I am trying to estimate the most likely number ok K using MCMC (Markov Chain Monte-Carlo Inference Of Clusters From Genotype Data) function in Geneland R-package by Gilles Guillot et al. I am a lit bit confused when it comes to varnpop and freq.model arguments
In the package reference manual https://cran.r-project.org/web/packages/Geneland/Geneland.pdf one may read:
varnpop = TRUE *should not* be used in conjunction with freq.model = "Correlated"
From the other hand, other manual http://www2.imm.dtu.dk/~gigu/Geneland/Geneland-Doc.pdf recommends example of MCMC usage which looks like this:
MCMC(coordinates=coord, geno.dip.codom=geno, varnpop=TRUE, npopmax=10, spatial=TRUE, freq.model="Correlated", nit=100000, thinning=100, path.mcmc="./")
I am not sure how to reconcile these two contradictory pieces of information, any suggestions?
You can use it, but you have to be aware that this could detect spurious clusters, by detecting some subtle differentiation.
Dear Dragica,
thanks for your response. To sum up, it is better not to use this option, because the results may be strange (I have actually obtained such spurious results, hence my question).
was it too much clusters, or wierd clustering? or both? Have you checked for isolation by distance in your sample? if there is some proof of it, better not to use geneland at all. tess might be beter solution according to safner et all.
- Badges
- Science topic
- Similar topics
- Mathematics
- Statistics
- Statistical Software
- R Statistical Package