I am investigating the presence of convergent evolution in a dataset containing 20 trait variables. I need to test for convergence on each trait individually, I am trying to set up a loop to do this. However, I am getting errors on my loops and I am not sure why. I can run each variable independently in the function perfectly.
I am using the package windex and am using the function test.windex. This function uses a data.frame containing information about which species are the focal ones and the traits that one wishes to test convergence on. The function also requires a phylogenetic tree for the species included in the data.frame.
To create a reproducible example I am using the sample data supplied with the package windex as my data is confidential (I have run the following and get the same errors as with my own data).
data(sample.data) #data.frame containing the focal species and variables
data(sample.tree) #phylogentic tree
head(sample.data)
species focals bm1 bm2 bm3
1 s4 0 13.03895 17.2201554 11.43644
2 s7 0 18.22705 15.2427947 22.75245
3 s8 0 12.38588 10.5858736 13.80216
4 s9 0 24.79114 8.1148456 23.38717
5 s11 1 28.20126 -2.9911114 15.63215
6 s12 1 29.45775 0.9225023 12.09184
ou1 ou2 ou3 bin
1 13.03895 17.220155 11.43644 1
2 18.22705 15.242795 22.75245 2
3 12.38588 10.585874 13.80216 3
4 24.79114 8.114846 23.38717 4
5 21.22215 21.936316 20.30037 5
6 21.24501 20.952824 20.88650 6
#My loop, it is the traits that I need to loop for each trait variable in the sample.data
sapply(sample.data[3:8], function(x) test.windex(sample.data,sample.tree,traits= x,
focal=sample.data[,2], reps=1000,plot=TRUE,col="light grey"))
This code generates the error: Error in .subset(x, j) : only 0's may be mixed with negative subscripts
Called from: [.data.frame(dat, , traits)
I am assuming that it is some sort of an indexing problem, but I just can't seem to find a way around it. I tried this instead, but also go the same error:
traitsonly<-sample.data[3:8]
sapply(traitsonly, function(x) test.windex(sample.data,sample.tree,traits= x,
focal=sample.data[,2], reps=1000,plot=TRUE,col="light grey"))
Any help would be greatly appreciated.
From the help page of test.windex it accepts column number or column name.
traits Column numbers (or names) of the traits for which you want to calculate a Wheatsheaf index.
So either of these should work.
library(windex)
sapply(3:8, function(x)
test.windex(sample.data,sample.tree,traits= x,
focal=sample.data[,2], reps=1000,plot=TRUE,col="light grey")
) -> plot
Or
sapply(names(sample.data)[3:8], function(x)
test.windex(sample.data,sample.tree,traits= x,
focal=sample.data[,2], reps=1000,plot=TRUE,col="light grey")
) -> plot