plotBinomial: Construct regression plots of species' pairwise influences on...

In nicholasjclark/BBS.occurrences: BBS community composition and co-occurrence analysis

Description

Construct regression plots of species' pairwise influences on occurrence probabilities using model output from lassoBinomial

Usage

plotBinomial(lassoBinomial, cutoff)

Arguments

lassoBinomial	A model object returned from lassoBinomial_comm
cutoff	Positive numeric value indicating the minimum quantile of biotic coefficients' absolute values (excluding 0's) that are considered as reflective of an important influence on occurrence probability. Default is 0.05, meaning that the top 95 percent of biotic coefficients are retained when performing the polynomial regression

Details

Species' pairwise influences on occurrence probabilities are extracted from lassoBinomial$coefficients and predicted by their respective habitat niche and phylogenetic distances (extracted from data("Bird.ecol.distances") and data("Bird.phy.distances")) using a second-order polynomial regression of the form lm(Influence ~ poly(Phy.dist,2) + poly(Ecol.dist,2)). Only pairwise influences whose absolute magnitudes are above the specified cutoff quantile are used in the regression

Value

A ggplot2 object visualising predicted habitat niche and phylogenetic distance regression lines and 99 captured by each predictor

nicholasjclark/BBS.occurrences documentation built on July 19, 2020, 8:31 p.m.