SDMWorkflows

The goal of SDMWorkflows is to make a workflow for Species distribution models for Sustainscapes

Installation

You can install the development version of SDMWorkflows like so:

remotes::install_github("Sustainscapes/SDMWorkflows")

Example

This is a basic example which shows you how to solve a common problem:

library(SDMWorkflows)
## basic example code

We will start by generating a list of species to be checked

Spp <- c("Abies concolor", "Abies lowiana", "Canis lupus", "Cannis lupus")

In this case we have four taxa to check, however we know that Abies concolor and Abies lowiana are synonyms for the accepted name of Abies concolor and that the second version of Canis lupus is badly written, it would be expected that the Clean_Taxa() function will recognize that there are only 2 species here and return a data frame with these together with their taxonomy resolution,

Final_List <- Clean_Taxa(Spp)
#> Joining, by = "Taxa"
#> Joining, by = "matched_name2"

Which yields the following table, the resolved species is the Species Column

Taxa	matched_name2	confidence	canonicalName	kingdom	phylum	order	family	genus	species	rank
Abies concolor	Abies concolor	98	Abies concolor	Plantae	Tracheophyta	Pinales	Pinaceae	Abies	Abies concolor	SPECIES
Abies lowiana	Abies lowiana	98	Abies lowiana	Plantae	Tracheophyta	Pinales	Pinaceae	Abies	Abies concolor	SPECIES
Canis lupus	Canis lupus	99	Canis lupus	Animalia	Chordata	Carnivora	Canidae	Canis	Canis lupus	SPECIES