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dcgerard / updog

Flexible Genotyping of Polyploids using Next Generation Sequencing Data
https://dcgerard.github.io/updog/
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Option `model = "f1ppdr"` is very unstable. #2

Closed dcgerard closed 6 years ago

dcgerard commented 6 years ago

Describe the bug I run into issues of non-increasing likelihoods even on the basic datasets. Right now I just include a strong warning against using it. I will probably just remove this option before resubmitting to CRAN since there seems to be little interest in supporting it.

To Reproduce

library(updog)
library(tidyverse)
data("snpdat")

snpdat %>%
  filter(snp == "SNP3") ->
  smalldat

fout1 <- flexdog(refvec  = smalldat$counts[-1],
                 sizevec = smalldat$size[-1],
                 ploidy  = 6,
                 p1ref   = smalldat$counts[1],
                 p1size  = smalldat$size[1],
                 model   = "f1ppdr",
                 bias    = 0.5)

fout2 <- flexdog(refvec  = smalldat$counts[-1],
                 sizevec = smalldat$size[-1],
                 ploidy  = 6,
                 model   = "f1ppdr",
                 bias    = 0.5)
dcgerard commented 6 years ago

I removed support for model = "f1ppdr" in 728e90cd64d18a095c8f098b6fa0a8b043092892.