r - Fitting with ggplot2, geom_smooth and nls

Question

I am trying to fit data on an exponential decay function (RC like system) with equation:

My data are on the following dataframe:

dataset <- data.frame(Exp = c(4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6), t = c(0, 0.33, 0.67, 1, 1.33, 1.67, 2, 4, 6, 8, 10, 0, 33, 0.67, 1, 1.33, 1.67, 2, 4, 6, 8, 10, 0, 0.33, 0.67, 1, 1.33, 1.67, 2, 4, 6, 8, 10), fold = c(1, 0.957066345654286, 1.24139015724819, 1.62889151698633, 1.72008539595879, 1.82725412314402, 1.93164365299958, 1.9722929538061, 2.15842019312484, 1.9200507796933, 1.95804730344453, 1, 0.836176542548747, 1.07077717914707, 1.45471712491441, 1.61069357875771, 1.75576377806756, 1.89280913889538, 2.00219054189937, 1.87795513639311, 1.85242493827193, 1.7409346372629, 1, 0.840498729335292, 0.904130905000499, 1.23116185602517, 1.41897551928886, 1.60167656534099, 1.72389226836308, 1.80635095956481, 1.76640786872057, 1.74327897001172, 1.63581509884482))

I have 3 experiment (Exp: 4, 5 and 6) data I want to fit each experiment on the given equation.

I have managed to do it for of the experiment by subsetting my data and using the parameter calculated by nls

test <- subset(dataset,Exp==4)
fit1 = nls(fold ~ 1+(Vmax*(1-exp(-t/tau))),
  data=test,
  start=c(tau=0.2,Vmax=2))
ggplot(test,aes(t,fold))+
  stat_function(fun=function(t){1+coef(fit1)[[2]]*(1-exp(-t/coef(fit1)[[1]]))})+
  geom_point()

But if I try to use the geom_smooth function directly on the full dataset with this code

d <- ggplot(test,aes(t,fold))+
   geom_point()+
   geom_smooth(method="nls", 
     formula='fold~1+Vmax*(1-exp(-t/tau))',
     start=c(tau=0.2,Fmax=2))
print(d)

I get the following error:

Error in model.frame.default(formula = ~fold, data = data, weights = weight) : 
  variable lengths differ (found for '(weights)')
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf

Is there anything wrong with my syntax? I would have this one working in order to use the same function on the dataset and using group to have one fit per Exp level.

Answer 1

There are several problems:

1. formula is a parameter of nls and you need to pass a formula object to it and not a character.
2. ggplot2 passes y and x to nls and not fold and t.
3. By default, stat_smooth tries to get the confidence interval. That isn't implemented in predict.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 intervals

Edit:

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)