Package: evobiR 2.1

Heath Blackmon

evobiR: Evolutionary Biology in R

Comparative analysis of continuous traits influencing discrete states, and utility tools to facilitate comparative analyses. Implementations of ABBA/BABA type statistics to test for introgression in genomic data.

Authors:Michelle M. Jonika, Maximos Chin, Nathan Anderson, Richard H. Adams, Jeffery P. Demuth, and Heath Blackmon

evobiR_2.1.tar.gz
evobiR_2.1.zip(r-4.5)evobiR_2.1.zip(r-4.4)evobiR_2.1.zip(r-4.3)
evobiR_2.1.tgz(r-4.4-any)evobiR_2.1.tgz(r-4.3-any)
evobiR_2.1.tar.gz(r-4.5-noble)evobiR_2.1.tar.gz(r-4.4-noble)
evobiR_2.1.tgz(r-4.4-emscripten)evobiR_2.1.tgz(r-4.3-emscripten)
evobiR.pdf |evobiR.html✨
evobiR/json (API)

# Install 'evobiR' in R:

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

Bug tracker:https://github.com/coleoguy/evobir/issues

Datasets:

hym.tree - Phylogenetic tree
mite.trait - Phenotype data for mites
trees - 10 Phylogenetic trees

On CRAN:

20 exports 14 stars 2.43 score 71 dependencies 3 mentions 103 scripts 209 downloads

Last updated 4 months agofrom:81a898a105. Checks:OK: 5 NOTE: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Sep 05 2024
R-4.5-win	NOTE	Sep 05 2024
R-4.5-linux	NOTE	Sep 05 2024
R-4.4-win	OK	Sep 05 2024
R-4.4-mac	OK	Sep 05 2024
R-4.3-win	OK	Sep 05 2024
R-4.3-mac	OK	Sep 05 2024

Exports:AncCond CalcD CalcPopD countTrees fix.simmap FuzzyMatch getNe GetTipRates make.simmap2 Pfaa Pfsa Pfss plot.phyloscaled ReOrderAlignment ResSel SampleTrees scaleTreeRates SlidingWindow SuperMatrix WinCalcD

Dependencies:ade4 ape castor cli clusterGeneration coda codetools colorspace combinat cpp11 DEoptim deSolve digest doParallel expm fansi farver fastmatch foreach geiger generics ggplot2 ggseqlogo glue gridExtra gtable igraph isoband iterators jsonlite labeling lattice lifecycle magrittr maps MASS Matrix mgcv mnormt munsell mvtnorm naturalsort ncbit nlme numDeriv optimParallel phangorn phytools pillar pixmap pkgconfig quadprog R6 RColorBrewer Rcpp RcppArmadillo RcppEigen rlang RSpectra scales scatterplot3d segmented seqinr sp subplex tibble utf8 vctrs viridis viridisLite withr

Evolutionary biology in R (evobiR) tutorial

Michelle Jonika, Jeffery Demuth, and Richard A. Adams, and Heath Blackmon

Rendered fromevolutionary.biology.in.R.Rmdusingknitr::rmarkdownon Sep 05 2024.

Last update: 2022-12-20
Started: 2015-10-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
evobiR: Evolutionary Biology in R	evobiR-package evobiR
simulated SNP data	1.fasta 3.fasta
Calculate the mean of a continuous character at transitions in a binary charachter	AncCond
Calculate Patterson's D-statistic	CalcD CalcPopD
Calculate the number of times a set of topologies occur	countTrees
Fix a stochastic map with failed edges	fix.simmap
Find Close Matches in a tree and dataset	FuzzyMatch
Calculate the variance effective population size	getNe
Calculate the rate of evolution on the leaves of a phylogeny	GetTipRates
Gnatocerus measurements	horn.beetle.csv
Phylogenetic tree	hym.tree
Modified stochastic mapping which is resistant to model failure	make.simmap2
phenotype data for mites	mite.trait
Calculate the proportion of different classes of fusions as a fraction of all fusions	Pfaa Pfsa Pfss
Phylogenetic visualization of heterogenity in discrete character evolution	plot.phyloscaled
Re-order sequences based on starting position	ReOrderAlignment
Selection on Residuals	ResSel
Select a random sample of trees	SampleTrees
Phylogeneitc analysis of heterogeneity in discrete character evolution	scaleTreeRates
Sliding window analysis	SlidingWindow
creates a supermatrix from multiple gene alignments	SuperMatrix
10 Phylogenetic trees	trees trees.mite
100 Phylogenetic trees	trees.nex
Calculate Patterson's D-statistic in sliding windows	WinCalcD