Package 'pestr'

EPPO Data Services token variable

Description

check_eppo_token should be used after create_eppo_token to check if the token is correctly recognized by EPPO Data Services API. As a reference it uses link to Xylella fastidiosa hosts database - XYLEFA eppocode. If token is recognized there will be no message. In other cases function will show following messages: No internet connection or Forbidden (HTTP 403).

Usage

check_eppo_token(token)

Arguments

token

object of class pestr_token.

Value

Silent NULL when there is no error, otherwise message.

See Also

To obtain your free EPPO token please register to EPPO Data Services https://data.eppo.int/

Examples

## Not run: 
eppo_token <- create_eppo_token("abcdef123456")
check_eppo_token(eppo_token)

## End(Not run)

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EPPO Data Services token variable

Description

create_eppo_token makes token thats should be saved in a variable and used argument for eppo_tabletools_hosts, eppo_tabletools_pests, eppo_tabletools_cat and eppo_tabletools_taxo functions. It contains token of class string, that is needed to communicate with EPPO Data Services API.

Usage

create_eppo_token(x)

Arguments

x

A string.

Value

Token to access EPPO Data Services API in format recognized by eppo_tabletools_* functions.

See Also

To obtain your free EPPO token please register https://data.eppo.int/

Examples

## Not run: 
  create_eppo_token("12345678abcdef")

## End(Not run)

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Citation helper tools

Description

Citation returns citation of EPPO Data Services and/or EPPO Global Database in bibtex format. To save the output into file use output argument with destination file name.

Usage

eppo_citation(cite, output = NULL)

Arguments

cite	string. Possible values: 'data_services', 'global_database' or 'both'.
output	string. Name of the file to which output will be saved. If NULL (default) results will be printed to console.

Value

citation of EPPO Data Services, EPPO Global Database or both in bibtex format.

Examples

eppo_citation("data_services")
eppo_citation("global_database")
eppo_citation("both")

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EPPO Data Services Database connection tools

Description

eppo_database_check checks if there is a file eppocodes.sqlite and informs user if it is outdated and should be downloaded. eppo_database_download downloads database in SQLite format directly. The downloaded file is zip archive. On Linux this database will be extracted automatically. On Windows user will need to extract the file manually. eppo_database_connect allows user to connect to SQLite database downloaded from EPPO Data Services.

Usage

eppo_database_check(filepath = getwd(), filename = "eppocodes.sqlite")

eppo_database_download(filepath = getwd())

eppo_database_connect(filepath = getwd(), filename = "eppocodes.sqlite")

Arguments

filepath	A string with path where eppocodes.sqlite file is stored. By default it points to working directory.
filename	A string with name of the file. By default it takes name eppocodes.sqlite.

Value

Checks if database file exist in directory, if it is outdated, and establishes SQLite database connection

Manual download

If you will, you can download database directly from EPPO Data Services https://data.eppo.int

Examples

## Not run: 
#to check if the db file exist in the directory (default working directory)

eppo_database_check(filepath = getwd())

#to download EPPO SQLite database into directory (default working directory).
#If you are Windows user, after download finishes you will need to unzip file
#manualy.

eppo_database_download(filepath = getwd())

#prior to use functions that check pest names in SQLite database,
#you need to set up connection to SQLite database. Doing so is
#straightforward with function below (once per sesion):

eppo_connection <- eppo_database_connect(filepath = getwd(),
                                         filename = "eppocodes.sqlite")

## End(Not run)

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EPPO Data Services SQLite Database search tools

Description

eppo_names_table checks if string (names or parts of the names) provided by user match any name in the EPPO database. If strings match any name in database, data frame with all names matching codeid, as well as preferred (binary), language and EPPOcode is returned.

Arguments

names_vector	A vector with organism or viruses names (or part of the names) to be checked for existence in EPPO SQLite Database.
sqlConnection	connection to SQLite EPPO Database. By default NULL; function will automatically connect to database with default credentials.

Value

Check if provided names are present in EPPO SQLite Database. Creates list which contains: data frame with matching names in database and their codeids, character vector of names from names_vector which do not match any entry in database, data frame with preferred names and their codeids, and data frame containing all names matching codeids of preferred names. Last data frame contains also column with preferred (binary), codelang (two letter character with language code), and EPPOcode.

Using with other functions

Output of the function might be passed to functions:

• eppo_tabletools_names

• eppo_tabletools_cat

• eppo_tabletools_hosts

• eppo_tabletools_distribution

Examples

## Not run: 
  ##This code needs SQLite dabatase in working directory
  test_names <- c("Xylella", "dog", "leafhopper")
  test_names_table <- eppo_names_table(test_names)

## End(Not run)

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EPPO Data Services information table

Description

eppo_table_full creates table in human friendly format with data on pest preferred name, synonyms and common names, hosts, categorization, taxonomy and its distribution.

Usage

eppo_table_full(names_vector, sqlConnection, token)

Arguments

names_vector	A vector with organism names (or part of the names) to be checked for existence in EPPO SQLite Database.
sqlConnection	connection to SQLite EPPO Database. By default NULL; function will automatically connect to database with default credentials.
token	An object containing EPPO API token created via create_eppo_token.

Value

Wraps results of function from eppo_tabletools, namely: eppo_tabletools_names, eppo_tabletools_hosts, eppo_tabletools_cat, eppo_tabletools_taxo, and eppo_tabletools_distri into one compact, human readable table.

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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)

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