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pestr (development version)

New functions

  • eppo_citation returns citation of EPPO resources in bibtex format.

Documentation updates

  • update README, correct typos, styling, add comments, etc.

Misc

  • new hex sticker

pestr 0.8.2

Function updates

  • 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.

pestr 0.8.1

New functions and tests

  • null_eppocodes function checks if provided vector of eppocodes is empty, and returns NULL if needed. Function is tested.

Fixed issues

  • eppo_tabletools_ family functions now correctly handle results of eppo_names_table, when there are no valid eppocodes.
  • refactor and adjust eppo_database_download fail gracefully.
  • corrected typos in documentation

pestr 0.8.0

Vignettes

  • updated petr workflow vignette.
  • updated Example workflow of checking taxons affecting Abies alba vignette.

New functions and updates

  • 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.

Fixed issues and smaller functionalities

  • updated documentation of functions, including examples, typos, etc. (#11)
  • added "devel" on Ubuntu 18.04 to github actions.
  • removed stringr and DT from Suggested dependencies as the are no longer in need.

pestr 0.7.4

New and updated test.

  • updated sample database (on 2020-Jan-06).(#19)
  • updated eppo_tabletools_hosts test including changes in function behavior.
  • if eppo_token is incorrect, functions return invisible NULL.(#18)

Fixed issues and smaller functionalities

  • Updated description of usage in README.
  • Changed license to MIT.
  • eppo_tabletools_hosts and eppo_tabletools_pests now include row with eppocode for which there is no data.

pestr 0.7.3

New functions

  • 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)
  • Updated eppo_json_wrapper and eppo_csv_download helpers to fail gracefully.(#18)

New and updated tests

  • Updated tests include mocking to support testing on CI and CRAN without using token, or connect to EPPO API, or download csv files.
  • EPPO REST responses are stored in RDS, so they can be mocked while testing if the creation of tables works correctly.(#19)
  • Now test are only checking if it inherits from pestr_token class.
  • mocked files and SQLite db is up to date on 04-Jan-2020.(#19)
  • Added tests for eppo_tabletools_pests.

New vignettes

  • Vignette showing how to use output of eppo_tabletools_pests() to check taxonomy of pest infecting Abies alba. (#8)

Fixed issues and smaller functionalities

  • Encrypted token for tests is no longer needed for all functions besides API helper since functions are mocked. (#12)
  • Updated sample database.
  • Updated tidyr::nest and dplyr functions arguments. (#20 #16)
  • Deleted dplyr package from imports. Package now only uses :: to access dplyr functions.
  • Deleted pryr for dependencies at it was only used to check if eppo_token is S3 class.
  • Deleted RCurl from dependencies since now package relies on httr and curl to connect with REST API, download csv files or download SQLite database.
  • All test now use correct syntax to load packages (e.g. library('dplyr') instead of library(dplyr)).
  • Added hex sticker.
  • Added lifcycle badges

pestr 0.7.2

New functions

  • new function eppo_tabletools_pests returning pests of hosts.

Known issues

  • eppo_tabletools_pests needs testing.

pestr 0.7.1

Fixed issues

  • updated comment in eppo_names_table
  • deleted unused dependency from vignette
  • added condition to download db file only if one does not exist in eppo_database_download

pestr 0.7.0

New vignette

Added pestr Workflow vignette with example usage of pestr package functions -- fix (#8).

Fixed issues

Added some formatting to NEWS.md

pestr 0.6.4

Fixed issues

Corrected table name in eppo_tabletools_host function.

pestr 0.6.3

Fixed issues

eppo_tabletools_host -- some small fixes in code and now returns table with NA, when there is no record in DB.

pestr 0.6.2

Fixed issues

eppo_tabletools_hosts correctly joins hosts names with their classes.

pestr 0.6.1

Fixed issues

eppo_tabletools_distri correctly joins countries with continents, without repeating names of some countries (e.g. USA, China).

pestr 0.6.0

New functions

  • eppo_table_full -- joins compact results of eppo_names_tables() and eppo_tabletools into one compact table.

pestr 0.5.0

New functions

  • eppo_tabletools_distri -- takes result of eppo_names_tables() and creates table with distribution of pests (continent and country level).

pestr 0.4.0

New functions

  • eppo_tabletools_cat() -- takes result of eppo_names_tables() and creates table with categorization of each pest.

Bug fixes

Fixed bug in eppo_tabletools_hosts() function. Now it returns correct values, in compact table.

pestr 0.3.0

New functions

  • eppo_tabletools_cat() -- takes result of eppo_names_tables() and creates table with categorization of each pest.

pestr 0.2.0

New functions

  • eppo_tabletools_hosts() -- takes result of eppo_names_tables() and creates table with hosts of each pest.

pestr 0.1.0

New functions

  • 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;

Issues to solve

  • Unify table outputs (#17)
  • Encrypt EPPO API token so test could run also on TravisCI (#12) FIXED
  • Code comments (#11)
  • Documentation (#10)
  • Additional tests (?) (#9)
  • Test for 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
  • Add new list item - tables formatted in the same way as they are formatted in EPPO template (#7)
  • Internationalization of package (#5) and (#6)
  • Hosts and categorization paste some values double into string, small fix is needed for both test and function FIXED

TODOs

  • taxize package can be helpful with correction of organism names.