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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
  )

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.