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funrar 1.5.0

NEW FEATURES

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

INTERNAL CHANGES

• Fix uses of the Matrix package for their next version
• Reorganized documentation to please goodpractice

USER-FACING CHANGES

• 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.

funrar 1.4.1

BUG FIX

• fix use of tidytext for upcoming version (#42, thanks @juliasilge !)
• remove dependency on dplyr to avoid breaking due to next dplyr release

funrar 1.4.0

NEW FEATURES

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

BUG FIX

• 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

funrar 1.3.1

BUG FIX

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

funrar 1.3.0

NEW FEATURES

• 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().

BUG FIX

• Warning when distinctiveness equals NaN in distinctiveness_stack() (#30).

funrar 1.2.2

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

funrar 1.2.1

• 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).

funrar 1.2.0

• 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.

funrar 1.1.1

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

funrar 1.1.0

• 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.

funrar 1.0.3

• 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.

funrar 1.0.2

• 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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.