Package index • delimtools

All functions

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