In RemkoDuursma/plantecophys: Modelling and Analysis of Leaf Gas Exchange Data

photosyn() : Comparison of simulation time

library(GasExchangeR)
library(Maeswrap)
library(plyr)

setwd("g:/work/projects/HFE/WTC/MAESPA_fluxmodelling")
source("./Rfunctions/photosyn.R")

h <- readhrflux("./MAESPArunfolder/hrflux.dat")

simTime <- function(df){

  t1 <- system.time(run1 <- photosyn(PAR=df$PAR, VPD=df$VPD, TLEAF=df$TAIR))
  t2 <- system.time(run1 <- photosyn2(PPFD=df$PAR, VPD=df$VPD, Tleaf=df$TAIR))
  t1 <- t1[[3]]
  t2 <- t2[[3]]
  return(c(t1,t2))
}

k <- c(0.1,0.25,0.5,1:10)
n <- nrow(h)
N <- floor(k*n)

r <- list()
for(i in seq_along(k)){

  # randomly selected rows
  rows <- sample(1:n, N[i], replace=TRUE)

  r[[i]] <- simTime(h[rows,])

}
r <- do.call(rbind, r)

plot(log10(N), log10(r[,1]), type='o', pch=21, bg="black",
     xlab=expression(log["10"]*(Sample~size)),
     ylab=expression(log["10"]*(Computing~time)),
     ylim=c(min(log10(r)), max(log10(r))))
points(log10(N), log10(r[,2]), type='o', pch=21, bg="white")
legend("topleft", c("GasExchangeR (fortran)","photosyn2() (R)"),
       lty=1, pch=21, pt.bg=c("black","white"))

w

RemkoDuursma/plantecophys documentation built on April 6, 2021, 2:45 a.m.