R/Data.Plots.r
In rcheshire/FishGraph: Visualizations for fishery stock-assessment.
Defines functions
Data.Plots
Documented in
Data.Plots
#' Plot of available data from the output of an assessment
#' The function \code{Data.Plots} generates a timeseries plot of the different data sources. Optionally, the size of the points for the age, length, and weight composition can be proportion to the sample size of input data
#'
#' @param x an R list with output from the assessment model.
#' @param DataName string used in plot titles. Defaults to argument \code{x}.
#' #' @param draft modifies plots for use in a report. When \code{FALSE} main titles
#' are omitted.
#' @param draft modifies plots for use in a report. When \code{FALSE} main titles
#' are omitted.
#' @param graphics.type a vector of graphics file types to which graphics are saved.
#' When \code{NULL}, no plots are saved.
#' @param use.color plots are made in grayscale when \code{FALSE}
#' @param scaleSize a boolean whether to scale size of point for age and length composition based on the sample size. Default is FALSE
#' @param cexval cex multiplier of squares to make continuous bar if desired
#' @param fill a boolean whether to fill the point, this is useful for diagnosing how much overlap occurs in the points, Default if TRUE
#' @param sampleName a character string of the length and age composition name to search for in the tseries matrix. Do not include the '.'. Default is 'neff'
#'
#' @return Graphics
#'
#' @author MT Vincent
#'
#' @examples \donttest{
#' Data.Plots(gag)
#' }
#' @export
#'
###########################################################################################
## R function to make plot of data input into assessment
## Part of FishGraph
## spp 50 year 17 rows cex=1.5
## spp1 45
## spp 45 years 18 rows cex=1.75
## 35 years 13 rows cex = 2.2
Data.Plots <- function(x, DataName = deparse(substitute(x)), draft = TRUE,
graphics.type = NULL, use.color = TRUE, scaleSize=FALSE,cexval=1,fill=TRUE,sampleName="neff")
{
###########################################################################################
### Check for x$t.series data frame:
if (! ("t.series" %in% names(x)))
{ ErrText = (paste("Component ", deparse(substitute(x)),
"$t.series not found.", sep = ""))
warning(ErrText, immediate. = TRUE)
return(invisible(-1))
}
ts = x$t.series
## Replace time series values with NA for less than 0 values
ts[ts<0]=NA
### Check for other needed data:
if (! ("year" %in% names(x$t.series)))
{ warning("Year variable not found in Index.plots!", immediate. = TRUE)
return(invisible(-1))
}
## Get the years of available catch by fishery
years = ts$year
## midyr = mean(years)
minyr=min(years)-(min(years)%%5)
maxyr=max(years)+ifelse((max(years)%%5)==0,0,5-(max(years)%%5))
midyr=.5
xyears=(years-minyr)/(maxyr-minyr)
## Get years of available CPUE by fishery
CPUEcols=grep("^U.*ob",names(ts))
CPUEs=ts[,CPUEcols]
tmp=names(ts)[CPUEcols]
## remove the first 2 and last 3 characters from string to get name of fleet
CPUENames=substr(substr(tmp,3,nchar(tmp)),1,nchar(tmp)-5)
## Landings
Landingcols=grep("^L.*ob",names(ts))
Landing=ts[,Landingcols]
tmp=names(ts)[Landingcols]
LandingNames=substr(substr(tmp,3,nchar(tmp)),1,nchar(tmp)-5)
## Discards
Discardcols=grep("^D.*ob",names(ts))
Discard=ts[,Discardcols]
tmp=names(ts)[Discardcols]
DiscardNames=substr(substr(tmp,3,nchar(tmp)),1,nchar(tmp)-5)
## Length compositions
Lengthcols=grep(paste0("^lcomp.*",sampleName),names(ts))
LengthN=ts[,Lengthcols]
tmp=names(ts)[Lengthcols]
LengthNames=substr(substr(tmp,7,nchar(tmp)),1,nchar(tmp)-7-nchar(sampleName))
## Get the samples size of the length compositon
## Age compositions
Agecols=grep(paste0("^acomp.*",sampleName),names(ts))
AgeN=ts[,Agecols]
tmp=names(ts)[Agecols]
AgeNames=substr(substr(tmp,7,nchar(tmp)),1,nchar(tmp)-7-nchar(sampleName))
## Check which data sources are used in this assessment
PlotCPUE=ifelse(length(CPUENames)==0,FALSE,TRUE)
PlotLanding=ifelse(length(LandingNames)==0,FALSE,TRUE)
PlotDiscard=ifelse(length(DiscardNames)==0,FALSE,TRUE)
PlotLength=ifelse(length(LengthNames)==0,FALSE,TRUE)
PlotAge=ifelse(length(AgeNames)==0,FALSE,TRUE)
## Calculate what the height of the y axis must be to plot all of these
## Gives 2 spaces for
pt=1
ttl=2
ycount = length(CPUENames)*pt + length(LandingNames)*pt + length(DiscardNames)*pt + length(LengthNames)*pt + length(AgeNames)*pt + PlotCPUE*ttl + PlotLanding*ttl + PlotDiscard*ttl + PlotLength*ttl + PlotAge*ttl
spacer=1/(ycount-2)
AllNames=c(LandingNames,DiscardNames,CPUENames,LengthNames,AgeNames)
if (use.color){
colvec <- rainbow(length(unique(AllNames)), s = 0.9, v = 0.65, start = 0.1, end = 1)
if (length(unique(AllNames)) == 1) colvec = "gray55"
} else {
colvec <- gray.colors(length(unique(AllNames)), start = 0.2, end = 0.8)
}
fishcols=data.frame(names=unique(AllNames),col=colvec)
## Make the plot with the right dimensions for the plot
savepar = FGSetPar(draft)
PlotTitle=ifelse(draft, paste(DataName,"Data Availability"),"")
if (draft){ par(mar=c(2.5,1+max(nchar(AllNames)),3,3+max(nchar(AllNames))))
} else{ par(mar=c(2.5,1+max(nchar(AllNames)),.5,3+max(nchar(AllNames))))}
plot(NA,xlim=c(0,1),ylim=c(-1,0),main=PlotTitle,axes=FALSE,frame.plot=TRUE,ylab='',xlab='Year',cex=1.5)
axis(1,at=seq(0,1,length.out=length(seq(minyr,maxyr,5))),labels=seq(minyr,maxyr,5),cex.axis=1.1)
counter=spacer
savecount=NULL
## Put in Landings title and data available points
if (PlotLanding){
counter=counter-spacer
text(midyr,counter,"Landings",cex=1.25,adj=c(0.5,0))
counter=counter-spacer
if (length(LandingNames)==1){
points(xyears[!is.na(Landing)],rep(counter,length(xyears[!is.na(Landing)])),pch=22,lwd=3,bg=ifelse(fill,fishcols[fishcols$names==LandingNames,2],"transparent"),cex=cexval,col=fishcols[fishcols$names==LandingNames,2])
savecount=c(savecount,counter)
counter=counter-spacer
} else {
for (i in 1:length(LandingNames)) {
points(xyears[!is.na(Landing[,i])],rep(counter,length(xyears[!is.na(Landing[,i])])),pch=22,lwd=3,bg=ifelse(fill,fishcols[fishcols$names==LandingNames[i],2],"transparent"),cex=cexval,col=fishcols[fishcols$names==LandingNames[i],2])
savecount=c(savecount,counter)
counter=counter-spacer
} #For Landing length
} #if length ==1
} #End if plot Landing
## Put in Discard title and data available point
if (PlotDiscard){
counter=counter-spacer
text(midyr,counter,"Discards",cex=1.25,adj=c(0.5,0))
counter=counter-spacer
if (length(DiscardNames)==1){
points(xyears[!is.na(Discard)],rep(counter,length(xyears[!is.na(Discard)])),pch=22,lwd=3,bg=ifelse(fill,fishcols[fishcols$names==DiscardNames,2],"transparent"),cex=cexval,col=fishcols[fishcols$names==DiscardNames,2])
savecount=c(savecount,counter)
counter=counter-spacer
} else {
for (i in 1:length(DiscardNames)) {
points(xyears[!is.na(Discard[,i])],rep(counter,length(xyears[!is.na(Discard[,i])])),pch=22,lwd=3,bg=ifelse(fill,fishcols[fishcols$names==DiscardNames[i],2],"transparent"),cex=cexval,col=fishcols[fishcols$names==DiscardNames[i],2])
savecount=c(savecount,counter)
counter=counter-spacer
} #For Discard length
} #if length ==1
} #End if plot Discard
## Put in CPUE title and available data
if (PlotCPUE){
counter=counter-spacer
text(midyr,counter,"Abundance Indices",cex=1.25,adj=c(0.5,0))
counter=counter-spacer
if (length(CPUENames)==1){
points(xyears[!is.na(CPUEs)],rep(counter,length(xyears[!is.na(CPUEs)])),pch=22,lwd=3,bg=ifelse(fill,fishcols[fishcols$names==CPUENames,2],"transparent"),cex=cexval,col=fishcols[fishcols$names==CPUENames,2])
savecount=c(savecount,counter)
counter=counter-spacer
} else {
for (i in 1:length(CPUENames)) {
points(xyears[!is.na(CPUEs[,i])],rep(counter,length(xyears[!is.na(CPUEs[,i])])),pch=22,lwd=3,bg=ifelse(fill,fishcols[fishcols$names==CPUENames[i],2],"transparent"),cex=cexval,col=fishcols[fishcols$names==CPUENames[i],2])
savecount=c(savecount,counter)
counter=counter-spacer
} #For CPUE length
} #if length==1
} #End if plot CPUE
## Put in Length comp data availability with option for size of points
if (PlotLength){
counter=counter-spacer
text(midyr,counter,"Length Composition",cex=1.25,adj=c(0.5,0))
counter=counter-spacer
if (length(LengthNames)==1){
ifelse(scaleSize,cexmult <- (LengthN[!is.na(LengthN)&LengthN>0]/max(LengthN,na.rm=TRUE))*cexval ,cexmult <- cexval)
points(xyears[!is.na(LengthN)&LengthN>0],rep(counter,length(xyears[!is.na(LengthN)&LengthN>0])),pch=22,lwd=3,bg=ifelse(fill,fishcols[fishcols$names==LengthNames,2],"transparent"),cex=cexmult,col=fishcols[fishcols$names==LengthNames,2])
savecount=c(savecount,counter)
counter=counter-spacer
} else {
for (i in 1:length(LengthNames)) {
ifelse(scaleSize,cexmult <- (LengthN[(!is.na(LengthN[,i])&LengthN[,i]>0),i]/max(LengthN,na.rm=TRUE))*cexval ,cexmult <- cexval)
points(xyears[(!is.na(LengthN[,i])&LengthN[,i]>0)],rep(counter,length(xyears[(!is.na(LengthN[,i])&LengthN[,i]>0)])),pch=22,lwd=3,bg=ifelse(fill,fishcols[fishcols$names==LengthNames[i],2],"transparent"),cex=cexmult,col=fishcols[fishcols$names==LengthNames[i],2])
savecount=c(savecount,counter)
counter=counter-spacer
} #For Length length
} #if length==1
} #End if plot Length
## Put in Age comp data availability with option for size of points
if (PlotAge){
counter=counter-spacer
text(midyr,counter,"Age Composition",cex=1.25,adj=c(0.5,0))
counter=counter-spacer
if (length(AgeNames)==1){
ifelse(scaleSize,cexmult <- (AgeN[!is.na(AgeN)]/max(AgeN,na.rm=TRUE))*cexval ,cexmult <- cexval)
points(xyears[!is.na(AgeN)],rep(counter,length(xyears[!is.na(AgeN)])),pch=22,lwd=3,bg=ifelse(fill,fishcols[fishcols$names==AgeNames,2],"transparent"),cex=cexmult,col=fishcols[fishcols$names==AgeNames,2])
savecount=c(savecount,counter)
counter=counter-spacer
} else {
for (i in 1:length(AgeNames)) {
ifelse(scaleSize,cexmult <- (AgeN[!is.na(AgeN[,i]),i]/max(AgeN,na.rm=TRUE))*cexval ,cexmult <- cexval)
points(xyears[!is.na(AgeN[,i])],rep(counter,length(xyears[!is.na(AgeN[,i])])),pch=22,lwd=3,bg=ifelse(fill,fishcols[fishcols$names==AgeNames[i],2],"transparent"),cex=cexmult,col=fishcols[fishcols$names==AgeNames[i],2])
savecount=c(savecount,counter)
counter=counter-spacer
} #For Age length
} #if length==1
} #End if plot Age
axis(2,at=savecount,labels=AllNames,las=2,cex.axis=1.1)
legend(1.05, -0.5, bty='n', xpd=NA, legend=fishcols[,1], pch=22, pt.bg=fishcols[,2],col=fishcols[,2],cex=1.1,yjust=0.5,lwd=3,lty=NA)
### If writing graphics files, make sure there is a directory for them:
if (! is.null(graphics.type)){
write.graphs <- TRUE
GraphicsDirName <- paste(DataName, "-figs", sep="")
FGCheckGraphDir(GraphicsDirName)
} else { write.graphs <- FALSE }
if (write.graphs) FGSavePlot(GraphicsDirName, DataName, GraphName = "data_availability", graphics.type)
# Restore graphics parameters and return:
par(savepar)
return(invisible(0))
}
#End Function
rcheshire/FishGraph documentation built on Feb. 23, 2024, 11:27 a.m.
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Defines functions Data.Plots
Documented in Data.Plots
#' Plot of available data from the output of an assessment
#' The function \code{Data.Plots} generates a timeseries plot of the different data sources. Optionally, the size of the points for the age, length, and weight composition can be proportion to the sample size of input data
#'
#' @param x an R list with output from the assessment model.
#' @param DataName string used in plot titles. Defaults to argument \code{x}.
#' #' @param draft modifies plots for use in a report. When \code{FALSE} main titles
#' are omitted.
#' @param draft modifies plots for use in a report. When \code{FALSE} main titles
#' are omitted.
#' @param graphics.type a vector of graphics file types to which graphics are saved.
#' When \code{NULL}, no plots are saved.
#' @param use.color plots are made in grayscale when \code{FALSE}
#' @param scaleSize a boolean whether to scale size of point for age and length composition based on the sample size. Default is FALSE
#' @param cexval cex multiplier of squares to make continuous bar if desired
#' @param fill a boolean whether to fill the point, this is useful for diagnosing how much overlap occurs in the points, Default if TRUE
#' @param sampleName a character string of the length and age composition name to search for in the tseries matrix. Do not include the '.'. Default is 'neff'
#'
#' @return Graphics
#'
#' @author MT Vincent
#'
#' @examples \donttest{
#' Data.Plots(gag)
#' }
#' @export
#'
###########################################################################################
## R function to make plot of data input into assessment
## Part of FishGraph
## spp 50 year 17 rows cex=1.5
## spp1 45
## spp 45 years 18 rows cex=1.75
## 35 years 13 rows cex = 2.2
Data.Plots <- function(x, DataName = deparse(substitute(x)), draft = TRUE,
graphics.type = NULL, use.color = TRUE, scaleSize=FALSE,cexval=1,fill=TRUE,sampleName="neff")
{
###########################################################################################
### Check for x$t.series data frame:
if (! ("t.series" %in% names(x)))
{ ErrText = (paste("Component ", deparse(substitute(x)),
"$t.series not found.", sep = ""))
warning(ErrText, immediate. = TRUE)
return(invisible(-1))
}
ts = x$t.series
## Replace time series values with NA for less than 0 values
ts[ts<0]=NA
### Check for other needed data:
if (! ("year" %in% names(x$t.series)))
{ warning("Year variable not found in Index.plots!", immediate. = TRUE)
return(invisible(-1))
}
## Get the years of available catch by fishery
years = ts$year
## midyr = mean(years)
minyr=min(years)-(min(years)%%5)
maxyr=max(years)+ifelse((max(years)%%5)==0,0,5-(max(years)%%5))
midyr=.5
xyears=(years-minyr)/(maxyr-minyr)
## Get years of available CPUE by fishery
CPUEcols=grep("^U.*ob",names(ts))
CPUEs=ts[,CPUEcols]
tmp=names(ts)[CPUEcols]
## remove the first 2 and last 3 characters from string to get name of fleet
CPUENames=substr(substr(tmp,3,nchar(tmp)),1,nchar(tmp)-5)
## Landings
Landingcols=grep("^L.*ob",names(ts))
Landing=ts[,Landingcols]
tmp=names(ts)[Landingcols]
LandingNames=substr(substr(tmp,3,nchar(tmp)),1,nchar(tmp)-5)
## Discards
Discardcols=grep("^D.*ob",names(ts))
Discard=ts[,Discardcols]
tmp=names(ts)[Discardcols]
DiscardNames=substr(substr(tmp,3,nchar(tmp)),1,nchar(tmp)-5)
## Length compositions
Lengthcols=grep(paste0("^lcomp.*",sampleName),names(ts))
LengthN=ts[,Lengthcols]
tmp=names(ts)[Lengthcols]
LengthNames=substr(substr(tmp,7,nchar(tmp)),1,nchar(tmp)-7-nchar(sampleName))
## Get the samples size of the length compositon
## Age compositions
Agecols=grep(paste0("^acomp.*",sampleName),names(ts))
AgeN=ts[,Agecols]
tmp=names(ts)[Agecols]
AgeNames=substr(substr(tmp,7,nchar(tmp)),1,nchar(tmp)-7-nchar(sampleName))
## Check which data sources are used in this assessment
PlotCPUE=ifelse(length(CPUENames)==0,FALSE,TRUE)
PlotLanding=ifelse(length(LandingNames)==0,FALSE,TRUE)
PlotDiscard=ifelse(length(DiscardNames)==0,FALSE,TRUE)
PlotLength=ifelse(length(LengthNames)==0,FALSE,TRUE)
PlotAge=ifelse(length(AgeNames)==0,FALSE,TRUE)
## Calculate what the height of the y axis must be to plot all of these
## Gives 2 spaces for
pt=1
ttl=2
ycount = length(CPUENames)*pt + length(LandingNames)*pt + length(DiscardNames)*pt + length(LengthNames)*pt + length(AgeNames)*pt + PlotCPUE*ttl + PlotLanding*ttl + PlotDiscard*ttl + PlotLength*ttl + PlotAge*ttl
spacer=1/(ycount-2)
AllNames=c(LandingNames,DiscardNames,CPUENames,LengthNames,AgeNames)
if (use.color){
colvec <- rainbow(length(unique(AllNames)), s = 0.9, v = 0.65, start = 0.1, end = 1)
if (length(unique(AllNames)) == 1) colvec = "gray55"
} else {
colvec <- gray.colors(length(unique(AllNames)), start = 0.2, end = 0.8)
}
fishcols=data.frame(names=unique(AllNames),col=colvec)
## Make the plot with the right dimensions for the plot
savepar = FGSetPar(draft)
PlotTitle=ifelse(draft, paste(DataName,"Data Availability"),"")
if (draft){ par(mar=c(2.5,1+max(nchar(AllNames)),3,3+max(nchar(AllNames))))
} else{ par(mar=c(2.5,1+max(nchar(AllNames)),.5,3+max(nchar(AllNames))))}
plot(NA,xlim=c(0,1),ylim=c(-1,0),main=PlotTitle,axes=FALSE,frame.plot=TRUE,ylab='',xlab='Year',cex=1.5)
axis(1,at=seq(0,1,length.out=length(seq(minyr,maxyr,5))),labels=seq(minyr,maxyr,5),cex.axis=1.1)
counter=spacer
savecount=NULL
## Put in Landings title and data available points
if (PlotLanding){
counter=counter-spacer
text(midyr,counter,"Landings",cex=1.25,adj=c(0.5,0))
counter=counter-spacer
if (length(LandingNames)==1){
points(xyears[!is.na(Landing)],rep(counter,length(xyears[!is.na(Landing)])),pch=22,lwd=3,bg=ifelse(fill,fishcols[fishcols$names==LandingNames,2],"transparent"),cex=cexval,col=fishcols[fishcols$names==LandingNames,2])
savecount=c(savecount,counter)
counter=counter-spacer
} else {
for (i in 1:length(LandingNames)) {
points(xyears[!is.na(Landing[,i])],rep(counter,length(xyears[!is.na(Landing[,i])])),pch=22,lwd=3,bg=ifelse(fill,fishcols[fishcols$names==LandingNames[i],2],"transparent"),cex=cexval,col=fishcols[fishcols$names==LandingNames[i],2])
savecount=c(savecount,counter)
counter=counter-spacer
} #For Landing length
} #if length ==1
} #End if plot Landing
## Put in Discard title and data available point
if (PlotDiscard){
counter=counter-spacer
text(midyr,counter,"Discards",cex=1.25,adj=c(0.5,0))
counter=counter-spacer
if (length(DiscardNames)==1){
points(xyears[!is.na(Discard)],rep(counter,length(xyears[!is.na(Discard)])),pch=22,lwd=3,bg=ifelse(fill,fishcols[fishcols$names==DiscardNames,2],"transparent"),cex=cexval,col=fishcols[fishcols$names==DiscardNames,2])
savecount=c(savecount,counter)
counter=counter-spacer
} else {
for (i in 1:length(DiscardNames)) {
points(xyears[!is.na(Discard[,i])],rep(counter,length(xyears[!is.na(Discard[,i])])),pch=22,lwd=3,bg=ifelse(fill,fishcols[fishcols$names==DiscardNames[i],2],"transparent"),cex=cexval,col=fishcols[fishcols$names==DiscardNames[i],2])
savecount=c(savecount,counter)
counter=counter-spacer
} #For Discard length
} #if length ==1
} #End if plot Discard
## Put in CPUE title and available data
if (PlotCPUE){
counter=counter-spacer
text(midyr,counter,"Abundance Indices",cex=1.25,adj=c(0.5,0))
counter=counter-spacer
if (length(CPUENames)==1){
points(xyears[!is.na(CPUEs)],rep(counter,length(xyears[!is.na(CPUEs)])),pch=22,lwd=3,bg=ifelse(fill,fishcols[fishcols$names==CPUENames,2],"transparent"),cex=cexval,col=fishcols[fishcols$names==CPUENames,2])
savecount=c(savecount,counter)
counter=counter-spacer
} else {
for (i in 1:length(CPUENames)) {
points(xyears[!is.na(CPUEs[,i])],rep(counter,length(xyears[!is.na(CPUEs[,i])])),pch=22,lwd=3,bg=ifelse(fill,fishcols[fishcols$names==CPUENames[i],2],"transparent"),cex=cexval,col=fishcols[fishcols$names==CPUENames[i],2])
savecount=c(savecount,counter)
counter=counter-spacer
} #For CPUE length
} #if length==1
} #End if plot CPUE
## Put in Length comp data availability with option for size of points
if (PlotLength){
counter=counter-spacer
text(midyr,counter,"Length Composition",cex=1.25,adj=c(0.5,0))
counter=counter-spacer
if (length(LengthNames)==1){
ifelse(scaleSize,cexmult <- (LengthN[!is.na(LengthN)&LengthN>0]/max(LengthN,na.rm=TRUE))*cexval ,cexmult <- cexval)
points(xyears[!is.na(LengthN)&LengthN>0],rep(counter,length(xyears[!is.na(LengthN)&LengthN>0])),pch=22,lwd=3,bg=ifelse(fill,fishcols[fishcols$names==LengthNames,2],"transparent"),cex=cexmult,col=fishcols[fishcols$names==LengthNames,2])
savecount=c(savecount,counter)
counter=counter-spacer
} else {
for (i in 1:length(LengthNames)) {
ifelse(scaleSize,cexmult <- (LengthN[(!is.na(LengthN[,i])&LengthN[,i]>0),i]/max(LengthN,na.rm=TRUE))*cexval ,cexmult <- cexval)
points(xyears[(!is.na(LengthN[,i])&LengthN[,i]>0)],rep(counter,length(xyears[(!is.na(LengthN[,i])&LengthN[,i]>0)])),pch=22,lwd=3,bg=ifelse(fill,fishcols[fishcols$names==LengthNames[i],2],"transparent"),cex=cexmult,col=fishcols[fishcols$names==LengthNames[i],2])
savecount=c(savecount,counter)
counter=counter-spacer
} #For Length length
} #if length==1
} #End if plot Length
## Put in Age comp data availability with option for size of points
if (PlotAge){
counter=counter-spacer
text(midyr,counter,"Age Composition",cex=1.25,adj=c(0.5,0))
counter=counter-spacer
if (length(AgeNames)==1){
ifelse(scaleSize,cexmult <- (AgeN[!is.na(AgeN)]/max(AgeN,na.rm=TRUE))*cexval ,cexmult <- cexval)
points(xyears[!is.na(AgeN)],rep(counter,length(xyears[!is.na(AgeN)])),pch=22,lwd=3,bg=ifelse(fill,fishcols[fishcols$names==AgeNames,2],"transparent"),cex=cexmult,col=fishcols[fishcols$names==AgeNames,2])
savecount=c(savecount,counter)
counter=counter-spacer
} else {
for (i in 1:length(AgeNames)) {
ifelse(scaleSize,cexmult <- (AgeN[!is.na(AgeN[,i]),i]/max(AgeN,na.rm=TRUE))*cexval ,cexmult <- cexval)
points(xyears[!is.na(AgeN[,i])],rep(counter,length(xyears[!is.na(AgeN[,i])])),pch=22,lwd=3,bg=ifelse(fill,fishcols[fishcols$names==AgeNames[i],2],"transparent"),cex=cexmult,col=fishcols[fishcols$names==AgeNames[i],2])
savecount=c(savecount,counter)
counter=counter-spacer
} #For Age length
} #if length==1
} #End if plot Age
axis(2,at=savecount,labels=AllNames,las=2,cex.axis=1.1)
legend(1.05, -0.5, bty='n', xpd=NA, legend=fishcols[,1], pch=22, pt.bg=fishcols[,2],col=fishcols[,2],cex=1.1,yjust=0.5,lwd=3,lty=NA)
### If writing graphics files, make sure there is a directory for them:
if (! is.null(graphics.type)){
write.graphs <- TRUE
GraphicsDirName <- paste(DataName, "-figs", sep="")
FGCheckGraphDir(GraphicsDirName)
} else { write.graphs <- FALSE }
if (write.graphs) FGSavePlot(GraphicsDirName, DataName, GraphName = "data_availability", graphics.type)
# Restore graphics parameters and return:
par(savepar)
return(invisible(0))
}
#End Function
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