cpr_classify_endem {canaper}R Documentation

Classify phylogenetic endemism

Description

Given the results of cpr_rand_test(), classifies phylogenetic endemism according to CANAPE scheme of Mishler et al. 2014.

Usage

cpr_classify_endem(df)

Arguments

df

Input data frame. Must have the following columns:

  • pe_obs_p_upper: Upper p-value comparing observed phylogenetic endemism to random values

  • pe_alt_obs_p_upper: Upper p-value comparing observed phylogenetic endemism on alternate tree to random values

  • rpe_obs_p_upper: Upper p-value comparing observed relative phylogenetic endemism to random values

Details

For a summary of the classification scheme, see: http://biodiverse-analysis-software.blogspot.com/2014/11/canape-categorical-analysis-of-palaeo.html # nolint

Value

Object of class data.frame with column endem_type (character) added. Values of endem_type type include paleo (paleoendemic), neo (neoendemic), ⁠not significant⁠ (what it says), mixed (mixed endemism), and super (super-endemic; both pe_obs and pe_obs_alt are highly significant).

References

Mishler, B., Knerr, N., González-Orozco, C. et al. (2014) Phylogenetic measures of biodiversity and neo- and paleo-endemism in Australian Acacia. Nat Commun, 5: 4473. doi:10.1038/ncomms5473

Examples


set.seed(12345)
data(phylocom)
rand_test <- cpr_rand_test(
  phylocom$comm, phylocom$phy,
  null_model = "curveball", metrics = c("pe", "rpe"), n_reps = 10
)
cpr_classify_endem(rand_test)


[Package canaper version 1.0.0 Index]