问题
I am an R newbie trying to fit plant photosynthetic light response curves (saturating, curvilinear) to a particular model accepted by experts. The goal is to get estimated coefficient values for Am, Rd, and LCP. Here is the error I keep getting:
Error in numericDeriv(form[[3L]], names(ind), env) :
Missing value or an infinity produced when evaluating the model
I have switched around the starting values a number of times, but still no luck. Help? Thanks you in advance. Example dataset below.
photolrc= c(3.089753, 6.336478, 7.737142, 8.004812, 8.031599)
PARlrc= c(48.69624, 200.08539, 499.29840, 749.59222, 1250.09363)
curvelrc<-data.frame(PARlrc,photolrc)
curve.nlslrc = nls(photolrc ~ Am*(1-((1-(Rd/Am))^(1-(PARlrc/LCP)))),start=list(Am=(max(photolrc)-min(photolrc)),Rd=-min(photolrc),LCP= (max(photolrc)-1)))
coef(curve.nlslrc)
回答1:
minpack.lm to the rescue:
library(minpack.lm)
curve.nlslrc = nlsLM(photolrc ~ Am*(1-((1-(Rd/Am))^(1-(PARlrc/LCP)))),
start=list(Am=(max(photolrc)-min(photolrc)),
Rd=-min(photolrc),
LCP= (max(photolrc)-1)),
data = curvelrc)
coef(curve.nlslrc)
# Am Rd LCP
#8.011311 1.087484 -20.752957
plot(photolrc ~ PARlrc, data = curvelrc)
lines(0:1300,
predict(curve.nlslrc,
newdata = data.frame(PARlrc = 0:1300)))
If you pass start = list(Am = 8, Rd = 1, LCP = -20)
to nls
you also get a successful fit.
I don't know if the parameter values are sensible estimates considering the science behind this. Can LCP be negative?
来源:https://stackoverflow.com/questions/33265467/nls-troubles-missing-value-or-an-infinity-produced-when-evaluating-the-model