Package: Rtapas 1.2

Rtapas: Random Tanglegram Partitions

Applies a given global-fit method to random partial tanglegrams of a fixed size to identify the associations, terminals, and nodes that maximize phylogenetic (in)congruence. It also includes functions to compute more easily the confidence intervals of classification metrics and plot results, reducing computational time. See "Llaberia-Robledillo et al. (2023, <doi:10.1093/sysbio/syad016>)".

Authors:Mar Llaberia-Robledillo [aut, cre, cph], Juan A. Balbuena [aut, cph], José Ignacio Lucas-Lledó [aut, cph], Oscar Alejandro Pérez-Escobar [aut, cph]

Rtapas_1.2.tar.gz
Rtapas_1.2.zip(r-4.5)Rtapas_1.2.zip(r-4.4)Rtapas_1.2.zip(r-4.3)
Rtapas_1.2.tgz(r-4.4-any)Rtapas_1.2.tgz(r-4.3-any)
Rtapas_1.2.tar.gz(r-4.5-noble)Rtapas_1.2.tar.gz(r-4.4-noble)
Rtapas_1.2.tgz(r-4.4-emscripten)Rtapas_1.2.tgz(r-4.3-emscripten)
Rtapas.pdf |Rtapas.html✨
Rtapas/json (API)

# Install 'Rtapas' in R:

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

Bug tracker:https://github.com/mllaberia/rtapas/issues

Datasets:

CP_500tr - Nuclear and chloroplast dataset of orchids
CPtr - Nuclear and chloroplast dataset of orchids
NUC_500tr - Nuclear and chloroplast dataset of orchids
NUCtr - Nuclear and chloroplast dataset of orchids
am_matrix - Amph_trem dataset
amphipod - Amph_trem dataset
amphipod_1000tr - Amph_trem dataset
np_matrix - Nuclear and chloroplast dataset of orchids
pp_treesPACo_cong - Nuclear and chloroplast dataset of orchids
pp_treesPACo_incong - Nuclear and chloroplast dataset of orchids
trematode - Amph_trem dataset
trematode_1000tr - Amph_trem dataset

On CRAN:

3.70 score 5 stars 10 scripts 172 downloads 15 exports 45 dependencies

Last updated 6 months agofrom:df64cc56b0. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 11 2024
R-4.5-win	OK	Nov 11 2024
R-4.5-linux	OK	Nov 11 2024
R-4.4-win	OK	Nov 11 2024
R-4.4-mac	OK	Nov 11 2024
R-4.3-win	OK	Nov 11 2024
R-4.3-mac	OK	Nov 11 2024

Exports:assoc_mat geo_D gini_ci gini_RSV link_freq linkf_CI max_cong max_incong one2one_f paco_ss paraF prob_statistic tangle_gram trimHS_maxC trimHS_maxI

Dependencies:ape cli cluster clusterGeneration coda codetools combinat cpp11 DEoptim digest distory doParallel expm fastmatch foreach generics glue igraph iterators lattice lifecycle magrittr maps MASS Matrix mgcv mnormt nlme numDeriv optimParallel paco parallelly permute phangorn phytools pkgconfig plyr quadprog Rcpp rlang scatterplot3d stringi stringr vctrs vegan

Help page	Topics
amph_trem dataset	amphipod amphipod_1000tr amph_trem am_matrix trematode trematode_1000tr
Create an host-symbiont association matrix	assoc_mat
Geodesic distance between trees	geo_D
Plot the confidence intervals of Gini coefficient	gini_ci
The Gini coefficient adjusted for negative attributes (Raffinetti, Siletti, & Vernizzi, 2015)	gini_RSV
Frequency of host-symbiont association	link_freq
Confidence intervals for the frequency of host-symbiont association	linkf_CI
Algortihm for maximizing congruence between two phylogenies	max_cong
Algortihm for maximizing incongruence between two phylogenies	max_incong
Nuclear and chloroplast dataset of orchids	CPtr CP_500tr np_matrix NUCtr NUC_500tr nuc_cp pp_treesPACo_cong pp_treesPACo_incong
Maximum number of unique one-to-one association over a number of runs	one2one_f
Procrustes Approach to Cophylogeny (PACo) of the host and symbiont configurations	paco_ss
Test of host-symbiont coevolution	paraF
Frequencies of the associations for the posterior probability trees	prob_statistic
Tanglegram of the host-symbiont frequencies	tangle_gram
Trims the H-S association matrix maximizing the congruence	trimHS_maxC
Trims the H-S association matrix maximizing the incongruence	trimHS_maxI

Package: Rtapas 1.2

Rtapas: Random Tanglegram Partitions

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)