make a rudimentary colony input file

This takes a long format data frame of CKMR frequencies and a corresponding one of genotypes of individuals (gotta have LocIdx and alle1 and alle2 columns, which give the integer representation of the alleles). Then it spits out a colony file with allele freqs either specified (by default) or not.

ckmr2colony(
  CKF,
  CKG,
  freqs_known = TRUE,
  outfile = "Colony2.dat",
  err_rate = c(0.01),
  drop_rate = c(0.01)
)

Arguments

CKF

a data frame like long_markers that has the allele freqs and indexes, etc.

CKG

a data frame of genotype data. It needs to have these columns:

id

the identifier of the individual

Locus

the names of the loci

LocIdx

the index of the locus (should correspond exactly to CKF)

alle1

The integer index of the allelic type of the first gene copy in the indiv.

alle2

The integer index of the allelic type of the second gene copy in the indiv.

freqs_known

set to FALSE if you want Colony to estimate the allele freqs. Otherwise it will just use the freqs from CKF (This makes a lot of sense if you have 10,000 individuals but you don't want to run all of them in Colony)

outfile

path to the output file to send this to

err_rate

the per-locus rate of mis-genotyped loci assumed for the analysis. Recycles to the proper length.

drop_rate

the per-locus rate of assumed for the analysis. Recycles to the proper length.

Details

The idea is that you use this to follow up on clusters of pairs that look like they might be sibs of some sort. This spits out a Colony2.dat file that can be run with Colony. To change different settings and options for the run, you just hand edit that output file.