inst/helperCode/Big_Looper2.0.r
In tmcd82070/CAMP_RST: CAMP RST R Routines
# # ---- Update packages. This is rarely done. Usually immediately before a new release.
# pkgs <- dir(.libPaths("//LAR-FILE-SRV/Data/PSMFC_CampRST/ThePlatform/CAMP_RST20170115-campR1.1.0/R/library"))
# notThese <- dir("C:/Program Files/R/R-3.5.0/library")
# pkgs <- pkgs[!(pkgs %in% c(notThese,c("campR","EnvCovDBpostgres")))]
#
# install.packages(pkgs,"C:/ThePlatform/CAMP_RST20180415-campR2.0/R/library")
# ---- Set variables necessary for Big Looper completion.
RVersion <- "3.5.0"
TestingPlatform <- "CAMP_RST20181023-campR2.0.10" # What the CAMP people will use; i.e., the static R in the Platform. Use this most of the time.
excelName <- "theExcel"
# excelName <- "theExcel2"
# ---- Set the reports you want to run. Use the key below.
# reportRun <- c("A","B","C","D","E","F","G","H","I","J","K","L","M","N","O","P","Q","R","S","T","U","V","W","X","Y","Z")
# reportRun <- c("A","B","C","D","E","F","G","H","I","J","K","L","M","N","O","P")
reportRun <- c("A","B","C","R","S","T")
reportRun <- c("G","R","S","T")
# reportRun <- c("K","L","M","N","O","P")
# reportRun <- c("B","R")
# reportRun <- c("Q")
# reportRun <- c("R","S")
# ---- Assign the version of R to use. A real check uses the version of R CAMP people use.
#.libPaths(paste0("C:/Users/jmitchell/Documents/R/win-library/",RVersion))
.libPaths(paste0("//lar-file-srv/Data/PSMFC_CampRST/ThePlatform/",TestingPlatform,"/R/library"))[1]
# ---- Get necessary packages in order.
# install.packages(c("RODBC","mvtnorm"))
# require("RODBC",lib.loc=paste0("C:/Users/jmitchell/Documents/R/win-library/",RVersion))
# require("mvtnorm",lib.loc=paste0("C:/Users/jmitchell/Documents/R/win-library/",RVersion))
# require("splines",lib.loc=paste0("C:/Users/jmitchell/Documents/R/win-library/",RVersion))
unloadNamespace("campR")
unloadNamespace("RODBC")
detach("package:RPostgres",unload=TRUE)
detach("package:campR", unload=TRUE)
require(campR)
# # ---- Read in updated functions, if updated before updating of package.
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/run_passage.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/tableDeleter.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/passageWithLifeStageAssign.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/F.lifestage.passage.forkLength.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/makeFake_release.df.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/est_passage.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/est_efficiency.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/eff_model.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/bootstrap_passage.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/getTogetherCovarData.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/estCovar.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/reMap.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/reMap2.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/checkValidCovars.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/plot_passage.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/release_summary.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/catch_model.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/plot_catch_model.R")
# ---- Read in the desired Excel scheme. This is kept in the helperCode folder of the inst folder
# ---- in the campR package development folder in CAMP_RST20160601.
theExcel <- read.csv(paste0("//lar-file-srv/Data/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/inst/helperCode/",excelName,".csv"))
rownames(theExcel) <- NULL
# theExcel <- theExcel[!is.na(theExcel$siteID),]
# theExcel <- theExcel[!(theExcel$streamName == "Sacramento River" & theExcel$Season %in% c(2014,2015)),] # Exclude out years that seemingly have no releases.
# ---- Modify theExcel further here, if desired. Otherwise, delete or comment out.
# theExcel <- theExcel[c(1,5,13,15,24,26,32,52,73),] # For Enh Eff development (no RBDD)
# theExcel <- theExcel[c(1,5,13,15,24,26,32,36,52,73),] # For Enh Eff development (yes RBDD)
# theExcel <- theExcel[c(23),] # For Enh Eff development (only RBDD)
# theExcel <- theExcel[theExcel$streamName == "American River",] # American
# theExcel <- theExcel[theExcel$streamName == "Feather River",] # Feather
# theExcel <- theExcel[theExcel$streamName == "Stanislaus River",] # Stanislaus
# theExcel <- theExcel[theExcel$streamName == "Sacramento River",] # Sacramento
# theExcel <- theExcel[!(theExcel$streamName == "Sacramento River"),] # All but Sacramento
# theExcel <- theExcel[theExcel$siteID == 5000,] # Herringer Riffle
# theExcel <- theExcel[theExcel$siteID == 52000 & !is.na(theExcel$siteID),] # Gateway Riffle
# ---- Monthly testing runs for enhanced efficiency.
# theExcel <- theExcel[theExcel$siteID == 5000 & !is.na(theExcel$siteID),] # Herringer Riffle + Excel2.csv
# theExcel <- theExcel[theExcel$siteID == 42000 & !is.na(theExcel$siteID),] # Herringer Riffle + Excel2.csv
theExcel <- theExcel[83,]
theExcel$Season <- 2007
theExcel$minvisitTime <- "1/1/2007"
theExcel$maxvisitTime <- "7/1/2007"
# ---- Tell the Big Looper where to put all the output.
theStem <- paste0("\\\\lar-file-srv/Data/PSMFC_CampRST/ThePlatform/",TestingPlatform)
outStem <- paste0(theStem,"/Outputs")
# ---- Identify the possible reports we can run, and folder stems we can create.
# ---- This section should not be ameliorated.
nn <- c("label","folder","report","function")
a <- c("A" ,"EstProdAllRunsLSReport" ,"ls.run.passage" ,"passageWithLifeStageAssign")
b <- c("B" ,"EstProdAllRunsReport" ,"run.passage" ,"F.run.passage")
c <- c("C" ,"PassageEst_FL_Fall" ,"lifestage.passage.forkLength" ,"F.lifestage.passage.forkLength")
d <- c("D" ,"AllCatchTable" ,"all.catch" ,"F.allCatch.table")
e <- c("E" ,"ByCatchTable" ,"by.catch" ,"F.byCatch.table")
f <- c("F" ,"ChinookByDate" ,"chinook.by.date" ,"F.chinookByDate.table")
g <- c("G" ,"ReleaseSummary" ,"release.summary" ,"F.release.summary")
h <- c("H" ,"SizeByDate" ,"size.by.date" ,"F.size.by.date")
i <- c("I" ,"LengthFreq" ,"length.freq" ,"F.length.frequency")
j <- c("J" ,"WeeklyEffortReport" ,"weekly.effort" ,"F.weekly.effort")
k <- c("K" ,"AutoLS_2Group_YesWgt" ,"auto.ls.2grp_yWgt" ,"F.lifestage.passage.assignLS2group")
l <- c("L" ,"AutoLS_2Group_NoWgt" ,"auto.ls.2grp_nWgt" ,"F.lifestage.passage.assignLS2groupNoWeight")
m <- c("M" ,"AutoLS_3Group_YesWgt" ,"auto.ls.3grp_yWgt" ,"F.lifestage.passage.assignLS3group")
n <- c("N" ,"AutoLS_3Group_NoWgt" ,"auto.ls.3grp_nWgt" ,"F.lifestage.passage.assignLS3groupNoWeight")
o <- c("O" ,"AutoLS_2or3_AutoWgt" ,"auto.ls.2or3grp_autoWgt" ,"F.lifestage.passage.assignLS")
p <- c("P" ,"AutoLS_2or3_NoWgt" ,"auto.ls.2or3grp_nWgt" ,"F.lifestage.passage.assignLSNoWeight")
q <- c("Q" ,"Enhanced_Eff_Get_Betas" ,"run.passage.enh" ,"F.run.passage.enh")
r <- c("R" ,"EstProdAllRunsReportENH" ,"run.passage.enheffT" ,"F.run.passage")
s <- c("S" ,"EstProdAllRunsLSReportENH" ,"ls.run.passage.enheffT" ,"passageWithLifeStageAssign")
t <- c("T" ,"PassageEst_FL_FallENH" ,"lifestage.passage.forkLength.enheffT","F.lifestage.passage.forkLength")
u <- c("U" ,"AutoLS_2Group_YesWgtENH" ,"auto.ls.2grp_yWgt.enheffT" ,"F.lifestage.passage.assignLS2group")
v <- c("V" ,"AutoLS_2Group_NoWgtENH" ,"auto.ls.2grp_nWgt.enheffT" ,"F.lifestage.passage.assignLS2groupNoWeight")
w <- c("W" ,"AutoLS_3Group_YesWgtENH" ,"auto.ls.3grp_yWgt.enheffT" ,"F.lifestage.passage.assignLS3group")
x <- c("X" ,"AutoLS_3Group_NoWgtENH" ,"auto.ls.3grp_nWgt.enheffT" ,"F.lifestage.passage.assignLS3groupNoWeight")
y <- c("Y" ,"AutoLS_2or3_AutoWgtENH" ,"auto.ls.2or3grp_autoWgt.enheffT" ,"F.lifestage.passage.assignLS")
z <- c("Z" ,"AutoLS_2or3_NoWgtENH" ,"auto.ls.2or3grp_nWgt.enheffT" ,"F.lifestage.passage.assignLSNoWeight")
aa <- c("AA","AnnualizeCovars" ,"annualize.covars" ,"annualizeCovars")
# ---- Clean up our requested report list for use in making folders.
masterReports <- as.data.frame(rbind(a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z,aa),stringsAsFactors=FALSE)
names(masterReports) <- nn
rownames(masterReports) <- NULL
masterReports <- masterReports[masterReports$label %in% reportRun,]
# ---- Build up the request folder structure.
streamNames <- unique(paste0(theExcel$streamName,"--",theExcel$Site))
nStreamNames <- length(streamNames)
reportLabels <- masterReports$label
reportFolders <- masterReports$folder
reportTitles <- masterReports$report
nReports <- length(reportFolders)
# ---- Helper function to make directories, if they don't already exist.
makeTheDir <- function(theDir){
ifelse(!dir.exists(file.path(theDir)), dir.create(file.path(theDir),showWarnings=TRUE,recursive=TRUE), FALSE)
theDir <- NULL
}
# ---- Set all the global variables away from the default that you want.
# db.file <<- "..\\Data\\CAMP.mdb"
# output.dir <<- "..\\outputs"
# sql.code.dir <<- file.path(find.package("campR"),"sql")
# samplePeriodCutTime <<- "04:00:00"
# max.ok.gap <<- 2
# fishingGapMinutes <<- 10080
# knotMesh <<- 15
# halfConeMulti <<- 2
# sample.size.forkLength <<- 100
# sample.size.forkLengthAndWeight <<- 100
# weight.prop.forkLength <<- 0.5
# forkLength.mean.diff <<- 10
# time.zone <<- "America/Los_Angeles"
# Yes.code <<- 1
# No.code <<- 2
# seed <<- 884
# forkLengthCutPoints <<- data.frame(lifeStage=c("FL1 leq 41mm","FL2 42-72mm","FL3 73-110mm","FL4 geq 111mm"),cutPoints=c(41,72,110,9999))
# passageRounder <<- 4
# eff.min.spline.samp.size <<- 10
# unassd.sig.digit <<- 1
#i <- j <- k <- 1
# ---- If we are building annualized covariates for enhnaced efficiency, we need this.
if( "AA" %in% reportRun ){
annual_records <- NULL
}
# ---- Given the 'theExcel', loop over the streams.
for(i in 1:nStreamNames){
# ---- Reduce the master 'theExcel' to one stream.
theStreamName <- strsplit(streamNames[i],"--",fixed=TRUE)[[1]][1] #as.character(droplevels(streamNames[i]))
theSiteName <- strsplit(streamNames[i],"--",fixed=TRUE)[[1]][2]
the1stExcel <- theExcel[theExcel$streamName == theStreamName & theExcel$Site == theSiteName,]
seasons <- unique(the1stExcel$Season)
nSeasons <- length(seasons)
# ---- Make individual folder for the stream.
makeTheDir(paste0(outStem,"/",theStreamName,"--",theSiteName))
# ---- Given the stream, loop over the seasons.
for(j in 1:nSeasons){
# ---- Reduce the stream-based 'theExcel' to one record (Season).
theSeason <- seasons[j]
the2ndExcel <- the1stExcel[the1stExcel$Season == theSeason,]
# ---- Given we are going to compile reports for this Season,
# ---- create a folder structure to house the results.
# ---- Make individual folder for a Season.
makeTheDir(paste0(outStem,"/",paste0(theStreamName,"--",theSiteName),"/",theSeason))
# ---- Given the Season, loop over the desired reports.
for(k in 1:nReports){
theReportLabel <- reportLabels[k]
theReportFolder <- reportFolders[k]
theReportTitle <- reportTitles[k]
# ---- Make individual folder for a report
makeTheDir(paste0(outStem,"/",paste0(theStreamName,"--",theSiteName),"/",theSeason,"/",theReportFolder))
# ---- At this point, we're ready to create reports for this row in 'theExcel.'
taxon <- 161980 # taxon <- 161989 # steelhead / rainbow trout
ci <- TRUE
site <- the2ndExcel$siteID
siteText <- as.character(droplevels(the2ndExcel$Site))
min.date <- as.character(as.Date(the2ndExcel$minvisitTime,format="%m/%d/%Y"))
max.date <- as.character(as.Date(the2ndExcel$maxvisitTime,format="%m/%d/%Y"))
by <- "All"
outFileStem <- paste0(outStem,"/",paste0(theStreamName,"--",theSiteName),"/",theSeason,"/",theReportFolder)
outFile <- paste0(theReportTitle,"-",siteText)
outAll <- paste0(outFileStem,"/",outFile,"-")
# ---- Set up the db.file text string, so R knows where to find the database.
if(theStreamName == 'Sacramento River'){
#db.file <- "L:/PSMFC_CampRST/ThePlatform/CAMP_RST20161212-campR1.0.0/Data/TestingDBs/CAMP_RBDD_19June20151/CAMP.mdb"
db.file <- paste0(theStem,"/Data/TestingDBs/newRBDDCAMP_17July2017/CAMP.mdb")
#db.file <- "C:/Users/jmitchell/Desktop/Test/CAMP.mdb"
} else if(theStreamName == 'American River'){
db.file <- paste0(theStem,"/Data/TestingDBs/newAmericanCAMP_21July2017/CAMP.mdb")
#db.file <- "C:/Users/jmitchell/Desktop/Test/American/CAMP.mdb"
#db.file <- "L:/PSMFC_CampRST/ThePlatform/CAMP_RST20161212-campR1.0.0/Data/oldTestingDBs/CAMPAmerican2013_2015Database_23June2015/CAMP.mdb"
#db.file <- "C:/ThePlatform/CAMP_RST20180509-campR2.0/Data/CAMP.mdb"
} else if(theStreamName == 'Feather River'){
db.file <- paste0(theStem,"/Data/TestingDBs/newFeatherCAMP_15Aug2018/CAMP.mdb")
} else if(theStreamName == 'Stanislaus River'){
db.file <- paste0(theStem,"/Data/TestingDBs/newStanislausCAMP_20Sept2018/CAMP.mdb")
} else if(theStreamName == 'Mokelumne River'){
db.file <- paste0(theStem,"/Data/TestingDBs/newMokelumneCAMP_10Aug2017/CAMP.mdb")
} else if(theStreamName == "Knight's Landing"){
db.file <- paste0(theStem,"/Data/TestingDBs/CAMPKnightsTinsdaleNEW_04Feb2016/CAMP.mdb")
} else if(theStreamName == "Battle Clear"){
db.file <- paste0(theStem,"/Data/TestingDBs/newClearBattleCAMP_20July2017/CAMP.mdb")
} else if(theStreamName == "Tisdale Weir"){
db.file <- paste0(theStem,"/Data/TestingDBs/CAMPTisdale_18Sept2018/CAMP.mdb")
}
# ---- Given the appropriate text string, connect to the database.
cat(paste("DB file:", db.file, "\n"))
ch <- odbcConnectAccess(db.file)
close(ch)
# ---- Create the by lifestage and run report.
if( theReportLabel == "A" ){
by <- "All"
outAll <- paste0(outFileStem,"/",outFile,"-")
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file=outAll,ci=TRUE,autols=FALSE,nls=NULL,weightuse=NULL,enhmodel=FALSE)
}
# ---- Create the ALL runs report -- NO ENHANCED EFFICIENCY.
if( theReportLabel == "B" ){
# ---- Run function run.passage over the four possible temporal periods.
for(byj in 1:4){
if(byj == 1){by <- 'day' }
else if(byj == 2){by <- 'week' }
else if(byj == 3){by <- 'month'}
else if(byj == 4){by <- 'year' }
outAll <- paste0(outFileStem,"/",by,"-",outFile,"-")
output.file <- outAll
F.run.passage(site,taxon,min.date,max.date,by=by,output.file=outAll,ci=TRUE,enhmodel=FALSE)
# ---- If desired, remove some of the output.
#theFiles <- dir(outFileStem)
#theFiles <- theFiles[grep("Late fall|Spring|Winter|Unassigned",theFiles)]
#file.remove(paste0(outFileStem,"/",theFiles))
}
}
# ---- Create the forklength report.
if( theReportLabel == "C" ){
# ---- Run function lifestage.passage.forkLength over the four possible temporal periods.
for(byj in 1:4){
if(byj == 1){by <- 'day' }
else if(byj == 2){by <- 'week' }
else if(byj == 3){by <- 'month'}
else if(byj == 4){by <- 'year' }
outAll <- paste0(outFileStem,"/",by,"-",outFile,"-")
output.file <- outAll
F.lifestage.passage.forkLength(site, taxon, min.date, max.date,by,output.file=output.file,ci=TRUE,enhmodel=FALSE)
}
}
# ---- Create the all-catch table.
if( theReportLabel == "D" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.allCatch.table( site,min.date,max.date,output.file)
}
# ---- Create the by-catch table.
if( theReportLabel == "E" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.byCatch.table(site,min.date,max.date,output.file)
}
# ---- Create the Chinook-by-date report.
if( theReportLabel == "F" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.chinookByDate.table(site,min.date,max.date,output.file)
}
# ---- Create the release summary report.
if( theReportLabel == "G" ){
runs <- c(1,3,5,4) # Spring, Fall, Late Fall Winter
run.names <- c('Spring','Fall','Late Fall','Winter')
for(l in 1:4){
run <- runs[l]
run.name <- run.names[l]
outAll <- paste0(outFileStem,"/",outFile,".",run.name,"-")
output.file <- outAll
F.release.summary(site,taxon,run,min.date,max.date,output.file)
}
}
# ---- Create the size-by-date report.
if( theReportLabel == "H" ){
runs <- c(1,3,5,4) # Spring, Fall, Late Fall, Winter
run.names <- c('Spring','Fall','Late Fall','Winter')
for(l in 1:4){
run <- runs[l]
run.name <- run.names[l]
outAll <- paste0(outFileStem,"/",outFile,".",run.name,"-")
output.file <- outAll
F.size.by.date(site,taxon,run,min.date,max.date,output.file)
}
}
# ---- Create the length frequency report.
if( theReportLabel == "I" ){
runs <- c(1,3,5,4) # Spring, Fall, Late Fall, Winter
run.names <- c('Spring','Fall','Late Fall','Winter')
for(l in 1:4){
run <- runs[l]
run.name <- run.names[l]
outAll <- paste0(outFileStem,"/",outFile,".",run.name,"-","_ls=F")
output.file <- outAll
F.length.frequency(site,taxon,run,min.date,max.date,output.file,by.lifestage=FALSE)
outAll <- paste0(outFileStem,"/",outFile,".",run.name,"-","_ls=T")
output.file <- outAll
F.length.frequency(site,taxon,run,min.date,max.date,output.file,by.lifestage=TRUE)
}
}
# ---- Create the weekly effort report.
if( theReportLabel == "J" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.weekly.effort(site,taxon,min.date,max.date,outAll)
}
# ---- Create automatic lifestage report: lifestage to 2 groups and use weight variable.
if( theReportLabel == "K" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=2,weightuse=TRUE,enhmodel=FALSE)
}
# ---- Create automatic lifestage report: lifestage to 2 groups and don't use weight variable.
if( theReportLabel == "L" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=2,weightuse=FALSE,enhmodel=FALSE)
}
# ---- Create automatic lifestage report: lifestage to 3 groups and use weight variable.
if( theReportLabel == "M" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=3,weightuse=TRUE,enhmodel=FALSE)
}
# ---- Create automatic lifestage report: lifestage to 3 groups and don't use weight variable.
if( theReportLabel == "N" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=3,weightuse=FALSE,enhmodel=FALSE)
}
# ---- Create automatic lifestage report: let program decide 2 or 3 groups and use weight variable.
if( theReportLabel == "O" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=1,weightuse=TRUE,enhmodel=FALSE)
}
# ---- Create automatic lifestage report: let program decide 2 or 3 groups and don't use weight variable.
if( theReportLabel == "P" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=1,weightuse=FALSE,enhmodel=FALSE)
}
# ---- Create enhanced efficiency beta estimates and associated plots and output.
if( theReportLabel == "Q" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
# ---- The fitting of enhanced efficiency models is assumed to be done in R directly; i.e., not via the Platform.
# ---- Read in the specialized functions for this task explicitly.
#require(splines)
#require(mvtnorm)
# ---- Git working directory.
source("//lar-file-srv/Data/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/inst/enhEffCode/get_release_data.enh.R")
source("//lar-file-srv/Data/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/inst/enhEffCode/run_passage.enh.R")
source("//lar-file-srv/Data/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/inst/enhEffCode/est_passage.enh.R")
source("//lar-file-srv/Data/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/inst/enhEffCode/est_efficiency.enh.R")
source("//lar-file-srv/Data/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/inst/enhEffCode/eff_model.enh.R")
source("//lar-file-srv/Data/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/inst/enhEffCode/passageWithLifeStageAssign.enh.R")
# ---- Function run.passage.enh expects a 'by' that isn't used.
by <- 'year'
output.file <- outAll
F.run.passage.enh(site,taxon,min.date,max.date,by=by,output.file=outAll,ci=TRUE)
}
# ---- Create the ALL runs report -- WITH ENHANCED EFFICIENCY.
if( theReportLabel == "R" ){
# ---- Run function run.passage over the four possible temporal periods.
for(byj in 1:4){
if(byj == 1){by <- 'day' }
else if(byj == 2){by <- 'week' }
else if(byj == 3){by <- 'month'}
else if(byj == 4){by <- 'year' }
outAll <- paste0(outFileStem,"/",by,"-",outFile,"-")
output.file <- outAll
enhmodel <- TRUE
F.run.passage(site,taxon,min.date,max.date,by=by,output.file=outAll,ci=TRUE,enhmodel=enhmodel)
# ---- If desired, remove some of the output.
#theFiles <- dir(outFileStem)
#theFiles <- theFiles[grep("Late fall|Spring|Winter|Unassigned",theFiles)]
#file.remove(paste0(outFileStem,"/",theFiles))
}
}
# ---- Create the by lifestage and run report -- YES ENHANCED EFFICIENCY.
if( theReportLabel == "S" ){
by <- "All"
outAll <- paste0(outFileStem,"/",outFile,"-")
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file=outAll,ci=TRUE,autols=FALSE,nls=NULL,weightuse=NULL,enhmodel=TRUE)
}
# ---- Create the forklength report -- YES ENHANCED EFFICIENCY.
if( theReportLabel == "T" ){
# ---- Run function lifestage.passage.forkLength over the four possible temporal periods.
for(byj in 1:4){
if(byj == 1){by <- 'day' }
else if(byj == 2){by <- 'week' }
else if(byj == 3){by <- 'month'}
else if(byj == 4){by <- 'year' }
outAll <- paste0(outFileStem,"/",by,"-",outFile,"-")
output.file <- outAll
F.lifestage.passage.forkLength(site, taxon, min.date, max.date,by,output.file=output.file,ci=TRUE,enhmodel=TRUE)
}
}
# ---- Create automatic lifestage report: lifestage to 2 groups and use weight variable -- YES ENHANCED EFFICIENCY.
if( theReportLabel == "U" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=2,weightuse=TRUE,enhmodel=TRUE)
}
# ---- Create automatic lifestage report: lifestage to 2 groups and don't use weight variable -- YES ENHANCED EFFICIENCY.
if( theReportLabel == "V" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=2,weightuse=FALSE,enhmodel=TRUE)
}
# ---- Create automatic lifestage report: lifestage to 3 groups and use weight variable -- YES ENHANCED EFFICIENCY.
if( theReportLabel == "W" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=3,weightuse=TRUE,enhmodel=TRUE)
}
# ---- Create automatic lifestage report: lifestage to 3 groups and don't use weight variable -- YES ENHANCED EFFICIENCY.
if( theReportLabel == "X" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=3,weightuse=FALSE,enhmodel=TRUE)
}
# ---- Create automatic lifestage report: let program decide 2 or 3 groups and use weight variable -- YES ENHANCED EFFICIENCY.
if( theReportLabel == "Y" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=1,weightuse=TRUE,enhmodel=TRUE)
}
# ---- Create automatic lifestage report: let program decide 2 or 3 groups and don't use weight variable -- YES ENHANCED EFFICIENCY.
if( theReportLabel == "Z" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=1,weightuse=FALSE,enhmodel=TRUE)
}
# ---- Estimate annualized covariates. We build this report here in the Big Looper; all others create external output.
if( theReportLabel == "AA" ){
# aa_record <- annualizeCovars(site,min.date,max.date,theSeason,taxon)
# output.file <- paste0(outFileStem,"/",outFile,"-",theSeason)
# save(aa_record,file=paste0(output.file,"-","aa_record.RData"))
# annual_records <- rbind(annual_records,aa_record)
# ---- It is likely the loop broke, it was done in pieces, etc. So, read in each of the aa_records,
# ---- from all their folders. Be sure theExcel is everything you want to include. To use this part,
# ---- turn off the four lines above used to make aa_record and save it.
# ---- After all aa_records are made, run this whole section. To be safe, you can do use_data after.
output.file <- paste0(outFileStem,"/",outFile,"-",theSeason)
load(file=paste0(output.file,"-","aa_record.RData"))
annual_records <- rbind(annual_records,aa_record)
# ---- Check to see if we have considered the last aa_record, so as to save the final built annual_records.
if(i == nStreamNames & j == nSeasons & k == nReports){
# ---- Estimate a grand mean, per site.
for(ss in 1:length(unique(annual_records$site))){
siteMean <- apply(annual_records[annual_records$site == unique(annual_records$site)[ss],],2,function(x) mean(x[!is.nan(x) & !is.na(x)]))
siteMean[names(siteMean) == "Season"] <- -9999
annual_records <- rbind(annual_records,siteMean)
}
# --- Check that all -9999 have records filled in. No NA!
var <- "bdMeanForkLength"
ind <- annual_records$site == site & annual_records$Season != -9999 & !is.na(annual_records[,var])
est <- mean(annual_records[ind,var])
annual_records[annual_records$site == site & annual_records$Season == -9999,var] <- est
var <- "bdMeanMoonProp"
ind <- annual_records$site == site & annual_records$Season != -9999 & !is.na(annual_records[,var])
est <- mean(annual_records[ind,var])
annual_records[annual_records$site == site & annual_records$Season == -9999,var] <- est
var <- "bdMeanNightProp"
ind <- annual_records$site == site & annual_records$Season != -9999 & !is.na(annual_records[,var])
est <- mean(annual_records[ind,var])
annual_records[annual_records$site == site & annual_records$Season == -9999,var] <- est
devtools::use_data(annual_records,internal=FALSE,overwrite=TRUE)
}
# ---- End of all section to do at once.
}
}
}
}
tmcd82070/CAMP_RST documentation built on April 6, 2022, 12:07 a.m.
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
# # ---- Update packages. This is rarely done. Usually immediately before a new release.
# pkgs <- dir(.libPaths("//LAR-FILE-SRV/Data/PSMFC_CampRST/ThePlatform/CAMP_RST20170115-campR1.1.0/R/library"))
# notThese <- dir("C:/Program Files/R/R-3.5.0/library")
# pkgs <- pkgs[!(pkgs %in% c(notThese,c("campR","EnvCovDBpostgres")))]
#
# install.packages(pkgs,"C:/ThePlatform/CAMP_RST20180415-campR2.0/R/library")
# ---- Set variables necessary for Big Looper completion.
RVersion <- "3.5.0"
TestingPlatform <- "CAMP_RST20181023-campR2.0.10" # What the CAMP people will use; i.e., the static R in the Platform. Use this most of the time.
excelName <- "theExcel"
# excelName <- "theExcel2"
# ---- Set the reports you want to run. Use the key below.
# reportRun <- c("A","B","C","D","E","F","G","H","I","J","K","L","M","N","O","P","Q","R","S","T","U","V","W","X","Y","Z")
# reportRun <- c("A","B","C","D","E","F","G","H","I","J","K","L","M","N","O","P")
reportRun <- c("A","B","C","R","S","T")
reportRun <- c("G","R","S","T")
# reportRun <- c("K","L","M","N","O","P")
# reportRun <- c("B","R")
# reportRun <- c("Q")
# reportRun <- c("R","S")
# ---- Assign the version of R to use. A real check uses the version of R CAMP people use.
#.libPaths(paste0("C:/Users/jmitchell/Documents/R/win-library/",RVersion))
.libPaths(paste0("//lar-file-srv/Data/PSMFC_CampRST/ThePlatform/",TestingPlatform,"/R/library"))[1]
# ---- Get necessary packages in order.
# install.packages(c("RODBC","mvtnorm"))
# require("RODBC",lib.loc=paste0("C:/Users/jmitchell/Documents/R/win-library/",RVersion))
# require("mvtnorm",lib.loc=paste0("C:/Users/jmitchell/Documents/R/win-library/",RVersion))
# require("splines",lib.loc=paste0("C:/Users/jmitchell/Documents/R/win-library/",RVersion))
unloadNamespace("campR")
unloadNamespace("RODBC")
detach("package:RPostgres",unload=TRUE)
detach("package:campR", unload=TRUE)
require(campR)
# # ---- Read in updated functions, if updated before updating of package.
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/run_passage.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/tableDeleter.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/passageWithLifeStageAssign.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/F.lifestage.passage.forkLength.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/makeFake_release.df.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/est_passage.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/est_efficiency.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/eff_model.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/bootstrap_passage.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/getTogetherCovarData.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/estCovar.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/reMap.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/reMap2.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/checkValidCovars.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/plot_passage.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/release_summary.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/catch_model.R")
# source("L:/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/R/plot_catch_model.R")
# ---- Read in the desired Excel scheme. This is kept in the helperCode folder of the inst folder
# ---- in the campR package development folder in CAMP_RST20160601.
theExcel <- read.csv(paste0("//lar-file-srv/Data/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/inst/helperCode/",excelName,".csv"))
rownames(theExcel) <- NULL
# theExcel <- theExcel[!is.na(theExcel$siteID),]
# theExcel <- theExcel[!(theExcel$streamName == "Sacramento River" & theExcel$Season %in% c(2014,2015)),] # Exclude out years that seemingly have no releases.
# ---- Modify theExcel further here, if desired. Otherwise, delete or comment out.
# theExcel <- theExcel[c(1,5,13,15,24,26,32,52,73),] # For Enh Eff development (no RBDD)
# theExcel <- theExcel[c(1,5,13,15,24,26,32,36,52,73),] # For Enh Eff development (yes RBDD)
# theExcel <- theExcel[c(23),] # For Enh Eff development (only RBDD)
# theExcel <- theExcel[theExcel$streamName == "American River",] # American
# theExcel <- theExcel[theExcel$streamName == "Feather River",] # Feather
# theExcel <- theExcel[theExcel$streamName == "Stanislaus River",] # Stanislaus
# theExcel <- theExcel[theExcel$streamName == "Sacramento River",] # Sacramento
# theExcel <- theExcel[!(theExcel$streamName == "Sacramento River"),] # All but Sacramento
# theExcel <- theExcel[theExcel$siteID == 5000,] # Herringer Riffle
# theExcel <- theExcel[theExcel$siteID == 52000 & !is.na(theExcel$siteID),] # Gateway Riffle
# ---- Monthly testing runs for enhanced efficiency.
# theExcel <- theExcel[theExcel$siteID == 5000 & !is.na(theExcel$siteID),] # Herringer Riffle + Excel2.csv
# theExcel <- theExcel[theExcel$siteID == 42000 & !is.na(theExcel$siteID),] # Herringer Riffle + Excel2.csv
theExcel <- theExcel[83,]
theExcel$Season <- 2007
theExcel$minvisitTime <- "1/1/2007"
theExcel$maxvisitTime <- "7/1/2007"
# ---- Tell the Big Looper where to put all the output.
theStem <- paste0("\\\\lar-file-srv/Data/PSMFC_CampRST/ThePlatform/",TestingPlatform)
outStem <- paste0(theStem,"/Outputs")
# ---- Identify the possible reports we can run, and folder stems we can create.
# ---- This section should not be ameliorated.
nn <- c("label","folder","report","function")
a <- c("A" ,"EstProdAllRunsLSReport" ,"ls.run.passage" ,"passageWithLifeStageAssign")
b <- c("B" ,"EstProdAllRunsReport" ,"run.passage" ,"F.run.passage")
c <- c("C" ,"PassageEst_FL_Fall" ,"lifestage.passage.forkLength" ,"F.lifestage.passage.forkLength")
d <- c("D" ,"AllCatchTable" ,"all.catch" ,"F.allCatch.table")
e <- c("E" ,"ByCatchTable" ,"by.catch" ,"F.byCatch.table")
f <- c("F" ,"ChinookByDate" ,"chinook.by.date" ,"F.chinookByDate.table")
g <- c("G" ,"ReleaseSummary" ,"release.summary" ,"F.release.summary")
h <- c("H" ,"SizeByDate" ,"size.by.date" ,"F.size.by.date")
i <- c("I" ,"LengthFreq" ,"length.freq" ,"F.length.frequency")
j <- c("J" ,"WeeklyEffortReport" ,"weekly.effort" ,"F.weekly.effort")
k <- c("K" ,"AutoLS_2Group_YesWgt" ,"auto.ls.2grp_yWgt" ,"F.lifestage.passage.assignLS2group")
l <- c("L" ,"AutoLS_2Group_NoWgt" ,"auto.ls.2grp_nWgt" ,"F.lifestage.passage.assignLS2groupNoWeight")
m <- c("M" ,"AutoLS_3Group_YesWgt" ,"auto.ls.3grp_yWgt" ,"F.lifestage.passage.assignLS3group")
n <- c("N" ,"AutoLS_3Group_NoWgt" ,"auto.ls.3grp_nWgt" ,"F.lifestage.passage.assignLS3groupNoWeight")
o <- c("O" ,"AutoLS_2or3_AutoWgt" ,"auto.ls.2or3grp_autoWgt" ,"F.lifestage.passage.assignLS")
p <- c("P" ,"AutoLS_2or3_NoWgt" ,"auto.ls.2or3grp_nWgt" ,"F.lifestage.passage.assignLSNoWeight")
q <- c("Q" ,"Enhanced_Eff_Get_Betas" ,"run.passage.enh" ,"F.run.passage.enh")
r <- c("R" ,"EstProdAllRunsReportENH" ,"run.passage.enheffT" ,"F.run.passage")
s <- c("S" ,"EstProdAllRunsLSReportENH" ,"ls.run.passage.enheffT" ,"passageWithLifeStageAssign")
t <- c("T" ,"PassageEst_FL_FallENH" ,"lifestage.passage.forkLength.enheffT","F.lifestage.passage.forkLength")
u <- c("U" ,"AutoLS_2Group_YesWgtENH" ,"auto.ls.2grp_yWgt.enheffT" ,"F.lifestage.passage.assignLS2group")
v <- c("V" ,"AutoLS_2Group_NoWgtENH" ,"auto.ls.2grp_nWgt.enheffT" ,"F.lifestage.passage.assignLS2groupNoWeight")
w <- c("W" ,"AutoLS_3Group_YesWgtENH" ,"auto.ls.3grp_yWgt.enheffT" ,"F.lifestage.passage.assignLS3group")
x <- c("X" ,"AutoLS_3Group_NoWgtENH" ,"auto.ls.3grp_nWgt.enheffT" ,"F.lifestage.passage.assignLS3groupNoWeight")
y <- c("Y" ,"AutoLS_2or3_AutoWgtENH" ,"auto.ls.2or3grp_autoWgt.enheffT" ,"F.lifestage.passage.assignLS")
z <- c("Z" ,"AutoLS_2or3_NoWgtENH" ,"auto.ls.2or3grp_nWgt.enheffT" ,"F.lifestage.passage.assignLSNoWeight")
aa <- c("AA","AnnualizeCovars" ,"annualize.covars" ,"annualizeCovars")
# ---- Clean up our requested report list for use in making folders.
masterReports <- as.data.frame(rbind(a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z,aa),stringsAsFactors=FALSE)
names(masterReports) <- nn
rownames(masterReports) <- NULL
masterReports <- masterReports[masterReports$label %in% reportRun,]
# ---- Build up the request folder structure.
streamNames <- unique(paste0(theExcel$streamName,"--",theExcel$Site))
nStreamNames <- length(streamNames)
reportLabels <- masterReports$label
reportFolders <- masterReports$folder
reportTitles <- masterReports$report
nReports <- length(reportFolders)
# ---- Helper function to make directories, if they don't already exist.
makeTheDir <- function(theDir){
ifelse(!dir.exists(file.path(theDir)), dir.create(file.path(theDir),showWarnings=TRUE,recursive=TRUE), FALSE)
theDir <- NULL
}
# ---- Set all the global variables away from the default that you want.
# db.file <<- "..\\Data\\CAMP.mdb"
# output.dir <<- "..\\outputs"
# sql.code.dir <<- file.path(find.package("campR"),"sql")
# samplePeriodCutTime <<- "04:00:00"
# max.ok.gap <<- 2
# fishingGapMinutes <<- 10080
# knotMesh <<- 15
# halfConeMulti <<- 2
# sample.size.forkLength <<- 100
# sample.size.forkLengthAndWeight <<- 100
# weight.prop.forkLength <<- 0.5
# forkLength.mean.diff <<- 10
# time.zone <<- "America/Los_Angeles"
# Yes.code <<- 1
# No.code <<- 2
# seed <<- 884
# forkLengthCutPoints <<- data.frame(lifeStage=c("FL1 leq 41mm","FL2 42-72mm","FL3 73-110mm","FL4 geq 111mm"),cutPoints=c(41,72,110,9999))
# passageRounder <<- 4
# eff.min.spline.samp.size <<- 10
# unassd.sig.digit <<- 1
#i <- j <- k <- 1
# ---- If we are building annualized covariates for enhnaced efficiency, we need this.
if( "AA" %in% reportRun ){
annual_records <- NULL
}
# ---- Given the 'theExcel', loop over the streams.
for(i in 1:nStreamNames){
# ---- Reduce the master 'theExcel' to one stream.
theStreamName <- strsplit(streamNames[i],"--",fixed=TRUE)[[1]][1] #as.character(droplevels(streamNames[i]))
theSiteName <- strsplit(streamNames[i],"--",fixed=TRUE)[[1]][2]
the1stExcel <- theExcel[theExcel$streamName == theStreamName & theExcel$Site == theSiteName,]
seasons <- unique(the1stExcel$Season)
nSeasons <- length(seasons)
# ---- Make individual folder for the stream.
makeTheDir(paste0(outStem,"/",theStreamName,"--",theSiteName))
# ---- Given the stream, loop over the seasons.
for(j in 1:nSeasons){
# ---- Reduce the stream-based 'theExcel' to one record (Season).
theSeason <- seasons[j]
the2ndExcel <- the1stExcel[the1stExcel$Season == theSeason,]
# ---- Given we are going to compile reports for this Season,
# ---- create a folder structure to house the results.
# ---- Make individual folder for a Season.
makeTheDir(paste0(outStem,"/",paste0(theStreamName,"--",theSiteName),"/",theSeason))
# ---- Given the Season, loop over the desired reports.
for(k in 1:nReports){
theReportLabel <- reportLabels[k]
theReportFolder <- reportFolders[k]
theReportTitle <- reportTitles[k]
# ---- Make individual folder for a report
makeTheDir(paste0(outStem,"/",paste0(theStreamName,"--",theSiteName),"/",theSeason,"/",theReportFolder))
# ---- At this point, we're ready to create reports for this row in 'theExcel.'
taxon <- 161980 # taxon <- 161989 # steelhead / rainbow trout
ci <- TRUE
site <- the2ndExcel$siteID
siteText <- as.character(droplevels(the2ndExcel$Site))
min.date <- as.character(as.Date(the2ndExcel$minvisitTime,format="%m/%d/%Y"))
max.date <- as.character(as.Date(the2ndExcel$maxvisitTime,format="%m/%d/%Y"))
by <- "All"
outFileStem <- paste0(outStem,"/",paste0(theStreamName,"--",theSiteName),"/",theSeason,"/",theReportFolder)
outFile <- paste0(theReportTitle,"-",siteText)
outAll <- paste0(outFileStem,"/",outFile,"-")
# ---- Set up the db.file text string, so R knows where to find the database.
if(theStreamName == 'Sacramento River'){
#db.file <- "L:/PSMFC_CampRST/ThePlatform/CAMP_RST20161212-campR1.0.0/Data/TestingDBs/CAMP_RBDD_19June20151/CAMP.mdb"
db.file <- paste0(theStem,"/Data/TestingDBs/newRBDDCAMP_17July2017/CAMP.mdb")
#db.file <- "C:/Users/jmitchell/Desktop/Test/CAMP.mdb"
} else if(theStreamName == 'American River'){
db.file <- paste0(theStem,"/Data/TestingDBs/newAmericanCAMP_21July2017/CAMP.mdb")
#db.file <- "C:/Users/jmitchell/Desktop/Test/American/CAMP.mdb"
#db.file <- "L:/PSMFC_CampRST/ThePlatform/CAMP_RST20161212-campR1.0.0/Data/oldTestingDBs/CAMPAmerican2013_2015Database_23June2015/CAMP.mdb"
#db.file <- "C:/ThePlatform/CAMP_RST20180509-campR2.0/Data/CAMP.mdb"
} else if(theStreamName == 'Feather River'){
db.file <- paste0(theStem,"/Data/TestingDBs/newFeatherCAMP_15Aug2018/CAMP.mdb")
} else if(theStreamName == 'Stanislaus River'){
db.file <- paste0(theStem,"/Data/TestingDBs/newStanislausCAMP_20Sept2018/CAMP.mdb")
} else if(theStreamName == 'Mokelumne River'){
db.file <- paste0(theStem,"/Data/TestingDBs/newMokelumneCAMP_10Aug2017/CAMP.mdb")
} else if(theStreamName == "Knight's Landing"){
db.file <- paste0(theStem,"/Data/TestingDBs/CAMPKnightsTinsdaleNEW_04Feb2016/CAMP.mdb")
} else if(theStreamName == "Battle Clear"){
db.file <- paste0(theStem,"/Data/TestingDBs/newClearBattleCAMP_20July2017/CAMP.mdb")
} else if(theStreamName == "Tisdale Weir"){
db.file <- paste0(theStem,"/Data/TestingDBs/CAMPTisdale_18Sept2018/CAMP.mdb")
}
# ---- Given the appropriate text string, connect to the database.
cat(paste("DB file:", db.file, "\n"))
ch <- odbcConnectAccess(db.file)
close(ch)
# ---- Create the by lifestage and run report.
if( theReportLabel == "A" ){
by <- "All"
outAll <- paste0(outFileStem,"/",outFile,"-")
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file=outAll,ci=TRUE,autols=FALSE,nls=NULL,weightuse=NULL,enhmodel=FALSE)
}
# ---- Create the ALL runs report -- NO ENHANCED EFFICIENCY.
if( theReportLabel == "B" ){
# ---- Run function run.passage over the four possible temporal periods.
for(byj in 1:4){
if(byj == 1){by <- 'day' }
else if(byj == 2){by <- 'week' }
else if(byj == 3){by <- 'month'}
else if(byj == 4){by <- 'year' }
outAll <- paste0(outFileStem,"/",by,"-",outFile,"-")
output.file <- outAll
F.run.passage(site,taxon,min.date,max.date,by=by,output.file=outAll,ci=TRUE,enhmodel=FALSE)
# ---- If desired, remove some of the output.
#theFiles <- dir(outFileStem)
#theFiles <- theFiles[grep("Late fall|Spring|Winter|Unassigned",theFiles)]
#file.remove(paste0(outFileStem,"/",theFiles))
}
}
# ---- Create the forklength report.
if( theReportLabel == "C" ){
# ---- Run function lifestage.passage.forkLength over the four possible temporal periods.
for(byj in 1:4){
if(byj == 1){by <- 'day' }
else if(byj == 2){by <- 'week' }
else if(byj == 3){by <- 'month'}
else if(byj == 4){by <- 'year' }
outAll <- paste0(outFileStem,"/",by,"-",outFile,"-")
output.file <- outAll
F.lifestage.passage.forkLength(site, taxon, min.date, max.date,by,output.file=output.file,ci=TRUE,enhmodel=FALSE)
}
}
# ---- Create the all-catch table.
if( theReportLabel == "D" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.allCatch.table( site,min.date,max.date,output.file)
}
# ---- Create the by-catch table.
if( theReportLabel == "E" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.byCatch.table(site,min.date,max.date,output.file)
}
# ---- Create the Chinook-by-date report.
if( theReportLabel == "F" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.chinookByDate.table(site,min.date,max.date,output.file)
}
# ---- Create the release summary report.
if( theReportLabel == "G" ){
runs <- c(1,3,5,4) # Spring, Fall, Late Fall Winter
run.names <- c('Spring','Fall','Late Fall','Winter')
for(l in 1:4){
run <- runs[l]
run.name <- run.names[l]
outAll <- paste0(outFileStem,"/",outFile,".",run.name,"-")
output.file <- outAll
F.release.summary(site,taxon,run,min.date,max.date,output.file)
}
}
# ---- Create the size-by-date report.
if( theReportLabel == "H" ){
runs <- c(1,3,5,4) # Spring, Fall, Late Fall, Winter
run.names <- c('Spring','Fall','Late Fall','Winter')
for(l in 1:4){
run <- runs[l]
run.name <- run.names[l]
outAll <- paste0(outFileStem,"/",outFile,".",run.name,"-")
output.file <- outAll
F.size.by.date(site,taxon,run,min.date,max.date,output.file)
}
}
# ---- Create the length frequency report.
if( theReportLabel == "I" ){
runs <- c(1,3,5,4) # Spring, Fall, Late Fall, Winter
run.names <- c('Spring','Fall','Late Fall','Winter')
for(l in 1:4){
run <- runs[l]
run.name <- run.names[l]
outAll <- paste0(outFileStem,"/",outFile,".",run.name,"-","_ls=F")
output.file <- outAll
F.length.frequency(site,taxon,run,min.date,max.date,output.file,by.lifestage=FALSE)
outAll <- paste0(outFileStem,"/",outFile,".",run.name,"-","_ls=T")
output.file <- outAll
F.length.frequency(site,taxon,run,min.date,max.date,output.file,by.lifestage=TRUE)
}
}
# ---- Create the weekly effort report.
if( theReportLabel == "J" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.weekly.effort(site,taxon,min.date,max.date,outAll)
}
# ---- Create automatic lifestage report: lifestage to 2 groups and use weight variable.
if( theReportLabel == "K" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=2,weightuse=TRUE,enhmodel=FALSE)
}
# ---- Create automatic lifestage report: lifestage to 2 groups and don't use weight variable.
if( theReportLabel == "L" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=2,weightuse=FALSE,enhmodel=FALSE)
}
# ---- Create automatic lifestage report: lifestage to 3 groups and use weight variable.
if( theReportLabel == "M" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=3,weightuse=TRUE,enhmodel=FALSE)
}
# ---- Create automatic lifestage report: lifestage to 3 groups and don't use weight variable.
if( theReportLabel == "N" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=3,weightuse=FALSE,enhmodel=FALSE)
}
# ---- Create automatic lifestage report: let program decide 2 or 3 groups and use weight variable.
if( theReportLabel == "O" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=1,weightuse=TRUE,enhmodel=FALSE)
}
# ---- Create automatic lifestage report: let program decide 2 or 3 groups and don't use weight variable.
if( theReportLabel == "P" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=1,weightuse=FALSE,enhmodel=FALSE)
}
# ---- Create enhanced efficiency beta estimates and associated plots and output.
if( theReportLabel == "Q" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
# ---- The fitting of enhanced efficiency models is assumed to be done in R directly; i.e., not via the Platform.
# ---- Read in the specialized functions for this task explicitly.
#require(splines)
#require(mvtnorm)
# ---- Git working directory.
source("//lar-file-srv/Data/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/inst/enhEffCode/get_release_data.enh.R")
source("//lar-file-srv/Data/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/inst/enhEffCode/run_passage.enh.R")
source("//lar-file-srv/Data/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/inst/enhEffCode/est_passage.enh.R")
source("//lar-file-srv/Data/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/inst/enhEffCode/est_efficiency.enh.R")
source("//lar-file-srv/Data/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/inst/enhEffCode/eff_model.enh.R")
source("//lar-file-srv/Data/PSMFC_CampRST/ThePlatform/CAMP_RST20160601-DougXXX-4.5/R-Interface/campR/inst/enhEffCode/passageWithLifeStageAssign.enh.R")
# ---- Function run.passage.enh expects a 'by' that isn't used.
by <- 'year'
output.file <- outAll
F.run.passage.enh(site,taxon,min.date,max.date,by=by,output.file=outAll,ci=TRUE)
}
# ---- Create the ALL runs report -- WITH ENHANCED EFFICIENCY.
if( theReportLabel == "R" ){
# ---- Run function run.passage over the four possible temporal periods.
for(byj in 1:4){
if(byj == 1){by <- 'day' }
else if(byj == 2){by <- 'week' }
else if(byj == 3){by <- 'month'}
else if(byj == 4){by <- 'year' }
outAll <- paste0(outFileStem,"/",by,"-",outFile,"-")
output.file <- outAll
enhmodel <- TRUE
F.run.passage(site,taxon,min.date,max.date,by=by,output.file=outAll,ci=TRUE,enhmodel=enhmodel)
# ---- If desired, remove some of the output.
#theFiles <- dir(outFileStem)
#theFiles <- theFiles[grep("Late fall|Spring|Winter|Unassigned",theFiles)]
#file.remove(paste0(outFileStem,"/",theFiles))
}
}
# ---- Create the by lifestage and run report -- YES ENHANCED EFFICIENCY.
if( theReportLabel == "S" ){
by <- "All"
outAll <- paste0(outFileStem,"/",outFile,"-")
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file=outAll,ci=TRUE,autols=FALSE,nls=NULL,weightuse=NULL,enhmodel=TRUE)
}
# ---- Create the forklength report -- YES ENHANCED EFFICIENCY.
if( theReportLabel == "T" ){
# ---- Run function lifestage.passage.forkLength over the four possible temporal periods.
for(byj in 1:4){
if(byj == 1){by <- 'day' }
else if(byj == 2){by <- 'week' }
else if(byj == 3){by <- 'month'}
else if(byj == 4){by <- 'year' }
outAll <- paste0(outFileStem,"/",by,"-",outFile,"-")
output.file <- outAll
F.lifestage.passage.forkLength(site, taxon, min.date, max.date,by,output.file=output.file,ci=TRUE,enhmodel=TRUE)
}
}
# ---- Create automatic lifestage report: lifestage to 2 groups and use weight variable -- YES ENHANCED EFFICIENCY.
if( theReportLabel == "U" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=2,weightuse=TRUE,enhmodel=TRUE)
}
# ---- Create automatic lifestage report: lifestage to 2 groups and don't use weight variable -- YES ENHANCED EFFICIENCY.
if( theReportLabel == "V" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=2,weightuse=FALSE,enhmodel=TRUE)
}
# ---- Create automatic lifestage report: lifestage to 3 groups and use weight variable -- YES ENHANCED EFFICIENCY.
if( theReportLabel == "W" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=3,weightuse=TRUE,enhmodel=TRUE)
}
# ---- Create automatic lifestage report: lifestage to 3 groups and don't use weight variable -- YES ENHANCED EFFICIENCY.
if( theReportLabel == "X" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=3,weightuse=FALSE,enhmodel=TRUE)
}
# ---- Create automatic lifestage report: let program decide 2 or 3 groups and use weight variable -- YES ENHANCED EFFICIENCY.
if( theReportLabel == "Y" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=1,weightuse=TRUE,enhmodel=TRUE)
}
# ---- Create automatic lifestage report: let program decide 2 or 3 groups and don't use weight variable -- YES ENHANCED EFFICIENCY.
if( theReportLabel == "Z" ){
outAll <- paste0(outFileStem,"/",outFile,"-")
output.file <- outAll
F.passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci=TRUE,autols=TRUE,nls=1,weightuse=FALSE,enhmodel=TRUE)
}
# ---- Estimate annualized covariates. We build this report here in the Big Looper; all others create external output.
if( theReportLabel == "AA" ){
# aa_record <- annualizeCovars(site,min.date,max.date,theSeason,taxon)
# output.file <- paste0(outFileStem,"/",outFile,"-",theSeason)
# save(aa_record,file=paste0(output.file,"-","aa_record.RData"))
# annual_records <- rbind(annual_records,aa_record)
# ---- It is likely the loop broke, it was done in pieces, etc. So, read in each of the aa_records,
# ---- from all their folders. Be sure theExcel is everything you want to include. To use this part,
# ---- turn off the four lines above used to make aa_record and save it.
# ---- After all aa_records are made, run this whole section. To be safe, you can do use_data after.
output.file <- paste0(outFileStem,"/",outFile,"-",theSeason)
load(file=paste0(output.file,"-","aa_record.RData"))
annual_records <- rbind(annual_records,aa_record)
# ---- Check to see if we have considered the last aa_record, so as to save the final built annual_records.
if(i == nStreamNames & j == nSeasons & k == nReports){
# ---- Estimate a grand mean, per site.
for(ss in 1:length(unique(annual_records$site))){
siteMean <- apply(annual_records[annual_records$site == unique(annual_records$site)[ss],],2,function(x) mean(x[!is.nan(x) & !is.na(x)]))
siteMean[names(siteMean) == "Season"] <- -9999
annual_records <- rbind(annual_records,siteMean)
}
# --- Check that all -9999 have records filled in. No NA!
var <- "bdMeanForkLength"
ind <- annual_records$site == site & annual_records$Season != -9999 & !is.na(annual_records[,var])
est <- mean(annual_records[ind,var])
annual_records[annual_records$site == site & annual_records$Season == -9999,var] <- est
var <- "bdMeanMoonProp"
ind <- annual_records$site == site & annual_records$Season != -9999 & !is.na(annual_records[,var])
est <- mean(annual_records[ind,var])
annual_records[annual_records$site == site & annual_records$Season == -9999,var] <- est
var <- "bdMeanNightProp"
ind <- annual_records$site == site & annual_records$Season != -9999 & !is.na(annual_records[,var])
est <- mean(annual_records[ind,var])
annual_records[annual_records$site == site & annual_records$Season == -9999,var] <- est
devtools::use_data(annual_records,internal=FALSE,overwrite=TRUE)
}
# ---- End of all section to do at once.
}
}
}
}
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