pgls.report {mmodely}

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)