Changes in version 1.9.9 (2019-12-25) + noncore_members removed + Added aggregate_rare function + Bioc polishing Changes in version 1.9.2 (2019-12-25) + Divergence function rewritten for clarity * Switched from sapply to vapply + Removed noncore_abundance + Fixing plot_core axis labeling + is.compositional function added + spreadplot function added + removed ready made themes from functions + Renamed is.compositional to is_compositional + Fixed a bug in core_members (also non-compositional detection now allowed) + removed rm.na option from aggregate_taxa + Deprecating noncore_* functions (replacing with rare_* functions everywhere) + Removed variable_members function + Support removed from R-3.3.3 and lower Changes in version 1.5.4 (2018-11-20) + Removed theme() commands from functions to give the choice to user + Fixed bug in merge_taxa2 + Fixed bug in Pielou's evenness + New functions: readcount, bfratio, aggregate_top_taxa + rewritten aggregate_taxa and moved the top argument in the new function aggregate_top_taxa + plot_composition function: new options for sample.sort and otu.sort + Added Phylum level to taxonomy tables in example data sets * New function: dominant + The diversities function is now replaces by alpha function. The alpha is more generic and can return also other alpha diversity indices. + plot_frequencies function now only returns the ggplot object + Renamed the global function into alpha + Renamed arguments rarity.detection and rarity.prevalence into detection and prevalence in the rarity function + Added Chao1 index in richness function + In atlas1006 data set, pseudocount of +1 in otu table has been removed to facilitate comparison with sequencing data sets and to avoid confusion + In atlas1006 data set, only a single replicate per subject-time combination is chosen (at random) + New function collapse_replicates has been added + Abundance matrices (otu tables) for all example data sets now starting from 0 without pseudocount + Changed the default for the detection argument in the richness function to detection=0 + removed rarity.threshold and rarity.prevalence options from the alpha function + Various minor fixes; see github commits for many more details o Color order in plot_landscape legend now follows the factor levels of the col argument o Fixed example in remove_samples CHANGES IN VERSION 1.1.2 # New features o Added plot_abundances function o Added Chao1 index in richness function o In atlas1006 data set, pseudocount of +1 in otu table has been removed to facilitate comparison with sequencing data sets and to avoid confusion o In atlas1006 data set, only a single replicate per subject-time combination is chosen (at random) o New function collapse_replicates has been added # Major changes o Abundance matrices (otu tables) for all example data sets now starting from 0 without pseudocount # Minor changes o Changed the default for the detection argument in the richness function to detection=0 o Color order in plot_landscape legend now follows the factor levels of the col argument o Various minor fixes; see github commits for many more details CHANGES IN VERSION 1.1.1 (2017-30-11) o Added index "observed" in function global o New options added to transform: scale, log10p o New bioc devel version CHANGES IN VERSION 0.99.8 (2017-08-21) o Added new function merge_taxa2 o Added sample names in divergence output o coreset option added in divergence o plot_taxa_prevalence argument "detection" added o transform argument removed from plot_composition for simplicity o data/DynamicsIBD data set and associated documentation removed to shrink the package o inst/extdata/qiita data sets and associated documentation removed to shrink the package o Baxter data removed to save space o Utilities that do not belong to the package moved to maintenance branch CHANGES IN VERSION 0.99.6 (2017-07-21) o Fixed bug in transform option "clr" o "lineplot" option added in plot_composition CHANGES IN VERSION 0.99.5 (2017-07-07) o fixed vignette headers o heat function now takes also labels as input for order.rows and order.cols o added age_group and bmi_group for easy access to standard groupings of these variables o package homepage host location changed to master:docs/ CHANGES IN VERSION 0.99.3 (2017-06-05) o Reduced the number of dependencies o Removed marginal functionality CHANGES IN VERSION 0.99.1 (2017-05-15) o Major rewrite of the package o Switched to support the phyloseq class o HTML vignette added o A separate online tutorial added o Removed less essential functionality and dependencies CHANGES IN VERSION 0.99.0 (2014-09-14) o First draft of the BioC release version CHANGES IN VERSION 0.3.63 (2012-12-24) o separated MySQL/preprocessing functions into a distinct package, HITChipDB CHANGES IN VERSION 0.3.43 (2012-09-28) o added relative.abundance function o polished estimate.diversity function o added functions: richness, evenness, diversity CHANGES IN VERSION 0.3.15 (2012-08-31) o FetchHITChipAtlas and run.profiling.script validated against each other o default imputation removed from run.profiling.script; this had considerable effect on normalized data CHANGES IN VERSION 0.3.13 (2012-08-30) o standardized the pipeline; output validated against previous atlas version CHANGES IN VERSION 0.3.05 (2012-08-22) o added MDS.classical and MDS.isometric to project.data CHANGES IN VERSION 0.3.02 (2012-06-20) o calculate.stability function added o added L2->species option to levelmap function o estimate.diversity function updated. Detection thresholds applied with richness and evenness o estimate.min.threshold mode detection improved o cross.correlate function added CHANGES IN VERSION 0.3.01 (2012-06-19) o draft version for GitHub CHANGES IN VERSION 0.2.04 (2012-06-15) o RMySQL removed from explicit dependencies CHANGES IN VERSION 0.2.03 (2012-06-06) o hitchip.phylodistance added o cross-hyb control functions added CHANGES IN VERSION 0.2.02 (2012-06-03) o annotation functions added CHANGES IN VERSION 0.2.01 (2012-05-31) o removed absolute scale matrices from run.profiling.script output. The idea is that just one log10 file for each phylogenetic level is outputted, and the user can then use other reading/analysis routines to read the data, convert to original non-log domain if necessary, etc. This is to provide a unique output format to avoid mistakes. o save.data and tree.display removed from run.profiling.script arguments o combined get.phylogeny and get.phylogeny.MITChip o moved plotting functions from run.profiling.script into a separate function profiling.hclust; o removed the option to read profiling parameters from R file in ReadParameters function o output file name phylogenyinfo.tab changed into phylogenyinfo-nspecies.tab o made run.profiling.script modular with respect to preprocessing, plotting, data storage, and logging o added instructions in the vignette on reading the final data CHANGES IN VERSION 0.12.14 (2012-05-10) o added pitchipdb in PITChip array name list in profiling.R CHANGES IN VERSION 0.12.12 (2012-05-02) o added MITChip level 0 o added separate get.phylogeny.MITChip function to include level 0 for MITChip CHANGES IN VERSION 0.12.10 (2012-04-17) o automatized the levels and methods output within run.profiling.script o now providing also non-logarithmized data matrices in the run.profiling.script output o added in run.profiling.script save.image(paste(params$wdir, "/tmp.RData", sep = "")) to enable the use of data from the current workspace during a session o multcomp replaced by parallel in dependencies o Removed "Use existing data from the workspace" (useDB) option. Problems when called from within a function. More clear and modular when the run.profiling.script is used for preprocessing, and any new plots are performed as separate steps based on the profiling output files if needed. o Moved run.profiling.script plots to their own functions and added usage examples to vignette. CHANGES IN VERSION 0.12.08 (2012-04-05) o detailed protocol added to the vignette o hierarchical clustering method moved from complete to ward in profiling script as it was in some of the previous versions o 'level 0' added in MITChip profiling o removed featureprofile from output files to save disk space, typically not needed o added remove.nonspecific.oligos option to run.profiling.script and FetchHITChipAtlas functions (through get.phylogeny) o summarize.probesets modified to include levels both in the form of "level.1" and "level 1" CHANGES IN VERSION 0.12.06 (2012-04-04) o fixed PITChip-specific issues o removed parallel from dependencies to allow compatibility with R-2.12.2 CHANGES IN VERSION 0.12.05 (2012-03-29) o removed background correction from profiling script (run.profiling.script) o kept standard normalizations: none, minmax, quantile - others removed o now using 16S phylogeny in profiling script. Other option removed o polishing of the functions o merged funcions from the phyloarray package o removed minmax, quantnorm from profiling.R functions CHANGES IN VERSION 0.12.04 (2012-03-28) o removed the additional background correction step which resulted in considerable information loss based on external validations CHANGES IN VERSION 0.12.01 (2012-03-23) o PlotMatrix updates CHANGES IN VERSION 0.0.12 (2012-03-15) o multicore removed from dependencies o vignette updated o R-2.12.1 required CHANGES IN VERSION 0.0.10 (2012-03-06) o standard profiling script included o added selected.samples in fetch.sample.info CHANGES IN VERSION 0.0.08 (2012-02-25) o Atlas preprocessing finalized. For usage examples, see vignette. CHANGES IN VERSION 0.0.05 (2012-02-22) o atlas functions added and polished CHANGES IN VERSION 0.0.02 (2012-02-06) o profiling_010.r script functions and dependencies added CHANGES IN VERSION 0.0.01 (2012-01-12) o First version based on profiling script version 010