colonyR package provides an interface between R and the Colony software
for parentage analysis (see http://www.zsl.org/science/software/colony). The
package was developed and has been used on a GNU/Linux platform.
colonyR relies on having Colony installed on the system, independently from
R. The Colony executable might be accessible either from
$PATH or it can be
copied directly in the R script folder (see
?colRun from R).
The functions documentation should be enough to get you up and running. Details about the parameters are to be found in the pdf manual accompanying Colony itself.
This R package has been working nicely for me until now, but be aware that I also had troubles when trying to run it on simulated genotypes (resulting in Colony crashes, for which I did not find the reason until now).