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NEWS.md

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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.