Multifunc Michaelis-Menten

MMmultifunc.R

library(multifunc)

#A function to get mm coefs
mmCoef <- function(adf){
  options(warn=2)
  
  mod <- try(nls(funcMaxed~Vm*Diversity/(K+Diversity), start=list(Vm=1, K=5),
      data=adf))
  
  options(warn=0)
  
  #if there was a problem, catch it and just return NAs for this coefficient
  if("try-error" %in% class(mod)) return(rep(NA, 4))
  
  out <- c(coef(mod), coef(summary(mod))[,2])
  names(out) <- c("Vm", "K", "se.Vm", "se.K")
  out
}

#see ?getFuncsMaxed for code to generate germanyThresh
mmGermany <- ddply(germanyThresh, "thresh", mmCoef)


ggplot(mmGermany, aes(x=thresh, y=K, ymin=K-1.96*se.K, ymax=K+1.96*se.K)) +
  geom_ribbon(fill="grey50", alpha=0.8) +
  geom_point() + 
  theme_bw() +
  stat_hline(yintercept=0, lwd=2, lty=2)



ggplot(mmGermany, aes(x=thresh, y=Vm, ymin=Vm-1.96*se.Vm, ymax=Vm+1.96*se.Vm)) +
  geom_ribbon(fill="grey50", alpha=0.8) +
  geom_point() + 
  theme_bw() +
  stat_hline(yintercept=0, lwd=2, lty=2)


#see the vignette on how to generate bdThreshes
mmBD <- ddply(bdThreshes,c("location", "thresholds"), mmCoef)


ggplot(mmBD, aes(x=thresholds, y=K, ymin=K-1.96*se.K, ymax=K+1.96*se.K)) +
  #geom_ribbon(fill="grey50", alpha=0.8) +
  geom_point() + 
  theme_bw() +
  stat_hline(yintercept=0, lwd=2, lty=2) +
  facet_wrap(~location) +
  ylim(c(-1,16))