View of /trunk/gadgetMerluza2015/scripts/all_Plots.r

####################################################################################################
#                              SOURCE FILE TO RUN ALL PLOT-SCRIPTS
#   From this source-script we can execute the 3 kinds of plots groups (diagnosis, results and 
# projections) together or separately in one or three pdf documents selecting pdfPlot TRUE or FALSE
#                     created: camilo.saavedra@vi.ieo.es (02/07/2013)
####################################################################################################

# VERY IMPORTANT: Set working directory to source file location
# setwd("~/scripts/")

# Select some figures before plotting. Name and number of documents withing plots
runN <- "1" # Ordinal number of the run
load("R.data/annualUpdate.RData") # Load annual updated data used for pdf names

##################### CHOOSE HOW DO YOU WANT TO PRINT YOUR PLOTS ###################################

# Executing pdf objects: The four pdf objects must be executed
pdfPlot <- FALSE  # If TRUE writes all plots in one pdf, if FALSE writes each plot in various pdf
pdfDiag <- FALSE # If TRUE writes all diagnosis plots in one pdf, if FALSE writes in various pdf
pdfResu <- FALSE # If TRUE writes all results plots in one pdf, if FALSE writes in various pdf
pdfPrj <- FALSE # If TRUE writes all projections plots in one pdf, if FALSE writes in various pdf

# Check and transform all pdf objects to FALSE if pdfPlot is TRUE
if(pdfPlot) {pdfDiag <- FALSE; pdfResu <- FALSE; pdfProj <- FALSE} 

################################## PLOTS ###########################################################

# Select the working directory to execute the next source scripts
wd <- getwd()

# Opens pdf document if we want to plot all figures in the same document (pdfPlot=TRUE)
if(pdfPlot) { 
  plotName <- paste("WGHMM", substr((lastYear+1), 3,4), ".", runN, sep="") # pdf name
  pdf(file=paste("../plots/", plotName, ".pdf", sep=""), height=7, width=10.5)}

############################### Diagnosis plots ####################################################

setwd(paste(wd, "/scripts.diag", sep=""))

if(pdfDiag) { 
  plotName <- paste("WGHMM", substr((lastYear+1), 3,4), ".", runN, sep="") # pdf name
  pdf(file=paste("../../plots/plots.diag/", plotName, ".Diag",".pdf", sep=""), height=7, width=10.5)}

##### Convergence plots #####
#source ("plot_Sensitivity.r")
# input function: "../functions/pdfPlot.r"
# input file: "../../model/sens.txt"
# output plot: "../../plots/plots.diag/plot_SensFree.pdf"
# output plot: "../../plots/plots.diag/plot_SensFix.pdf"

##### Summary of likelihood scores #####
source ("plot_LikeSummary.r")
# input function: "../functions/pdfPlot.r"
# input file: "../../out/hke.lik.summ.out"
# output plot: "../../plots/plots.diag/plot_LikeWeight.pdf"
# output plot: "../../plots/plots.diag/plot_LikeSumm.pdf"

##### Catchability in abundance indices (sp and pt surveys) by 15 cm length class #####
source ("plot_INDEX.r")
# input function: "../functions/pdfPlot.r"
# input file for every length range (N = 1:3 ranges): "../../out/SpIndex15.N.print"
# output plot: "../plots/plots.diag/plot_INDEX-ObsExp.pdf"

##### Catchability in abundance indices (sp and pt) by 15cm length class (25-40; 40-55; 55-70) #####
source ("plot_CPUE.r")
# input function: "../functions/pdfPlot.r"
# input file: "../../out/SpCPUE15cm.1.print"
# input file: "../../out/SpCPUE15cm.2.print"
# input file: "../../out/SpCPUE15cm.3.print"
# input file: "../../data/ld-15cm-sp_cpue.in"
# input file: "../../out/Sp85CPUE15cm.1.print"
# input file: "../../out/Sp85CPUE15cm.2.print"
# input file: "../../out/Sp85CPUE15cm.3.print"
# input file: "../../data/ld-15cm-sp_cpue85.in"
# input file: "../../out/PtCPUE15cm.1.print"
# input file: "../../out/PtCPUE15cm.2.print"
# input file: "../../out/PtCPUE15cm.3.print"
# input file: "../../data/ld-15cm-pt_cpue.in"
# output plot: "../plots/plots.diag/plot_CPUE-ObsExp.pdf" 

##### Landings observed and expected (histogram and density plots) #####
source ("plot_ObsExp.r")
# input function: "../functions/pdfPlot.r"
# input file: "../../out/expected.landings.ld"
# input file: "../../out/expected.landings1.ld"
# input file: "../../out/expected.cdlandings.ld"
# input file: "../../out/expected.discards.ld"
# input file: "../../out/expected-sp_surv.ld"
# input file: "../../out/expected-pt_surv.ld"
# input file: "../../out/expected-cdAut_surv.ld"
# input file: "../../data/ld-2cm-land82-93.in"
# input file: "../../data/ld-2cm-land94-end.in"
# input file: "../../data/ld-2cm-land-Cd94-04.in"
# input file: "../../data/ld-2cm-disc.in"
# input file: "../../data/ld-2cm-sp-surv.in"
# input file: "../../data/ld-2cm-cdAut-surv.in"
# input file: "../../data/ld-2cm-pt-surv.in"
# output plot: "../../plots/plots.diag/plot_ObsExp.pdf"
# output plot: "../../plots/plots.diag/plot_ObsExpSurvey.pdf"

##### Landings observed and expected (bubles plots) #####
source ("plot_ObsExpBuble.r")
# input function: "../functions/pdfPlot.r"
# input file: "../../model/hke.likelihood"
# input file: "../../out/expected.landings1.ld"
# input file: "../../out/expected.landings.ld"
# input file: "../../out/expected.cdlandings.ld"
# input file: "../../out/expected.discards.ld"
# input file: "../../out/expected-sp_surv.ld"
# input file: "../../out/expected-pt_surv.ld"
# input file: "../../out/expected-cdAut_surv.ld"
# output plot: "../../plots/plots.diag/plots_ObsExpBuble.pdf"
# output plot: "../../plots/plots.diag/plots_ObsExpBubleSurvey.pdf"

if (pdfDiag){dev.off()}
setwd(wd)

############################# Results plots ########################################################

setwd(paste(wd, "/scripts.results", sep=""))

if(pdfResu) { 
  plotName <- paste("WGHMM", substr((lastYear+1), 3,4), ".", runN, sep="") # pdf name
  pdf(file=paste("../../plots/plots.results/", plotName, ".Results",".pdf", sep=""), height=7, width=10.5)}

##### PLot selectivity for sp and pt survey and for total catches ######
#source("plot_Selectivity.r")
# input function: "../functions/pdfPlot.r"
# input function: "../functions/logit.r"
# input function: "../functions/andersen.r"
# input file: "../../model/params.out"
# output file: "../../plots/plots.results/plot_SelectPattern.pdf"

##### PLot growth curve #####
source("plot_Growth.r")
# input function: "../functions/pdfPlot.r"
# source file: "../functions/vonb.r"
# input file: "../../model/params.out"
# output file: "../../plots/plots.results/plot_GrowthVB.pdf"

##### Summary tables hkeLen and hkeAge ##### 
source("table_Summary.r")
# input data: "../R.data/annualUpdate.RData"
# input file: "../../out/hkeLenN.out"
# input file: "../../out/hkeLenC.out"
# input file: "../../out/hkeLenL.out"
# input file: "../../out/hkeLenD.out"
# input file: "../../data/RData.matOgives"
# input file: "../../out/hkeAgeN.out"
# input file: "../../out/hkeAgeC.out"
# input file: "../../out/hkeAgeL.out"
# input file: "../../out/hkeAgeD.out"
# input file: "../../out/hke.std.out"
# output data: "../R.data/hakeLen.RData"
# output data: "../R.data/hakeAge.RData"
# output file: "../../tables/tables.results/hkeLen.csv"
# output file: "../../tables/tables.results/hkeAge.csv"

##### Summary plot Gadget #####
source("plot_Summary.r")
# input function: "../functions/pdfPlot.r"
# input file: "../../tables/tables.results/hkeLen.csv"
# input file: "../../tables/tables.results/hkeAge.csv"
# output data: "../R.data/sumDat.RData"
# output table: "../../tables/tables.results/sumDat.csv"
# output table: "../../tables/tables.results/tab_summary.pdf"
# output plot: "../../plots/plots.results/plot_StkRec-Refpts.pdf"
# output plot: "../../plots/plots.results/plot_Summary.pdf"
# output plot: "../../plots/plots.results/FComp.pdf"

##### F by quarter #####
source("plot_FQuarter.r")
# input function: "../functions/pdfPlot.r"
# input data: "../R.data/annualUpdate.RData"
# input file: "../../out/hkeAgeC.out"
# output file: "../../plots/plots.results/plot_FQuarter.pdf"

##### Mean length at age #####
source("plot_LenAtAge.r")
# input function: "../functions/pdfPlot.r"
# input file: "../../out/hke.std.out"
# output plot: "../../plots/plots.results/plot_LengthAtAge.pdf"

##### N and C by length #####
source("plot_ByLength.r")
#