version 1.5.xx (2014-04-17) + Incorporating biom-format support with the biom2MRexperiment, MRexperiment2biom and load_biome function. + Added uniqueFeatures, filterData, aggregateByTaxonomy / aggTax, plotFeature and calculateEffectiveSamples functions. + Renamed MRfisher to fitPA (presence-absence fisher test). + Added warnings for normalization + Added fitDO (Discovery odds ratio test) and fitMeta (original metastats). + Added match.call() info to fitZig output + Fixed missing E-Step bounds version 1.2.xx (2013-08-20) + Our paper got accepted and is available! + Added methods for MRexperiment objects (colSums,colMeans,rowSums,rowMeans, usage is for example colSums(obj) or colSums(obj,norm=TRUE)) (09-25) + Added two new functions, plotOrd and plotRare - a function to plot PCA/MDS coordinates and rarefaction effect (09-04,09-18) + Updated MRfisher to include thresholding for presence-absence testing (08-19) + Updated comments (roxygen2) style for all the functions using the Rd2roxygen package (07-13) + Updated plotCorr and plotMRheatmap to allow various colors/not require trials(07-13) + Rewrote vignette (and switched to knitr) version 1.1.xx (last update 2013-06-25) + Rewrote load_meta and load_metaQ to be faster/use less memory + Modified cumNormStat to remove NA samples from calculations (example would be samples without any counts) + Re-added plotGenus' jitter + Fixed uniqueNames call in the MR tables + Changed thanks to Kasper Daniel Hansen's suggestions the following: plotOTU and plotGenus both have much better auto-generated axis MRtable, MRfulltable, MRcoefs have a sort by p-value option now MRtable, MRfulltable, MRcoefs now have an extra option to include unique numbers for OTU features (default would automatically add them previously) cumNorm.R - now returns the object as well - not just replacing the environment 0 Still need to turn the fitZig output to S3, consider subsetting function address low p-values version 1.0.0: (2013-03-29) + Release!