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

#### Defines functions TTEM.fun

```# TTEM - Based on PmaxT1 + GR50M
TTEM.fun <- function(time, Temp, G, Tc, sigmaTc, Tb, ThetaT, b) {
Pmax <- PmaxT1.fun(Temp, G, Tc, sigmaTc)
GR50 <- GRT.M.fun(Temp, Tc, Tb, ThetaT)
GR50 <- ifelse(GR50<=0, 1e-06, GR50)
plogis(b * (log(time) - log(1/GR50)) )*Pmax
}
"TTEM" <- function(){
fct <- function(x, parm) {
S <- TTEM.fun(x[,1], x[,2], parm[,1], parm[,2], parm[,3], parm[,4],
parm[,5], parm[,6])
}
names <- c("G", "Tc", "sigmaTc", "Tb", "ThetaT", "b")
ss <- function(data){
data <- subset(data, is.finite(data[,1])==T)
result <- c()
TempF <- factor(data[,2])
for(i in 1:length(levels(TempF))){
temp <- subset(data, data[,2] == levels(TempF)[i])
x <- temp[,1]; y <- temp[,3]
modT <- try(drm(y ~ x, fct=LL.3()), silent=T)
#modT <- try(nls(y ~ NLSLL.3(x, a, b, c)), silent=T)
if(class(modT) == "try-error") {res <- as.numeric(levels(TempF)[i])
result <- c(result, res) }
}
dataset_cum <- subset(data, is.finite(data[,1])==T)
if(is.null(result)!=T){
for(i in 1:length(result)) dataset_cum <- subset(dataset_cum, dataset_cum[,2] != result[i])}
TempF <- factor(dataset_cum[,2])

x1 <- dataset_cum[,1]
x2 <- dataset_cum[,2]
y <- dataset_cum[,3]

modI <- drm(y ~ x1, fct=LL.3(), curveid=TempF, pmodels=list(~1,~TempF-1,~TempF-1), data=dataset_cum)
psiLevels <- as.numeric(levels(TempF))
b <- -coef(modI)[1]
Pmax <- coef(modI)[2:(length(psiLevels)+1)]
modPmax <- drm(Pmax ~ psiLevels, fct=PmaxT1())
G <- coef(modPmax)[1]; Tc1 <- coef(modPmax)[2]; sigmaTc <- coef(modPmax)[3]

GR50 <- 1/coef(modI)[(length(psiLevels)+2):length(coef(modI))]
modGR <- drm(GR50 ~ psiLevels, fct=GRT.M())
Tc2 <- coef(modGR)[1]; Tb <- coef(modGR)[2]; ThetaT <- coef(modGR)[3]
Tc <- (Tc1 + Tc2)/2
#temp <- c(G, Tc, sigmaTc, k, Tb, ThetaT, b)
#print(temp)
return(c(G, Tc, sigmaTc, Tb, ThetaT, b)) }
text <- "Thermal-time model with shifted exponential for Pmax and Mesgaran model for GR50"
GR <- function(parms, respl=50, reference="control", type="relative", Temp){
G <- as.numeric(parms[1]); Tc <- as.numeric(parms[2])
sigmaTc <- as.numeric(parms[3]);
Tb <- as.numeric(parms[4]); ThetaT <- as.numeric(parms[5])
b <- as.numeric(parms[6])
g <- respl/100
if(type=="absolute"){
.Pmax <- PmaxT1.fun(Temp, G, Tc, sigmaTc)
.Pmax <- ifelse(.Pmax > 0, .Pmax, 0)
.temp2 <- (.Pmax - g)/g
.temp2 <- ifelse(.temp2 < 0, 0, .temp2)
.GR50 <- GRT.M.fun(Temp, Tc, Tb, ThetaT)
.GR50 <- ifelse(.GR50>0, .GR50, 0)
res <- as.numeric( exp( - (1/b)*log(.temp2) + log(1/.GR50) ) )
EDp <- 1/res
.GR <- EDp
EDder1 <- 1/.GR * ((1/b) * ((1/g) * (.Pmax/G)/((1/g) * (.Pmax - g))))/exp(-(1/b) *log((1/g) * (.Pmax - g)) + log(1/.GR50))^2
EDder2 <- 1/.GR * (ThetaT * (( (Temp - Tb)/(Tc - Tb))^2 )/(.GR50*ThetaT)^2/(1/.GR50) + (1/b) * ( (G * (exp(-(Tc - Temp)/sigmaTc) * (1/sigmaTc)))/((.Pmax - g))))/(1/.GR)^2
EDder3 <- -(1/.GR * ((1/b) * ((1/g) * (G * (exp(-(Tc - Temp)/sigmaTc) * ((Tc - Temp)/sigmaTc^2)))/((1/g) * (.Pmax - g))))/(1/.GR)^2)
EDder4 <- (1/.GR) * (ThetaT * ((1/(Tc - Tb) - (Temp - Tb)/(Tc - Tb)^2) * (Temp - Tb) - (1 - (Temp - Tb)/(Tc - Tb)))/((1 - (Temp - Tb)/(Tc - Tb)) * (Temp - Tb))^2/(1/.GR50))/(1/.GR)^2
EDder5 <- -(1/.GR * (1/((1 - (Temp - Tb)/(Tc - Tb)) * (Temp - Tb))/(1/.GR50))/(1/.GR)^2)
EDder6 <- -(1/.GR * (1/b^2 * log((1/g) * ((G * (1 - exp(-(Tc - Temp)/sigmaTc))) - g)))/(1/.GR)^2)
EDder <- c(EDder1, EDder2, EDder3, EDder4, EDder5, EDder6)
} else{ if(type=="relative") {
.Pmax <- PmaxT1.fun(Temp, G, Tc, sigmaTc)
.Pmax <- ifelse(.Pmax > 0, .Pmax, 0)
.temp2 <- (1 - g)/g
.GR50 <- GRT.M.fun(Temp, Tc, Tb, ThetaT)
.GR50 <- ifelse(.GR50>0, .GR50, 0)
res <- as.numeric( exp( - (1/b)*log(.temp2) + log(1/.GR50) ) )
EDp <- 1/res
.GR <- EDp
EDder1 <- 0
EDder2 <- (1/.GR) * (ThetaT * (((Temp - Tb)/(Tc - Tb))^2 )/(.GR50*ThetaT)^2/(1/.GR50))/(1/.GR)^2
EDder3 <- 0
EDder4 <- (1/.GR) * (ThetaT * ((1/(Tc - Tb) - (Temp - Tb)/(Tc - Tb)^2) * (Temp - Tb) - (1 - (Temp - Tb)/(Tc - Tb)))/(.GR50*ThetaT)^2/(1/.GR50))/(1/.GR)^2
EDder5 <- -(1/.GR * (1/((1 - (Temp - Tb)/(Tc - Tb)) * (Temp - Tb))/(1/.GR50))/(1/.GR)^2)
EDder6 <- -(1/.GR * (1/b^2 * log((1/g) * (1 - g)))/(1/.GR)^2)
EDder <- c(EDder1, EDder2, EDder3, EDder4, EDder5, EDder6)
} }
return(list(EDp, EDder))
}
deriv1 <- function(x, parm){
#Approximation by using finite differences

d1.1 <- TTEM.fun(x[,1], x[,2], parm[,1], parm[,2], parm[,3],
parm[,4], parm[,5], parm[,6])
d1.2 <- TTEM.fun(x[,1], x[,2], (parm[,1] + 10e-6), parm[,2], parm[,3],
parm[,4], parm[,5], parm[,6])
d1 <- (d1.2 - d1.1)/10e-6

d2.1 <- TTEM.fun(x[,1], x[,2], parm[,1], parm[,2], parm[,3],
parm[,4], parm[,5], parm[,6])
d2.2 <- TTEM.fun(x[,1], x[,2], parm[,1], (parm[,2] + 10e-6), parm[,3],
parm[,4], parm[,5], parm[,6])
d2 <- (d2.2 - d2.1)/10e-6

d3.1 <- TTEM.fun(x[,1], x[,2], parm[,1], parm[,2], parm[,3],
parm[,4], parm[,5], parm[,6])
d3.2 <- TTEM.fun(x[,1], x[,2], parm[,1], parm[,2], (parm[,3] + 10e-6),
parm[,4], parm[,5], parm[,6])
d3 <- (d3.2 - d3.1)/10e-6

d4.1 <- TTEM.fun(x[,1], x[,2], parm[,1], parm[,2], parm[,3],
parm[,4], parm[,5], parm[,6])
d4.2 <- TTEM.fun(x[,1], x[,2], parm[,1], parm[,2], parm[,3],
(parm[,4] + 10e-6), parm[,5], parm[,6])
d4 <- (d4.2 - d4.1)/10e-6

d5.1 <- TTEM.fun(x[,1], x[,2], parm[,1], parm[,2], parm[,3],
parm[,4], parm[,5], parm[,6])
d5.2 <- TTEM.fun(x[,1], x[,2], parm[,1], parm[,2], parm[,3],
parm[,4], (parm[,5] + 10e-6), parm[,6])
d5 <- (d5.2 - d5.1)/10e-6

d6.1 <- TTEM.fun(x[,1], x[,2], parm[,1], parm[,2], parm[,3],
parm[,4], parm[,5], parm[,6])
d6.2 <- TTEM.fun(x[,1], x[,2], parm[,1], parm[,2], parm[,3],
parm[,4], parm[,5], (parm[,6] + 10e-6))
d6 <- (d6.2 - d6.1)/10e-6

cbind(d1, d2, d3, d4, d5, d6)
}

returnList <- list(fct=fct, ssfct=ss, names=names, text=text, edfct=GR, deriv1 = deriv1)
class(returnList) <- "drcMean"
invisible(returnList)
}
```
OnofriAndreaPG/drcSeedGerm documentation built on Oct. 9, 2019, 3:45 p.m.