select_reefish_species: Select sequences and species from BOLD which are in Reef Life...

In Grelot/geogendivr: Geographic Gene Diversity in R

Usage

select_reefish_species(prparedResBold.fishbaseValid, reefishSurveySpecies, countSequencesbySpeciesThreshold=2)

Arguments

prparedResBold.fishbaseValid	A curated dataframe generated by prepare_bold_res and fishbase_name_species_bold with 81 columns including "fishbase_name_species"
reefishSurveySpecies	A dataframe describing reef fish species abundance and biomass for 7100 spatial survey geographical position and 11 columns including "TAXONOMIC_NAME"
countSequencesbySpeciesThreshold	a numeric value (default value = 2), species with a number of sequences equal or lower than this threshold are filtered out

Value

A dataframe with individual sequences as row and 81 descriptors as column. Species who are not in Reef Life Survey database has been removed.

Author(s)

Pierre-Edouard GUERIN, Stephanie MANEL

Examples

## load BOLD specimen and sequence data with matching taxa "Pomacanthidae"
data(requestPomacanthidaeBOLD)
## load RLS species data
data(reefishSurveySpecies)
## filter and mutate
prparedResBold <- prepare_bold_res(resBold,
                                   marker_code="COI-5P",
                                   species_names=TRUE, 
                                   coordinates=TRUE, 
                                   ambiguities=TRUE, 
                                   min_length=420,
                                   max_length=720
                                  )
## validate species names
prparedResBold.fishbaseValid <- fishbase_name_species_bold(prparedResBold)
reefishBold <- select_reefish_species(prparedResBold.fishbaseValid,
                       reefishSurveySpecies,
                      countSequencesbySpeciesThreshold=2
                      )
print(reefishBold)

Grelot/geogendivr documentation built on Sept. 3, 2020, 6:25 p.m.