msm: Fit a Multispecies Model

In wkmor1/msmod: Fit Multispecies Models

Description

Fit a Multispecies Model

Usage

msm(y, sites, x, species, traits, data, site_re = FALSE, type = c("mstm",
  "jsdm"), method = c("glmer", "jags", "stan"), ...)

Arguments

y	Character. Column name of response variable, species occurrences.
sites	Character. Column name of site variable.
x	Character. Column names of site level predictor variables.
species	Character. Column name of species variable.
traits	Character. Column names of species trait variables. Ignore
data	A data.frame containing the variables for the model.
site_re	Logical. Should a site level random effect be included.
type	The type of model to fit either 'mstm', multispecies trait model, or 'jsdm', joint species distribution model.
method	The method used to fit the model.
...	Further arguments to pass on to model fitting functions.

Examples

msm_glmer <- msm('present', 'plot', 'logit_rock', 'species', 'ln_sla', eucs)
msm_glmer_probit <- msm('present', 'plot', 'logit_rock', 'species', 'ln_sla',
  eucs, family = binomial(link = 'probit'))
msm_jags <- msm('present', 'plot', 'logit_rock', 'species', data = eucs, type = 'jsdm',
  method = 'jags')

wkmor1/msmod documentation built on May 4, 2019, 7:34 a.m.