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Package: laser 2.4-1

Dan Rabosky

laser: Likelihood Analysis of Speciation/Extinction Rates from Phylogenies

laser implements maximum likelihood methods based on the birth-death process to test whether diversification rates have changed over time and whether rates vary among lineages.

Authors:Dan Rabosky, Klaus Schliep

laser_2.4-1.tar.gz
laser_2.4-1.zip(r-4.7-any)laser_2.4-1.zip(r-4.6-any)laser_2.4-1.zip(r-4.5-any)
laser_2.4-1.tgz(r-4.6-any)laser_2.4-1.tgz(r-4.5-any)
laser_2.4-1.tar.gz(r-4.7-any)laser_2.4-1.tar.gz(r-4.6-any)
laser_2.4-1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
laser/json (API)

# Install 'laser' in R:

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

Datasets:

agamids - Ultrametric Phylogeny of Australian Agamid Lizards
plethodon - Plethodon
rtrees5 - Random Phylogenetic Trees
rtrees50 - Random Phylogenetic Trees
warblers - Branching times from phylogeny of North American Dendroica warblers

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.08 score 2 stars 60 scripts 23 downloads 47 exports 50 dependencies

Last updated from:d4b5245f08. Checks:7 ERROR, 2 OK. Indexed: no.

Target	Result	Time
linux-devel	ERROR	142
source / vignettes	OK	208
linux-release	ERROR	127
macos-release	ERROR	110
macos-oldrel	ERROR	99
windows-devel	ERROR	93
windows-release	ERROR	112
windows-oldrel	ERROR	78
wasm-release	OK	118

Exports:bd birthdeathSim calcLHbd checkbasal combinations DDL DDX fitBOTHVAR fitdAICrc fitdAICrc.batch fitEXVAR fitSPVAR gamStat getBtimes getBtimes.batch getLikelihood.BOTHVAR getLikelihood.EXVAR getLikelihood.SPVAR getSpeciationtimes gsr lambda.crown.ms01 lambda.stem.ci lambda.stem.ml lambda.stem.ms01 lambdaFx mccrTest muFx node.sons plotLtt plotNodeNumbers.phylo plotRate pTt.BOTHVAR pTt.EXVAR pTt.SPVAR pureBirth rhoFxn.BOTHVAR rhoFxn.EXVAR rhoFxn.SPVAR scaleBranchingtimes truncateTree yule2rate yule3rate yule4rate yule5rate yuleint2 yuleSim yuleWindow

Dependencies:ape backports checkmate cli clusterGeneration coda codetools colorspace combinat cpp11 DEoptim deSolve digest doParallel expm foreach future future.apply geiger generics globals glue igraph iterators lattice lifecycle listenv magrittr maps MASS Matrix mnormt mvtnorm ncbit nlme numDeriv optimParallel osqp parallelly phangorn phytools pkgconfig progressr Rcpp RcppArmadillo rlang S7 scatterplot3d subplex vctrs

Help page	Topics
LASER	laser-package laser
Ultrametric Phylogeny of Australian Agamid Lizards	agamids
Fit Rate-Constant Birth-Death Model to Branching Times	bd
birthdeathSim	birthdeathSim
Calculate Likelihood of Branching Times Under Birth-Death Model	calcLHbd
Fit Density Dependent Speciation Model to Branching Times	DDL DDX
Test for Rate Variation Using delta-AICrc Test Statistic	fitdAICrc
Generate Null Distribution of dAICrc	fitdAICrc.batch
Fit model with continuous-time varying speciation/extinction rates to phylogeny	fitBOTHVAR fitEXVAR fitSPVAR
gamStat	gamStat
Get Branching Times From Parenthetic-Format Tree ('Newick')	getBtimes
Branching Times for Batch of Phylogenies	getBtimes.batch
Estimate speciation rates for crown and stem groups	lambda.crown.ms01 lambda.stem.ci lambda.stem.ml lambda.stem.ms01
Conduct monte carlo constant rates (gamma statistic) test	mccrTest
plethodon	plethodon
plotLtt	plotLtt
Plot phylogenetic tree with node numbers	plotNodeNumbers.phylo
Plot speciation and extinction rates through time	plotRate
pureBirth	pureBirth
Random Phylogenetic Trees	rtrees5 rtrees50
Scale Branching Times	scaleBranchingtimes
Truncate a Set of Branching Times	truncateTree
Branching times from phylogeny of North American Dendroica warblers	warblers
yule-n-rate	yule-n-rate yule2rate yule3rate yule4rate yule5rate
yuleSim	yuleSim
Fit Yule Model (Pure Birth) to Temporal Window of Branching Times	yuleWindow

Package: laser 2.4-1

laser: Likelihood Analysis of Speciation/Extinction Rates from Phylogenies

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)