R/juveniles_BioEnCompareRelationships.R

In wStockhausen/rPacificCod: Functions related to the Pacific cod IBM

#'
#' @title Plot the bioenergetic relationships for juvenile Pacific cod
#'
#' @description Function to plot the bioenergetic relationships for juvenile Pacific cod.
#'
#' @param W - weights, in g
#' @param T - temperatures, in deg C
#'
#' @return list of \code{ggplot2}-type plots
#'
#' @import ggplot2
#' @import magrittr
#' @import reshape2
#'
#' @family juvenile bioenergetic functions
#'
#' @import magrittr
#'
#' @export
#'
juvBioenergetics_PlotRelationships<-function(
           W=seq(from=3.0,to=10.0,by=0.2), #--weights (g)
           T=seq(from=0.0,to=20.0,by=2.0)  #--temperatures (degrees)
                                                  ){
  plots<-list();

  dfrFRs<-data.frame(T=T,respiration=juv_fR(T),consumption=juv_fC(T));
  dfrp<-reshape2::melt(dfrFRs,id.vars="T",variable.name="response");
  p <- ggplot2::ggplot(data=dfrp,mapping=ggplot2::aes_string(x="T",y="value",colour="response"));
  p <- p + ggplot2::geom_line();
  p <- p + ggplot2::labs(x="temperature (deg C)",y="functional response",
                         subtitle="functional responses");
  #print(p);
  plots[["functional responses"]]<-p;

  dfrRCs<-data.frame(W=W,respiration=juv_Ra(W),consumption=juv_Ca(W));
  dfrp<-reshape2::melt(dfrRCs,id.vars="W",variable.name="type");
  p <- ggplot2::ggplot(data=dfrp,mapping=ggplot2::aes_string(x="W",y="value",colour="type"));
  p <- p + ggplot2::geom_line();
  p <- p + ggplot2::labs(x="weight (g)",y="allometry (g/g/d)",
                         subtitle="respiration and consumption")
  #print(p);
  plots[["respiration and consumption"]]<-p;

  p <- p + ggplot2::scale_y_log10();
  #print(p);
  plots[["ln(respiration and consumption)"]]<-p;

  dfrCGT<-data.frame("T"=T,"GT"=juv_GT(T),"CT"=juv_CT(T));
  dfrp<-reshape2::melt(dfrCGT,id.vars="T",variable.name="type");
  p <- ggplot2::ggplot(data=dfrp,mapping=ggplot2::aes_string(x="T",y="value",colour="type"));
  p <- p + ggplot2::geom_line();
  p <- p + ggplot2::labs(x="temperature",y="mass equivalent (g/d)",
                         subtitle="growth and consumption");
  #print(p);
  plots[["growth and consumption"]]<-p;

  #--calculate growth
  dfrG<-juv_BioEnGrowth(W,T);
  #--plot growth as a function of weight at different temperatures
  dfrp<-dfrG;
  dfrp$T<-as.factor(dfrp$T)
  p <- ggplot2::ggplot(data=dfrp,mapping=ggplot2::aes_string(x="W",y="G",colour="T"));
  p <- p + ggplot2::geom_line();
  p <- p + ggplot2::labs(x="weight",y="growth (J/g fish/d)",
                         subtitle="growth at a fixed temperature");
  plots[["g(W|T)"]]<-p;

  #--plot growth as a function of temperature at different weights
  dfrp<-dfrG;
  dfrp$W<-as.factor(dfrp$W)
  p <- ggplot2::ggplot(data=dfrp,mapping=ggplot2::aes_string(x="T",y="G",colour="W"));
  p <- p + ggplot2::geom_line();
  p <- p + ggplot2::labs(x="temperature",y="growth (J/g fish/d)",
                         subtitle="growth at a fixed weight");
  plots[["g(T|W)"]]<-p;

  #--compare GT with G(w=6.8,T)
  dfrGTw<-juv_BioEnGrowth(W=6.8,T);
  dfrGTw$W<-as.factor(dfrGTw$W);

  dfrp<-cbind(dfrGTw,dfrCGT[,2:3]);
  dfrp = reshape2::melt(dfrp,id.vars=c("W","T"),factorsAsStrings=TRUE);
  dfrp$variable = as.character(dfrp$variable);
  dfrp %<>% subset(variable %in% c("G","GT"))
  dfrp$variable[dfrp$variable=="G"]  = "bioenergetics";
  dfrp$variable[dfrp$variable=="GT"] = "empirical";
  p <- ggplot2::ggplot(data=dfrp,mapping=ggplot2::aes_string(x="T",y="value",colour="variable"));
  p <- p + ggplot2::geom_line();
  p <- p + ggplot2::labs(x="temperature",y="G(T|W=6.8g) [J/g fish/day]",colour="calculation",
                         subtitle="comparison of specific growth from \nbioenergetics and empirical equations");
  plots[["g(T|W=6.8g)"]]<-p;

  return(plots);
}

#'
#' @title Plot the bioenergetic relationships for juvenile Pacific cod
#'
#' @description Function to plot the bioenergetic relationships for juvenile Pacific cod.
#'
#' @param W - weights, in g
#' @param T - temperatures, in deg C
#' @param EDc - energy density of P. cod
#'
#' @return list of \code{ggplot2}-type plots
#'
#' @details
#' \itemize{
#' \item{fitted growth- from \code{\link{juv_GT}}, based on eq. S8}
#' \item{fitted respiration -from \code{\link{juv_MT}}, based on eq. S5}
#' \item{estimated consumption - from \code{\link{juv_CT}}, based on eq. S9}
#' \item{estimated respiration - from \code{\link{juv_Ra}}*\code{\link{juv_fR}}, based on eq.s S2 and S6}
#' }
#'
#' @import ggplot2
#' @import tibble
#'
#' @family juvenile bioenergetic functions
#'
#' @export
#'
juvBioenergetics_CompareRelationships<-function(
           W=6.8,                           #--weights (g)
           T=seq(from=0.0,to=20.0,by=2.0),  #--temperatures (degrees)
           EDc=4138                         #--energy density of P. cod (J/g fish)
                                                  ){
  plots<-list();

  gt<-juv_GT(T);          #--J/g fish/day (fitted growth)
  mt<-juv_MT(T);          #--?? units (fitted respiration)
  ct<-juv_CT(T,W);        #--J/g fish/day (estimated consumption)
  rt<-juv_Ra(W)*juv_fR(T);#--J/g fish/day (estimated respiration)
  dfrCGT<-tibble::tibble("T"=T,
                         `specific growth(T); eq. S8`=gt,
                         `respiration(T); eq. S5 (units??)`=mt,
                         `specific consumed energy(T,W); eq. S9`=ct,
                         `specific respiration(T,W); eq.s S2 and S6`=rt);
  dfrp<-reshape2::melt(dfrCGT,id.vars="T",variable.name="type");
  p <- ggplot2::ggplot(data=dfrp,mapping=ggplot2::aes_string(x="T",y="value",colour="type"));
  p <- p + ggplot2::geom_line();
  p <- p + ggplot2::ylim(c(0,NA));
  p <- p + ggplot2::labs(x="temperature",
                         y="energy equivalent (J/g fish/day)",
                         subtitle=paste0("comparison for ",W,"g fish"));
  print(p);
  plots[["GCR"]]<-p;
  # p <- ggplot2::ggplot(data=dfrp,mapping=ggplot2::aes_string(x="T",y="value",colour="type"));
  # p <- p + ggplot2::geom_line();
  # p <- p + ggplot2::facet_grid(rows=ggplot2::vars(type),scales="free_y");
  # #p <- p + ggplot2::ylim(c(0,NA));
  # p <- p + ggplot2::labs(x="temperature",y="mass equivalent (g/day)")
  # print(p);
  # plots[["GCRbyT"]]<-p;

  return(plots);
}