Package: OUwie 2.13

Jeremy Beaulieu

OUwie: Analysis of Evolutionary Rates in an OU Framework

Estimates rates for continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck based Hansen models that allow both the strength of the pull and stochastic motion to vary across selective regimes. Beaulieu et al (2012).

Authors:Jeremy M. Beaulieu <[email protected]>, Brian O'Meara <[email protected]>

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OUwie.pdf |OUwie.html✨
OUwie/json (API)

# Install 'OUwie' in R:

install.packages('OUwie', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/thej022214/ouwie/issues

Datasets:

trait - An example dataset
trait - An example dataset
tree - An example dataset
tree - An example dataset

On CRAN:

8.13 score 9 stars 150 scripts 790 downloads 22 mentions 19 exports 85 dependencies

Last updated 3 months agofrom:892d71dacf. Checks:OK: 7. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Oct 26 2024
R-4.5-win	OK	Oct 26 2024
R-4.5-linux	OK	Oct 26 2024
R-4.4-win	OK	Oct 26 2024
R-4.4-mac	OK	Oct 26 2024
R-4.3-win	OK	Oct 26 2024
R-4.3-mac	OK	Oct 26 2024

Exports:check.identify fix.kappa getModelAvgParams getModelTable getOUParamStructure hOUwie hOUwie.fixed hOUwie.recon hOUwie.sim hOUwie.thorough hOUwie.walk OUwie OUwie.anc OUwie.boot OUwie.contour OUwie.dredge OUwie.fixed OUwie.format OUwie.sim

Dependencies:ape bitops cli clusterGeneration coda codetools colorspace combinat corHMM corpcor cpp11 data.table deldir DEoptim deSolve digest doParallel expm fansi farver foreach future future.apply geiger generics GenSA ggplot2 globals glue gmp gridExtra gtable igraph interp isoband iterators jsonlite labeling lattice lhs lifecycle listenv magrittr maps MASS Matrix mgcv mnormt munsell mvtnorm ncbit nlme nloptr nnet numDeriv optimParallel paleotree parallelly phangorn phylolm phytools pillar pkgconfig plyr png quadprog R6 RColorBrewer Rcpp RcppEigen RCurl reshape2 rlang Rmpfr scales scatterplot3d stringi stringr subplex tibble utf8 vctrs viridis viridisLite withr

hOUwie User Guide

Rendered fromhOUwieStarterGuide.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2023-01-19
Started: 2023-01-18

New additions as of OUwie 2.1

Jeremy M. Beaulieu and Brian C. O'Meara

Rendered fromOUwie_2.1_adds.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2024-08-27
Started: 2020-05-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A test of regime identifiability	check.identify
Propose new values This proposes new values using a normal distribution centered on the original parameter values, with desired standard deviation. If any proposed values are outside the bounds, it will propose again.	dent_propose
Sample points from along a ridge	dent_walk
An example dataset	trait tree
Adjust tree for matrix condition	fix.kappa
Model average the parameter estimates over severl hOUwie fits.	getModelAvgParams
Generate a table from a set of hOUwie models describing their relative fit to data.	getModelTable
Generate a continuous model parameter structure	getOUParamStructure
Fit a joint model of discrete and continuous characters via maximum-likelihood.	hOUwie
Fit a joint model of discrete and continuous characters via maximum-likelihood with fixed regimes.	hOUwie.fixed
Reconstruct the marginal probability of discrete node states under the hOUwie model.	hOUwie.recon
Simulate a discrete and continuous character following a Markov and Ornstein-Uhlenbeck model.	hOUwie.sim
Rerun a set of hOUwie models with the best mappings of the set.	hOUwie.thorough
Sample points from along a ridge for a hOUwie model	hOUwie.walk
Generalized Hansen models	OUwie
Estimate ancestral states given a fitted OUwie model	OUwie.anc
Parametric bootstrap function	OUwie.boot
Generates data for contour plot of likelihood surface	OUwie.contour
Generalized Detection of shifts in OU process	OUwie.dredge
Generalized Hansen model likelihood calculator	OUwie.fixed
Format data and tree for OUwie	OUwie.format
Generalized Hansen model simulator	OUwie.sim
Plot the dented samples This will show the univariate plots of the parameter values versus the likelihood as well as bivariate plots of pairs of parameters to look for ridges.	plot.dentist
Contour plot	plot.OUwie.contour
Print dentist print summary of output from dent_walk	print.dentist
Summarize dentist Display summary of output from dent_walk	summary.dentist