View source: R/cpr_classify_endem.R
cpr_classify_endem | R Documentation |
Given the results of cpr_rand_test()
, classifies phylogenetic endemism
according to CANAPE scheme of Mishler et al. 2014.
cpr_classify_endem(df)
df |
Input data frame. Must have the following columns:
|
For a summary of the classification scheme, see: http://biodiverse-analysis-software.blogspot.com/2014/11/canape-categorical-analysis-of-palaeo.html # nolint
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).
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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/ncomms5473")}
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)
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