Package index • canaper

Community matrix randomization

cpr_rand_comm(): Randomize a single community matrix

cpr_iter_sim(): Simulate the number of iterations needed to generate a random community that is sufficiently different from the original community

Randomization tests

The main focus of this package, conducting randomization tests of biodiversity metrics

cpr_rand_test(): Run a randomization analysis for one or more biodiversity metrics

Classification

Functions to classify the results of the randomization test

cpr_classify_endem(): Classify phylogenetic endemism

cpr_classify_signif(): Classify statistical significance

Datasets

Datasets included in this package

acacia: Acacia example data

biod_example: Biodiverse example data

phylocom: Phylocom example data

biod_results: Output from Biodiverse

Color palettes

Colors for plotting classification results

cpr_make_pal(): Make a palette of colors for plotting CANAPE results

mishler_endem_cols: Original color palette for plotting results of CANAPE

cpr_endem_cols: CVD-friendly color palette for plotting results of CANAPE

cpr_endem_cols_2: CVD-friendly color palette for plotting results of CANAPE, version 2

cpr_endem_cols_3: CVD-friendly color palette for plotting results of CANAPE, version 3

cpr_endem_cols_4: CVD-friendly color palette for plotting results of CANAPE, version 4

mishler_signif_cols: Original color palette for plotting results of CANAPE

cpr_signif_cols: CVD-friendly color palette for plotting results of randomization test

cpr_signif_cols_2: CVD-friendly color palette for plotting results of randomization test, version 2