sam_example_schoolfield_nlme.R

# load package
library(nlsLoop)
library(nlme)
library(ggplot2)
library(dplyr)

# create dummy data
example <- data.frame(expand.grid(K = 280:330, rep = 1:3))

# create dummy params
params <- data.frame(rep = 1:3, 
                     ln.c = rnorm(3, mean = 1, sd = 0.5),
                     Ea = rnorm(3, mean = 0.6, sd = 0.2),
                     Eh = rnorm(3, mean = 3, sd = 0.5),
                     Th = rnorm(3, mean = 320, sd = 3))

# create rate data
example <- merge(example, params, by = 'rep') %>%
  mutate(log_rate = schoolfield.high(ln.c, Ea, Eh, Th, temp = K, Tc = 10),
         rep = as.factor(rep))

# quickplot
ggplot(example) +
         geom_line(aes(K, log_rate, col = factor(rep)))
         
# example mixed model code for a single species
# the trickiest part here is knowing how many 0s after the each parameter you need in the start = argument
# not needed here as we have no fixed effect factors
# set up controls
control <- nlmeControl(maxIter = 10000, tol = 1e-15)
MM <- nlme(log_rate ~ schoolfield.high(ln.c, Ea, Eh, Th, temp = K, Tc = 10),
                        data = example,
                        fixed = list(ln.c + Ea + Eh + Th ~ 1),
                        random =  pdDiag(ln.c + Ea + Eh ~ 1), # doesn't seem to fit with Th in. Too little random variance
                        na.action = na.omit,
                        groups = ~ rep,  
                        start = c(1, 0.6, 3, 320),
                        control = control)