Create tables for EPPO Pest Risk Assessment

pestr package hexsticker

### Load packages
library("pestr")
library("dplyr")

Overview

EPPO Express Pest Risk Analysis – PM5/5(1) Additional guidance – requires information that can be easily obtained using pestr package functions. Particularly the information needed for Stage 2. Pest Risk Assessment:

For the purpose of this vignette, lets assume that you are working on well known pest – Anoplophora chinensis. This beetle is know for it’s voracious larvae which bore into the wood of living trees. More detailed info can be found at EPPO Datasheet: Anoplophora chinensis.

Please bear in mind that the workflow presented in this vignette can be also adjusted to other Pest Risk Analyses / Assessments of other authorities with some basic knowledge on R tools like dplyr, tidyr or stringr.

Prior to downloading data, please ensure that you set up variables.

### assign token to variable
eppo_token <- create_eppo_token("<<your eppo token>>")
### assign name to variable
ac_name <- "Anoplophora chinensis"
### assign eppocode to variable
ac_eppocode <- "ANOLCN" 
### assign database connection to variable
eppoDB <- eppo_database_connect()

Taxonomy and names of pest

ac_names_table <- eppo_names_tables(ac_name, eppo_DB)

ac_other_names <- eppo_tabletools_names(ac_names_table) %>%
  .[2] %>%
  dplyr::select(Other_names) %>%
  unlist()

ac_taxonomy <- eppo_tabletools_taxo(
  token = eppo_token,
  raw_eppocodes = ac_eppocode,
  use_raw_codes = TRUE
  )

Host of pest – as text or as table

ac_hosts <- eppo_tabletools_hosts(
  token = eppo_token,
  raw_eppocodes = ac_eppocode,
  use_raw_codes = TRUE
  )

Categorization table

ac_categorization <- eppo_tabletools_cat(
  token = eppo_token,
  raw_eppocodes = ac_eppocode,
  use_raw_codes = TRUE
  )

Distribution of pest

ac_distribution <- eppo_tabletools_distri(
  token = eppo_token,
  raw_eppocodes = ac_eppocode,
  use_raw_codes = TRUE
  )