# Helper Functions for Species Delimitation Analysis

## Documentation for package ‘delimtools’ version 0.2.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

delimtools-package | Helper Functions for Species Delimitation Analysis
abgd_tbl | A Command-Line Interface for ABGD - Automatic Barcode Gap Discovery
asap_tbl | A Command-Line Interface for ASAP - Assemble Species by Automatic Partitioning
as_dwc | Rename Columns using Darwin Core Standard Terms
bgmyc_ci | Confidence Intervals for Species Delimitations Methods
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
confidence_intervals | Confidence Intervals for Species Delimitations Methods
delimtools | Helper Functions for Species Delimitation Analysis
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
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_ci | Confidence Intervals for Species Delimitations Methods
gmyc_tbl | Turns GMYC Results Into a Tibble
haplotype_tbl | Summarise Haplotypes Down to One Row
hap_collapse | Removes Duplicated Sequences from Alignment
hap_unite | Unite Haplotype Summaries with Species Delimitation Outputs
locmin_ci | Confidence Intervals for Species Delimitations Methods
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_ci | Confidence Intervals for Species Delimitations Methods
mptp_tbl | A Command-Line Interface for mPTP - multi-rate Poisson Tree Processes
report_delim | Report Unique Species Partitions