v0.7.1-alpha

WIP:  Fix issues with taxa package breaking changes

Potential fix for #111

0.7.0

MicrobiomeR 0.7.0

• Added biomodality_coefficient function from modes.
• Removed modes from DESCRIPTION and NAMESPACE.
• Fixed bug from breaking changes in metacoder.

0.6.1

MicrobiomeR 0.6.1

• Added StagedInstall: false to DESCRIPTION file.

0.6.0

MicrobiomeR 0.6.0

• Improved documentation of ordination methods and distances.
• Deprecated select_otu_table parameter for alpha_diversity_plot.
• Added site deployment key to travis-ci.com
• Migrated continuous integration to travis-ci.com
• Fixed height of stat comparisons.

0.5.2

MicrobiomeR 0.5.2

• Ran devtools::spell_check() on the package to fix spelling.
• Added deployment of pkgdown site to .travis.yml.

0.5.1

Changes and Bug Fixes

• A specific bug was introduced that prevented local machines and Travis CI servers from building
  the package.

  • This bug is attributed to a dplyr update (0.7.8 -> 0.8.0.1)
  • See Joss branch #79
  • See Joss debug branch #82
  • See dplyr issue #4213
  • See Travis CI forum post

• Updated the paper for submission

• Added the JOSS paper and draft vignette

• Changed correlation plots

  • Removed color from background
  • Removed hard coded plot limits
  • Added "1:1" line and Average lines
  • Added a trans parameter to transform the x and y axis

• Changed function names

  • From create_metacoder to create_taxmap
  • From agglomerate_metacoder to agglomerate_taxmap
  • From melt_metacoder to melt_taxmap

• Bugs

  • Fixed output_dir bug where error should have been a warning
  • Fixed correlation plot bug where treatments were on the wrong axis.
  • Fixed output message for heat tree plots.

• Fixed build-check Notes and Warnings

0.4.1

Changes

• Fixed wilcoxon pvalue in analysis vignette.
• Updated default color palette for stacked_barplot function.

0.4.0

MicrobiomeR

An R package for microbiome analysis that incorporates phyloseq,
metacoder, taxa, and microbiome in order to standardize and simplify common microbiome workflows.

Installation

We are currently not on CRAN or Bioconductor:

library(devtools) # Load the devtools package
install_github("vallenderlab/MicrobiomeR") # Install the package

Workflow Features

• Standardization of data wrangling.
  • Phyloseq for data import.
  • Taxa for the primary data object (Taxmap).
  • Proprietary data formatting and validation.
• Phyloseq inspired filtering for taxa::taxmap objects.
  • Metacoder/taxa for mainstream filtering.
  • Proprietary basic filtering for samples, taxonomies, and OTUs.
  • Proprietary advanced filtering (phyloseq-style).
  • Other Proprietary filtering functions for observation data.
• Metacoder enabled statistical analysis functions.
• Various visualization options.
  • Output Directories
  • Color Palettes
  • Heat Trees
  • Correlation Plots
  • Stacked Bar Plot
  • Alpha Diversity Plot
  • Ordination Plot