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