Changelog

Source: NEWS.md

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 loggging 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.