Perform Phylogenetic Path Analysis

A comprehensive and easy to use R implementation of confirmatory phylogenetic path analysis as described by Von Hardenberg and Gonzalez-Voyer (2012) .


News

  • IMPORTANT: Faulty model averaging has been fixed. This was often introduced due to differences in matrix ordering. Avering results from versions before 0.2.1 should NOT be trusted.

  • Using ape::corBrownian() no longer returns an error.

  • Averaging is less likely to fail due to errors in nlme::intervals().

  • phylo_path() has become more streamlined with functionality moved to other functions. The phylopath object now containts all necessary models and data, summary() is used to obtain the results table, and best() and average() are used to extract and fit the best or average model. See the vignette for details.

  • Model averaging for arbitrary models is now possible with average_DAGs().

  • Model averaging now supports both conditional and full model averaging.

  • Both the old est_DAG() and the new average_DAGs() now return objects of a new class fitted_DAG, that has it's seperate plot method. The plot method for objects of class DAG has been simplified.

  • Model averaging now returns standard errors and confidence intervals based on the MuMIn package (issue #1).

  • A new function plot_coefs for plotting regression coefficients and their confidence intervals has been added.

Reference manual

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install.packages("phylopath")

0.2.3 by Wouter van der Bijl, 3 months ago


https://github.com/Ax3man/phylopath


Report a bug at https://github.com/Ax3man/phylopath/issues


Browse source code at https://github.com/cran/phylopath


Authors: Wouter van der Bijl


Documentation:   PDF Manual  


GPL-3 license


Imports ape, DiagrammeR, dplyr, ggm, ggplot2, igraph, MuMIn, nlme, parallel, pbapply, purrr, tibble, tidyr

Suggests knitr, rmarkdown


See at CRAN