I am using the R package Introgress to study introgression of SNPs between the northern and southern extents of the lodgepole X jack pine hybrid zone in western Canada.
When I use the compare.clines function with the code: comp.out
I have no idea about the package, syntax or the error code, but regarding "need two or more classes to fit a multinom model" are you sure the vector (variable) is indicated as factor, often needed for classification issue? You can check this with class(df$class_stuff).
Update: I think I have found the issue and I thought I would post it here in case someone else runs into the same one.
The compare.clines function in the introgress package does not seem to work if the minor allele frequency is less than 5% or (0.05) in both of the hybrid zones being compared.
Once I removed those SNPs, the compare.clines function worked!!
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