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evolvability

evovability is an R-package for calculating evolvability parameters from G-matrices (see Hansen and Houle 2008 https://doi.org/10.1111/j.1420-9101.2008.01573.x and Bolstad et al. 2014 https://doi.org/10.1098/rstb.2013.0255) and for fitting phylogenetic comparative models that link the rate of evolution of a trait to the state of another evolving trait (see Hansen et al. 2021 Systematic Biology https://doi.org/10.1093/sysbio/syab079).

The package includes two vignettes. One on analyzing rates of evolution and one on fitting phylogenetic mixed models.

The latest version of the package can be downloaded by devtools::install_github(repo = "GHBolstad/evolvability", build_vignettes = TRUE)

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Version

Install

install.packages('evolvability')

Monthly Downloads

244

Version

2.0.0

License

GPL (>= 2)

Maintainer

Geir H Bolstad

Last Published

December 8th, 2021

Functions in evolvability (2.0.0)

meanStdGMCMC

Mean standardize the posterior distribution of a G-matrix
phylH

Phylogenetic heritability
evolvabilityMeansMCMC

Calculate posterior distribution of average evolvability parameters of a G-matrix
simulate_rate

Simulating evolutionary rate model
round_and_format

Rounds and formats in the same function
evolvabilityMeans

Calculate average evolvability parameters of a G-matrix
rate_gls

Generalized least squares rate model
randomBeta

Generating selection gradients/vectors in random directions.
macro_pred

Macroevolutionary predictions
summary.evolvabilityBetaMCMC

Summarizing posterior distribution of evolvability parameters over a set of selection gradients
meanStdG

Mean standardize a variance matrix
plot.simulate_rate

Plot of simulate_rate object
rate_gls_boot

Bootstrap of the rate_gls model fit
plot.rate_gls

Plot of rate_gls object
rate_gls_sim

Simulate responses from rate_gls fit
evolvabilityBetaMCMC2

Calculate posterior distribution of evolvability parameters from a selection gradient estimated with uncertainty
summary.evolvabilityBeta

Summarizing evolvability parameters over a set of selection gradients
Almer

Linear mixed model with correlated random effects structure
evolvabilityBeta

Calculate evolvability parameters along a set of selection gradients
GLS

Generalized least square
Almer_boot

Parametric bootstrap on Almer model fit
Almer_SE

Linear mixed model for response variables with uncertainty
evolvability-package

Calculation of Evolvability Parameters
evolvabilityBetaMCMC

Calculate posterior distribution of evolvability parameters from a set of selection gradients
Almer_sim

Simulate responses from Almer fit
conditionalG

Computing a conditional sub-matrix of G