Changelog

Source: NEWS.md

MicrobiomeR 0.8.0

  • Fixed heat-tree rank generation so each rank is filtered independently and nodes are sized by retained descendant OTU counts.
  • Clarified the heat-tree node-size interpretation in the package documentation.
  • Removed the outdated lab location and improved documentation readability.
  • Restored stacked barplot sample labels and removed y-axis baseline padding (#109).
  • Completed package citation metadata and usage guidance (#33).
  • Made the .rda input-validation test independent of the test working directory.
  • Reduced routine test and vignette build time with deterministic, clearly labeled example-data subsets while preserving the full exported datasets.

MicrobiomeR 0.6.2

  • Added compatibility shims for upstream metacoder/taxa API drift, including a local parse_phyloseq() fallback for the upstream ranks_ref bug and removal of stale modes and taxa import paths.

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

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.