hap_unite: Unite Haplotype Summaries with Species Delimitation Outputs

In delimtools: Helper Functions for Species Delimitation Analysis

Unite Haplotype Summaries with Species Delimitation Outputs

Description

hap_unite() returns a single tbl_df combining all results from haplotype_tbl or collapse_others with results from delim_join or delim_consensus.

Usage

hap_unite(hap_tbl, delim)

Arguments

hap_tbl	output from haplotype_tbl or collapse_others.
delim	output from delim_join or delim_consensus.

Details

Many functions in this package relies on the usage of unique haplotypes due to known issues when using identical or duplicated sequences for species delimitation analysis. Thus, these outputs will very often refer only to unique haplotypes within a given dataset, which can be determined by using functions like hap_collapse. Assuming that a duplicated or identical sequence should share the same properties as the first sequence of the group has, hap_unite() combines the output of haplotype_tbl with the output of delim_join. Alternativelly, one may use collapse_others and delim_consensus as well. This output may be used for downstream analysis or to determine in which cluster a given sequence belongs.

Value

an object of class tbl_df.

Author(s)

Pedro S. Bittencourt

Examples

# get haplotype table
hap_tbl <- haplotype_tbl(geophagus)

# unite
hap_unite(hap_tbl, geophagus_delims)

delimtools documentation built on April 3, 2025, 9:28 p.m.