DrK-Lo
commented
9 years ago Would using R and "system()" as a front to call other programs written in C (Bayenv, LFMM, etc) count under this umbrella?
Open smanel opened 9 years ago
DrK-Lo
commented
9 years ago Would using R and "system()" as a front to call other programs written in C (Bayenv, LFMM, etc) count under this umbrella?
darencard
commented
9 years ago Having a wrapper for many popular stand-alone programs would be welcomed by many I think. No sense in re-inventing the wheel, though in some cases it may be necessary to reimplement things. It would be especially helpful to provide integration with the other capabilities (e.g., plotting) in R. I also think that the pseudo-GUI environment provided by RStudio and certain packages could bridge the gap to those with little experience with large genetic datasets.
smanel
commented
9 years ago Yes using R and "system()" as a front to call other programs (Bayenv, LFMM) if possible would be very useful... The same for the detection of population genetic structure like STRUCTURE or other bayesian clustering approaches...
thibautjombart
commented
9 years ago I can see the appeal but this typically poses dependency problems and will make a package trickier to get onto CRAN. The use the system() for system calls is also probably fairly platform dependent.
On Mon, Mar 9, 2015 at 1:05 PM, Manel notifications@github.com wrote:
Yes using R and "system()" as a front to call other programs (Bayenv, LFMM) if possible would be very useful... The same for the detection of population genetic structure like STRUCTURE or other bayesian clustering approaches...
— Reply to this email directly or view it on GitHub https://github.com/NESCent/r-popgen-hackathon/issues/7#issuecomment-77849289 .
KlausVigo
commented
9 years ago What would be the requisites for a population genetics task view or mailing list on CRAN, like the task view and the mailing list for phylogentics and comparative methods? This would give pop gene users in R an overview over available packages and available functionality right on the R website and a source for FAQs.
thibautjombart
commented
9 years ago They exist already: http://cran.r-project.org/web/views/Genetics.html
https://stat.ethz.ch/mailman/listinfo/r-sig-genetics
R-sig-genetics has been massively under-used so far - just a matter of getting the right people in though.
On Mon, Mar 9, 2015 at 6:32 PM, klash notifications@github.com wrote:
What would be the requisites for a population genetics task view or mailing list on CRAN, like the task view http://cran.r-project.org/web/views/Phylogenetics.html and the mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-phylo for phylogentics and comparative methods? This would give pop gene users in R an overview over available packages and available functionality right on the R website and a source for FAQs.
— Reply to this email directly or view it on GitHub https://github.com/NESCent/r-popgen-hackathon/issues/7#issuecomment-77914283 .
Not fully clear of how and what but a suggestion below on how promoting R packages in population genetics, since it is probably one of the end-product of our working group (?): A way to do is to publish well –driven applications using (almost) only R packages (already existing and developed during the hackathon): it can help users to better know about and to see the possibilities. This requires using free existing databases already published, and to address hot topic questions in populations genetics (e.g. detection of climatic signal of selection, ....). It would be wonderful to have unpublished databases, but probably not possible.