Package: delimtools 0.3.5

Pedro Bittencourt

delimtools: Helper Functions for Species Delimitation Analysis

Helpers functions to process, analyse, and visualize the output of single locus species delimitation methods.

Authors:Pedro Bittencourt [aut, cre, cph], Rupert Collins [aut, ctb, cph], Tomas Hrbek [aut, ctb], Tomas Flouri [ctb], Sarah Lutteropp [ctb], Paschalia Kapli [ctb]

delimtools_0.3.5.tar.gz
delimtools_0.3.5.tar.gz(r-4.7-x86_64)delimtools_0.3.5.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
delimtools/json (API)

# Install 'delimtools' in R:

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

Bug tracker:https://github.com/legallab/delimtools/issues

Pkgdown/docs site:https://legallab.github.io

Datasets:

geophagus - Cytochrome C Oxidase Sequences of Geophagus Eartheaters
geophagus_beast - Geophagus Eartheaters Ultrametric Tree
geophagus_bootstraps - Geophagus Eartheaters Bootstrap Trees
geophagus_delims - Geophagus Eartheaters Species Partitions
geophagus_info - Geophagus Earthearts Associated Metadata
geophagus_posterior - Geophagus Eartheaters Posterior Trees
geophagus_raxml - Geophagus Eartheaters Phylogram

On CRAN:

5.64 score 4 stars 3 scripts 387 downloads 42 exports 72 dependencies

Last updated from:7233273cde. Checks:12 FAIL, 3 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	FAIL	115
linux-devel-x86_64	OK	201
source / vignettes	OK	216
linux-release-arm64	FAIL	115
linux-release-x86_64	OK	191
macos-release-arm64	FAIL	123
macos-release-x86_64	FAIL	195
macos-oldrel-arm64	FAIL	125
macos-oldrel-x86_64	FAIL	278
windows-devel-arm64	FAIL	292
windows-devel-x86_64	FAIL	77
windows-release-arm64	FAIL	279
windows-release-x86_64	FAIL	68
windows-oldrel-x86_64	FAIL	78
wasm-release	FAIL	113

Exports:abgd abgd_tbl as_dwc asap asap_tbl best_partition bgmyc bgmyc_ci bgmyc_tbl boot_dna check_delim check_identifiers clean_dna collapse_others delim_autoplot delim_autoplot2 delim_brewer delim_consensus delim_join delim_tbl drop_sequences dwc_terms get_delim_cols get_dwc gmyc gmyc_ci gmyc_tbl hap_collapse hap_unite haplotype_tbl locmin_ci locmin_tbl match_ratio min_brlen morph_tbl mptp mptp_ci mptp_mcmc mptp_support mptp_tbl report_delim spec.list

Dependencies:ape aplot base64enc bslib cachem cli cpp11 digest dplyr evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver fs gdtools generics ggfun ggiraph ggplot2 ggplotify ggtree glue gridGraphics gtable highr htmltools htmlwidgets isoband jquerylib jsonlite knitr labeling lattice lazyeval lifecycle magrittr MASS memoise mime nlme patchwork pillar pkgconfig purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown S7 sass scales stringi stringr systemfonts tibble tidyr tidyselect tidytree tinytex treeio utf8 vctrs viridisLite withr xfun yaml yulab.utils

Installing Species Delimitation Softwares

Rendered frominstall.Rmdusingknitr::rmarkdown

Last update: 2025-09-29
Started: 2025-03-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Helper Functions for Species Delimitation Analysis	delimtools-package delimtools
Automatic Barcode Gap Discovery (ABGD)	abgd
A Command-Line Interface for ABGD - Automatic Barcode Gap Discovery	abgd_tbl
Rename Columns using Darwin Core Standard Terms	as_dwc
ASAP - Assemble Species by Automatic Partitions	asap
A Command-Line Interface for ASAP - Assemble Species by Automatic Partitioning	asap_tbl
Select the Best Partition from a Delimitation Result	best_partition best_partition.abgd best_partition.asap
Public API Run Bayesian GMYC species delimitation	bgmyc
Turns bGMYC Results Into a Tibble	bgmyc_tbl
Checks If Two or More Species Delimitation Outputs are (Nearly) Equal	check_delim
Checks for Differences Between Identifiers in Metadata and DNA Sequence Files	check_identifiers
Removes Gaps, Ambiguities and Missing Data from DNA Sequences	clean_dna
Summarise Haplotype Metadata Down to One Row	collapse_others
Confidence Intervals for Species Delimitations Methods	bgmyc_ci confidence_intervals gmyc_ci locmin_ci mptp_ci
Plot Phylogenetic Trees With Species Delimitation Partitions	delim_autoplot
Plot Phylogenetic Trees With Species Delimitation Partitions	delim_autoplot2
Customize Delimitation Colors	delim_brewer
Estimate a Majority-Vote Consensus	delim_consensus
Join Multiple Species Delimitation Methods Outputs	delim_join
Generating a Delimitation Hypothesis Table	delim_tbl
Remove Sequences of a DNAbin list object	drop_sequences
Print Darwin Core Terms, Definitions and Examples as Bullet Lists	dwc_terms
Cytochrome C Oxidase Sequences of Geophagus Eartheaters	geophagus
Geophagus Eartheaters Ultrametric Tree	geophagus_beast
Geophagus Eartheaters Bootstrap Trees	geophagus_bootstraps
Geophagus Eartheaters Species Partitions	geophagus_delims
Geophagus Earthearts Associated Metadata	geophagus_info
Geophagus Eartheaters Posterior Trees	geophagus_posterior
Geophagus Eartheaters Phylogram	geophagus_raxml
Extract Labels and Colors from Species Delimitation Partitions	get_delim_cols
Get Darwin Core Terms and Definitions	get_dwc
Run the GMYC Species Delimitation Analysis	gmyc
Turns GMYC Results Into a Tibble	gmyc_tbl
Removes Duplicated Sequences from Alignment	hap_collapse
Unite Haplotype Summaries with Species Delimitation Outputs	hap_unite
Summarise Haplotypes Down to One Row	haplotype_tbl
Turns Local Minima Results into a Tibble	locmin_tbl
Compute Agreement Between Alternative Species Delimitation Partitions	match_ratio
A function to report the smallest tip-to-tip distances in a phylogenetic tree	min_brlen
Generating a Morphological Delimitation Table	morph_tbl
Run mPTP species delimitation (Maximum Likelihood)	mptp
Run mPTP species delimitation (MCMC)	mptp_mcmc
Extract MCMC support values	mptp_support
A Command-Line Interface for mPTP - multi-rate Poisson Tree Processes	mptp_tbl
Report Unique Species Partitions	report_delim
Get species list from a delimitation result	spec.list spec.list.gmyc
Summary of a Bayesian GMYC (bGMYC) delimitation	summary.bgmyc_fit