checkpnr: A function to distinct the cooccurence of species pairs from...

In JotSoSerious/cooccurExtra: An extension use of R package "cooccur"

Description

This is a function of the package "cooccurExtra". The main idea of this function is distincting the cooccurence ("positive", "negative", or "random") of species pairs from a "cooccur" ouput model object. It provides an output of table in the class of data frame to show probabilities as well as the classifying positive, negative or no cooccurence associations between species in each pair.

Usage

checkpnr(cooccur.mod)

Arguments

cooccur.mod

An model object generated by "cooccur" function from package "cooccur".

Value

Returns a data frame with all the needed pairs of species as well as the p-values and the cooccurence between the species in each pair.

sp1_name	Name of a specie in a pair.
sp2_name	Name of the other specie in a pair.
p_gt	Probabilities for rejecting classifying positive and negative associations between the species in each pairs.
PNR	The cooccurence associations ("positive", "negative", or "random") between the species in each pairs.

Author(s)

Yingjia Jot He

Examples

  # ask for the model generated by "coocana" (with splits)
  data(modelca)
  ModelCOC <- modelca$Model$`Full Data`

  # the default with two kinds of plots
  mytest <- checkpnr(ModelCOC)

  # show the output
  mytest

JotSoSerious/cooccurExtra documentation built on Oct. 30, 2019, 8:03 p.m.