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##
## BioCro/R/idbp.R by Fernando Ezequiel Miguez Copyright (C) 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/
##
##
idbp <- function(data, phenoControl=list()){
## should have t
if(any(is.na(data)))
stop("missing data are not allowed")
dnames <- c("ThermalT","Stem","Leaf","Root","Rhizome","Grain","LAI")
if(any(is.na(unlist(lapply(names(data),pmatch,dnames)))))
warning("data names and/or order might be wrong")
phenoP <- phenoParms()
phenoP[names(phenoControl)] <- phenoControl
TPcoefs <- as.vector(unlist(phenoP)[1:6])
n1dat <- numeric(6)
for(i in 1:6) n1dat[i] <- nrow(data[data[,1] <= TPcoefs[i],])
## coefficients for the first stage
if(n1dat[1] > 1){
dat1 <- data[c(1,n1dat[1]),]
delta.dat1 <- dat1[2,] - dat1[1,]
c1s.r <- (delta.dat1[5] / dat1[1,5])/delta.dat1[1]
}else{
if(n1dat[1] == 1){
warning("only one row for phen stage 1")
}else{
warning("zero rows for phen stage 1")
}
dat1 <- data[1,]
delta.dat1 <- dat1
c1s.r <- -1e-4
}
rsum.dat1 <- sum(delta.dat1[2:4])
c1s <- c(delta.dat1[2:4]/rsum.dat1,c1s.r)
c1s <- as.vector(unlist(c(c1s[2:1],c1s[3:4])))
## coefficients for the second stage
dat2 <- data[n1dat[1:2],]
delta.dat2 <- dat2[2,] - dat2[1,]
rsum.dat2 <- sum(delta.dat2[2:4])
c2s.r <- (delta.dat2[5] / dat2[1,5])/delta.dat2[1]
c2s <- c(delta.dat2[2:4]/rsum.dat2,c2s.r)
c2s <- as.vector(unlist(c(c2s[2:1],c2s[3:4])))
## coefficients for the third stage
dat3 <- data[n1dat[2:3],];## print(dat3)
delta.dat3 <- dat3[2,] - dat3[1,];## print(delta.dat3)
delta.dat3[delta.dat3 < 0] <- 1e-6
rsum.dat3 <- sum(delta.dat3[2:5])
c3s <- c(delta.dat3[2:5]/rsum.dat3)
c3s <- as.vector(unlist(c(c3s[2:1],c3s[3:4])))
## coefficients for the fourth stage
dat4 <- data[n1dat[3:4],]
delta.dat4 <- dat4[2,] - dat4[1,]; ##print(delta.dat4)
delta.dat4[delta.dat4 < 0] <- 1e-6
rsum.dat4 <- sum(delta.dat4[2:5])
c4s <- c(delta.dat4[2:5]/rsum.dat4)
c4s <- as.vector(unlist(c(c4s[2:1],c4s[3:4])))
## coefficients for the fifth stage
dat5 <- data[n1dat[4:5],]; ##print(dat5); print(n1dat[4:5])
delta.dat5 <- dat5[2,] - dat5[1,]; ##print(delta.dat5)
delta.dat5[delta.dat5 < 0] <- 1e-6
rsum.dat5 <- sum(delta.dat5[2:5])
c5s <- c(delta.dat5[2:5]/rsum.dat5)
c5s <- as.vector(unlist(c(c5s[2:1],c5s[3:4])))
## coefficients for the sixth stage
dat6 <- data[n1dat[5:6],]
delta.dat6 <- dat6[2,] - dat6[1,]
delta.dat6[delta.dat6 < 0] <- 1e-6
rsum.dat6 <- sum(delta.dat6[2:6])
c6s <- c(delta.dat6[2:6]/rsum.dat6)
c6s <- as.vector(unlist(c(c6s[2:1],c6s[3:5])))
cfs <- as.vector(unlist(c(c1s,c2s,c3s,c4s,c5s,c6s)))
cfs
}
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