R/plotAQ.R

In serbinsh/biocro: Simulation of Energycane and Sugarcane

## 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)
        }
    }
    
}