Package: delimtools 0.2.2

Pedro Bittencourt

delimtools: Helper Functions for Species Delimitation Analysis

Helpers functions to process, analyse, and visualize the output of single locus species delimitation methods. For full functionality, please install suggested software at <https://legallab.github.io/delimtools/articles/install.html>.

Authors:Pedro Bittencourt [aut, cre, cph], Rupert Collins [aut, ctb, cph], Tomas Hrbek [aut, ctb]

delimtools_0.2.2.tar.gz
delimtools_0.2.2.zip(r-4.7)delimtools_0.2.2.zip(r-4.6)delimtools_0.2.2.zip(r-4.5)
delimtools_0.2.2.tgz(r-4.6-any)delimtools_0.2.2.tgz(r-4.5-any)
delimtools_0.2.2.tar.gz(r-4.7-any)delimtools_0.2.2.tar.gz(r-4.6-any)
delimtools_0.2.2.tgz(r-4.6-emscripten)
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:

5.56 score 4 stars 3 scripts 346 downloads 32 exports 72 dependencies

Last updated from:763efec224. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	194
source / vignettes	OK	277
linux-release-x86_64	OK	178
macos-release-arm64	OK	190
macos-oldrel-arm64	OK	215
windows-devel	OK	203
windows-release	OK	149
windows-oldrel	OK	139
wasm-release	OK	160

Exports:abgd_tbl as_dwc asap_tbl bgmyc_ci bgmyc_tbl boot_dna check_delim check_identifiers clean_dna collapse_others delim_autoplot delim_autoplot2 delim_brewer delim_consensus delim_join drop_sequences dwc_terms get_delim_cols get_dwc gmyc_ci gmyc_tbl hap_collapse hap_unite haplotype_tbl locmin_ci locmin_tbl match_ratio min_brlen morph_tbl mptp_ci mptp_tbl report_delim

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
A Command-Line Interface for ABGD - Automatic Barcode Gap Discovery	abgd_tbl
Rename Columns using Darwin Core Standard Terms	as_dwc
A Command-Line Interface for ASAP - Assemble Species by Automatic Partitioning	asap_tbl
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
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
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
A Command-Line Interface for mPTP - multi-rate Poisson Tree Processes	mptp_tbl
Report Unique Species Partitions	report_delim