R/GRT.Ex.R In OnofriAndreaPG/drcSeedGerm: Statistical approaches for data analyses in seed germination assays

Defines functions GRT.Exb.funGRT.Ex.fun

```# Exponential with switch-off (Catara et al., 2017)
#Original. ThetaT is not comparable to the other models
GRT.Ex.fun <- function(Temp, Tb, ThetaT, k, Tc) {
GR50 <- ((Temp - Tb)/ThetaT) * (1 - exp(k * (Temp - Tc)))
return(ifelse(GR50 < 0 , 0 , GR50)) }
"GRT.Ex" <- function(){
fct <- function(x, parm) {
GR50 <- GRT.Ex.fun(x, parm[,1], parm[,2], parm[,3], parm[,4])
return(GR50) }
names <- c("Tb", "ThetaT", "k", "Tc")
ss <- function(data){
pos <- which( data[,2]==max(data[,2]) )
len <- length( data[,2] )

reg1 <- data[1:pos, ]
reg2 <- data[pos:len, ]
x1 <- reg1[,1]; y1 <- reg1[, 2]
x2 <- reg2[,1]; y2 <- reg2[, 2]

ss1 <- coef( lm(y1 ~ x1) )
ThetaT <- 1/ss1[2]
Tb <- - ss1[1] * ThetaT
ss2 <- coef( lm((1-y2) ~ x2) )
k <- ss2[2]
To <- - ss2[1] / k
Tc <- (1 - ss2[1])/ss2[2]

return(c(Tb, ThetaT, k, Tc))}
deriv1 <- function(x, parm){
#Approximation by using finite differences
d1.1 <- GRT.Ex.fun(x, parm[,1], parm[,2], parm[,3],
parm[,4])
d1.2 <- GRT.Ex.fun(x, (parm[,1] + 10e-6), parm[,2], parm[,3],
parm[,4])
d1 <- (d1.2 - d1.1)/10e-6

d2.1 <- GRT.Ex.fun(x, parm[,1], parm[,2], parm[,3],
parm[,4])
d2.2 <- GRT.Ex.fun(x, parm[,1], (parm[,2] + 10e-6), parm[,3],
parm[,4])
d2 <- (d2.2 - d2.1)/10e-6

d3.1 <- GRT.Ex.fun(x, parm[,1], parm[,2], parm[,3],
parm[,4])
d3.2 <- GRT.Ex.fun(x, parm[,1], parm[,2], (parm[,3] + 10e-6),
parm[,4])
d3 <- (d3.2 - d3.1)/10e-6

d4.1 <- GRT.Ex.fun(x, parm[,1], parm[,2], parm[,3],
parm[,4])
d4.2 <- GRT.Ex.fun(x, parm[,1], parm[,2], parm[,3],
(parm[,4] + 10e-6))
d4 <- (d4.2 - d4.1)/10e-6

cbind(d1, d2, d3, d4)
}

text <- "Exponential effect of temperature on GR50 (Masin et al., 2017)"
returnList <- list(fct=fct, ssfct=ss, names=names, text=text, deriv1 = deriv1)
class(returnList) <- "drcMean"
invisible(returnList)
}

# Exponential with switch-off (From Masin et al., 2017 - modified)
GRT.Exb.fun <- function(Temp, Tb, ThetaT, k, Tc) {
GR50 <- ((Temp - Tb)/ThetaT) * ((1 - exp(k * (Temp - Tc)))/(1 - exp(k * (Tb - Tc))))
return(ifelse(GR50 < 0 , 0 , GR50)) }
"GRT.Exb" <- function(){
fct <- function(x, parm) {
GR50 <- GRT.Exb.fun(x, parm[,1], parm[,2], parm[,3], parm[,4])
return(GR50) }
names <- c("Tb", "ThetaT", "k", "Tc")
ss <- function(data){
pos <- which( data[,2]==max(data[,2]) )
len <- length( data[,2] )

reg1 <- data[1:pos, ]
reg2 <- data[pos:len, ]
x1 <- reg1[,1]; y1 <- reg1[, 2]
x2 <- reg2[,1]; y2 <- reg2[, 2]

ss1 <- coef( lm(y1 ~ x1) )
ThetaT <- 1/ss1[2]
Tb <- - ss1[1] * ThetaT
ss2 <- coef( lm((1-y2) ~ x2) )
k <- ss2[2]
To <- - ss2[1] / k
Tc <- (1 - ss2[1])/ss2[2]
return(c(Tb, ThetaT, k, Tc))}

deriv1 <- function(x, parm){
#Approximation by using finite differences
d1.1 <- GRT.Exb.fun(x, parm[,1], parm[,2], parm[,3],
parm[,4])
d1.2 <- GRT.Exb.fun(x, (parm[,1] + 10e-6), parm[,2], parm[,3],
parm[,4])
d1 <- (d1.2 - d1.1)/10e-6

d2.1 <- GRT.Exb.fun(x, parm[,1], parm[,2], parm[,3],
parm[,4])
d2.2 <- GRT.Exb.fun(x, parm[,1], (parm[,2] + 10e-6), parm[,3],
parm[,4])
d2 <- (d2.2 - d2.1)/10e-6

d3.1 <- GRT.Exb.fun(x, parm[,1], parm[,2], parm[,3],
parm[,4])
d3.2 <- GRT.Exb.fun(x, parm[,1], parm[,2], (parm[,3] + 10e-6),
parm[,4])
d3 <- (d3.2 - d3.1)/10e-6

d4.1 <- GRT.Exb.fun(x, parm[,1], parm[,2], parm[,3],
parm[,4])
d4.2 <- GRT.Exb.fun(x, parm[,1], parm[,2], parm[,3],
(parm[,4] + 10e-6))
d4 <- (d4.2 - d4.1)/10e-6

cbind(d1, d2, d3, d4)
}

text <- "Exponential effect of temperature on GR50 (Type II - Masin et al., 2017)"
returnList <- list(fct=fct, ssfct=ss, names=names, text=text, deriv1 = deriv1)
class(returnList) <- "drcMean"
invisible(returnList)
}
```
OnofriAndreaPG/drcSeedGerm documentation built on Oct. 9, 2019, 3:45 p.m.