eppo_tabletools: EPPO table manipulation tools

In mczyzj/pestr: Interface to Download Data on Pests and Hosts from 'EPPO'

EPPO table manipulation tools

Description

eppo_tabletools_names creates tables with names – preferred, common and synonyms – of pests. It is particularly useful for creating whole table with eppo_table_full, otherwise it might be more informative to use eppo_names_tables which provides additional information for your query. eppo_tabletools_hosts creates tables with hosts of pests. eppo_tabletools_cat creates tables with categorization of pests. eppo_tabletools_taxo creates tables with taxonomy of pests/hosts. eppo_tabletools_distri creates tables with distribution of pests. eppo_tabletools_pests creates table with pests of host. All functions return both long table and compact, human friendly table.

Usage

eppo_tabletools_names(names_tables)

eppo_tabletools_hosts(
  names_tables = NULL,
  token,
  raw_eppocodes = NULL,
  use_raw_codes = FALSE
)

eppo_tabletools_cat(
  names_tables = NULL,
  token,
  raw_eppocodes = NULL,
  use_raw_codes = FALSE
)

eppo_tabletools_taxo(
  names_tables = NULL,
  token,
  raw_eppocodes = NULL,
  use_raw_codes = FALSE
)

eppo_tabletools_distri(
  names_tables = NULL,
  raw_eppocodes = NULL,
  use_raw_codes = FALSE
)

eppo_tabletools_pests(
  names_tables = NULL,
  token,
  raw_eppocodes = NULL,
  use_raw_codes = FALSE
)

Arguments

names_tables	A list of tables created via eppo_names_tables().
token	An object containing EPPO API token created via create_eppo_token().
raw_eppocodes	A character vector of eppocodes. Use with caution, and ONLY when sure that provided eppocodes are correct.
use_raw_codes	logical. Default FALSE. Set TRUE if you want to provide eppocodes directly.

Value

List containing two data frames. First is in a long format, and each row contains synonyms and names in other languages in respect to preferred names. The second data frame contains coerced synonyms and other names to single cell for each preferred name.

See Also

EPPO Data services https://data.eppo.int/ and EPPO Global Database https://gd.eppo.int/

Examples

## Not run: 
 ## the code below requires SQLite DB in the working directory
 ## which can be downloaded with eppo_database_download function
 test_names <- eppo_names_tables(c("Xylella", "Poacea"))
 # get data on naming
 eppo_tabletools_names(test_names)

 ## below functions connect to EPPO Global Database or EPPO Global Services
 ## they need connection to internet.

 # get data on distribution
 eppo_tabletools_distri(test_names)
 # you can also get data using eppocodes directly
 eppo_tabletools_distri(raw_eppocodes = c("XYLEFA", "1GRAF"),
                        use_raw_codes = TRUE)

 ## below functions, beside internet connection require also valid token that
 ## can be obtained after free of charge registration at EPPO Data Services

 # first create token variable:
 create_eppo_token("paste_your_token_here")

 # then use result of eppo_names_tables or raw eppocodes to query REST API
 # get data on hosts
 eppo_tabletools_hosts(test_names, eppo_token)
 eppo_tabletools_hosts(token = eppo_token,
                       raw_eppocodes = c("XYLEFA", "1GRAF"),
                       use_raw_codes = TRUE)

 # get data on categorization
 eppo_tabletools_cat(test_names, eppo_token)
 eppo_tabletools_cat(token = eppo_token,
                       raw_eppocodes = c("XYLEFA", "1GRAF"),
                       use_raw_codes = TRUE)

 # get data on taxonomy
 eppo_tabletools_taxo(test_names, eppo_token)
 eppo_tabletools_taxo(token = eppo_token,
                       raw_eppocodes = c("XYLEFA", "1GRAF"),
                       use_raw_codes = TRUE)

 # get data on pests
 eppo_tabletools_pests(test_names, eppo_token)
 eppo_tabletools_pests(token = eppo_token,
                       raw_eppocodes = c("XYLEFA", "1GRAF"),
                       use_raw_codes = TRUE)

## End(Not run)

mczyzj/pestr documentation built on Feb. 27, 2024, 8:58 p.m.