The l1ou package provides functions to study trait evolution from comparative data and detect past changes in the expected mean trait values, as well as convergent evolution. It uses the Ornstein-Uhlenbeck process along a phylogenetic tree, which can model a changing adaptive landscape over time and over lineages. Shifts can be detected from multiple traits, assuming that all traits shifted along the same lineages. Estimation is very fast thanks to lasso techniques, and the user can choose from multiple information criteria for model selection, including a phylognetic BIC. Citation:
From within R:
install.packages("devtools") library(devtools) install_github("glmgen/genlasso") install_github("khabbazian/l1ou")
Windows users will first need to install Rtools.
To resolve dependencies, first install the following packages from CRAN, then the knitr package. From within R:
install.packages(c("igraph", "phylolm", "lars", "grplasso", "magic", "Rcpp")) install.packages("knitr")
Download genlasso version 1.3 R package from CRAN archive (link). From within R:
install.packages("genlasso_1.3.tar.gz", repos=NULL, type="source") ``` Now in the shell, with asterisks to be replaced with the correct version number: ```shell git clone https://github.com/khabbazian/l1ou.git R CMD build l1ou R -e 'install.packages("l1ou_*.**.tar.gz")'
major changes are indicated below.
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