Note that the data input format allows only 10 characters for the species name, so I suggest if your species names are longer than 10 characters use the function abbreviate, for example, to shorten all names to no longer than 10 characters. Also, within the function WritePhylip I concatenate species names and their number of individuals per species leaving plenty of space.
Also, mess around with the options in the "system" call to get what you want. For example, I used "R", "W" and "Y", meaning replace old outfile (R), then turn on within species analyses (W), then accept all options (Y). E..g, if you don't have an old outfile, then you obviously don't need to replace the old file with the "R" command.
(p.s. I have not tried this on a windows machine).
Here is example output:
> datout names2 dat...1. dat...2. 1 VarAIn_VarAest 0.000110 -0.000017 2 VarAIn_VarAest -0.000017 0.000155 3 VarAIn_VarEest 0.790783 -0.063097 4 VarAIn_VarEest -0.063097 0.981216 5 VarAIn_VarAreg 1.000000 -0.107200 6 VarAIn_VarAreg -0.151800 1.000000 7 VarAIn_VarAcorr 1.000000 -0.127600 8 VarAIn_VarAcorr -0.127600 1.000000 9 VarAIn_VarEreg 1.000000 -0.064300 10 VarAIn_VarEreg -0.079800 1.000000 11 VarAIn_VarEcorr 1.000000 -0.071600 12 VarAIn_VarEcorr -0.071600 1.000000 13 VarAOut_VarEest 0.790734 -0.063104 14 VarAOut_VarEest -0.063104 0.981169 15 VarAOut_VarEreg 1.000000 -0.064300 16 VarAOut_VarEreg -0.079800 1.000000 17 VarAOut_VarEcorr 1.000000 -0.071600 18 VarAOut_VarEcorr -0.071600 1.000000 19 logL_withvar_df -68.779770 6.000000 20 logL_withoutvar_df -68.771450 3.000000 21 chisq_df -0.016640 3.000000 22 chisq_p 1.000000 -999.000000
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