NEWS.md
Following the changes done in the previous release 1.0.0, related to the adaptation to the new versions 10.0 of STICS and 1.5.0 of JavaSTICS.
The main changes are mainly related to the adaptation to the new versions 10.0 of STICS
and 1.5.0 of JavaSTICS, to homogenization of arguments names in functions and to fixes.
Prepared templates for STICS V10.
FIXES:
Bugs fixed for generation of soil, ini and tec XML files from excel files.
Fixed reading of observation and simulation results files in case of USM selection (arg. usm_name)
tec file of associated plant no more searched in case of a single plant in gen_usms_xml2txt
DOC:
Completed doc for generation of XML files from excel files.
Updated general doc.
DESCRIPTION / NAMESPACE: updates linked to new functions
Tests
Functions:
Files:
Tutorial: minor fix for use-xml-files (working dir creation)
get_sim / get_obs / get_file / get_file_ refactoring added some controls now taking into account a usms file path in functions fixed issues related to intercrops data loading added data.frame columns detection for filtering data on dates
functions for manipulating xml files taking into account a new kind of STICS parameter dependency (for plant and soil layers dependent parameters)
set_param_txt: fix for setting values for varietal parameters
gen_obs: fixes generating multiple files from a sheet generating files from a single observed variable
gen_usms_xml2txt now compatible with lai forcing added optional argument for checking files now removing files before each files generation
get_sim: new function replacing get_daily_results
get_daily_results: has been set to deprecated (a warning is displayed)
set_param_value: changed error output to warning if any parameter name does not exist
gen_tec_xml: now taking into account specific parameters linked to cut crops management
gen_ini_xml: fix for crop identifiers management (plant 1 or 2)
get_usms_list: changed error output to warning when the usms file does not exist
force_param_value: now uses either parameters names including () or _ for indexed ones (for example lai(n) or lai_n)
get_param_xml, set_param_xml: checks have been added for detecting parameters duplicates in tec files
get_obs, get_daily_results: removed useless columns from return, simplification
download_usm_xl, download_usm_csv: added verbose argument for masking warnings/displays, added overwriting case
read_params_table : new function for getting parameters tables either from csv files or excel files sheets
get_param_txt: added varieties management, earlier return when param is null, catching names ending with numerical indices, get varietal parameter, reading now parameters attached to several layers or fertilizations, added examples files for STICS version 8.5
Manipulating_Stics_XML_files.Rmd: using XML file for the latest model version for displaying files fragments as examples
get_stics_versions_compat, manage_stics_versions.R: added NA management in data
get_file: added plant names in output (for obs and daily data), fixed issue and tests added for intercropping case
get_daily_results: renamed class attribute to cropr_simulation, use of tibble::as_tibble(), mixed calculation using get_plants_nb, always returns a list, added optional usm_name arg, uses now get_plant_name instead, added javastics_path argument if plant files are located in it, dual variables name syntax (i.e. lai_n or lai(n) for example), taking into account intercrops management
functions refactoring for getting observations and daily outputs
get_var_info: now using partial matching on name column also
static_help: new function for generating html files from package functions help, some fixes and updates for vignettes
new function for downloading csv files from examples
new functions for managing model versions information and examples
get_obs* functions: fixes and optimization, added associated data and tests
force_param_values: fix for one line tibble
set_param_xml: output dir checking
force_param_values: new function for forcing model parameters
get_report_results: new function for extracting data from reports files
get_param_info: added using of a specific XML file, attribute for STICS version, unique for parameters names list, building a filter before dplyr::filter
functions added to manage STICS versions data
get_obs, get_plant_name: using usms.xml file outside of a STICS workspace, parsing mixed crops, file checking,usms_list renamed as usm_name
gen_*_xml functions: fix for usms name column
get_plant_name: getting now plant files list outside mapply call
get_param_value: returns a named list even if only one parameter, fix for param_name nb > 1, without parameters names in args;returned for each file
xmlDocument class: fix for checking ids validity
removed useless scripts for generating XML files
get_plants_nb: is now an interface to get either plants number from an xml file or a text file, returning an usms named vector
download_data: fix select
gen_usms_xml2txt: silent error when blanks in workspace_path, fix javastics workspace use,
get_stics_versions_compat: all data as character, study_case_1 added
gen_usms_obs: added usms_list
All functions code and help now using the get_examples_path function
get_examples_path: new function for getting files examples according to their type (txt, XML, csv,…) and embedded STICS versions data
gen_varmod: forcing to add variable not in STICS output variables for a given version, now checks if a variable exists, dual variable syntax (i.e. lai_n or lai(n))
set_param_txt: set value per soil layer, per variety
get_usms_files: taking into account 2 plant files folders (but without duplicates checks), taking into account varieties management
get_usms_list: returns now a character vector of usms names
get_param_xml: without parameters names in args;returned for each file, name of the XML file added to the output