NEWS.md

In vallenderlab/MicrobiomeR: Analyze Microbiome Data

MicrobiomeR 0.6.1

• Added StagedInstall: false to DESCRIPTION file.

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.

MicrobiomeR 0.5.2

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

MicrobiomeR 0.5.1

• 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

MicrobiomeR 0.5.0

• 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

MicrobiomeR 0.4.1

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

MicrobiomeR 0.4.0

Renamed functions

• get_alpha_diversity_measures to alpha_diversity_measures

Added functions

• Added stacked_barplots, alpha_diversity_plots, ordination_plots
• Added save_stacked_barplots, save_alpha_diversity_plots, save_ordination_plots

Deprecated functions

• Removed save_barplot

• Updated vignettes.

MicrobiomeR 0.3.1

• Added code coverage.

MicrobiomeR 0.3.0

• Changed function names
• From get_treatment_matrix to treatment_matrix
• From get_output_dir to output_dir
• From get_correlation_plots to correlation_plots
• From get_correlation_data to correlation_data
• From get_plot_limits to plot_limits
• From get_heat_tree_plots to heat_tree_plots
• From get_heat_tree_parameters to heat_tree_parameters
• From object_handler to create_metacoder

MicrobiomeR 0.2.4

• Added new tests
• Correlation plot tests
• Heat tree tests
• Metacoder Formatting tests
• Phyloseq tests

MicrobiomeR 0.2.3

Documentation Updates

• Updated documentation for create_pub_table function.

Tests Added

• Added tests for utils.R

MicrobiomeR 0.2.2

Functional Changes

• Added support for multiple treatments for some plots
• get_heat_tree_plots now produces a metacoder::heat_tree_matrix.
• correlation_plot now produces multiple plots for data with more that 2 treatments.
• Added the get_treatment_matrix function
• Added the get_correlation_data function
• Updated analysis vignette to demonstrate more than 2 treatment groups.
• Updated internal data files.
• Added new metadata file with 3 treatment groups (nephele_metadata3.txt).
• Formatted Treatment Group metadata.
• Updated public datasets.
• Removed Greengenes datasets.
• Added Silva data with 3 treatment groups.
• Added the color-palettes vignette.

MicrobiomeR 0.2.1

Features Added

• Added permanova function for generating permanova stats.
• Added top_coefficients_barplot for generating a plot of the top coefficients output from the permanova function.

Tests Added

• Added tests for permanova.R.

MicrobiomeR 0.2.0

Documentation Updates

• Added vignettes to package and pkgdown config.
• About
• Introduction
• Data Wrangling
• Filtering
• Analysis
• Added reference sections to pkgdown config corresponding to @family tag.
• Import
• Formatting
• Validation
• Filtering (Basic, Advanced, Other)
• Visualization
• Color Palettes

Functional Changes

• Renamed sample_filter to sample_id_filter.
• Renamed get_phyloseq_obj to create_phyloseq.
• Renamed format_metacoder_object to as_custom_format.
• Updated vlookup and get_color_palette parameters.
• Added the root_phyloseq_tree function.
• Fixed minor bugs in code and docs.

MicrobiomeR 0.1.3

• Added custom css for pkgdown.
• Added more sections including authors and vignettes to _pkgdown.yml.
• Fixed @importFrom sections for crayon.

MicrobiomeR 0.1.2

• Added ordination.R for ordination plots.
• Added tests for ordination plots.

MicrobiomeR 0.1.1

• Added logging and better warning messages.

MicrobiomeR 0.1.0

• Changed to a semantic versioning scheme.
• Added barplot.R file of stacked barplot functions.
• Improved get_alpha_diversity_measures function.
• Added a NEWS.md file to track changes to the package.
• Added simple tests for stacked_barplot and alpha_diversity_plot.

MicrobiomeR 0.0.9.2

• Fixes to heat tree plots

MicrobiomeR 0.0.9.1

• Added barplot.R file of stacked barplot functions.

vallenderlab/MicrobiomeR documentation built on Aug. 30, 2019, 11:24 p.m.