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I am getting an error message in a call to nlme and cannot understand what is happening. I explain the steps below in the hope that someone can explain the error and how to correct it. STEP 1: Data set: name: marouane.data. This is a data frame whose first few lines are as follows: > marouane.data[1:13,] species plant leaf irradiance photosynthesis chlorophyll 1 Asclepias.incarnata 1 1 0 -2.091359 0.02619 2 Asclepias.incarnata 1 1 50 1.153241...

...y outputs the initial estimates. I can also use the nlsList with this function to get the separate nonlinear fits by group. However, I get an error message when using the nlme function. Here is the relevent code: fit<-nlsList(photosynthesis~photo(irradiance,Q,Am,LCP)|species/plant/leaf,da ta=marouane.data, + na.action=na.omit) This works, showing that the function "photo" works as a self-starting function. nlme(model=photosynthesis~photo(irradiance,Q,Am,LCP), + data=marouane.data,fixed=Q+Am+LCP~1, + random=Q+Am+LCP~1|species,na.action=na.omit) Error: subscript out of bounds This i...

I am having difficulty understanding the syntax of the nlme() function for nonlinear mixed models. The data frame is called Marouane.chlorophyll. The model involves a dependent variable (Absorb) and an independent variable (Ch.surf), which are both numeric variables in the data frame. The data are hierarchically grouped as Espece, Plante nested within Espece, and Feuille nested within Plante (i.e. leaves within plants within...