spatialpoints_bold: Function to transform curated BOLD dataframe into sp...

In Grelot/geogendivr: Geographic Gene Diversity in R

Description

Given a BOLD individual georeferenced sequences dataframe and a projection CRS, this function will return a spatialpoints object with all coordinates of individual sequences.

Usage

spatialpoints_bold(reefishBold, projectionCRS="+init=epsg:3347")

Arguments

reefishBold	A dataframe with individual sequences as row and 81 descriptors as column. Mandatory fields : lon, lat, species_name, fishbase_species_name, genus_name, family_name, order_name, class_name, sequence
projectionCRS	Interface class to the PROJ projection and transformation system. Default value is "+init=epsg:3347"

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
                      )
## transform curated BOLD dataframe into sp spatialpoints object
spatialpoints_bold(reefishBold, projectionCRS="+init=epsg:3347")

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