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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.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.