R/plotAQ.R

In BioCro: Simulation of Biomass Crops

##
##  BioCro/R/plotAQ.R by Fernando Ezequiel Miguez  Copyright (C) 2007-2009
##
##  This program is free software; you can redistribute it and/or modify
##  it under the terms of the GNU General Public License as published by
##  the Free Software Foundation; either version 2 or 3 of the License
##  (at your option).
##
##  This program is distributed in the hope that it will be useful,
##  but WITHOUT ANY WARRANTY; without even the implied warranty of
##  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
##  GNU General Public License for more details.
##
##  A copy of the GNU General Public License is available at
##  http://www.r-project.org/Licenses/
##
##

## helper plotting functions

## Function to plot A/Q curves
##
## data are assumed to have
##
## col 1: trt
## col 2 (optional): other treatment factor
## col 2: Assimilation
## col 3: Quantum flux
## col 4: Temperature
## col 5: Relative humidity
## col 6 (optional): Reference CO2

plotAQ <- function(data,fittd,
                   id.col=1,
                   trt.col=2,
                   ylab="CO2 Uptake",
                   xlab="Quantum flux",
                   by=c("trt","ID"),type="o",...){

  by <- match.arg(by)
  Acol <- trt.col + 1
  Qp.col <- trt.col + 2

  if(missing(fittd) || is.null(fittd)){
    if(by == "trt"){
      plot1 <- xyplot(data[,Acol] ~ data[,Qp.col] | factor(data[,trt.col]),
                      ylab = ylab,
                      xlab = xlab,
                      type = type, ...)
                      
      plot(plot1)
    }else{
      plot1 <- xyplot(data[,Acol] ~ data[,Qp.col] | factor(data[,id.col]),
                      ylab = ylab,
                      xlab = xlab,
                      type = type, ...)
      plot(plot1)
    }
  }else{
    stopifnot(length(fittd) == nrow(data))
    if(by == "trt"){
      plot1 <- xyplot(data[,Acol] + fittd ~ data[,Qp.col] | factor(data[,trt.col]),
                      ylab = ylab, 
                      xlab = xlab,
                      type = type, ...)
      plot(plot1)
    }else{
      plot1 <- xyplot(data[,Acol] + fittd ~ data[,Qp.col] | factor(data[,id.col]),
                      ylab = ylab, 
                      xlab = xlab,
                      type = type, ...)
      plot(plot1)
    }
  }

}