GLMER: Fit a fixed-structure generalized linear mixed-effects model

In timnewbold/StatisticalModels: What the package does (short line)

Fit a fixed-structure generalized linear mixed-effects model

Description

Fit a generalized linear mixed-effects model with a fixed model structure

Usage

GLMER(modelData,responseVar,fitFamily,fixedStruct,
                      randomStruct,saveVars=character(0),REML=TRUE,
                     optimizer="bobyqa",maxIters=10000)

Arguments

modelData	A data frame containing the response variable, and all fixed and random effects in the specified model structure
responseVar	The response variable to fit in the model
fitFamily	The family to use for the generalized linear mixed effects model
fixedStruct	The fixed effects to include, in the format of a glmer model-call
randomStruct	The random effects to include, in the format of a glmer call
saveVars	Any variables in the original data frame to retain in the model data frame for later analysis
REML	Whether to use Restricted Maximum Likelihood for fitting the model. Alternative is simple maximum likelihood. Default is to use REML
optimizer	The GLMER optimizer to use. Options are 'bobyqa' (the default) and 'Nelder_Mead'
maxIters	The maximum number of iterations to allow by the optimizer (default is 10,000)

Value

model: the model

data: the dataset used in to fit the model, i.e. a subset of the original data frame, containing only the variables fit in the model, variables specified to be saved, and with any rows containing NA values removed

Author(s)

Tim Newbold <[e-mail]>

Examples

# Load example data (site-level effects of land use on biodiversity from the PREDICTS database)
data(PREDICTSSiteData)

# Run a model of log-transformed total abundance as a function of land use, human population density
# and distance to nearest road (with an interaction between human population density
# and road distance)
m1 <- GLMER(modelData = PREDICTSSites,responseVar = "LogAbund",fitFamily = "gaussian",
fixedStruct = "LandUse+poly(logHPD.rs,2)+poly(logDistRd.rs,2)+poly(logHPD.rs,2):poly(logDistRd.rs,2)",
randomStruct = "(1|SS)+(1|SSB)",REML = TRUE)

timnewbold/StatisticalModels documentation built on Aug. 25, 2023, 4:58 p.m.