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High-Performance Open-Source Archive

NEWS

funrar 1.5.0

Added a new vignette named “other_functions” to document recently added functions. You can access it through vignette("other_functions", package = "funrar")

Remove warnings regarding relative abundances for the distinctiveness_*() functions as they can perfectly work with absolute abundances giving the same results.
Fix typo in name of sparse matrices vignette.

Implement distinctiveness_global() to compute occurrence based distinctiveness at the global/regional level using only a distance matrix

Fix tests that used data.frame() now with explicit stringAsFactors values for compatibility with R 4.0.0
Add missing tests on bad inputs for some functions

Test explicitly for matrix type in rarity_dimensions() for compatibility with R 4.0.0

Add _tidy() aliases for each _stack() function for easier reading (fix #29).
distinctiveness_stack() returns NA as distinctiveness values for absent species (#30).
New definition of functional distinctiveness based on range see distinctiveness_range().
New definition of functional distinctiveness based on range with different formula see distinctiveness_alt().

Fix a bug in the test of distinctiveness_dimensions() that generated errors on cran server.

Add Authors’ ORCID and all contributors;
funrar paper is now included in DESCRIPTION, README.md and has a proper CITATION file;
Fix typos in documentation;
Transformation from tidy data.frame to sparse matrix is now possible using stack_to_matrix(x, sparse = TRUE) (#25);
Add a warning message when using only continuous traits with function comput_dist_matrix(), as it defaults to Gower’s distance (#27);
Specification in help that functional distances need to be scaled between 0 and 1 prior to distinctiveness computation (#26).

Split rarity_dimensions() in two more explicit functions: uniqueness_dimensions() and distinctiveness_dimensions() split corresponding tests;
Add internal function to compute multiple functional distance matrix using a single trait table (combination_trait_dist());
distinctiveness() now fully conserve the dimnames of the provided site-species matrix.

Add tests for rarity_dimensions();
rarity_dimensions() now comprises both Uniqueness and Distinctiveness;
Remove packages StatMatch, microbenchmark & reshape2 from suggested packages.

Made make_absolute() defunct because it was based on false assumptions and would not give back matrices of relative abundances;
Improved examples of make_relative(), uniqueness(), distinctiveness() to compute across single communities or regional pools;
Add rarity_dimensions() function to measure the different facets of rarity according to the trait;
Add center and scale arguments in compute_dist_matrix() to scale traits before computing distance, these arguments are sensitive to the specific distance metric used;
Use markdown with roxygen2 to generates documentation.

Corrected bug so that dense matrices can be transformed to stack data frame using matrix_to_stack() (#19),
Updated citation for Violle et al. 2017,
Use package goodpractice to enforce better code style,
Add is_relative() function to test if matrix contains relative abundances, scarcity() and distinctiveness() now warns if it is not the case (#21),
Conditional use microbenchmark following CRAN advice.

Added functions to convert absolute abundance matrix to relative abundance matrix, make_relative() and reverse function make_absolute(),
Added a NEWS.md file to track changes to the package.

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