Package index • delimtools

All functions

abgd_tbl(): A Command-Line Interface for ABGD - Automatic Barcode Gap Discovery

as_dwc(): Rename Columns using Darwin Core Standard Terms

asap_tbl(): A Command-Line Interface for ASAP - Assemble Species by Automatic Partitioning

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

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_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_tbl(): A Command-Line Interface for mPTP - multi-rate Poisson Tree Processes

report_delim(): Report Unique Species Partitions