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NEWS
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version 1.25.xx (2019)
+ Added 'wrenchNorm' function
+ Added option to use IHW as p-value adustment method in 'MRcoefs'
+ Modified 'expSummary' slot in 'MRexperiment' object to be of class 'list' instead of 'environment'
+ Added results classes for 'fitZig' and 'fitFeatureModel' results
version 1.21.xx (2018)
+ Numerous changes. Added greater flexibility to fitFeatureModel
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!