R/plotRawData.R

In wStockhausen/rPIBKC: Package to run the PIBKC stock assessment

#'
#'@title Plot raw survey and fishery data.
#'
#'@description Function to plot raw survey and fishery data.
#'
#'@param srvData - survey data dataframe, path to csv file, or NULL
#'@param fshData - fisheries data dataframe, path to csv file, or NULL
#'@param yr2 - starting year for 2nd arithmetic scale plot
#'@param pdfType - probability distribution for error bars
#'@param ci - confidence interval for error bar plots
#'@param verbose - flag (T/F) to print diagnostics, etc
#'@param showPlot - flag (T/F) to show plots immediately
#'
#'@details Biomass units are assumed to be in t, abundance units in ones.
#'
#'@return list with named elements
#'\itemize{
#'  \item srvData - dataframe w/ abundance is in ones and biomass is in t
#'  \item fshData - dataframe w/ catch biomass is in t
#'  \item plots - list with ggplot2 objects 
#'  \itemize{
#'      \item retained catch time series
#'      \item retained catch time series, recent time period
#'      \item discard catch time series
#'      \item discard catch time seies, recent time period
#'      \item survey biomass time series
#'      \item survey biomass time series, recent time period
#'      \item survey biomass time series, log10-scale
#'  }
#'}
#'
#'@import ggplot2
#'@importFrom wtsUtilities selectFile
#'
#'@export
#'
plotRawData<-function(srvData=NULL,
                      fshData=NULL,
                      yr2=1990,
                      pdfType='lognormal',
                      ci=0.95,
                      verbose=FALSE,
                      showPlot=FALSE
                      ){
    if (is.null(fshData)|is.character(fshData)) fshData<-getFisheryData(fshData);
    if (is.null(srvData)|is.character(srvData)) srvData<-getSurveyData(srvData);
    
    plots<-list();

    #--fishery data--
    if (!is.null(fshData)){
        pd<-position_dodge(0.2);
        fp<-fshData;
        fp$category<-factor(fp$category,levels=c("legal","sublegal","females","all"))
        #plot retained catch fishery data
        fpp<-fp[fp$type=='retained',];
        p <- ggplot(aes_string(x='year',y='catch',colour='category',fill='gear',shape='gear'),
                    data=fpp);
        p <- p + geom_point(position=pd,size=3);
        p <- p + geom_line( position=pd,size=1,alpha=1);
        p <- p + ylab("Fishery Catch (t)");
        p <- p + facet_grid(fishery~type,scales="free_y");
        pF1 <- p;
        if (showPlot) print(pF1);
        cap<-paste0("Figure &&fno. Time series of retained PIBKC catch in the directed fishery.")
        plots[[cap]]<-pF1;
    
        pF2 <- p %+% fpp[fpp$year>=yr2,];
        if (showPlot) print(pF2);
        cap<-paste0("Figure &&fno. Time series of retained PIBKC catch in the directed fishery (recent time period).")
        plots[[cap]]<-pF2;
        
        #plot bycatch fishery data
        fpp<-fp[(fp$type=='discard')&(!is.na(fp$catch)),];
        p <- ggplot(aes_string(x='year',y='catch',colour='category',fill='gear',shape='gear'),
                    data=fpp);
        p <- p + geom_point(position=pd,size=3);
        p <- p + geom_line( position=pd,size=1,alpha=1);
        p <- p + ylab("Fishery Catch (t)");
        p <- p + facet_grid(fishery~type,scales="free_y");
        pF1 <- p;
        if (showPlot) print(pF1);
        cap<-paste0("Figure &&fno. Time series of PIBKC bycatch in the crab and groundfish fisheries.")
        plots[[cap]]<-pF1;
    
        pF2 <- p %+% fpp[fpp$year>=yr2,];
        if (showPlot) print(pF2);
        cap<-paste0("Figure &&fno. Time series of PIBKC bycatch in the crab and groundfish fisheries (recent time period).")
        plots[[cap]]<-pF2;
        
        rm(fp,fpp,p,pF1, pF2);
    }

    #---survey data---
    if (!is.null(srvData)){
        #compute confidence intervals for survey data
        res<-rPIBKC::calcCIs(srvData$value,srvData$cv,pdfType=pdfType,ci=ci);
        srvData$lci<-res$lci;
        srvData$uci<-res$uci;
    
        #plot survey biomass
        bSD1<-srvData[(srvData$type=='biomass')&(srvData$category!='total'),];
        bSD1$category<-factor(bSD1$category,levels=c('immature','mature','legal'))
        ymx <- sort(bSD1$uci,decreasing=TRUE)[6];
        pd<-position_dodge(0.2);
        p <- ggplot(aes_string(x='year',y='value',colour='sex',fill='sex',shape='sex'),data=bSD1);
        p <- p + geom_errorbar(aes_string(ymin='lci',ymax='uci'),position=pd,width=0.8,linetype=1);
        p <- p + geom_point(position=pd,size=3);
        p <- p + geom_line( position=pd,size=1,alpha=1);
        p <- p + coord_cartesian(ylim=c(0,ymx));
        p <- p + ylab("Survey Biomass (t)");
        p <- p + facet_grid(category~.);
        pS1 <- p;
        if (showPlot) print(pS1);
        cap<-paste0("  \nFigure &&fno. Time series of NMFS EBS bottom trawl survey biomass for PIKC.",
                    " Confidence intervals shown are ",100*ci," CI's, assuming ",pdfType," error distributions.  \n")
        plots[[cap]]<-pS1;
    
        bSD2<-bSD1[bSD1$year>=yr2,];
        ymx <- sort(bSD2$uci,decreasing=TRUE)[1];
        pS2 <- p %+% bSD2
        pS2 <- pS2 + coord_cartesian(ylim=c(0,ymx));
        if (showPlot) print(pS2);
        cap<-paste0("  \nFigure &&fno. Time series of NMFS EBS bottom trawl survey biomass for PIKC (recent time period).",
                    " Confidence intervals shown are ",100*ci," CI's, assuming ",pdfType," error distributions.  \n")
        plots[[cap]]<-pS2;
    
        bSD3<-bSD1;
        bSD3$value<-log10(bSD3$value);
        bSD3$uci<-log10(bSD3$uci);
        bSD3$lci<-log10(bSD3$lci);
        ymx <- sort(bSD3$uci,decreasing=TRUE)[1];
        pS3 <- p %+% bSD3;
        pS3 <- pS3 + coord_cartesian(ylim=NULL);
        pS3 <- pS3 + ylab("log10-scale Survey Biomass (t)");
        if (showPlot) print(pS3);
        cap<-paste0("Figure &&fno. Log10-scale time series of NMFS EBS bottom trawl survey biomass for PIKC.",
                    " Confidence intervals shown are ",100*ci," CI's, assuming ",pdfType," error distributions.  \n")
        plots[[cap]]<-pS3;
        
        rm(bSD1,bSD2,bSD3,p,pS1,pS2,pS3);
    }

    return(invisible(list(srvData=srvData,
                          fshData=fshData,
                          plots=plots)));
}