Fitting with ggplot2, geom_smooth and nls
There are several problems:
formulais a parameter ofnlsand you need to pass a formula object to it and not a character.- ggplot2 passes
yandxtonlsand notfoldandt. - By default,
stat_smoothtries to get the confidence interval. That isn't implemented inpredict.nls.
In summary:
d <- ggplot(test,aes(x=t, y=fold))+ #to make it obvious I use argument names instead of positional matching geom_point()+ geom_smooth(method="nls", formula=y~1+Vmax*(1-exp(-x/tau)), # this is an nls argument, #but stat_smooth passes the parameter along start=c(tau=0.2,Vmax=2), # this too se=FALSE) # this is an argument to stat_smooth and # switches off drawing confidence intervalsEdit:
After the major ggplot2 update to version 2, you need:
geom_smooth(method="nls", formula=y~1+Vmax*(1-exp(-x/tau)), # this is an nls argument method.args = list(start=c(tau=0.2,Vmax=2)), # this too se=FALSE)