R/covarPlot.r

In tmcd82070/CAMP_RST: CAMP RST R Routines

#'@export
#'
#'@title covarPlot
#'  
#'@description For a trap, plot efficiency against an environmental covariate 
#'  and the covariate against time.
#'  
#'@param covar A unit-length character specifying the covariate of interest with
#'  its associated unit, e.g., \code{turbidity_ntu}.
#'  
#'@param df A data frame containing at least numerator and denominator 
#'  efficiency information, i.e., variables \code{nCaught} and \code{nReleased}.
#'  
#'@param dbCovar A data frame containing queried data from a CAMP database for 
#'  one environmental covariate.
#'  
#'@param trap A unit-length numeric corresponding to a \code{trapPositionID}.
#'  
#'@param eff.ind.inside A logical vector identifying which visit dates 
#'  correspond to dates within a fishing period, as defined by when efficiency 
#'  trials took place.
#'  
#'@param bsplBegDt The first date, via the spline-1959-1960 paradigm, to which 
#'  all efficiency years and dates collapse.
#'  
#'@param fit An enhanced-efficiency model fit object resulting from function
#'  \code{glm}.
#'  
#'@return Plots to screen, as described in the description.
#'  
#'@details The function is intended to be called as part of a larger script. As
#'  such, the function itself doesn't include any \code{png} statements or 
#'  \code{dev.off()} of the same.
#'  
#'@seealso \code{estCovar}
#'  
#'@author WEST Inc.
#'  
#' @examples
#' \dontrun{
#' covarPlot("turbidity_ntu",obs.eff.df,dbTurb,57004,eff.ind.inside)
#'}

covarPlot <- function(covar,df,dbCovar,trap,eff.ind.inside,bsplBegDt,fit){
  
  # covar <- "temp_c"
  # df <- obs.eff.df
  # dbCovar <- dbTpPG
  # trap <- 57001
  # eff.ind.inside <- eff.ind.inside
  
  #   ---- We give the function all the data, so restrict to the trap.  
  df <- df[df$TrapPositionID == trap,]
  effdf <- df[!is.na(df$efficiency),]
  
  #   ---- Plot of efficiency versus covariate.
  if(covar %in% names(effdf)){
    
    #   ---- Color points from different years.  Looking for interactions wrt to time. 
    cols <- c("red","orange","yellow","green","blue","purple","brown","black")
    col.i <- as.factor(as.POSIXlt(effdf$batchDate)$year - min(as.POSIXlt(effdf$batchDate)$year) + 1)
    
    # if(covar %in% names(fit$coefficients)){
    #   covarGrid <- seq(min(df[!is.na(df$nCaught),covar]),max(df[!is.na(df$nCaught),covar]),length.out=100)
    #   phat <- predict(fit,newdata=list(deparse(substitute(covar))=covarGrid))
    #   
    #   phat <- predict(fit,newdata=list(turbidity_ntu=covarGrid,bdMeanForkLength=rep(mean(df[!is.na(df$nCaught),]$bdMeanForkLength),length.out=length(covarGrid))))
    # }
    
    plot(effdf[,covar],100*effdf$efficiency,col=cols[col.i],type="p",pch=19,xlab=NA,ylab='Efficiency (%)',main=paste0(covar," at ",effdf$TrapPositionID[1]))
  } else {
    plot(1,1)
  }
  
  #   ---- Plot of variable 3 versus time with smoother. Currently assumes 1 entry in the list df.covar.
  if(covar %in% names(df)){
    
    bsplBegDt$mon + 1
    
    #   ---- Find the range with respect to the data we use.
    xS <- df$batchDate
    yS <- df[!is.na(df$nCaught),covar]

    #   ---- Find the range with respect to the data recorded.  
    xD <- dbCovar[dbCovar$subSiteID == trap,]$measureDate
    yD <- dbCovar[dbCovar$subSiteID == trap,3]
    
    xm <- min(xD[!is.na(xD)])
    xM <- max(xD[!is.na(xD)])
    ym <- min(yS[!is.na(yS)])
    yM <- max(yS[!is.na(yS)])

    #plot(xD,yD,xlab=NA,ylab=NA,xaxt='n',yaxt='n',xlim=c(xm,xM),ylim=c(ym,yM),type="p",cex=0.25,pch=19,main=paste0(covar," at ",df$TrapPositionID[1]))
    plot(xD,yD,xlab='Date',ylab=covar,xlim=c(xm,xM),ylim=c(ym,yM),type="p",cex=0.25,pch=19,main=paste0(covar," at ",df$TrapPositionID[1]))
    #par(new=TRUE)
    #plot(xS[eff.ind.inside],yS[eff.ind.inside],xlab='Date',ylab=covar,xlim=c(xm,xM),ylim=c(ym,yM),type="l",col="red")

  } else {
    plot(1,1)
  }
  
}