smithsonian/epicc-name-match

Shiny app that matches scientific names to the EPICC taxonomy

This repo is now archived since the same results can be achieved using OpenRefine in a simpler way.

EPICC Name Match

A Shiny app to help the NMNH Paleo collection on their digitization efforts. The app tries to match the scientific names from labels in the collection to the taxonomy by EPICC (Eastern Pacific Invertebrate Communities of the Cenozoic).

This app takes the string in the column "Taxonomy" of a csv file and matches it with the Taxonomy from EPICC. The process tries to find a match taking into account the variety of ways that a scientific name can appear.

The process tries to match the string by looking at possible ways a scientific name is written in a collection label by trying to match:

• Genus
• Genus (Subgenus)
• Genus species
• Genus species Author
• Genus (Subgenus) species
• Genus (Subgenus) species Author
• Synonym

If no matches are found, the system will try to find a match by performing an approximate string matching to a scientific name or a synonym.

Running in local computer

To test the app locally, without the need of a server, just install R and Shiny. Then, run a command that will download the source files from Github.

R version 3.3 or better is required. After starting R, copy and paste these commands:

install.packages(c("shiny", "DT", "dplyr", "stringr", "stringdist", "futile.logger"))

library(shiny)
runGitHub("EPICC-name-match", "Smithsonian")

Please note that the installation of the required packages may take a few minutes to download and install.

Installation in Shiny server

This app requires the following R packages:

• shiny
• DT
• dplyr
• stringr
• stringdist
• futile.logger

To install:

install.packages(c("shiny", "DT", "dplyr", "stringr", "stringdist", "futile.logger"))