NEWS
aa05dcce
 version 1.15.xx (2016)
 	+ Added 'mergeMRexperiment' function
 	+ Replaced RUnit with testthat library for unit testing
 	+ Adding multiple upgrades and changes throughout
552624f1
 	+ Deprecated the load_* functions and created load* function.
9a964a43
 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"
30b095c3
 	+ Fixed s2 miscalculation in calcZeroComponent
da6bbd1f
 version 1.11.xx (2015)
 	+ Adding fitFeatureModel - a feature based zero-inflated log-normal model.
88ed5d7c
 	+ Added MRcoefs,MRtable,MRfulltable support for fitFeatureModel output.
 	+ Added mention in vignette.
18700986
 	+ Added support for normalizing matrices instead of just MRexperiment objects.
 	+ Fixed cumNormStat's non-default qFlag option 
79ae68b7
 version 1.9.xx (2015)
29b13be6
 	+ Added flexibility in formula choice for fitTimeSeries
79ae68b7
 	+ Added readability in ssPermAnalysis
f8c701b5
 	+ Fixed default in plotClassTimeSeries (include = c("1",...))
eb3ffd7c
 	+ Added fitTimeSeries vignette
7284c919
 	+ Removed interactiveDisplay to namespace - moved to suggests
 	+ Fixed ordering of MRtable,MRfulltable first four columns
86e03520
 	+ modified df estimated through responsibilities
3e4d5fe3
 	+ renamed fitMeta to fitLogNormal - a more appropriate name
65e0e07d
 version 1.7.xx (2014-05-07)
e54e12aa
 	+ Added function plotBubble
7ec77ed5
 	+ Added parallel (multi-core) options to fitPA, fitDO
e54e12aa
 	+ 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
2ddba19e
 	+ (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)
e093bc69
 	+ (1.7.18) fitTimeSeries Including times series method for differentially abundant time intervals
b9482b9c
 	+ (1.7.20) Fixed minor bug for OTU level time series analyses and added plotClassTimeSeries
f98b43d4
 	+ (1.7.26) Added warning / fix if any samples are empty in cumNormStat
58e2f308
 	+ (1.7.27) Added a few unit tests
c8c0ac82
 	+ (1.7.29) Added interactiveDisplay to namespace (display function allows interactive exploration / plots through browser)
63ecea0f
 version 1.5.xx (2014-04-17)
218839b9
 	+ Incorporating biom-format support with the biom2MRexperiment, MRexperiment2biom and load_biome function.
240ea475
 	+ Added uniqueFeatures, filterData, aggregateByTaxonomy / aggTax, plotFeature and calculateEffectiveSamples functions.
679d9067
 	+ Renamed MRfisher to fitPA (presence-absence fisher test).
63ecea0f
 	+ Added warnings for normalization 
b327ef52
 	+ Added fitDO (Discovery odds ratio test) and fitMeta (original metastats).
927898ea
 	+ Added match.call() info to fitZig output
63ecea0f
 	+ Fixed missing E-Step bounds
d0c17b88
 version 1.2.xx (2013-08-20)
57a36c3d
 	+ 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) 
cd3d7e5b
 
7654e349
 version 1.1.xx (last update 2013-06-25)	
57a36c3d
 	+ 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
03d3c28b
 
57a36c3d
 	+ Changed thanks to Kasper Daniel Hansen's suggestions the following:
7654e349
 		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
57a36c3d
 	0 Still need to turn the fitZig output to S3, consider subsetting function address low p-values
bed02ed2
 
452e2105
 version 1.0.0: (2013-03-29)
57a36c3d
 	+ Release!