# R/findCiTransition.R In plantecophys: Modelling and Analysis of Leaf Gas Exchange Data

#### Documented in findCiTransition

```#' Calculate transition points for fitted A-Ci curves
#'@description Calculates the Ci at the transition points between Ac & Aj (point 1), and Aj and Ap (point 2). The latter is not NA only when TPU was estimated (and estimable), see \code{\link{fitaci}}, argument \code{fitTPU}.
#'@param object Either an object returned by \code{fitaci}, or a copy of the \code{Photosyn} function.
#'@param \dots Further arguments passed to the \code{Photosyn} function.
#'@details This function is also used by \code{fitaci}, the results are stored in elements \code{Ci_transition} and \code{Ci_transition2}.
#'@export
findCiTransition <- function(object, ...){

if(is.function(object)){
photofun <- object
} else {
photofun <- object\$Photosyn
}

O <- function(Ci, photofun, point, ...){
x <- photofun(Ci=Ci, ...)
if(point == 1){
Ac <- x\$Ac - x\$Rd
Aj <- x\$Aj - x\$Rd
return((Ac - Aj)^2)
}
if(point == 2){
Aj <- x\$Aj - x\$Rd
Ap <- x\$Ap - x\$Rd
return((Aj - Ap)^2)
}
}
p1 <- optimize(O, c(25,2000), photofun=photofun, point=1, ...)\$minimum

r <- photofun(Ci=500, ...)

if(r\$Ap >= 1000 | is.na(r\$Ap)){
p2 <- NA
} else {
p2 <- optimize(O, c(400,2000), photofun=photofun, point=2, ...)\$minimum
}

return(c(Ac_Aj=p1, Aj_Ap=p2))
}
```

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plantecophys documentation built on April 1, 2021, 1:06 a.m.