pgls.report: Report PGLS results as a table

In mmodely: Modeling Multivariate Origins Determinants - Evolutionary Lineages in Ecology

Report PGLS results as a table

Description

Output a spreadsheet ready tabular summary of a fit PGLS model

Usage

pgls.report(cd, f=formula('y~x'), l=1,k=1,d=1, 
            bounds=list(lambda=c(.2,1),kappa=c(.2,2.7),delta=c(.2,2.7)), 
            anova=FALSE, mod.no='NA', out='pgls.output-temp',QC.plot=FALSE)

Arguments

cd	a comparative data object, here created by 'comp.data'
f	the model formula (as acharacter string)
k	the fixed or 'ML' value for kappa
l	the fixed or 'ML' value for lambda
d	the fixed or 'ML' value for delta
bounds	a list of vectors of upper and lower bounds for kappa, lambda, and delta
anova	should an anova be run on the fit model and output to the terminal?
mod.no	the model number (can be the order that models were run)
out	the base filename to be printed out
QC.plot	should a quality control plot be output to screen?

Value

A summary results of a fit PGLS model with ANOVA and tabular spreadsheet ready csv filesystem output.

Examples

data.path <- system.file("extdata","primate-example.data.csv", package="mmodely")
data <- read.csv(data.path, row.names=1)
data$gn_sp <- rownames(data)

tree.path <- system.file("extdata","primate-springer.2012.tre", package="mmodely")
#5. RAxML phylogram based on the 61199 bp concatenation of 69 nuclear and ten mitochondrial genes. 
phyl <- ape::read.tree(tree.path)[[5]]

phyl <- trim.phylo(phylo=phyl, gs.vect=data$gn_sp)

comp <- comp.data(phylo=phyl, df=data)

pgls.report(comp, f=formula('OC~mass.Kg + DPL.km'), l=1,k=1,d=1,
             anova=FALSE, mod.no='555', out='', QC.plot=TRUE)

mmodely documentation built on May 31, 2023, 6:47 p.m.