I need to test a suite of argument conditions in order to find the best model (using the drc
package). That is, I'd like to store function arguments in a list and then call them into the drm()
function. The drc
package has a function (mselect()
) to do this, but it has been known to fail for unknown reasons (https://www.reddit.com/r/Rlanguage/comments/a1bu44/any_idea_what_im_doing_wrong_with_the_mselect/).
Example Data
library(drc) # This also loads in the S.alba data
data(S.alba)
head(S.alba)
Dose Herbicide DryMatter
1 0 Glyphosate 4.7
2 0 Glyphosate 4.6
3 0 Glyphosate 4.1
4 0 Glyphosate 4.4
5 0 Glyphosate 3.2
6 0 Glyphosate 3.0
Failed Attempt
# List of function arguments to be assessed e.g. drm(...fct = W1.4(fixed = c(NA, 0.1, NA, NA)
model_list <- list(curve = c(W1.4(fixed = c(NA, 0.1, NA, NA)),
LL.4(fixed = c(NA, 0.1, NA, NA))))
# Failed function, attempting to return a list of results
model_select <- function(data, mlist){
model = data %>%
drm(DryMatter ~ Dose, Herbicide, data = . , fct = mlist)
metric = AIC(model)
return(metric)
}
model_select(data = S.alba, mlist = model_list)
Error in drm(DryMatter ~ Dose, Herbicide, data = ., fct = mlist) : First entry in list to 'fct' NOT a function
Semi-Working Attempt
model_select_2 <- function(data){
model = data %>%
drm(DryMatter ~ Dose, Herbicide, data = . , fct = W1.4(fixed = c(NA, 0.1, NA, NA)))
metric = AIC(model)
return(metric)
}
model_select_2(data = S.alba)
model_select_2(data = S.alba)
[1] 106.9226
Desired Output
model_select(data = S.alba, mlist = model_list)
[1] W1.4-106.9226
[2] LL.4-99.54702
Part of the problem is how you are creating model_list
. You want to combine those values with list()
rather than c()
. The latter tried to combine them into the same object.
The next thing you can do is sapply
over the list of curves to get the result for each input. A working example would be
model_list <- list(curve = list(W1.4(fixed = c(NA, 0.1, NA, NA)),
LL.4(fixed = c(NA, 0.1, NA, NA))))
model_select <- function(data, mlist){
sapply(mlist$curve, function(curve){
model <- drm(DryMatter ~ Dose, Herbicide, data = data , fct = curve)
metric = AIC(model)
})
}
model_select(data = S.alba, mlist = model_list)
# [1] 106.92259 99.54702