version 1.15.xx (2016) + Added 'mergeMRexperiment' function + Added 'normFactors' and 'libSize' generics + Added 'fitMultipleTimeSeries' function + Replaced RUnit with testthat library for unit testing + Adding multiple upgrades and changes throughout + Deprecated the load_* functions and created load* function. version 1.13.xx (2015) + Upgrade support for biom-format vs. 2.0 + Fixed issue - "MRtable, etc will report NA rows when user requests more features than available" + Fixed s2 miscalculation in calcZeroComponent version 1.11.xx (2015) + Adding fitFeatureModel - a feature based zero-inflated log-normal model. + Added MRcoefs,MRtable,MRfulltable support for fitFeatureModel output. + Added mention in vignette. + Added support for normalizing matrices instead of just MRexperiment objects. + Fixed cumNormStat's non-default qFlag option version 1.9.xx (2015) + Added flexibility in formula choice for fitTimeSeries + Added readability in ssPermAnalysis + Fixed default in plotClassTimeSeries (include = c("1",...)) + Added fitTimeSeries vignette + Removed interactiveDisplay to namespace - moved to suggests + Fixed ordering of MRtable,MRfulltable first four columns + modified df estimated through responsibilities + renamed fitMeta to fitLogNormal - a more appropriate name version 1.7.xx (2014-05-07) + Added function plotBubble + Added parallel (multi-core) options to fitPA, fitDO + Fixed bug for fitMeta when useCSSoffset=FALSE and model matrix ncol==2 + (1.7.10) Updated default quantile estimate (.5) for low estimates + (1.7.10) Added short description on how to do multiple group comparisons + (1.7.15) Output of fitZig (eb) is now a result of limma::eBayes instead of limma::ebayes + (1.7.16) plotMRheatmap allows for sorting by any stat (not just sd) + (1.7.18) fitTimeSeries Including times series method for differentially abundant time intervals + (1.7.20) Fixed minor bug for OTU level time series analyses and added plotClassTimeSeries + (1.7.26) Added warning / fix if any samples are empty in cumNormStat + (1.7.27) Added a few unit tests + (1.7.29) Added interactiveDisplay to namespace (display function allows interactive exploration / plots through browser) 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!