create_eppo_token it does not create Global variable now. Instead user needs to assign it to a variable manually. This is also corrected in tests, vignettes and documentation.eppo_tabletools_taxo now correctly handles eppocodes with correct structure, but otherwise invalid. I.e. It returns NA when the eppocode is not in the EPPO Data Services instead of breaking.null_eppocodes function checks if provided vector of eppocodes is empty, and returns NULL if needed. Function is tested.eppo_tabletools_ family functions now correctly handle results of eppo_names_table, when there are no valid eppocodes.eppo_database_download fail gracefully.petr workflow vignette.Example workflow of checking taxons affecting Abies alba vignette.eppo_tabletools functions now can use “raw” eppocodes instead of result of eppo_names_tables function result to query EPPO Data Services and EPPO Global Database. New functionality works with raw_eppocodes and ’use_raw_codes` parameters.msg_helpers small wrapper over messages to reduce redundancy in code.stringr and DT from Suggested dependencies as the are no longer in need.eppo_tabletools_hosts test including changes in function behavior.eppo_token is incorrect, functions return invisible NULL.(#18)eppo_tabletools_hosts and eppo_tabletools_pests now include row with eppocode for which there is no data.check_eppo_token allows checking if eppo_token is correctly recognized by EPPO Data Services API.(#18)try_GET and eppo_try_urls helper wrappers to fail gracefully. (#18)eppo_json_wrapper and eppo_csv_download helpers to fail gracefully.(#18)inherits from pestr_token class.eppo_tabletools_pests.eppo_tabletools_pests() to check taxonomy of pest infecting Abies alba. (#8)tidyr::nest and dplyr functions arguments. (#20 #16)dplyr package from imports. Package now only uses :: to access dplyr functions.pryr for dependencies at it was only used to check if eppo_token is S3 class.RCurl from dependencies since now package relies on httr and curl to connect with REST API, download csv files or download SQLite database.library('dplyr') instead of library(dplyr)).lifcycle badgeseppo_tabletools_pests returning pests of hosts.eppo_tabletools_pests needs testing.eppo_names_tableeppo_database_downloadAdded pestr Workflow vignette with example usage of pestr package functions – fix (#8).
Added some formatting to NEWS.md
Corrected table name in eppo_tabletools_host function.
eppo_tabletools_host – some small fixes in code and now returns table with NA, when there is no record in DB.
eppo_tabletools_hosts correctly joins hosts names with their classes.
eppo_tabletools_distri correctly joins countries with continents, without repeating names of some countries (e.g. USA, China).
eppo_table_full – joins compact results of eppo_names_tables() and eppo_tabletools into one compact table.eppo_tabletools_distri – takes result of eppo_names_tables() and creates table with distribution of pests (continent and country level).eppo_tabletools_cat() – takes result of eppo_names_tables() and creates table with categorization of each pest.Fixed bug in eppo_tabletools_hosts() function. Now it returns correct values, in compact table.
eppo_tabletools_cat() – takes result of eppo_names_tables() and creates table with categorization of each pest.eppo_tabletools_hosts() – takes result of eppo_names_tables() and creates table with hosts of each pest.create_eppo_token() – stores EPPO token for further use;eppo_database_check() – checks if EPPO SQLite db exist in folder;eppo_database_connect() – connects to EPPO SQLite db;eppo_database_download() – downloads EPPO SQLite db from EPPO Data Services;eppo_names_tables() – checks if names in query exist in EPPO SQLite db and uses them to create table with preferred and non-preferred names, synonyms, and common names in other languages;eppo_tabletools_names() – takes result of eppo_names_tables() and creates table with proper formatting (names etc.) on long or condensed format;eppo_tabletools_taxo breaks – function does not return correct values (namely table has only one row with NA) for compact table, however when run manually everything is O.K. (#9) – Probably updating sample SQLite db for test will solve above issue FIXEDtaxize package can be helpful with correction of organism names.