Package {SticsRFiles}

Title:	Read and Modify STICS Input/Output Files
Version:	1.7.0
Description:	Manipulating input and output files of the 'STICS' crop model (Beaudouin et al. (2022) <doi:10.35690/978-2-7592-3679-4>). The package is based on the model software, which is accessible, as well as resources, on its web site https://stics.inrae.fr/eng/. Files are either 'JavaSTICS' XML files or text files used by the model 'fortran' executable. Most basic functionalities are reading or writing parameter names and values in both XML or text input files, and getting data from output files. Advanced functionalities include XML files generation from XML templates and/or spreadsheets, or text files generation from XML files by using 'xslt' transformation.
License:	LGPL (≥ 3)
URL:	https://github.com/SticsRPacks/SticsRFiles, https://doi.org/10.5281/zenodo.4443206
BugReports:	https://github.com/SticsRPacks/SticsRFiles/issues
Depends:	R (≥ 4.0.0)
Imports:	cli, crayon, curl, data.table, doParallel, dplyr (≥ 1.0.0), foreach, lubridate, methods, parallel, rlang, rstudioapi, semver, tibble, tidyr, tidyselect, tools, utils, XML, xml2, xslt
Suggests:	covr, formatR, knitr, learnr, readxl, rmarkdown, spelling, testthat
VignetteBuilder:	knitr
ByteCompile:	true
Config/roxygen2/version:	8.0.0
Encoding:	UTF-8
Language:	en-US
Collate:	'add_node_to_doc.R' 'add_stics_nodes.R' 'all_in_par.R' 'all_out_var.R' 'approx_vapour_pressure.R' 'attributes_list2matrix.R' 'check_choice_param.R' 'check_java_path.R' 'check_java_workspace.R' 'check_output_files.R' 'check_param_names.R' 'check_upgrade_versions.R' 'col_names_to_var.R' 'compute_date_from_day.R' 'compute_day_number.R' 'convert_xml2txt.R' 'convert_xml2txt_int.R' 'download_data.R' 'download_usm_xl.R' 'exist_param_xml.R' 'exists_javastics_pref.R' 'exists_param.R' 'expand_stics_names.R' 'extract.R' 'extract_workspace.R' 'global.R' 'file_document.R' 'find_names.R' 'force_param_values.R' 'gen_climate.R' 'gen_general_param_xml.R' 'gen_ini_doc.R' 'gen_ini_xml.R' 'gen_new_travail.R' 'gen_obs.R' 'gen_paramsti.R' 'gen_sol_xsl_file.R' 'gen_sols_xml.R' 'gen_sta_doc.R' 'gen_sta_xml.R' 'gen_tec_doc.R' 'gen_tec_xml.R' 'gen_usms_sols_doc.R' 'gen_usms_xml.R' 'gen_usms_xml2txt.R' 'gen_varmod.R' 'get_climate_txt.R' 'get_cores_nb.R' 'get_cultivars_list.R' 'get_cultivars_param.R' 'get_dev_stages.R' 'get_file.R' 'get_file_int.R' 'get_files_list.R' 'get_formalisms_xml.R' 'get_java_workspace.R' 'get_lai_forcing.R' 'get_name_value_file_value.R' 'get_obs.R' 'get_option_choice_param_values.R' 'get_options_choices.R' 'get_options_names.R' 'get_param_bounds.R' 'get_param_bounds_xml.R' 'get_param_formalisms.R' 'get_param_info_xml.R' 'get_param_names.R' 'get_param_names_xml.R' 'get_param_number.R' 'get_param_txt.R' 'get_param_type.R' 'get_param_value.R' 'get_param_xml.R' 'get_params_dict.R' 'get_params_from_doc.R' 'get_params_from_doc_attr.R' 'get_params_from_doc_node.R' 'get_params_from_table.R' 'get_plant_name.R' 'get_plants_nb.R' 'get_report_results.R' 'get_sim.R' 'get_soils_list.R' 'get_stics_versions_compat.R' 'get_used_param.R' 'get_usms_list.R' 'get_values_by_param.R' 'get_varmod.R' 'get_xml_base_doc.R' 'get_xml_base_node.R' 'get_xml_doc_example.R' 'get_xml_files_param_df.R' 'get_xml_stics_version.R' 'init_javastics_pref.R' 'is_os_name.R' 'is_stics_doc.R' 'is_stics_xml.R' 'javastics_cmd_util.R' 'javastics_path.R' 'manage_stics_versions.R' 'merge_nodesets.R' 'read_params_table.R' 'remove_node_from_doc.R' 'remove_parent_from_doc.R' 'replace_string_in_file.R' 'replace_txt_param_value.R' 'rewrite_xml_files.R' 'set_codeoptim.R' 'set_file_executable.R' 'set_java_workspace.R' 'set_param_txt.R' 'set_param_value.R' 'set_param_xml.R' 'set_sols_param_xml.R' 'set_usms_param_xml.R' 'setup_parallelism.R' 'static_help.R' 'stics_environment.R' 'stics_files_utils.R' 'upgrade_v10_v11.R' 'upgrade_v9_v10.R' 'upgrade_xml_files.R' 'var_to_col_names.R' 'xml_document.R' 'xml_files_functions.R' 'zzz.R'
NeedsCompilation:	no
Packaged:	2026-09-14 13:51:35 UTC; plecharpent
Author:	Patrice Lecharpentier [aut, cre], Remi Vezy [aut], Samuel Buis [aut], Michel Giner [aut], Timothee Flutre [aut], Thomas Robine [ctb], Amine Barkaoui [ctb], Patrick Chabrier [ctb], Julie Constantin [rev], Dominique Ripoche [rev], Marie Launay [rev], Alain Mollier [rev], Christine Le Bas [rev], Joel Leonard [rev]
Maintainer:	Patrice Lecharpentier <patrice.lecharpentier@inrae.fr>
Repository:	CRAN
Date/Publication:	2026-09-14 22:40:09 UTC

[ method for cropr_simulation

Description

This method ensure keeping the cropr_simulation attribute when subsetting a cropr_simulation list.

Usage

## S3 method for class 'cropr_simulation'
x[...]

Arguments

Value

A subset of a cropr_simulation, keeping its attribute

Examples

path <- file.path(get_examples_path("sti"), "workspace1")
sim <- SticsRFiles::get_sim(workspace = path)
# sim returns a `cropr_simulation` list

Approximate vapour pressure

Description

Approximates vapour pressure as the saturated vapour pressure at the daily mean air temperature using relative humidity. See section 9.3 of the STICS book, as well as M. Launay's explanations on the STICS forum (link).

Usage

approx_vapour_pressure(mean_temp, rel_humid)

Arguments

Value

numeric vector

Author(s)

Timothee Flutre

Examples

approx_vapour_pressure(15, 60)

Convert day number into date

Description

Computes the date corresponding to a given day number (or vector of) with reference to a start year. Typically, the start year should be the year of a STICS simulation start, but not necessarily.

Usage

compute_date_from_day(day, start_year)

Arguments

Value

Date vector

Author(s)

Timothee Flutre

Examples

compute_date_from_day(day = 290, start_year = 1994)

compute_date_from_day(day = 700, start_year = 1994)

compute_date_from_day(day = 999, start_year = 1994)

Convert date into day number

Description

Computes the day number corresponding to a given date (or vector of) from the first day of a start year. Typically, the start year should be the year of a STICS simulation start. Leap years are properly handled.

Usage

compute_day_from_date(date, start_year = NULL)

Arguments

Value

numeric vector

Author(s)

Timothee Flutre

Examples

compute_day_from_date(date = as.Date("2015-02-10"))
compute_day_from_date(date = "2015-02-10", start_year = 2014)

compute_day_from_date(date = as.Date("2009-02-10"), start_year = 2008)

dates <- c(as.Date("2008-02-10"), as.Date("2009-02-10"))
compute_day_from_date(date = dates, start_year = 2008)

Transforming a STICS xml file into a text file

Description

The input file according to his type (ini,plant,tec,station,soil,par) is converted to a text file readable by the STICS model (ficini.txt, ficplt1.txt,...)

Usage

convert_xml2txt(
  file,
  plant_id = 1,
  soil_name = NULL,
  out_dir = NULL,
  save_as = NULL,
  stics_version = "latest"
)

Arguments

Value

None

Examples

xml_path <- file.path(get_examples_path("xml"), "file_plt.xml")
convert_xml2txt(file = xml_path)
xml_path <- file.path(get_examples_path("xml"), "sols.xml")
convert_xml2txt(file = xml_path, soil_name = "soil_rice")

Download example USMs

Description

Download locally the example data from the data repository in the SticsRPacks organization.

Usage

download_data(
  branch = NULL,
  out_dir = tempdir(),
  example_dirs = NULL,
  stics_version = "latest",
  raise_error = FALSE
)

Arguments

Value

The path of the folder data have been downloaded into or NULL if the download fails and raise_error is FALSE.

Examples

# Getting data for a given example : study_case_1 and a given STICS version
download_data(example_dirs = "study_case_1", stics_version = "V9.0")
# raising an error instead of a message
download_data(
  example_dirs = "study_case_1", stics_version = "V9.0",
  raise_error = TRUE
)

Downloading a CSV usms data file example into a directory

Description

The file is an example that can be used for generating JavaSTICS usms.xml input file from parameters values stored in a CSV file using the function gen_usms_xml

Usage

download_usm_csv(
  file = NULL,
  out_dir = tempdir(),
  stics_version = "latest",
  overwrite = FALSE,
  verbose = FALSE
)

Arguments

Value

A vector of copied files path.

Examples

download_usm_csv()

Downloading an Excel usms data file example into a directory

Description

The file is an example that can be used for generating JavaSTICS input files from parameters values stored in Excel spreadsheet format (USMs, Ini, Soils, Tec, Station, ...). Each sheet contains parameters values to insert into XML files, with the help of these functions: gen_usms_xml, gen_sols_xml, gen_tec_xml, gen_sta_xml, gen_usms_xml, gen_ini_xml

Usage

download_usm_xl(
  file = NULL,
  out_dir = tempdir(),
  stics_version = "latest",
  overwrite = FALSE,
  verbose = FALSE,
  ...
)

Arguments

Value

A vector of copied files path.

Examples

download_usm_xl()

Extract an XML JavaSTICS workspace from a source workspace

Description

Extract an XML JavaSTICS workspace from a source workspace

Usage

extract_workspace(
  from_workspace,
  to_workspace,
  javastics,
  usm = NULL,
  use_mod_files = FALSE
)

Arguments

Value

None

Examples

## Not run: 
# Extract all usms from a source workspace to a target workspace
extract_workspace(
  "/path/to/source/workspace",
  "/path/to/target/workspace",
  "/path/to/javastics/dir"
)

# Extract only selected usms from a source workspace to a target workspace
extract_workspace("/path/to/source/workspace",
  "/path/to/target/workspace",
  "/path/to/javastics/dir",
  usm = c("SugarCane", "potato")
)

## End(Not run)

Generates files to force parameters values in STICS simulations

Description

Generates a param.sti file and sets code optim in new_travail.usm to force parameters values in STICS simulations (this function is typically called before SticsOnR::run_stics())

Usage

force_param_values(workspace, values, javastics, force = FALSE)

Arguments

Details

This function operates on STICS text input files. Do not use it before calling gen_usms_xml2txt(), otherwise param.sti and new_travail.usm files will be overwritten.

This function has been created to be called before SticsOnR::run_stics(). It can not work with SticsOnR::run_javastics(), that will overwrite param.sti and new_travail.usm files.

values can contain NA. In this case, the corresponding parameter(s) will not be forced (default value(s), i.e. read in STICS input files, will be used). If values==NA or values==NULL, not any parameter will be forced (all default values used).

Value

A logical status TRUE if successful, FALSE otherwise

See Also

SticsOnR::run_stics()

Examples

## Not run: 
example_txt_dir <- get_examples_path(file_type = "txt")
force_param_values(example_txt_dir,
  setNames(object = c(220, 330), c("stlevamf", "stamflax")),
  javastics = "/path/to/javastics"
)

## End(Not run)

Generate STICS general parameters xml file(s) from a template file according to a STICS version

Description

Generate STICS general parameters xml file(s) from a template file according to a STICS version

Usage

gen_general_param_xml(out_dir, stics_version = "latest", overwrite = FALSE)

Arguments

Details

Please see get_stics_versions_compat() for the full list of STICS versions that can be used for the argument stics_version.

Value

None

Examples

gen_general_param_xml(out_dir = tempdir())

gen_general_param_xml(
  out_dir = tempdir(),
  stics_version = "V10.0",
  overwrite = TRUE
)

Generate STICS ini xml file(s) from a template or an input file

Description

Generate STICS ini xml file(s) from a template or an input file

Usage

gen_ini_xml(
  param_df,
  file = NULL,
  out_dir,
  crop_tag = "Crop",
  stics_version = "latest"
)

Arguments

Details

Please see get_stics_versions_compat() for the full list of STICS versions that can be used for the argument stics_version.

param_df is a data.frame with the following format:

The first column gives the ini file name (to be generated), all following columns give the parameter value to put in the file, and each line denotes a separate ini file (for e.g. several USMs).

The first column name must contain the keyword ini or Ini or INI as a prefix to be detected (as shown in the table extract above).

If not given (the default, NULL), the function returns the template as is.

Value

None

Examples

library(readxl)

xl_path <- download_usm_xl(file = "inputs_stics_example.xlsx")

ini_param_df <- read_excel(xl_path, sheet = "Ini")
gen_ini_xml(
  out_dir = tempdir(),
  param_df = ini_param_df[1:2, ]
)

Generating observation data files from a data.frame

Description

Generating observation data files from a data.frame

Usage

gen_obs(df, out_dir, usms_list = NULL)

Arguments

Details

df is a data.frame with the following format:

• usm_name column contains usms names which are used as output .obs files names

• ian, mo, jo and jul are mandatory (year, month, day and julian date)

• Other columns one per variable contain observations values or NA

@seealso get_var_info for getting variable right syntax or searching a variable name.

Value

A return logical status indicating if any error when writing files (FALSE), TRUE when no errors.

Examples

xl_path <- download_usm_xl(file = "inputs_stics_example.xlsx")
obs_df <- read_params_table(file = xl_path, sheet_name = "Obs")
gen_obs(df = obs_df, out_dir = "/path/to/dest/dir")

Generate STICS sols xml file from a template or an input file

Description

Generate STICS sols xml file from a template or an input file

Usage

gen_sols_xml(file, param_df, template = NULL, stics_version = "latest")

Arguments

Details

Please see get_stics_versions_compat() for the full list of STICS versions that can be used for the argument stics_version.

param_df is a data.frame with the following format:

The first column gives the soil name, all following columns give the parameter values to put in the sols.xml file for each soil row.

The first column name must contain the keyword Soil or soil or SOIL as a prefix to be detected (as shown in the table extract above).

If not given (the default, NULL), the function returns the template as is.

Value

None

Examples

xl_path <- download_usm_xl(file = "inputs_stics_example.xlsx")

sols_param_df <- read_params_table(file = xl_path, sheet_name = "Soils")
gen_sols_xml(
  file = file.path(tempdir(), "sols.xml"),
  param_df = sols_param_df
)

Generate STICS sta xml file(s) from a template or an input file

Description

Generate STICS sta xml file(s) from a template or an input file

Usage

gen_sta_xml(param_df, file = NULL, out_dir, stics_version = "latest")

Arguments

Details

Please see get_stics_versions_compat() for the full list of STICS versions that can be used for the argument stics_version.

param_df is a data.frame with the following format:

The first column gives the sta file name (to be generated), all following columns give the parameter value to put in the file, and each line denotes a separate sta file (for e.g. several USMs).

The first column name must contain the keyword sta or Sta or STA as a prefix to be detected (as shown in the table extract above).

If not given (the default, NULL), the function returns the template as is.

Value

None

Examples

xl_path <- download_usm_xl(file = "inputs_stics_example.xlsx")
sta_param_df <- read_params_table(file = xl_path, sheet_name = "Station")
gen_sta_xml(out_dir = tempdir(), param_df = sta_param_df)

Generate STICS tec xml file(s) from a template or an input file

Description

Generate STICS tec xml file(s) from a template or an input file

Usage

gen_tec_xml(
  param_df,
  file = NULL,
  out_dir,
  stics_version = "latest",
  na_values = NA
)

Arguments

Details

Please see get_stics_versions_compat() for the full list of STICS versions that can be used for the argument stics_version.

param_df is a data.frame with the following format:

The first column gives the tec file name (to be generated), all following columns give the parameter value to put in the file, and each line denotes a separate tec file (for e.g. several USMs).

The first column name must contain the keyword tec or Tec or TEC as a prefix to be detected (as shown in the table extract above).

If not given (the default, NULL), the function returns the template as is.

Value

None

Examples

xl_path <- download_usm_xl(file = "inputs_stics_example.xlsx")
tec_param_df <- read_params_table(file = xl_path, sheet_name = "Tec")
gen_tec_xml(out_dir = tempdir(), param_df = tec_param_df[1:2, ])

Generate STICS usms xml file from a template or an input file

Description

Generate STICS usms xml file from a template or an input file

Usage

gen_usms_xml(file, param_df, template = NULL, stics_version = "latest")

Arguments

Details

Please see get_stics_versions_compat() for the full list of STICS versions that can be used for the argument stics_version.

param_df is a data.frame with the following format:

The first column gives the usm name, all following columns give the parameter values to put in the usms.xml file for each usm row.

The first column name must contain the keyword Usm or usm or USM as a prefix to be detected (as shown in the table extract above).

If not given (the default, NULL), the function returns the template as is.

Value

an invisible xml_document object

Examples

xl_path <- download_usm_xl(file = "inputs_stics_example.xlsx")
usms_param_df <- read_params_table(file = xl_path, sheet_name = "USMs")
gen_usms_xml(
  file = file.path(tempdir(), "usms.xml"),
  param_df = usms_param_df
)

Generating one or several usms directories from a javastics workspace content

Description

The function creates sets of input files for one or multiple usms from usms data stored in a JavaSTICS workspace. For multiple usms, sets will be generated into individual folders named with usm names. Observations files will be also copied if they are named ⁠[usm_name].obs⁠ For one usm, files will be generated either in the workspace directory or in a subdirectory.

Usage

gen_usms_xml2txt(
  javastics = NULL,
  workspace = NULL,
  out_dir = NULL,
  usm = NULL,
  stics_version = "latest",
  verbose = TRUE,
  dir_per_usm_flag = TRUE,
  java_cmd = "java",
  java_converter = FALSE,
  parallel = FALSE,
  cores = NA
)

Arguments

Value

A list with named elements: usms_path : created directories paths (for storing STICS input files), files : generated files list (in JavaSTICS workspace origin), copy_status : logical value vector, indicating if all files have been generated for each usm obs_copy_status : logical value vector, indicating if observation files have been successfully copied in usms directories

Examples

## Not run: 
javastics <- "/path/to/JavaSTICS/folder"
workspace <- "/path/to/workspace"

# For all usms
gen_usms_xml2txt(javastics, workspace)

# For an usms list
usm_list <- c("usm1", "usm2")
gen_usms_xml2txt(javastics, workspace, usms = usm_list)

## End(Not run)

Generating a var.mod type file

Description

Generating a daily variable list file from variables names

Usage

gen_varmod(
  workspace,
  var,
  append = FALSE,
  file_name = "var.mod",
  stics_version = "latest",
  force = FALSE,
  verbose = FALSE
)

Arguments

Details

Variable names can be found using get_var_info(). They are checked before writing. If any variable name does not exist, it will not be written by default, but the function will still write the variables that exist. force= TRUE may however be used to write variables that do not exist. Variables already present in a var.mod file can be listed using get_varmod().

Value

None

Examples

# generate a new file
gen_varmod(tempdir(), c("lai(n)", "hauteur"))
# Add a variable to the others
# var.mod will contain now "lai(n)","hauteur" and "masec(n)"
gen_varmod(tempdir(), "masec(n)", append = TRUE)

Read STICS input meteorology file

Description

Read the meteorology input for STICS ("climat.txt")

Usage

get_climate_txt(workspace, file_name = "climat.txt", preserve = TRUE)

Arguments

Value

A data.frame of the input meteorological variables used as input for the STICS model.

Note

The time-related variables are summarized into one POSIXct column named date.

Examples

path <- get_examples_path(file_type = "txt")
meteo_data <- get_climate_txt(path)

Get the cultivar names for an xml plant file (*_plt.xml)

Description

Extracts the cultivar names from a plant file

Usage

get_cultivars_list(file)

Arguments

Value

A vector of cultivar names

Examples

path <- get_examples_path(file_type = "xml")

# Read from a plant file (all cultivars available in a plant file)
cv_list <- get_cultivars_list(file = file.path(path, "file_plt.xml"))

Get the values of cultivar-specific parameters from an xml plant file (*_plt.xml)

Description

Extracts the values of cultivar-specific parameters from a plant file

Usage

get_cultivars_param(file)

Arguments

Value

A data.frame with one row per cultivar and one column per parameter

Examples

path <- get_examples_path(file_type = "xml")

# Read from a plant file (all cultivars available in a plant file)
cv_param_df <- get_cultivars_param(file = file.path(path, "file_plt.xml"))

Get developmental stages from simulations

Description

Extracts the values of developmental stages from simulations

Usage

get_dev_stages(
  sim,
  dev_vars = c("iplts", "imbs", "ilets", "igers", "idebdorms", "ifindorms", "ilevs",
    "iamfs", "ilaxs", "ilats", "iflos", "idrps", "inous", "idebdess", "imats", "irecs"),
  usm = NULL
)

Arguments

Value

List of data.frame, one per USM, with one row per developmental stage.

Author(s)

Timothee Flutre

See Also

get_sim

Examples

## Not run: 
simulations <- get_sim(workspace)
get_dev_stages(simulations, "iplts")

## End(Not run)

Getting examples files path attached to a STICS version for a given file type

Description

Getting examples files path attached to a STICS version for a given file type

Usage

get_examples_path(file_type, stics_version = "latest", overwrite = FALSE)

Arguments

Value

A directory path for examples files for given file type and STICS version or a vector of (for unknown file types "" is returned as path)

Examples

get_examples_path(file_type = "csv")

get_examples_path(file_type = c("csv", "sti"))

get_examples_path(file_type = "csv", stics_version = "V8.5")

Getting existing xml files path list per usm from an usms.xml file

Description

Getting existing xml files path list per usm from an usms.xml file

Usage

get_files_list(
  workspace,
  usm = NULL,
  usms_file = "usms.xml",
  file_type = NULL,
  only_existing = TRUE,
  javastics = NULL,
  use_mod_files = FALSE
)

Arguments

Details

The possible values for file_type are: "fplt", "finit", "fclim1", "fclim2", "fstation", "ftec", "sols", "pargen", "parnew", "usms", "mod"

Value

A named list (usms names) with files path in paths field and a logical vector in exist field indicating if the file exists or not.

See Also

See get_soils_list() to get all soils in a usm file, and get_usms_list() to get the list of usms.

Examples

## Not run: 

get_files_list(
  workspace = "/path/to/workspace",
  javastics = "/path/to/JavaSTICS/folder"
)

get_files_list(
  workspace = "/path/to/workspace",
  javastics = "/path/to/JavaSTICS/folder",
  usm = c("usm1", "usm3")
)

get_files_list(
  workspace = "/path/to/workspace",
  file_type = c("finit", "ftec")
)

get_files_list(
  workspace = "/path/to/workspace",
  use_mod_files = TRUE,
  javastics = "/path/to/JavaSTICS/folder"
)

## End(Not run)

Getting LAI forcing for each usm

Description

Is LAI forced for usms in usms.xml

Usage

get_lai_forcing(usm_file_path, usms_list = c())

Arguments

Details

Use get_usms_list() to get the list of the usm names for an usms.xml file.

Value

A named numeric vector with a Boolean value (TRUE = forced) for each usm

Examples

# Xml case
xml_usms <- file.path(get_examples_path(file_type = "xml"), "usms.xml")
get_lai_forcing(xml_usms)
get_lai_forcing(xml_usms, "wheat")
get_lai_forcing(xml_usms, c("wheat", "intercrop_pea_barley"))

Read STICS observation files (*.obs)

Description

Read STICS observation files from a JavaSTICS workspace and store data into a list per usm

Usage

get_obs(
  workspace,
  usm = NULL,
  var = NULL,
  dates = NULL,
  usms_file = NULL,
  javastics = NULL,
  verbose = TRUE,
  parallel = FALSE,
  cores = NA
)

Arguments

Details

The .obs files names must match USMs names, e.g. for a usm called "banana", the .obs file should be named banana.obs. For intercrops, the name should be suffixed by "p" for the principal and "a" for the associated plant.

If usm is not specified (or equal to NULL), the function reads the files from all usms in the workspace(s).

If usms_file is provided and if the associated plant file is found, the plant names in the "Plant" column of the generated data.frame are either the plant code (as specified in the plant file) or the name of the plant file, if the plant file is not found.

If usms_file is not specified, the plants are named "plant_1" by default (+ "plant_2" for intercrops).

Value

A list, where each element is a data.frame of observations for the given usm. The list is named after the USM name.

Intercrops are returned in a single data.frame, and are identified using either the "Plant" or "Dominance" columns.

See Details section for more information about the "Plant" column.

Examples

path <- file.path(get_examples_path(file_type = "obs"), "mixed")

# Get observations for all usms, but only banana has observations:
Meas <- get_obs(path)

# Get observations only for banana:
Meas_banana <- get_obs(path, "banana")

## Not run: 
# Get observations with real plant names when plant
# folder is not in the workspace:
get_obs(path, "banana", javastics = "/path/to/JavaSTICS/folder")

## End(Not run)

Finding parameters information using partial search words

Description

Helper function that returns names and descriptions of STICS input parameters from a partial name and/or descriptive keywords.

Usage

get_param_info(param = NULL, keyword = NULL, stics_version = "latest")

Arguments

Details

The function understand regex as input.

Value

A data.frame with information about parameter(s) with columns name, file, min, max, definition, unit and cultivar

Examples

# Find by parameter name (fuzzy search):
SticsRFiles::get_param_info("alb")
SticsRFiles::get_param_info("alb[e]?")

# Find by keyword (fuzzy search in parameter name and description):
SticsRFiles::get_param_info(keyword = "bdil")

# Find for a particular version:
SticsRFiles::get_param_info("alb", stics_version = "V9.0")

get_param_info()

Read STICS input parameters from text files

Description

Read STICS model input parameters from a usm in text format (STICS input) Generally used after calling building a usm with JavaSTICS.

Read a specific STICS model input parameter file. Users would generally use the wrapper get_param_txt() instead.

Usage

get_param_txt(
  workspace,
  param = NULL,
  plant_id = NULL,
  variety = NULL,
  value_id = NULL,
  exact = FALSE,
  stics_version = "latest",
  ...
)

get_ini_txt(file = "ficini.txt", stics_version, workspace = NULL)

get_general_txt(file = "tempopar.sti", workspace = NULL)

get_tmp_txt(file = "tempoparv6.sti", workspace = NULL)

get_plant_txt(file = "ficplt1.txt", variety = NULL, workspace = NULL)

get_tec_txt(
  file = "fictec1.txt",
  stics_version = "latest",
  several_fert = NULL,
  several_thin = NULL,
  is_pasture = NULL,
  workspace = NULL,
  ...
)

get_soil_txt(file = "param.sol", stics_version, workspace = NULL)

get_station_txt(file = "station.txt", workspace = NULL)

get_usm_txt(file = "new_travail.usm", plant_id = NULL, workspace = NULL)

Arguments

Details

If the variety is not given and a param is asked, the function will return the values for the variety that is simulated in the USM by checking the variete parameter in the technical file. If param is not provided by the user, the values from all varieties will be returned unless the user ask for a given variety.

several_fert, several_thin and is_pasture are read from the tmp file (tempoparv6.sti). get_param_txt() does it automatically. If you absolutely need to use directly get_tec_txt, please see example.

Value

A list of parameters value(s), or if param = NULL a list of all parameters:

A list of parameters, depending on the file/function:

Note

Users would generally use get_param_txt to identify parameters names and values and pass them to other functions.

The functions are compatible with intercrops. Users generally only use get_param_txt(), which is a wrapper for all these functions.

See Also

gen_varmod(),

get_param_txt().

Examples

path <- get_examples_path(file_type = "txt")

# Getting the interrow distance parameter value
get_param_txt(path, param = "interrang")

# Getting varietal parameters values
# Get the leaf lifespan of the variety used in the usm:
get_param_txt(workspace = path, param = "durvieF")
# Get the leaf lifespan of another variety available in the plant file:
get_param_txt(workspace = path, param = "durvieF", variety = "Furio")
# To get the values for several (or all) varieties, either put all varieties:
varieties <- c("Pactol", "Cherif", "Furio", "Dunia", "Volga", "Cecilia")
get_param_txt(workspace = path, param = "durvieF", variety = varieties)
# Or get it from the output of the function returning all parameters:
get_param_txt(workspace = path)$plant$plant1$durvieF

# Get parameters for a specific plant
get_param_txt(workspace = path, plant_id = 1)
get_param_txt(workspace = path, param = "durvieF", plant_id = 1)
get_param_txt(
  workspace = path, param = "durvieF", plant_id = 1,
  variety = varieties
)

# Get parameters for specific interventions or soil layers
get_param_txt(workspace = path, param = "amount", value_id = c(1, 3))
get_param_txt(workspace = path, param = "Hinitf", value_id = c(1, 3))
get_param_txt(workspace = path, param = "epc", value_id = c(1, 3))

## Not run: 
# Read the initialization file (ficini.txt):
library(SticsRFiles)
path <- file.path(get_examples_path(file_type = "txt"), "ficini.txt")
get_ini_txt(path)

# Read the tec file directly:

# First, get the parameters from the tmp file:
tmp <- get_tmp_txt(
  workspace = get_examples_path(file_type = "txt")
)
several_fert <- tmp$option_engrais_multiple == 1
several_thin <- tmp$option_thinning == 1
is_pasture <- tmp$option_pature == 1

# Then, get the technical parameters:
get_tec_txt(
  workspace = get_examples_path(file_type = "txt"),
  file = "fictec1.txt",
  several_fert = several_fert, several_thin = several_thin,
  is_pasture = is_pasture
)

## End(Not run)

Getting parameter values from xml files

Description

Extracting parameter values for a list of xml files and parameters

Usage

get_param_xml(
  file,
  param = NULL,
  select = NULL,
  select_value = NULL,
  value_id = NULL,
  ...
)

Arguments

Value

A list of parameter values for each file (a list of list)

Examples

# Soil file
file <- file.path(get_examples_path(file_type = "xml"), "sols.xml")

# For all soils
get_param_xml(file)
get_param_xml(file, c("argi", "norg"))

# With soil selection
# scalar parameters per soil
get_param_xml(file, c("argi", "norg"),
  select = "sol", select_value = c("solcanne", "solbanane")
)

# Crop management file
file <- file.path(get_examples_path(file_type = "xml"), "file_tec.xml")

# Getting parameters for irrigation (date and quantity)
get_param_xml(file, c("julapI_or_sum_upvt", "amount"))

Getting plants code from plant files list by usm

Description

Getting plants code from plant files list by usm

Usage

get_plant_code(plant_dir_path, plant_xml_names)

Arguments

Value

a named list of plant codes by usm

Getting xml plant files by usm from an usms.xml file

Description

Getting xml plant files by usm from an usms.xml file

Usage

get_plant_files(usms_file, usms = NULL)

Arguments

Value

A named list with usm names containing plant files names

Examples

## Not run: 
get_plant_files("path/to/usms.xml")

get_plant_files("path/to/usms.xml", c("usm1", "usm2")

## End(Not run)

Getting plant tag(s) from a plant files list by usm

Description

Getting plant tag(s) from a plant files list by usm

Usage

get_plant_id(usms_plant)

Arguments

Value

a list of plant tags by usm

Getting plants number per usm for all usms or selected from a usm name vector

Description

Extracting plant number from usms.xml or new_travail.usm file data

Usage

get_plants_nb(usms_file, usms_list = c())

Arguments

Details

Use get_usms_list() to get the list of the usm names for an usms.xml file.

Value

A named numeric vector of plants number per usm

Examples

# Xml case
xml_usms <- file.path(get_examples_path(file_type = "xml"), "usms.xml")
get_plants_nb(xml_usms)
get_plants_nb(xml_usms, "wheat")
get_plants_nb(xml_usms, c("wheat", "intercrop_pea_barley"))

# Txt case
txt_usm <- file.path(get_examples_path(file_type = "txt"), "new_travail.usm")
get_plants_nb(txt_usm)

Extracting data from the STICS report file

Description

Extracting data from the STICS report file

Usage

get_report_results(
  workspace,
  file_name = "mod_rapport.sti",
  usm = NULL,
  var_list = NULL
)

Arguments

Details

The data may be filtered using usm_name vector of usm names and and/or var_list vector of variables names. In the returned data.frame, variables names respect the same syntax as in the get_sim output.

Value

A data.frame

Examples

path <- get_examples_path(file_type = "sti")
get_report_results(workspace = path)

get_report_results(workspace = path, usm = c("DurumWheat", "grass"))

get_report_results(workspace = path, var_list = c("masec(n)", "QNplante"))

get_report_results(workspace = path, usm = c("DurumWheat", "grass"))

get_report_results(workspace = path)

get_report_results(workspace = path, file_name = "mod_rapportA.sti")

Load and format STICS daily output file(s)

Description

Reads and format daily output file(s) (mod_s*.sti) for usm(s) with possible selection on variable names, cumulative DOY and dates

Usage

get_sim(
  workspace,
  usm = NULL,
  var = NULL,
  dates = NULL,
  usms_file = NULL,
  javastics = NULL,
  verbose = TRUE,
  parallel = FALSE,
  cores = NA
)

Arguments

Details

If usm is not specified (or equal to NULL), the function reads the files from all usms in the workspace(s).

If usms_file is provided and if the associated plant file is found, the plant names in the "Plant" column of the generated data.frame are either the plant code (as specified in the plant file) or the name of the plant file, if the plant file is not found.

If usms_file is not specified, the plants are named "plant_1" by default (+ "plant_2" for intercrops).

Value

A list, where each element is a data.frame of simulation results for the given usm. The list is named after the USM name.

Intercrops are returned in a single data.frame, and are identified using either the "Plant" or "Dominance" columns.

See Details section for more information about the "Plant" column.

Examples

path <- get_examples_path(file_type = "sti")
sim_data <- get_sim(path, "banana")

Get the soil names for an usms.xml or sols.xml file

Description

Extracts the soil names from a USMs file, or from a soil file

Usage

get_soils_list(file, soil = NULL)

Arguments

Details

The file given as the file_path is either a "usms" file type to get all the soils used in a particular USM, or a soil file type ("sols") to get all soil types available in a soil file.

Value

A vector of soil names

Examples

path <- get_examples_path(file_type = "xml")

# Read from a usms file (soils used in a USM):
soil_list <- get_soils_list(file = file.path(path, "usms.xml"))

# Read from a soil file (all soil types available in a soil file)
soil_list <- get_soils_list(file = file.path(path, "sols.xml"))

soil_list <- get_soils_list(
  file = file.path(path, "usms.xml"),
  soil = c("solcanne", "sole")
)

Get the compatible STICS versions

Description

Get the versions of STICS that are fully compatible with this package.

Usage

get_stics_versions_compat(version_index = NULL)

Arguments

Value

A named list with the STICS versions compatible with this package ($versions_list), and the latest version in use ($latest_version) or an existing version selected using version_index.

Examples

# Getting the complete versions list
get_stics_versions_compat()

# Getting the first version
get_stics_versions_compat(1)

# Getting the previous version of the latest one
get_stics_versions_compat(-1)

Getting usms names list for an usms.xml file

Description

Extracting a usm names list from an usms.xml file

Usage

get_usms_list(file, usm = NULL)

Arguments

Value

A vector of usm names

Examples

path <- get_examples_path(file_type = "xml")

usms_list <- get_usms_list(file = file.path(path, "usms.xml"))

usms_list <- get_usms_list(
  file = file.path(path, "usms.xml"),
  usm = c("usm1", "usm2")
)

Find STICS output variable names and description

Description

Helper function that returns names and descriptions of STICS output variables from a partial name and/or descriptive keywords.

Usage

get_var_info(var = NULL, keyword = NULL, stics_version = "latest")

Arguments

Details

The function understand regex as input.

Value

A data.frame with information about variable(s) with columns name, definition, unit, type

Examples

# Find by variable name (fuzzy search):
SticsRFiles::get_var_info("lai")

# Find by keyword (fuzzy search in variable name and description):
SticsRFiles::get_var_info(keyword = "lai")

# Find for a particular version:
SticsRFiles::get_var_info("lai", stics_version = "V9.0")


get_var_info()

Get desired STICS outputs

Description

Get the STICS output variables (from var.mod file)

Usage

get_varmod(workspace, file_name = "var.mod")

Arguments

Details

A var.mod file can be created or modified using gen_varmod().

Value

The variables that will be returned by STICS

See Also

gen_varmod

Examples

get_varmod(get_examples_path(file_type = "txt"))

Extracting a data.frame of parameters values for an xml file or a set of (whatever the xml file kind)

Description

Extracting a data.frame of parameters values for an xml file or a set of (whatever the xml file kind)

Usage

get_xml_files_param_df(file_path, param_names = NULL, wide_shape = FALSE)

Arguments

Details

An extract of returned data.frames with the 2 formats from an usms.xml file as input

• Default data.frame long format

name: a file name or an usm or soil name type: type of file param: param name id: NA for scalar, integer id for vectors parameters value: parameter value

• wide data.frame format

name: a file name or an usm or soil name type: type of file all other columns names correspond to parameter names, with indices as suffix for multiple values (as in _tec.xml files)

Value

A single long data.frame with name, type, param, id and value columns, value is of type character. or a wide a data.frame with name, type, and all other columns correspond to parameter names, with indices as suffix for multiple values (as in _tec.xml files for water supply, N supply, ...)

Examples

## Not run: 
dir_path <- get_examples_path("xml")

get_xml_files_param_df(
  file_path = file.path(dir_path, "sols.xml")
)

files_list <- file.path(dir_path, c("sols.xml", "usms.xml", "param_gen.xml"))
# long format (default)
get_xml_files_param_df(file_path = files_list)

# wide format
get_xml_files_param_df(file_path = files_list, wide_shape = TRUE)

## End(Not run)

Getting years from file(s) names(s)

Description

Getting years from file(s) names(s)

Usage

get_year_from_file_name(file_path)

Arguments

Value

a vector of numeric years

Examples

#'
## Not run: 
get_year_from_file_name(
  c("path/to/weather.year1", "path/to/weather.year2")
)
# should return c(year1, year2)

get_year_from_file_name(
  c("path/to/weather.year1", "path/to/weather.year3")
)
# should return c(year1, year2, year3)

## End(Not run)

Evaluating if the OS is a Mac OS type

Description

Evaluating if the OS is a Mac OS type

Usage

is_mac()

Value

TRUE/FALSE

Examples

is_mac()

Search if a STICS parameter exist

Description

Tells if one or more parameter names are valid STICS input parameters.

Usage

is_stics_param(param, stics_version = "latest")

Arguments

Value

A boolean vector: TRUE if the parameter exist, FALSE otherwise

See Also

get_param_info() for interactive use.

Examples

is_stics_param(c("adil", "adilmax", "unknown"))

Search if a STICS variable exist

Description

Tells if one or more variable names are valid STICS output variables.

Usage

is_stics_var(var, stics_version = "latest", verbose = FALSE)

Arguments

Value

A boolean vector: TRUE if the variable exist, FALSE otherwise

See Also

get_var_info() for interactive use.

Examples

is_stics_var(c("lai(n)", "masec(n)", "unknown"))

Evaluating if the OS is a unix like type

Description

Evaluating if the OS is a unix like type

Usage

is_unix()

Value

TRUE/FALSE

Examples

is_unix()

Evaluating if the OS is a windows type

Description

Evaluating if the OS is a windows type

Usage

is_windows()

Value

TRUE/FALSE

Examples

is_windows()

Getting parameters data from tables files (Excel sheet, csv)

Description

Getting parameters data from tables files (Excel sheet, csv)

Usage

read_params_table(file_path, sheet_name = NULL, num_na = "NA", char_na = "NA")

Arguments

Details

After data are loaded, numerical and string NA values are replaced respectively with num_na or char_na

Value

A tibble of parameters

Examples

usm_xl_file <- download_usm_xl(
  file_name = "inputs_stics_example.xlsx",
  verbose = FALSE
)
read_params_table(usm_xl_file, sheet = "USMs")
usm_csv_file <- download_usm_csv(
  file = "inputs_stics_example_USMs.csv",
  stics_version = "V9.2"
)
read_params_table(file_path = usm_csv_file)

Set (replace) STICS input file parameters

Description

Replace or set an input parameter from an existing STICS input file.

Usage

set_param_txt(
  workspace,
  param,
  value,
  append = FALSE,
  plant_id = 1,
  variety = NULL,
  value_id = NULL,
  stics_version = "latest"
)

set_usm_txt(file = "new_travail.usm", param, value, append = FALSE)

set_station_txt(file = "station.txt", param, value, append = FALSE)

set_ini_txt(
  file = "ficini.txt",
  param,
  value,
  append = FALSE,
  plant_id = 1,
  value_id = NULL,
  stics_version = "latest"
)

set_general_txt(file = "tempopar.sti", param, value, append = FALSE)

set_tmp_txt(file = "tempoparv6.sti", param, value, append = FALSE)

set_plant_txt(
  file = "ficplt1.txt",
  param,
  value,
  append = FALSE,
  variety = NULL
)

set_tec_txt(
  file = "fictec1.txt",
  param,
  value,
  append = FALSE,
  value_id = NULL
)

set_soil_txt(
  file = "param.sol",
  param,
  value,
  value_id = NULL,
  stics_version = "latest"
)

Arguments

Details

The plant parameter can be either equal to 1, 2 for the associated plant in the case of intercrop, or c(1,2) for both Principal and associated plants. get_var_info is a helper function that returns all possible output variables. If the variety is not given and if param is a varietal parameter, the function will modify the value of param for the simulated variety, as given in the technical file.

Value

None

Note

gen_varmod is not used by set_param_txt. To replace the output variables required from STICS, please directly call gen_varmod.

Examples

# Getting example data path
path <- get_examples_path(file_type = "txt")

# Change the value of durvieF for the current variety:
set_param_txt(workspace = path, param = "durvieF", value = 245)

# Change the value of durvieF for another variety:
set_param_txt(
  workspace = path, param = "durvieF",
  variety = "Nefer", value = 178
)
# Change the value of soil parameter "cailloux" for all layers
# or a specific one
set_param_txt(workspace = path, param = "cailloux", value = 1)
set_param_txt(workspace = path, param = "cailloux", value_id = 2, value = 2)

# Change the value of parameter "amount" for all water supply interventions
# or a specific one
set_param_txt(workspace = path, param = "amount", value = 50)
set_param_txt(workspace = path, param = "amount", value_id = 2, value = 40)

Setting parameter values into xml files

Description

Setting parameter values for a parameter or a vector of and with a parameters values vector

Usage

set_param_xml(
  file,
  param,
  values,
  save_as = NULL,
  select = NULL,
  select_value = NULL,
  value_id = NULL,
  overwrite = FALSE,
  ...
)

Arguments

Details

It is possible to give several values for a parameter by passing a vector of values. For example, for two parameters with two values each: value= list(c(1,2), c(2.3,4.5))

Value

A logical value TRUE for operation success, FALSE otherwise

Examples

ex_path <- get_examples_path(file_type = "xml")

# Soil file

sol_path <- file.path(ex_path, "sols.xml")

# For scalar parameters per soil
# Setting all soils "argi" values to 50
set_param_xml(sol_path, "argi", 50, overwrite = TRUE)
# Getting changed values
# get_param_xml(sol_path, "argi")

# Setting a specific value to "argi" for "solcanne" soil
set_param_xml(
  file = sol_path, param = "argi", values = 56,
  select = "sol", select_value = "solcanne", overwrite = TRUE
)
# Getting changed values
# get_param_xml(sol_path, "argi",
#   select = "sol", select_value = "solcanne"
# )


# Setting a specific values to 2 parameters "argi" and
# "norg" for "solcanne" soil
set_param_xml(sol_path, c("argi", "norg"), list(100, 150),
  select = "sol", select_value = "solcanne", overwrite = TRUE
)
# Getting changed values
# get_param_xml(sol_path, c("argi", "norg"),
#   select = "sol", select_value = "solcanne"
# )


# For vector parameters per soil (5 values, one per soil layer)
set_param_xml(sol_path, c("epc", "HCCF"),
  select = "sol",
  select_value = c("solcanne", "solbanane"),
  values = list(c(20:24, 10:14), c(50:54, 40:44)),
  overwrite = TRUE
)

# Getting changed values
# get_param_xml(sol_path, c("epc", "HCCF"),
# select = "sol",
# select_value = c("solcanne", "solbanane")
# )

# For specific values of vector parameters
set_param_xml(sol_path, "HCCF",
  select = "sol",
  select_value = "solcanne",
  values = c(46.8, 48.5, 50.1),
  value_id = c(1, 3, 5),
  overwrite = TRUE
)

# Getting changed values
# get_param_xml(sol_path, "HCCF",
# select = "sol",
# select_value = "solcanne",
# value_id = c(1,3,5)
# )

# Crop management file

tec_path <- file.path(ex_path, "file_tec.xml")

# Modifying irrigations parameters
set_param_xml(tec_path, c("julapI_or_sum_upvt", "amount"),
  values = list(200:215, 20:35), overwrite = TRUE
)
# Getting changed values
# get_param_xml(tec_path, c("julapI_or_sum_upvt", "amount"))

Upgrade _ini.xml file(s) to a next major version

Description

Upgrade _ini.xml file(s) to a next major version

Usage

upgrade_ini_xml(file, out_dir, param_gen_file, overwrite = FALSE)

Arguments

Value

None

Examples

dir_path <- get_examples_path(file_type = "xml", stics_version = "V10.0")

upgrade_ini_xml(
  file = file.path(dir_path, "file_ini.xml"),
  out_dir = tempdir(),
  param_gen_file = file.path(dir_path, "param_gen.xml")
)

Upgrade _ini.xml file(s) from STICS version 10 to 11

Description

Upgrade _ini.xml file(s) from STICS version 10 to 11

Usage

upgrade_ini_xml_10_11(file, out_dir, overwrite = FALSE)

Arguments

Value

None

Examples

## Not run: 
dir_path <- get_examples_path(file_type = "xml", stics_version = "V10.0")

upgrade_ini_xml_10_11(
  file = file.path(dir_path, "file_ini.xml"),
  out_dir = tempdir()
)

## End(Not run)

Upgrade _ini.xml file(s) from STICS version 9 to 10

Description

Upgrade _ini.xml file(s) from STICS version 9 to 10

Usage

upgrade_ini_xml_9_10(file, out_dir, param_gen_file, overwrite = FALSE)

Arguments

Details

See SticsRFiles::get_stics_versions_compat() for listing versions

Value

None

Examples

## Not run: 
dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")

upgrade_ini_xml_9_10(
  file = file.path(dir_path, "file_ini.xml"),
  out_dir = tempdir(),
  param_gen_file = file.path(dir_path, "param_gen.xml")
)

## End(Not run)

Upgrade a param_gen.xml file to a next major version

Description

Upgrade a param_gen.xml file to a next major version

Usage

upgrade_param_gen_xml(file, out_dir, ..., overwrite = FALSE)

Arguments

Value

None

Examples

dir_path <- get_examples_path(file_type = "xml", stics_version = "V10.0")

upgrade_param_gen_xml(
  file = file.path(dir_path, "param_gen.xml"),
  out_dir = tempdir()
)

Upgrade a param_gen.xml file from STICS version 10 to 11

Description

Upgrade a param_gen.xml file from STICS version 10 to 11

Usage

upgrade_param_gen_xml_10_11(file, out_dir, ..., overwrite = FALSE)

Arguments

Value

None

Examples

## Not run: 
dir_path <- get_examples_path(file_type = "xml", stics_version = "V10.0")

upgrade_param_gen_xml_10_11(
  file = file.path(dir_path, "param_gen.xml"),
  out_dir = tempdir()
)

## End(Not run)

Upgrade a param_gen.xml file from STICS version 9 to 10

Description

Upgrade a param_gen.xml file from STICS version 9 to 10

Usage

upgrade_param_gen_xml_9_10(file, out_dir, overwrite = FALSE)

Arguments

Details

See get_stics_versions_compat() for listing versions

Value

None

Examples

## Not run: 
dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")

upgrade_param_gen_xml_9_10(
  file = file.path(dir_path, "param_gen.xml"),
  out_dir = tempdir()
)

## End(Not run)

Upgrade a param_newform.xml file to a next major version

Description

Upgrade a param_newform.xml file to a next major version

Usage

upgrade_param_newform_xml(
  file,
  out_dir,
  param_gen_file,
  ...,
  overwrite = FALSE
)

Arguments

Value

None

Examples

dir_path <- get_examples_path(file_type = "xml", stics_version = "V10.0")

upgrade_param_newform_xml(
  file = file.path(dir_path, "param_newform.xml"),
  out_dir = tempdir(),
  param_gen_file = file.path(dir_path, "param_gen.xml")
)

Upgrade a param_newform.xml file from STICS version 10 to 11

Description

Upgrade a param_newform.xml file from STICS version 10 to 11

Usage

upgrade_param_newform_xml_10_11(file, out_dir, ..., overwrite = FALSE)

Arguments

Value

None

Examples

## Not run: 
dir_path <- get_examples_path(file_type = "xml", stics_version = "V10.0")

upgrade_param_newform_xml_10_11(
  file = file.path(dir_path, "param_newform.xml"),
  out_dir = tempdir()
)

## End(Not run)

Upgrade a param_newform.xml file from STICS version 9 to 10

Description

Upgrade a param_newform.xml file from STICS version 9 to 10

Usage

upgrade_param_newform_xml_9_10(
  file,
  out_dir,
  param_gen_file,
  overwrite = FALSE
)

Arguments

Details

See SticsRFiles::get_stics_versions_compat() for listing versions

Value

None

Examples

## Not run: 
dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")

upgrade_param_newform_xml_9_10(
  file = file.path(dir_path, "param_newform.xml"),
  out_dir = tempdir(),
  param_gen_file = file.path(dir_path, "param_gen.xml")
)

## End(Not run)

Upgrade _plt.xml file(s) to a next major version

Description

Upgrade _plt.xml file(s) to a next major version

Usage

upgrade_plt_xml(
  file,
  out_dir,
  param_gen_file,
  param_newform_file,
  ...,
  overwrite = FALSE,
  warning = TRUE
)

Arguments

Value

None

Examples

dir_path <- get_examples_path(file_type = "xml", stics_version = "V10.0")

upgrade_plt_xml(
  file = file.path(dir_path, "file_plt.xml"),
  out_dir = tempdir(),
  param_gen_file = file.path(dir_path, "param_gen.xml"),
  param_newform_file = file.path(dir_path, "param_newform.xml")
)

Upgrade _plt.xml file(s) from version 10 to 11

Description

Upgrade _plt.xml file(s) from version 10 to 11

Usage

upgrade_plt_xml_10_11(file, out_dir, ..., overwrite = FALSE, warning = TRUE)

Arguments

Value

None

Examples

## Not run: 
dir_path <- get_examples_path(file_type = "xml", stics_version = "V10.0")

upgrade_plt_xml_10_11(
  file = file.path(dir_path, "file_plt.xml"),
  out_dir = tempdir()
)

## End(Not run)

Upgrade _plt.xml file(s) from STICS version 9 to 10

Description

Upgrade _plt.xml file(s) from STICS version 9 to 10

Usage

upgrade_plt_xml_9_10(
  file,
  out_dir,
  param_gen_file,
  param_newform_file,
  overwrite = FALSE
)

Arguments

Details

See get_stics_versions_compat() for listing versions

Value

None

Examples

## Not run: 
dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")

upgrade_plt_xml_9_10(
  file = file.path(dir_path, "file_plt.xml"),
  out_dir = tempdir(),
  param_gen_file = file.path(dir_path, "param_gen.xml"),
  param_newform_file = file.path(dir_path, "param_newform.xml")
)

## End(Not run)

Upgrade a sols.xml file to a next major version

Description

Upgrade a sols.xml file to a next major version

Usage

upgrade_sols_xml(file, out_dir, param_gen_file, overwrite = FALSE)

Arguments

Value

None

Examples

dir_path <- get_examples_path(file_type = "xml", stics_version = "V10.0")

upgrade_sols_xml(
  file = file.path(dir_path, "sols.xml"),
  out_dir = tempdir(),
  param_gen_file = file.path(dir_path, "param_gen.xml")
)

Upgrade a sols.xml file from STICS version 10 to 11

Description

Upgrade a sols.xml file from STICS version 10 to 11

Usage

upgrade_sols_xml_10_11(file, out_dir, overwrite = FALSE)

Arguments

Value

None

Examples

## Not run: 
dir_path <- get_examples_path(file_type = "xml", stics_version = "V10.0")

upgrade_sols_xml_10_11(
  file = file.path(dir_path, "sols.xml"),
  out_dir = tempdir()
)

## End(Not run)

Upgrade a sols.xml file from STICS version 9 to 10

Description

Upgrade a sols.xml file from STICS version 9 to 10

Usage

upgrade_sols_xml_9_10(file, out_dir, param_gen_file, overwrite = FALSE)

Arguments

Details

See SticsRFiles::get_stics_versions_compat() for listing versions

Value

None

Examples

## Not run: 
dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")

upgrade_sols_xml_9_10(
  file = file.path(dir_path, "sols.xml"),
  out_dir = tempdir(),
  param_gen_file = file.path(dir_path, "param_gen.xml")
)

## End(Not run)

Upgrade _sta.xml file(s) to a next major version

Description

Upgrade _sta.xml file(s) to a next major version

Usage

upgrade_sta_xml(file, out_dir, param_gen_file, overwrite = FALSE)

Arguments

Value

None

Examples

dir_path <- get_examples_path(file_type = "xml", stics_version = "V10.0")

upgrade_sta_xml(
  file = file.path(dir_path, "file_sta.xml"),
  out_dir = tempdir(),
  param_gen_file = file.path(dir_path, "param_gen.xml")
)

Upgrade _sta.xml file(s) from STICS version 10 to 11

Description

Upgrade _sta.xml file(s) from STICS version 10 to 11

Usage

upgrade_sta_xml_10_11(file, out_dir, overwrite = FALSE)

Arguments

Value

None

Examples

## Not run: 
dir_path <- get_examples_path(file_type = "xml", stics_version = "V10.0")

upgrade_sta_xml_10_11(
  file = file.path(dir_path, "file_sta.xml"),
  out_dir = tempdir()
)

## End(Not run)

Upgrade _sta.xml file(s) from STICS version 9 to 10

Description

Upgrade _sta.xml file(s) from STICS version 9 to 10

Usage

upgrade_sta_xml_9_10(file, out_dir, param_gen_file, overwrite = FALSE)

Arguments

Details

See SticsRFiles::get_stics_versions_compat() for listing versions

Value

None

Examples

## Not run: 
dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")

upgrade_sta_xml_9_10(
  file = file.path(dir_path, "file_sta.xml"),
  out_dir = tempdir(),
  param_gen_file = file.path(dir_path, "param_gen.xml")
)

## End(Not run)

Upgrade _tec.xml file(s) to a next major version

Description

Upgrade _tec.xml file(s) to a next major version

Usage

upgrade_tec_xml(
  file,
  out_dir,
  param_gen_file,
  param_newform_file,
  ...,
  overwrite = FALSE
)

Arguments

Value

None

Examples

dir_path <- get_examples_path(file_type = "xml", stics_version = "V10.0")

upgrade_tec_xml(
  file = file.path(dir_path, "file_tec.xml"),
  out_dir = tempdir(),
  param_gen_file = file.path(dir_path, "param_gen.xml"),
  param_newform_file = file.path(dir_path, "param_newform.xml")
)

Upgrade _tec.xml file(s) from version 10 to 11

Description

Upgrade _tec.xml file(s) from version 10 to 11

Usage

upgrade_tec_xml_10_11(file, out_dir, ..., overwrite = FALSE)

Arguments

Value

None

Examples

## Not run: 
dir_path <- get_examples_path(file_type = "xml", stics_version = "V10.0")

upgrade_tec_xml_10_11(
  file = file.path(dir_path, "file_tec.xml"),
  out_dir = tempdir()
)

## End(Not run)

Upgrade _tec.xml file(s) from STICS version 9 to 10

Description

Upgrade _tec.xml file(s) from STICS version 9 to 10

Usage

upgrade_tec_xml_9_10(
  file,
  out_dir,
  param_gen_file,
  param_newform_file,
  overwrite = FALSE
)

Arguments

Details

See get_stics_versions_compat() for listing versions

Value

None

Examples

## Not run: 
dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")

upgrade_tec_xml_9_10(
  file = file.path(dir_path, "file_tec.xml"),
  out_dir = tempdir(),
  param_gen_file = file.path(dir_path, "param_gen.xml"),
  param_newform_file = file.path(dir_path, "param_newform.xml")
)

## End(Not run)

Upgrade a usms.xml file to a next major version

Description

Upgrade a usms.xml file to a next major version

Usage

upgrade_usms_xml(file, out_dir, param_gen_file, overwrite = FALSE)

Arguments

Value

None

Examples

dir_path <- get_examples_path(file_type = "xml", stics_version = "V10.0")

upgrade_usms_xml(
  file = file.path(dir_path, "usms.xml"),
  out_dir = tempdir(),
  param_gen_file = file.path(dir_path, "param_gen.xml")
)

Upgrade a usms.xml file from STICS version 10 to 11

Description

Upgrade a usms.xml file from STICS version 10 to 11

Usage

upgrade_usms_xml_10_11(file, out_dir, overwrite = FALSE)

Arguments

Value

None

Examples

## Not run: 
dir_path <- get_examples_path(file_type = "xml", stics_version = "V10.0")

upgrade_usms_xml_10_11(
  file = file.path(dir_path, "usms.xml"),
  out_dir = tempdir()
)

## End(Not run)

Upgrade a usms.xml file from STICS version 9 to 10

Description

Upgrade a usms.xml file from STICS version 9 to 10

Usage

upgrade_usms_xml_9_10(file, out_dir, param_gen_file, overwrite = FALSE)

Arguments

Details

See get_stics_versions_compat() for listing versions

Value

None

Examples

## Not run: 
dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")

upgrade_usms_xml_9_10(
  file = file.path(dir_path, "usms.xml"),
  out_dir = tempdir(),
  param_gen_file = file.path(dir_path, "param_gen.xml")
)

## End(Not run)

Upgrade a Javastics STICS xml workspace directory to a next major version

Description

Upgrade a Javastics STICS xml workspace directory to a next major version

Usage

upgrade_workspace_xml(
  workspace,
  out_dir,
  ...,
  javastics = NULL,
  overwrite = FALSE,
  verbose = FALSE
)

Arguments

Value

None

Examples

## Not run: 
upgrade_workspace_xml(
  workspace = "/path/to/JavaSTICS/workspace",
  out_dir = "/path/to/an/output/directory",
  javastics = "/path/to/JavaSTICS/folder"
)

## End(Not run)