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 |