Package: RADstackshelpR 0.1.0

This vignette/article is designed to provide a fully reproducible example of how to use the RADstackshelpR package to optimize STACKS parameters. Each bash code chunk gives a generic example of code you could use to execute the STACKS pipeline. Each R code chunk uses extremely light (20 samples, ~200 SNPs), toy vcf files which are distributed with the package, in order to provide fully reproducible examples for end-users. These chunks should run successfully if you have successfully installed the package. | Demultiplex | Iterate over potential values for the 'm' parameter in the 'ustacks' module | Use RADstackshelpR to visualize the output of these 5 runs and determine the optimal value for the parameter 'm'. | Iterate over potential values for the 'M' parameter in the 'ustacks' module | Use RADstackshelpR to visualize the output of these 8 runs and determine the optimal value for the parameter 'M'. | Iterate over potential values for the 'n' parameter in the 'cstacks' module | Use RADstackshelpR to visualize the output of these 3 runs and determine the optimal value for 'n'.