Package: do3PCA 1.0.2

do3PCA: Probabilistic Phylogenetic Principal Component Analysis

Estimates probabilistic phylogenetic Principal Component Analysis (PCA) and non-phylogenetic probabilistic PCA. Provides methods to implement alternative models of trait evolution including Brownian motion (BM), Ornstein-Uhlenbeck (OU), Early Burst (EB), and Pagel's lambda. Also provides flexible biplot functions.

Authors:Daniel Caetano [aut, cre]

do3PCA_1.0.2.tar.gz
do3PCA_1.0.2.zip(r-4.7)do3PCA_1.0.2.zip(r-4.6)do3PCA_1.0.2.zip(r-4.5)
do3PCA_1.0.2.tgz(r-4.6-any)do3PCA_1.0.2.tgz(r-4.5-any)
do3PCA_1.0.2.tar.gz(r-4.7-any)do3PCA_1.0.2.tar.gz(r-4.6-any)
do3PCA_1.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
do3PCA/json (API)

# Install 'do3PCA' in R:

install.packages('do3PCA', repos = c('https://caetanods.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/caetanods/do3pca/issues

On CRAN:

3.30 score 1 stars 210 downloads 11 exports 105 dependencies

Last updated from:dc0eece3ed. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	203
source / vignettes	OK	268
linux-release-x86_64	OK	193
macos-release-arm64	OK	145
macos-oldrel-arm64	OK	112
windows-devel	OK	123
windows-release	OK	118
windows-oldrel	OK	141
wasm-release	OK	151

Exports:BrokenStick doBiplot loglik MCMCphylProbPCA MCMCProbPCA modelChoice phylProbPCA phylProbPCAJoint picProbPCA ProbPCA traitModelAIC

Dependencies:ADMM ape backports bit bit64 checkmate clarabel cli clipr cluster clusterGeneration coda codetools colorspace combinat corpcor cpp11 crayon CVXR dbscan DEoptim deSolve digest doParallel dotCall64 ellipse expm fastcluster fastmatch foreach future future.apply geiger generics glassoFast globals glue gmp gsignal highs hms igraph iterators labdsv lattice lifecycle listenv magrittr maotai maps MASS Matrix matrixcalc mclust mclustcomp mcmc mgcv mnormt mvMORPH mvtnorm ncbit nlme nloptr numDeriv optimParallel osqp parallelly pbmcapply phangorn phylolm phytools pillar pkgconfig pracma prettyunits progress quadprog R6 RANN ratematrix rbibutils Rcpp RcppArmadillo RcppDE RcppDist RcppEigen Rdimtools Rdpack readr rlang RSpectra Rtsne S7 scatterplot3d scs slam spam subplex tibble tidyselect tzdb utf8 vctrs vroom withr

do3PCA tutorial

Daniel S. Caetano

Rendered fromdo3PCA_tutorial.Rmdusingknitr::rmarkdownon May 07 2026.

Last update: 2025-08-05
Started: 2025-08-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Broken stick test for number of principal components	BrokenStick
Make biplot for any type of PCA	doBiplot
Probabilistic PCA likelihood function	loglik
MCMC for Probabilistic Phylogenetic PCA	MCMCphylProbPCA
MCMC for Probabilistic PCA	MCMCProbPCA
Automatic choice of number of principal components	modelChoice
Probabilistic Phylogenetic PCA	phylProbPCA
Probabilistic Phylogenetic PCA (Joint)	phylProbPCAJoint
Probabilistic PCA of independent contrasts (PIC-PCA)	picProbPCA
Probabilistic PCA	ProbPCA
Compute the MLE and AIC scores for a model of trait evolution	traitModelAIC