Reach and Parameter ts obs d
61. lication extens FPU Resetter dil _ IHMObjects pdb 6 20 201211 51 AM PDB File FPU excess ik 120 IHMObjects 6 20 201211 51 AM XML Document Dp Rim pos O LF9O EER 3 4 2010 12 38 PM EER File m MODFLW96 3 4 2010 12 38 PM Application PostProcessingShared dll 6 19 2012 9 43 AM Application extens hspfmsg wdm _ PostProcessingShared pdb 6 19 2012 9 43 AM PDB File HM 120 PostProcessingShared 6 19 2012 9 43 AM XML Document PreProcessingTemplate 4 21 2010 12 50 PM Windows Batch File 8 ConnectionManager dil _ ConnectionManager pdb 2 hass ent dil SE HspfEngine b Each folder contains a exe file Standard Post Processing contains 2 exe files that need to be opened the prior to the first model run on a system cc l Computer OS C INTB ReVerification Bin Post Processing Plugins ae ea ee File Edit View Tools Help Organize v Include in library Share with w Burn New folder 4 Favorites 3 Name H Desktop Command Line 1 Downloads di Head Reader SE Recent Places p Model Upload External d Standard Post Processing Internal 2TB 2 Water Balance z SAR Common V Tal R Ces Create External Data Database File Home SL amp cut 4 Ascending ae 53 Copy SoM El Descending c Double click and open the following exe files no action Format Painter agremsiesott jS Views Clipboard Ta Sort amp Filti necessary ju
62. lligator Allens Long Branch 2005 4 Sim lt data frame REACH al1 REACH ts all X LABEL head sim parameter all parameter dv all simulated method si mul ated name all name year all year month all month REACH parameter dv met hod 1 63 BOD NA simulated 2 6 3 BOD 4 067 simulated 3 63 BOD NA simulated 4 6 3 BOD 2 828 simulated 5 6 3 BOD 2 732 simulated 6 63 BOD 3 154 simulated ts name 1 Modeled Biological Oxygen Demand 5 mg L Alligator Allens Long Branch 2 Modeled Biological Oxygen Demand 5 mg L Alligator Allens Long Branch 3 Modeled Biological Oxygen Demand 5 mg L Alligator Allens Long Branch 4 Biological Oxygen Demand 5 mg L Alligator Allens Long Branch 5 Modeled Biological Oxygen Demand 5 mg L Alligator Allens Long Branch 6 Modeled Biological Oxygen Demand 5 mg L Alligator Allens Long Branch year month 1 2000 4 2 2001 4 3 2002 4 4 2003 4 5 2004 4 6 2005 4 Variables to define PARAMETER TP Reach 63 the only part that needs to be changed for file CIUsers johnf Downloads Appendix 20D 20ts 20 4 html 12 2 2013 11 05 22 AM the remainder of the code Appendix D ts R Subset by Reach and Parameter ts obs data lt subset obs obs REACH Reach amp obs paramet er PARAMETER ts sim datas subset sim si m REACH Reach amp si m paramet er PARAMETER Aggregrate and calculate means by year and month 0bserved aggdata lt suppressWarnings aggregate ts obs data by lis
63. lsborough ambient conc OTB County ambient conc OTB REACH 227 lt Hillsborough ambient conc OTB County ambient conc OTB REACH 229 lt Hillsborough Sort by county ambient conc _county lt data frame ambient conc OTB order ambient conc OTB County head ambient conc county REACH name date tn tkn NOX NH3 tp ORTHOP tss BOD 416 68 Double Branch 24JULO1 1 850 1 80 0 05 0 13 0 32 0 21 NA 1 86 417 68 Double Branch 18SEP01 1 260 1 22 0 04 0 04 0 18 0 10 NA 1 73 418 68 Double Branch 23 UL02 1 365 1 31 0 06 0 04 0 14 0 08 NA 2 00 419 68 Double Branch 20AUG02 1 191 1 10 0 09 0 06 0 16 0 07 NA 1 00 420 68 Double Branch 17SEP02 1 305 1 20 0 11 0 08 0 10 0 08 NA 1 00 421 68 Double Branch 10DEC02 1 102 1 02 0 08 0 10 0 14 0 08 NA 3 00 loc County 416 Hillsborough Hillsborough 417 Hillsborough Hillsborough 418 Hillsborough Hillsborough 419 Hillsborough Hillsborough 420 Hillsborough Hillsborough 421 Hillsborough Hillsborough change 0 to na ambient conc county ambient conc county 0 lt NA Subset data into seperate parameter data sets NAS are still present obs TKN na lt data frame cbind ambient conc county tkn ambient conc county County obs NH3 na lt data frame cbind ambient conc county NH3 ambient conc county County obs NOX na lt data frame cbind ambient conc county NOX ambient conc county County obs TN na lt data frame cbind ambient conc county tn ambient conc county County obs ORTHOP na lt
64. name cdf data name both lt rbind obs sim head both REACH parameter dv method label name 12 60 TN 1 000 observed Total Nitrogen mg L Bishop Mullet file CIUsers johnf Downloads Appendix 20C 20cdfs htm l 12 1 2013 7 22 32 PM Appendix C cdfs R 24 6 0 TN 0 790 observed Total Nitrogen mg L Bishop Mullet 97 60 TN 0 800 observed Total Nitrogen mg L Bishop Mull et 115 60 TN 1 117 observed Total Nitrogen mg L Bishop Mullet 1 13 60 TN 1 515 observed Total Nitrogen mg L Bishop Mullet 243 60 TN 4 230 observed Total Nitrogen mg L Bishop Mullet tail both REACH parameter dv met hod label 3621 60 TN 1 3198 simulated Modeled Total Nitrogen mg L 3622 6 0 TN 0 5142 simulated Modeled Total Nitrogen mg L 3623 60 TN 0 8237 simulated Modeled Total Nitrogen mg L 3639 60 TN 1 5882 simulated Modeled Total Nitrogen mg L 3646 60 TN 1 3110 simulated Modeled Total Nitrogen mg L 3653 60 TN 1 1502 simulated Modeled Total Nitrogen mg L name 3621 Bishop Mullet 3622 Bishop Mullet 3623 Bishop Mullet 3639 Bishop Mullet 3646 Bishop Mullet 3653 Bishop Mullet librari es library scales plots percentages Or ary gdp ot 2 plot cdf values for both observed and stimulated using stat ecdf pl lt ggplot both aes dv linetype method stat ecdf n 100 coord flip pl file CIUsers johnf Downloads Appendix 20C 20cdfs html 12 1 2013 7 22 32 PM Appendix C cdfs R observed simulated I 0 00
65. on_YearMonthDayTime 2 Createanewaccess database 3 Make backup copies of ReachHistory csv and ReachintegrationHistory csv 4 Import ReachHistory csv and ReachintegrationHistory csv into new access tables External Data ay ey Access Home Create Saved LinkedTable Excel Imports Database Import amp Link 5 In the Import Text Wizard select First Row Contains Field Names and No primary key then click Finish E Import Text Wizard What delimiter separates your fields Select the appropriate delimiter and see how your textis affected in the preview below Choose the delimiter that separates your fields Tab 01 01 2000 01 01 2000 01 01 2000 1 01 2000 4 01 01 2000 01 01 2000 Je 01 01 2000 01 01 2000 01 01 2000 1 01 2000 01 01 2000 01 01 2000 01 01 2000 01 01 2000 Semicolon Advanced Comma Other Text Qualifier none 99488831000000E 000 674998 76000000E 000 7T 81543875000000E 000 81448603000000E 000 1 18547764000000E 000 0605219B000000E4 001 53732967000000E 000 57300797000000E 000 02565527000000E 000 32288074000000E 000 89772949000000E 001 6 05295467000000E 000 i 72296143000000E 000 1 24012327000000E 000 25267148000000E 004 34649834000000E 004 p 79475122000000E 003 48061859000000E 002 7 6255652Z50000000E 003 24162622000000E 003 02676895000000E 004 1 67079443000000E 003
66. pe Observed data newdata size 3 colour black Se pz Warning Removed 6 rows containing missing values geom path Warning Removed 10 rows containing missing values geom point file Cl Users johnf Downloads A ppendix 20D 20ts 20 4 html 12 2 2013 11 05 22 AM Appendix D ts R HU Observed Observed 2 dv Simulated Simulated 10 pr ta i n rr er mjin PR d Fil DO 2 U Pat il F wil J I Ul dec year specifiy the theme for the plot this theme removes the default gray background and adds axes lines ts p3 lt ts p2 theme legend title element blank theme legend justification c 1 1 legend position c 1 1 theme panel border element rect colour black fill NA theme axis text element Text coloun black size 12 theme panel background element rect fill NA colour black theme legend key element rect fill NA 3 Warning Removed 6 rows containing missing values geom path Warning Removed 10 rows containing missing values geom point file CI Users johnf Downloads Appendix 20D 20ts 20 4 html 12 2 2013 11 05 22 AM Appendix D ts R Observed Simulated 2000 2002 2005 2008 2010 dec year add the x and y labels ts p4 lt ts p3 scale x_continuous breaks c 2000 2001 2002 2003 2004 QI QI Lon ah a ts p4 Warning Removed 6 rows containing missing values geom path Warning Removed 10 rows con
67. pl lt ggplot both aes dv linetype method stat ecdf n 100 coord flip pl file Cl Users johnf Downloads A ppendix 20C 20cdfs html 12 1 2013 7 22 32 PM Appendix C cdfs R 1 0 observed simulated 0 5 r mjo m rm OE mo 4 SI D Do iu si F F 50 Ui F K specifiy the theme for the plot this theme removes the default gray background and adds axes lines p2 lt pl theme legend title element bl ank theme legena justification c 1 1 legend position c 1 1 theme panel border element rect colour black fill NA LNemel axl Ss text element text colour black size 12 theme panel background element rect fill colour theme legend key element rect fill NA NA bk p2 file Cl Users johnf Downloads Appendix 20C 20cdfs htm1 12 1 2013 7 22 32 PM Appendix C cdfs R observed simulated 0 00 0 25 0 50 0 75 1 00 add the x and y labels p3 lt p2 scale y continuous labels percent imts c 0 00001 1 ylab Percentile xlab both l abel 1 p3 Warning Removed 2 rows containing missing values geom path Warning Removed 2 rows containing missing values geom path file Cl Users johnt Downloads A ppendix 20C 20cdfts html 12 1 2013 7 22 32 PM Appendix C cdfs R observed simulated Total Phosphorus mali 0 29 50 75 100 Percentile add title p4 lt p3 ggtitle paste OTB Waterhed Water Qu
68. re Is a missing value obs lt na omit data frame REACH Reach parameter PARAMETER dv cdf data observed method observed label cdf data X LABEL name cdf data name Sim lt na omit data frame REACH Reach parameter PARAMETER dv cdf data si mul ated method si mulated label cdf data X LABEL name cdf data name both lt rbind obs sim head both REACH parameter dv method label name 12 60 TP 0 240 observed Total Phosphorus mg L Bishop Mullet 24 60 TP 0 070 observed Total Phosphorus mg L Bishop Mullet 97 60 TP 0 250 observed Total Phosphorus mg L Bishop Mullet 1 13 60 TP 0 200 observed Total Phosphorus mg L Bishop Mullet 173 60 TP 0 295 observed Total Phosphorus mg L Bishop Mullet 243 60 TP 1 310 observed Total Phosphorus mg L Bishop Mull et tail both REACH parameter dv met hod label 3621 60 TP 0 1866 simulated Modeled Total Phosphorus mg L 3622 60 TP 0 0829 simulated Modeled Total Phosphorus mg L 3623 60 TP 0 1309 simulated Modeled Total Phosphorus mg L 3639 60 TP 0 2340 simulated Modeled Total Phosphorus mg L 3646 60 TP 0 2148 simulated Modeled Total Phosphorus mg L 3653 60 TP 0 1824 simulated Modeled Total Phosphorus mg L name 3621 Bishop Mullet 3622 Bishop Mullet 3623 Bishop Mullet 3639 Bishop Mullet 3646 Bishop Mullet 3653 Bishop Mullet 1 1 braries library scales plots percentages library ggpl ot2 plot cdf values for both observed and stimulated using stat ecdf
69. rom the list of possible simulation scenarios File Help CWUP_ Environmental_70 Consolidated WF scenario for water body impact assessment pumping at historical 1989 1990 then at CWUP_Off_Environmental Consolidated WF pumping off after 1990 1 day integration 1989 through 2006 2 day archiving for Modflo CWUP_Off WellMitigation Consolidated WF pumping off after 1990 1 day integration 1989 through May 2001 1 day archiving for M CWUP _Other UPsAt50PercPumping Consolidated WF scenario for other nearby WUPS at 50 pumping pumping at historical 1989 1990 the CWUP_WellMitigation_00Prescribed_200 Consolidated WF scenario for well mitigation pumping at historical 1989 1990 then at 0 mgd 1991 2 2 CWUP WellMitigation 90 90 Prescribed Consolidated WF scenario for well mitigation pumping at historical 1989 1990 then at 90 prescribed 1 CWUP WellMitigation 90Prescribed _ 200 Consolidated WF scenario for well mitigation pumping at historical 1989 1990 then at 90 prescribed 1 HotStartCheck Confirm hot start heads match source run heads 1 week simulation PEST_Run 12 year run for PEST PEST_ RunTest 1 week test run for PEST Short run to test pre processing Reaches Only INTB Calibration 1 day integration INTB Verification 1 day integration 2000 to 2009 INTB Verification 1 day integration 2000 only Cenisia INTE Verification 1 day integration 2000 and 2001 only Verification INTB Verification 1 day integra
70. rosoft ADO Ext 2 8 for DDL and Securi Pal Grapher 10 Type Librari 32 bit Aec32BitAppServer Library 32 bit AecJetDbServer Library _ 32 bit VBA server type library _ 3Dconnexion TDxInput 1 0 Type Library Ac32BitAppServer 1 0 Out of process server for 32 AcAuthEntities 17ENU tb 1 0 Type Library _ AcAuthEntitiesComLib ArcessihilitvCnlAdmin 1 0 Tyne ihrary dI nin TI Grapher 10 Type Library Location C Program Files Golden Software Grapher 10 grapher tb Language Standard 5 Batch File a Navigate to the installation file set up folder and open the bat file in a text editor ie Notebook Search ReVerifi File Edit View Tools Help Organize v Include in library v Share with v Burn New folder F r Name Date modified Type Size HI Desktop 11 24 2013 2 38 PM File folder Downloads T Recent Places 11 24 2013 2 38 PM File folder 11 24 2013 2 38 PM File folder External G 6 20 2012 2 32PM Windows Batch File 1 KB N Internal 2TB 2 11 4 2011 5 02PM CTLFile 31 KB amp SAR Common V IHM_Code mdb 12 1 2013 9 57 AM Microsoft Access 6 404 KB INTB mdb 12 1 2013 1 29PM Microsoft Access 1 485 772 KB 404 Libraries b Setthe file 1 equal to the program file location for Microsoft Access executable file Note mdb is the file extension for earlier versions of Access accdb is the file extension for newer versions of Access Use mbd for this model Note Microsof
71. s box File Tools sms Locations Constituents Time Series Help Scenarios D of 6 lt UNHE gt HILLS OBSERYED PERIPH SCRIPTRE SOUTHCB Time Series 2730 of 2730 available time series in list D not on WDH file Type WD WD File tam ret rain te ram ret tam ref tam ret ram tet WDM WE WD WD DM WD WD DM Di WD WM WD tam ret tam ret rain ret tam ret rain Tel rain ret rain ret rain ret rain ret rain ret rain ret rain ret rain ret rain ret rain ret Dates Reset Start Fairy tet DSH SOUTHEB SOUTHEB SOUTHEB mA SOUTHCE 13360 5000 5001 5002 5003 5004 5005 5006 5007 5008 5009 H End Current fessi E Common 1599 1 SEL RS Note In the constituent column are numbers ranging from 1 through 8 each corresponds to a SOUTHCE SOUTHCB SOUTHCB SUUTHEB SOUTHCE PSU THE HILLS HILLS HILLS HILLS HILLS HILLS HILLS HILLS HILLS HILLS to 2009 12 31 to 2009 12 31 Native Locations D of 304 K a JENE SQUTHCE Constituent Location 142 142 142 142 2a a Cata I a CT LT en pe beer ra ET ROCONI ROCON2 ROCONS ROCON4 ROCONS ROCONE ROCON ROCONS ROCONI ROCONZ TStep Units Start 19991 199971 1999 11 19897171 KE 19931 1999 11 1999 1 1 199971 1 1999 11 1999 11 1999 11 1999 1 1 1999 71 1 1999 11 modeled water quality variable as shown in the table below
72. st close the file rome Ris C3 _csPostProcessingContext e Command Line no Rata e Head Reader Plugin a iii e Model Upload ere e HotStart Builder e Output Summary e Water Balance 3 Default Debugging a Inthe ReVerification run folder open Bin Post Processing Plugins Standard Post Processing OutputSummary mdb w pnt G gt di Computer OSIS INTB ReVerification Bin Post Processing Plugins Standard Post Processing File Edit View Tools Help Organize Al Open Burn Mew folder B Desktop Mane Date modified Type T Dalar A ioni IDEE NR SELE O E EI SSR aR EPI ConnectionManager dill 6 19 2012 2 46 AM Application exte ecent Places External G L ConnectionManager pdb 6 19 2012 946 AM PDB File ernal G am K bi LITE Z ConnectionManager xml 6 19 2012 9 40 AM AML Document nternal 27 Ga SARC an _ Hotstart Builder plugin 6 5 2012 3 41 PM PLUGIN File ommon Bl HotstartBuilder exe 6 19 2012 9 46 AM Application a Ba tame Li HotstartBuilder exe config 6 19 2012 9 45 AM CONFIG Fite gt HotstartBuilder pdb 6 19 2012 9 46 AM PDB File b Documents F kra i d vini HotstartBuilder xml 6 19 2012 9 46 AM AML Document gt usic Ej IHMOutput_H mdb 4 25 2013 3 38 PM Microsoft Acces bs Pict ictures gt HE Vid IHMOutput M mdb 4 2 2013 3 38 PM Microsoft Acces fideos 3 Output Summary Database plugin 6 6 2012 11 04 AM PLUGIN File E OutputSummary
73. t summaryBy In County data NOX FUN c mean na rm TRUE keep names TRUE In TN mean lt summaryBy In County data TN FUN c mean na rm TRUE keep names TRUE In ORTHOP mean lt summaryBy n County data ORTHOP FUN c mean na rm TRUE keep names TRUE In TP_mean lt summaryBy In County data TP FUN c mean na rm TRUE keep names TRUE In TSS mean lt summaryBy In County data TSS FUN c mean na rm TRUE keep names TRUE In BOD mean lt summaryBy In County data BOD FUN c mean na rm TRUE keep names TRUE Merge the mean values into one data set using the function cbind mod2 lt chind TKN mean NH3 mean 2 NOX mean 2 IN meani 21 ORTHOP mean 2 e tele Ak TSS_mean 2 BOD mean 2 In TKN mean 2 In NH3 mean 2 In NOX mean 2 In TN mean 2 LO ORTHOP T meani 2I In TP mean di In TSS mean 2 ln BOD tee yy Add column names colnames mod2 lt c County SNA ana NIS mess NOX mean SW tee OR TOR mean WP nee Arsen a BOD mean In TKN mean Sie NE meani ln NOX mean kn TN mean In ORTHOP mean In TP mean SPa TSS meann In BOD mean head mod2 County TKN mean NH3 mean NOX mean TN mean ORTHOP mean TP mean 1 Hillsborough 4349 167 8 1714 4987 814 1 1410 2 Pinellas 4711 112 8 1510 5299 934 5 1385 TSS mean BOD mean In TKN mean In NH3 mean In NOX mean In TN mean 1 1779 6288 0 3986 2 688 1 88 0 1797 2 8629 1687 0 3626 2 820 2 05 0 159
74. t Office Suite must be 32 bit not 64 bit Edit Se Mew Help I A CA AAA S A AAA A a a AAA Run standard preprocessing Re Tee Tr Ser Serer eer reer ee er errr er ere er er er er rrr err filel filel file2 fx RunstandardPreProcessing REM RRRR RRR RRR RRR RR ERR RRR RRR RR RRR ee REM Compact the code DB to clear out storage used by temporary tables REM AUR URRY RRR RRR RRA Rr Rr AY filel Sfile2 compact REM Delete log Tiles REM i i i ee ww del modf low Modt lowMessages Log del modf lowModfstatus TXT del hspf error fi 6 Modeling Database Prior to executing the simulation for the first time Trust Security Settings need to be set a Open the INTB mdb database and click the file button in the top left corner and click Options Ali iu INTE Databas Home Create External Data Database Tools wa Save Information about INTB H Save Object As R10120_Janicki 006_O7B Integrated Modeh Design Presentations Training Workshop 4 IHM Install Save Database As E Open Pi Compact amp Repair Bi x Close Database n Help prevent and correct database file problems by using Compact and Repair zj INTE mdb Compact amp Repair Database h GutputSummarw mdb ah reach edits accdb zj IntervalErrorStateCa Manage Users amp Permissions z B Use passwords and permissions to allow or restrict the access of individuals Inf or groups of individuals to the objects in your database HIS Users
75. t ts obs datasyear ts obs datasmonth FUN mean na rm TRUE head aggdata Group 1 Group 2 REACH parameter dv method label name year month l 2000 1 63 NA 0 10833 NA NA NA 2000 1 2 2001 63 NA 0 17333 NA NA NA 2001 1 3 2002 1 63 NA 0 13250 NA NA NA 2002 1 4 2003 1 63 NA 0 08133 NA NA NA 2003 1 5 2004 l 63 NA 0 11556 NA NA NA 2004 1 6 2005 63 NA 0 11444 NA NA NA 2005 1 Si mul ated aggdata sim lt suppressWarnings aggregate ts sim data by list ts simdata year ts simdata month ts simdata parameter ts sim data name FUN mean na rm TRUE head aggdata sim Group 1 Group 2 Group 3 Group 4 REACH parameter l 2000 1 TP Alligator Allens Long Branch 6 3 NA 2 2001 TP Alligator Allens Long Branch 6 3 NA 3 2002 l TP Alligator Allens Long Branch 63 NA 4 2003 1 TP Alligator Allens Long Branch 6 3 NA 5 2004 1 TP Alligator Allens Long Branch 6 3 NA 6 2005 1 TP Alligator Allens Long Branch 6 3 NA dv method ts name year month 1 NaN NA NA NA 2000 1 2 NaN NA NA NA 2001 1 3 0 1504 NA NA NA 2002 l 4 0 1256 NA NA NA 2003 l 5 0 1874 NA NA NA 2004 1 6 0 1697 NA NA NA 2005 1 Change year to decimal year for plotting Observed aggdata dec year lt aggdata year aggdata month 12 1 12 head aggdata Group 1 Group 2 REACH parameter dv method label name year month 1 2000 1 63 NA 0 10833 NA NA NA 2000 1 2 2001 1 63 NA 0 17333 NA NA NA 2001 1 3 2002 1 63 NA 0 13250 NA NA NA 2002 1 4 2003 1 63 NA 0 08133 NA NA NA 2003 1 5 2004
76. taining missing values geom point file Cl Users johnf Downloads A ppendix 20D 20ts 20 4 html 12 2 2013 11 05 22 AM Appendix D ts R Observed Simulated 2000 2001 2002 2003 20040 2005 2006 2007 2008 2009 2010 Year add title ts p5 lt ts p4 ggtitle paste OTB Waterhed Water Quality n ts simdata name 1 Reach Reach sep See Warning Removed 6 rows containing missing values geom path Warning Removed 10 rows containing missing values geom point file Cl Users johnf Downloads A ppendix 20D 20ts 20 4 html 12 2 2013 11 05 22 AM Appendix D ts R OTB Waterhed Water Quality Allidator Allens Long Branch Reach 63 Observed Simulated 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 Year clean up legend ts po lt ts p5 scale colour manual values c dodgerblue4 scale shape manual values 1 ts p Warning Removed 6 rows containing missing values geom path Warning Removed 10 rows containing missing values geom point file Cl Users johnf Downloads A ppendix 20D 20ts 20 4 html 12 2 2013 11 05 22 AM Appendix D ts R OTB Waterhed Water Quality Allidator Allens Long Branch Reach 63 O Observed Simulated 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 Year save and export plot plot filename lt paste0 C Users john Documents old tampa bay water optimal model bf 5 Appendix D timeseries predicted amp obs
77. ter 1 60 O01 AN2000 Modeled Biological Oxygen Demand 5 mg L BOD 2 60 O01 AN2000 Modeled Ammonia mg L NH3 3 60 01 AN2000 Modeled Nitrate Nitrite mg L NOX 4 60 01 AN2000 Modeled Ortho Phosphorus mg L ORTHOP 5 60 01 AN2000 Modeled Total Kjeldahl Nitrogen mg L TKN 6 60 O01 AN2000 Modeled Total Nitrogen mg L TN simulated observed OP ABSOP OP2 year month season l NA NA NA NA NA 2000 1 Dry Nov May 2 NA NA NA NA NA 2000 1 Dry Nov May 3 NA NA NA NA NA 2000 1 Dry Nov May 4 NA NA NA NA NA 2000 1 Dry Nov May 5 NA NA NA NA NA 2000 1 Dry Nov May 6 NA NA NA NA NA 2000 1 Dry Nov May di m sim obs 1 467584 12 FS ser dala remove An BO ANIN TN Eno Tey En Tos all lt subset sim obs sim obs paramet er BOD sim obs parameter NH3 sim obs parameter NOX sim obs parameter ORTHOP sim obs parameter TKN sim obs parameter TN sim obs parameter TP sim obs parameter TSS head all REACH date X LABEL parameter 1 60 01 AN2000 Modeled Biological Oxygen Demand 5 mg L BOD 2 60 O01 AN2000 Modeled Ammonia mg L NH3 3 60 01 AN2000 Modeled Nitrate Nitrite mg L NOX 4 60 01 AN2000 Modeled Ortho Phosphorus mg L ORTHOP 5 60 01 AN2000 Modeled Total Kjeldahl Nitrogen mg L TKN 6 60 O01 AN2000 Modeled Total Nitrogen mg L TN simul ated observed OP ABSOP OP2 year month season NA NA NA NA NA 2000 1 Dry Nov May 2 NA NA NA NA NA 2000 1 Dry Nov May 3 NA NA NA NA NA 200
78. tion 1999 to 2009 VerificationPlus NTB Verification Plus three antecedent years 1 day integration 1996to2006 Simulation Control HSPF Control Modflow Control Output Control Post Sri Name ReVerification INTB Verification 1 day integration 2000 to 2009 io 1 1 2000 End Date 2317209 v Integration Time Step days 1 Preprocessing Batch File O INTB ReVerification _INTB_PreProcessing bat Timestamp Simulation Directory I Run Reaches Only 2 On the bottom half of the interface click on the Simulation Control Tab and browse to the preprocessing batch file shown above C OUTPUT CONTROL SETTINGS 1 On the bottom half of the interface click on the Output Control Tab and set the Sequence to None for the first simulation Name Description CWUP Environmental 70 Consolidated WF scenario for water body impact assessment pumping at historical 1989 1990 then at CWwUP Off Environmental Consolidated WF pumping off after 1990 1 day integration 1989 through 2006 2 day archiving for Modflo CWUP Off WellMitigation Consolidated WF pumping off after 1990 1 day integration 1989 through May 2001 1 day archiving for M CWUP_OtherWUPsAt50PercPumping Consolidated WF scenario for other nearby WUPS at 50 pumping pumping at historical 1989 1990 the CWUP WellMitigation 00Prescribed 200 Consolidated WF scenario for well mitigation pumping at historical 1989 1990 then at
79. ty NOX MOD model conc county County TN na lt data frame cbind model conc county TN MOD model conc county County ORTHOP na lt data frame cbind model conc county ORTHOP MOD model conc county County TP na lt data frame cbind model conc county TP MOD model conc county County TSS na lt data frame cbind model conc county TSS MOD model conc county County BOD na lt data frame cbind model conc county BOD MOD model conc county County head TKN na X1 X2 1 lt NA gt Hillsborough 2 lt NA gt Hillsborough 3 3 0536 Hillsborough 4 1 1275 Hillsborough 5 1 9214 Hillsborough 6 lt NA gt Hillsborough di m TKN na 1 29224 2 Remove NAs from all the data sets TKN lt na omit TKN na NH3 lt na omit NH3 na NOX lt na omit NOX na TN lt na omit TN na ORTHOP lt na omit ORTHOP na TPx na omit TP na TSS lt na om t TSS na BOD lt na omit BOD na head TKN X1 X2 3 3 0536 Hillsborough 4 1 1275 Hillsborough 5 1 9214 Hillsborough 8 1 7354 Hillsborough 9 1 0638 Hillsborough 10 1 5501 Hillsborough di m TKN 1 18218 2 Calculate the natural log as a new column in each dataset Have to include as character to ensure that R recognizes the value as a number and not as a leve os TKN In TKN MOD x log as numeric as character TKNI 1 NH3 In NH3 MOD lt log as numeric as character NH3 1 file Cl Users johnf Downloads Table 203 1 html 12 1 2013 7 25 11
80. y key 01 01 2000 91 01 2000 01 01 2000 1 01 2000 01 01 2000 01 01 2000 01 01 2000 01 01 2000 61 01 2000 1 01 2000 01 01 2000 01 01 2000 01 01 2000 01 01 2000 99488831000000E 000 57499876000000E 000 81543875000000E 000 81448603000000E 000 7B547764000000E 000 06052198000000E 001 53732967000000E 000 14573007 97000000E 000 025655527000000E 000 32288074000000E 000 B9772949000000E 001 05295467000000E 000 12256143000000E 000 24012732 7000000E G00 569427031 000000F 004 25267148 000000E 004 346498 34000000E 004 79475122000000E 003 48061859000000E 002 625565250000000E 003 2411626522000000E 003 026768 95000000E 004 4 67079443000000E 003 38516144000000E 002 70400572000000E 000 31876953000000E 002 31615266000000E 000 33915772000000E 000 99488831000000E 000 67499876000000E 000 B1543875000000E 000 651448603000000E 000 78547 764000000E 000 06052198000000E 001 5373296 7000000E 000 i 07300797000000E 000 02565527000000E 000 32288074000000E 000 8977T2949000000E 001 05295467000000E 000 72296143000000E 000 2401232 7000000E 000 l 2 11 Create anew guery in Access 12 Open the query in SQL view and paste the following statement and save SELECT ReachintegrationHistory FROM ReachintegrationHistory WHERE ReachintegrationHistory ReachID lt 473 ORDER BY ReachintegrationHistory Date ReachIntegrationHistory ReachlD 13 Right

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