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Functions included in this package allows users to painlessly connect to and extract data from EPPO Data Services / EPPO Global Database. Before you start using it you should register on: EPPO Data Services and obtain your token to access REST API.


You can install and use pestr development version from GitHub as follows:


Overview and Usage

Package include function that allow you to download SQLite database eppo_database_download (archive around 12 MB, after extraction around 45 MB). The database is needed for extracting eppocodes that are used in other functions from this package. Function included in eppo_tabletools_ family return both:

Before using functions that connect to REST API (hosts, categorization, taxonomy and pests) you should execute create_eppo_token function with string argument equal to your personal EPPO Data Services token. This function creates global variable eppo_token which should be parsed as an argument to functions that require token argument.

eppo_table_full allow to execute all the functions and return compact table with information on names, hosts, categorization, distribution and taxonomy – one row per one pest.

Feel free to contribute to this package and report issues via GitHub or email.

Example workflow

First you need to create token variable, use your token from EPPO Data Services.

create_eppo_token('<<your token>>')


eppo_database_download() #by default it downloads to working directory
#you can override this behaviour filepath argument

and extract the file manually to project working directory.

Put all the names that you are looking for into a vector, e.g.:

pests <- c(''Xylella', Cydia packardi', 'Drosophila suzuki')

and make connection to database.

eppo_SQLite <- eppo_database_connect()

pests names

Get pest names using:

pests_names_tables <- eppo_names_tables(pests, eppo_SQLite)

in result you will have list containing 4 tables:

You might parse results of this function directly to eppo_tabletools_ to obtain data. Other way is to use raw eppocodes as argument (this workflow is explained in Vignettes).

pests categorization


pests_cat <- eppo_tabletools_cat(pests_names_tables, eppo_token)

you will get as result you will get list with two elements:

pest hosts

pests_hosts <- eppo_tabletools_hosts(pests_names_tables, eppo_token)

result with two tables:

pests taxonomy

To get taxonomy use:

pests_taxo <- eppo_tabletools_taxo(pests_names_tables, eppo_token)

This function results are a list of two data frames:

pest distribution

The function extracting distribution from EPPO Global Database does not need eppo_token. It can be called like:

pest_distri <- eppo_tabletools_distri(pests_names_tables)

The result is a two element list:

pest names, categorization, distribution, taxonomy and hosts in one shot

Whole condensed table in one shot:

eppo_fulltable <- eppo_table_full(pests, eppo_SQLite, eppo_token)

which you can easily save as csv and use in a spreadsheet:

write.csv(eppo_fulltable, 'eppo_fulltable.csv')

hosts pests

Since the EPPO Data Services provides information on pest of particular host, you can easily access information with:

hosts <- c("Abies alba", "Triticum")

hosts_names_tables <- eppo_names_tables(pests, eppo_SQLite)
hosts_pests <- eppo_tabletools_taxo(hosts_names_tables, eppo_token)