R/plotCPool.R

In SoilR: Models of Soil Organic Matter Decomposition

#' Plots the output of \code{\link{getC}} or \code{\link{getReleaseFlux}} for
#' each pool over time
#' 
#' This function produces a plot with the C content or released C for each pool
#' over time. Needs as input a matrix obtained after a call to
#' \code{\link{getC}} or \code{\link{getReleaseFlux}}.
#' 
#' 
#' @param t A vector containing the time points for plotting.
#' @param mat A matrix object obtained after a call to \code{\link{getC}} or
#' \code{\link{getReleaseFlux}}
#' @param col A color palette specifying color lines for each pool (columns of
#' \code{mat}).
#' @param ... Other arguments passed to \code{link{plot}}.
plotCPool<-structure(
  function 
  (t,  
   mat, 
   col,   
   ...    
  )
  {
    n=ncol(mat)
    plot(t,mat[,1],type="l",col=col[1],...)
    for(i in 2:n){
      lines(t,mat[,i],col=col[i])
    }
  }
  ,
  ex=function(){
    years=seq(1901,2009,by=0.5)
    LitterInput=700 
    Ex=ThreepFeedbackModel14(
      t=years,ks=c(k1=1/2.8, k2=1/35, k3=1/100),C0=c(200,5000,500),
      F0=c(0,0,0), In=LitterInput, a21=0.1,a12=0.01,a32=0.005,a23=0.001,
      inputFc=C14Atm_NH
    )
    Ct=getC(Ex)
    Rt=getReleaseFlux(Ex)
    pal=rainbow(3)
    plotCPool(t=years,mat=Ct,col=pal,xlab="Time (yrs)",
              ylab="Carbon stocks",ylim=c(min(Ct),max(Ct)))
  }
)