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!
|