Changes in version 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 - Removed the outdated lab location and improved documentation readability.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. Changes in version 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. Changes in version 0.6.1 - Added StagedInstall: false to DESCRIPTION file. Changes in version 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. Changes in version 0.5.2 - Ran devtools::spell_check() on the package to fix spelling. - Added deployment of pkgdown site to .travis.yml. Changes in version 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 Changes in version 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 Changes in version 0.4.1 - Fixed wilcoxon pvalue in analysis vignette. - Updated default color palette for stacked_barplot function. Changes in version 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. Changes in version 0.3.1 - Added code coverage. Changes in version 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 Changes in version 0.2.4 - Added new tests - Correlation plot tests - Heat tree tests - Metacoder Formatting tests - Phyloseq tests Changes in version 0.2.3 Documentation Updates - Updated documentation for create_pub_table function. Tests Added - Added tests for utils.R Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 0.1.3 - Added custom css for pkgdown. - Added more sections including authors and vignettes to _pkgdown.yml. - Fixed @importFrom sections for crayon. Changes in version 0.1.2 - Added ordination.R for ordination plots. - Added tests for ordination plots. Changes in version 0.1.1 - Added logging and better warning messages. Changes in version 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. Changes in version 0.0.9.2 - Fixes to heat tree plots Changes in version 0.0.9.1 - Added barplot.R file of stacked barplot functions.