Fixed Readme files.
eppo_citation returns citation of EPPO resources in bibtex format.README, correct typos, styling, add comments, etc.NEWS.mdselect syntax in functions and testscreate_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 FIXED