Package: CRABS 1.2.0.9001

Bjørn Tore Kopperud

CRABS: Congruent Rate Analyses in Birth-Death Scenarios

Features tools for exploring congruent phylogenetic birth-death models. It can construct the pulled speciation- and net-diversification rates from a reference model. Given alternative speciation- or extinction rates, it can construct new models that are congruent with the reference model. Functionality is included to sample new rate functions, and to visualize the distribution of one congruence class. See also Louca & Pennell (2020) <doi:10.1038/s41586-020-2176-1>.

Authors:Bjørn Tore Kopperud [aut, cre], Sebastian Höhna [aut], Andrew F. Magee [aut], Jérémy Andréoletti [aut]

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NEWS

# Install 'CRABS' in R:

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

Bug tracker:https://github.com/afmagee/crabs/issues

Datasets:

primates - Primates phylogenetic tree
primates_ebd - RevBayes Primates birth-death model
primates_ebd_log - Primates birth-death model
primates_ebd_tess - TESS Primates birth-death model
primates_ebd_treepar - TreePar Primates birth-death model

On CRAN:

4.02 score 7 stars 5 scripts 201 downloads 14 exports 43 dependencies

Last updated 1 years agofrom:d1ccbd2fdb. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 17 2024
R-4.5-win	OK	Nov 17 2024
R-4.5-linux	OK	Nov 17 2024
R-4.4-win	OK	Nov 17 2024
R-4.4-mac	OK	Nov 17 2024
R-4.3-win	OK	Nov 17 2024
R-4.3-mac	OK	Nov 17 2024

Exports:congruent.models crabs.loglikelihood create.model full.plot.regularity.thresholds joint.congruent.models model2df read.RevBayes sample.basic.models sample.basic.models.joint sample.congruence.class sample.congruence.class.posterior sample.rates summarize.posterior summarize.trends

Dependencies:ape cli colorspace cpp11 deSolve digest dplyr fansi farver generics ggplot2 glue gtable isoband labeling latex2exp lattice lifecycle magrittr MASS Matrix mgcv munsell nlme patchwork pillar pkgconfig pracma purrr R6 RColorBrewer Rcpp rlang scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr

Help page	Topics
CRABS: Congruent Rate Analyses in Birth-death Scenarios	CRABS-package CRABS
Create a set of congruent models	congruent.models
Compute likelihood	crabs.loglikelihood
Computes the congruent class, i.e., the pulled rates.	create.model
Plots the rate functions after filtering them according to a given penalty and predefined thresholds.	full.plot.regularity.thresholds
Create a set of congruent models	joint.congruent.models
model2df	model2df
Plots the rate functions including the pulled rates.	plot.CRABS
Plots the rate functions	plot.CRABSset
Primates phylogenetic tree	primates
RevBayes Primates birth-death model	primates_ebd
Primates birth-death model	primates_ebd_log
TESS Primates birth-death model	primates_ebd_tess
TreePar Primates birth-death model	primates_ebd_treepar
Print method for CRABS object	print.CRABS
Title	print.CRABSposterior
Print method for CRABSset object	print.CRABSset
print.CRABSsets	print.CRABSsets
read RevBayes log file	read.RevBayes
Samples simple increase/decrease models through time with noise.	sample.basic.models
Jointly samples speciation and extinction trajectories through time, with noise.	sample.basic.models.joint
Stochastic exploration of congruent models.	sample.congruence.class
Stochastic exploration of congruent models for all samples in the posterior	sample.congruence.class.posterior
Sample custom functions through time.	sample.rates
Summarize trends in the posterior	summarize.posterior
Summarize trends in the congruence class	summarize.trends

Package: CRABS 1.2.0.9001

CRABS: Congruent Rate Analyses in Birth-Death Scenarios

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