Helper Functions for Species Delimitation Analysis


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Documentation for package ‘delimtools’ version 0.2.0

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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