In my last post, I discussed the use of odds ratios to characterize the association between edibility and binary mushroom characteristics for the mushrooms characterized in the UCI mushroom dataset. I did not, however, describe those co...

The bigmemory is an excellent package for handling big matrix in R. There are several sister packages provided by "The Bigmemory Project": biganalytics for analysis, bigtabulate for tabulation, bigalgebra for linear algebra functionality, synchronicity for synchronization via mutexes and interprocess communication and message passing.biganalytics provides a few functions for analysis: linear regression model, generalized linear regression model, and...

I provide here an R function to estimate gene diversity of diallelic sites (e.g. SNPs), given allele frequencies at each segregating site. The function takes three input parameters: maf: a numeric value (or vector) representing minor allele frequency at each site. Default is 0.5 nreads: size of each resampling experiment. Default is 10000. nreplicates: Number

I’m a HUGE fan of Structural Equation Modeling. Heck, I’ve even begun teaching short SEM workshops. (seriously, if you want, email me and we’ll talk). For those of you unfamiliar with the technique, it’s awesome for three main reasons. It’s a method of teasing apart direct and indirect interactions in your data. It allows you