Package 'SticsRFiles'

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

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)

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,
  start_date = lifecycle::deprecated()
)

Arguments

Value

numeric vector

Author(s)

Timothee Flutre

Examples

date <- as.Date("2015-02-10")
compute_day_from_date(date = date)

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

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

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

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,
  out_dir = NULL,
  save_as = NULL,
  stics_version = "latest",
  xml_file = lifecycle::deprecated(),
  plt_num = lifecycle::deprecated(),
  out_file = lifecycle::deprecated()
)

Arguments

Value

None

Examples

## Not run: 
xml_path <- "/path/to/corn_plt.xml"
javastics_path <- "/path/to/JavaSTICS/folder"
convert_xml2txt(file = xml_path, javastics = javastics_path)

## End(Not run)

Description

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

Usage

download_data(
  out_dir = tempdir(),
  example_dirs = NULL,
  stics_version = "latest",
  dir = lifecycle::deprecated(),
  version_name = lifecycle::deprecated()
)

Arguments

Value

The path to the folder where data have been downloaded

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")

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,
  csv_name = lifecycle::deprecated(),
  version_name = lifecycle::deprecated(),
  dest_dir = lifecycle::deprecated()
)

Arguments

Value

A vector of copied files path.

Examples

download_usm_csv()

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,
  xl_name = lifecycle::deprecated(),
  version_name = lifecycle::deprecated(),
  dest_dir = lifecycle::deprecated(),
  ...
)

Arguments

Value

A vector of copied files path.

Examples

download_usm_xl()

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,
  param_values = lifecycle::deprecated()
)

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)

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)

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",
  ini_in_file = lifecycle::deprecated(),
  param_table = lifecycle::deprecated(),
  out_path = lifecycle::deprecated()
)

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,]
)

Description

Generating observation data files from a data.frame

Usage

gen_obs(
  df,
  out_dir,
  usms_list = NULL,
  obs_table = lifecycle::deprecated(),
  out_path = lifecycle::deprecated()
)

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")

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",
  sols_in_file = lifecycle::deprecated(),
  sols_param = lifecycle::deprecated(),
  sols_out_file = lifecycle::deprecated(),
  sols_nb = lifecycle::deprecated()
)

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)

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",
  param_table = lifecycle::deprecated(),
  sta_in_file = lifecycle::deprecated(),
  out_path = lifecycle::deprecated()
)

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)

Description

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

Usage

gen_tec_xml(
  param_df = NULL,
  file = NULL,
  out_dir,
  stics_version = "latest",
  na_values = NA,
  param_table = lifecycle::deprecated(),
  tec_in_file = lifecycle::deprecated(),
  out_path = lifecycle::deprecated()
)

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, ])

Description

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

Usage

gen_usms_xml(
  file,
  param_df = NULL,
  template = NULL,
  stics_version = "latest",
  usms_out_file = lifecycle::deprecated(),
  usms_nb = lifecycle::deprecated(),
  usms_param = lifecycle::deprecated(),
  usms_in_file = lifecycle::deprecated()
)

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)

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 = c(),
  stics_version = "latest",
  verbose = TRUE,
  dir_per_usm_flag = TRUE,
  java_cmd = "java",
  java_converter = FALSE,
  javastics_path = lifecycle::deprecated(),
  workspace_path = lifecycle::deprecated(),
  target_path = lifecycle::deprecated(),
  usms_list = lifecycle::deprecated()
)

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 <- c("usm1", "usm2")
gen_usms_xml2txt(javastics, workspace, usm)


## End(Not run)

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,
  var_names = lifecycle::deprecated(),
  version = lifecycle::deprecated()
)

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.

Value

None

Examples

gen_varmod(tempdir(), c("lai(n)", "hauteur"))
# Add a variable to the others:
gen_varmod(tempdir(), "masec(n)", append = TRUE)
# NB: var.mod will have "lai(n)","hauteur" and "masec(n)"

Description

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

Usage

get_climate_txt(
  workspace,
  file_name = "climat.txt",
  preserve = TRUE,
  dirpath = lifecycle::deprecated(),
  filename = lifecycle::deprecated()
)

Arguments

Value

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

Note

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

Examples

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

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"))

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"))

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,
  version_name = lifecycle::deprecated()
)

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")

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"))

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,
  usm_name = lifecycle::deprecated(),
  var_list = lifecycle::deprecated(),
  dates_list = lifecycle::deprecated(),
  usms_filepath = lifecycle::deprecated(),
  javastics_path = lifecycle::deprecated()
)

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)

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

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")

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",
  dirpath = lifecycle::deprecated(),
  ...
)

get_ini_txt(
  file = "ficini.txt",
  stics_version,
  filepath = lifecycle::deprecated()
)

get_general_txt(file = "tempopar.sti", filepath = lifecycle::deprecated())

get_tmp_txt(file = "tempoparv6.sti", filepath = lifecycle::deprecated())

get_plant_txt(
  file = "ficplt1.txt",
  variety = NULL,
  filepath = lifecycle::deprecated()
)

get_tec_txt(
  file = "fictec1.txt",
  stics_version = "latest",
  several_fert = NULL,
  several_thin = NULL,
  is_pasture = NULL,
  filepath = lifecycle::deprecated(),
  ...
)

get_soil_txt(
  file = "param.sol",
  stics_version,
  filepath = lifecycle::deprecated()
)

get_station_txt(file = "station.txt", filepath = lifecycle::deprecated())

get_usm_txt(
  file = "new_travail.usm",
  plant_id = NULL,
  filepath = lifecycle::deprecated()
)

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 initialisation 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(file = file.path(get_examples_path(file_type = "txt"),
                                    "tempoparv6.sti"))
several_fert <- ifelse(tmp$option_engrais_multiple == 1, TRUE, FALSE)
several_thin <- ifelse(tmp$option_thinning == 1, TRUE, FALSE)
is_pasture <- ifelse(tmp$option_pature == 1, TRUE, FALSE)

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

## End(Not run)

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,
  xml_file = lifecycle::deprecated(),
  param_name = lifecycle::deprecated(),
  value = lifecycle::deprecated(),
  ...
)

Arguments

Value

A list of parameter values for each xml_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"))

Description

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

Usage

get_plants_nb(
  usms_file,
  usms_list = c(),
  usm_file_path = lifecycle::deprecated()
)

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)

Description

Extracting data from the STICS report file

Usage

get_report_results(
  workspace,
  file_name = "mod_rapport.sti",
  usm = NULL,
  var_list = NULL,
  usm_name = lifecycle::deprecated()
)

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")

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,
  usm_name = lifecycle::deprecated(),
  var_list = lifecycle::deprecated(),
  dates_list = lifecycle::deprecated(),
  usms_filepath = lifecycle::deprecated(),
  javastics_path = lifecycle::deprecated()
)

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")

Description

Extracts the soil names from a "usms.xml" file, or from a soil file

Usage

get_soils_list(
  file,
  soil = NULL,
  file_path = lifecycle::deprecated(),
  name = lifecycle::deprecated()
)

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"))

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)

Description

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

Usage

get_usms_files(
  workspace,
  usms_list = NULL,
  usms_file = "usms.xml",
  file_type = NULL,
  javastics = NULL,
  df_output = FALSE,
  workspace_path = lifecycle::deprecated(),
  file_name = lifecycle::deprecated(),
  javastics_path = lifecycle::deprecated()
)

Arguments

Details

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

Value

A named list with existing files path in each usm element

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

get_usms_files(
  workspace = "/path/to/workspace",
  javastics = "/path/to/JavaSTICS/folder",
  usm_list = c("usm1", "usm3")
)

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

## End(Not run)

Description

Extracting a usm names list from an usms.xml file

Usage

get_usms_list(
  file,
  usm = NULL,
  usm_path = lifecycle::deprecated(),
  name = lifecycle::deprecated()
)

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"))

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")

Description

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

Usage

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

Arguments

Value

The variables that will be returned by STICS

See Also

gen_varmod

Examples

get_varmod(get_examples_path(file_type = "txt"))

Description

Evaluating if the OS is a Mac OS type

Usage

is_mac()

Value

TRUE/FALSE

Examples

is_mac()

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"))

Description

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

Usage

is_stics_var(var, stics_version = "latest")

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"))

Description

Evaluating if the OS is a unix like type

Usage

is_unix()

Value

TRUE/FALSE

Examples

is_unix()

Description

Evaluating if the OS is a windows type

Usage

is_windows()

Value

TRUE/FALSE

Examples

is_windows()

Description

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

Usage

read_params_table(
  file,
  sheet_name = NULL,
  num_na = "NA",
  char_na = "NA",
  file_path = lifecycle::deprecated()
)

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 = "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",
  verbose = FALSE,
  stics_version = "V9.2"
)
read_params_table(file = usm_csv_file)

Description

Replace or set an input parameter from a pre-existing STICS input file.

Usage

set_param_txt(
  workspace,
  param,
  value,
  append = FALSE,
  plant_id = 1,
  variety = NULL,
  value_id = NULL,
  stics_version = "latest",
  dirpath = lifecycle::deprecated(),
  add = lifecycle::deprecated(),
  plant = lifecycle::deprecated(),
  layer = lifecycle::deprecated()
)

set_usm_txt(
  file = "new_travail.usm",
  param,
  value,
  append = FALSE,
  filepath = lifecycle::deprecated(),
  add = lifecycle::deprecated()
)

set_station_txt(
  file = "station.txt",
  param,
  value,
  append = FALSE,
  filepath = lifecycle::deprecated(),
  add = lifecycle::deprecated()
)

set_ini_txt(
  file = "ficini.txt",
  param,
  value,
  append = FALSE,
  plant_id = 1,
  layer = NULL,
  stics_version = "latest",
  filepath = lifecycle::deprecated(),
  add = lifecycle::deprecated()
)

set_general_txt(
  file = "tempopar.sti",
  param,
  value,
  append = FALSE,
  filepath = lifecycle::deprecated(),
  add = lifecycle::deprecated()
)

set_tmp_txt(
  file = "tempoparv6.sti",
  param,
  value,
  append = FALSE,
  filepath = lifecycle::deprecated(),
  add = lifecycle::deprecated()
)

set_plant_txt(
  file = "ficplt1.txt",
  param,
  value,
  append = FALSE,
  variety = NULL,
  filepath = lifecycle::deprecated(),
  add = lifecycle::deprecated()
)

set_tec_txt(
  file = "fictec1.txt",
  param,
  value,
  append = FALSE,
  value_id = NULL,
  filepath = lifecycle::deprecated(),
  add = lifecycle::deprecated()
)

set_soil_txt(
  file = "param.sol",
  param,
  value,
  layer = NULL,
  stics_version = "latest",
  filepath = lifecycle::deprecated()
)

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)

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,
  xml_file = lifecycle::deprecated(),
  out_path = lifecycle::deprecated(),
  param_name = lifecycle::deprecated(),
  param_value = lifecycle::deprecated(),
  value = lifecycle::deprecated(),
  ...
)

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"))

Description

Upgrading _ini.xml file(s) to a newer version

Usage

upgrade_ini_xml(
  file,
  out_dir,
  param_gen_file,
  stics_version = "V9.2",
  target_version = "V10.0",
  check_version = TRUE,
  overwrite = FALSE,
  ...
)

Arguments

Details

See SticsRFiles::get_stics_versions_compat() for listing versions

Value

None

Examples

dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")

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

Description

Upgrading a param_gen.xml file to a newer version

Usage

upgrade_param_gen_xml(
  file,
  out_dir,
  stics_version = "V9.2",
  target_version = "V10.0",
  check_version = TRUE,
  overwrite = FALSE
)

Arguments

Details

See get_stics_versions_compat() for listing versions

Value

None

Examples

dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")

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

Description

Upgrading a param_newform.xml file to a newer version

Usage

upgrade_param_newform_xml(
  file,
  out_dir,
  param_gen_file,
  stics_version = "V9.2",
  target_version = "V10.0",
  check_version = TRUE,
  overwrite = FALSE
)

Arguments

Details

See SticsRFiles::get_stics_versions_compat() for listing versions

Value

None

Examples

dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")

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")
)

Description

Upgrading _plt.xml file(s) to a newer version

Usage

upgrade_plt_xml(
  file,
  out_dir,
  param_newform_file,
  param_gen_file,
  stics_version = "V9.2",
  target_version = "V10.0",
  check_version = TRUE,
  overwrite = FALSE,
  ...
)

Arguments

Details

See get_stics_versions_compat() for listing versions

Value

None

Examples

dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")

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

Description

Upgrading a sols.xml file to a newer version

Usage

upgrade_sols_xml(
  file,
  out_dir,
  param_gen_file,
  stics_version = "V9.2",
  target_version = "V10.0",
  check_version = TRUE,
  overwrite = FALSE
)

Arguments

Details

See SticsRFiles::get_stics_versions_compat() for listing versions

Value

None

Examples

dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")

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

Description

Upgrading _sta.xml file(s) to a newer version

Usage

upgrade_sta_xml(
  file,
  out_dir,
  param_gen_file,
  stics_version = "V9.2",
  target_version = "V10.0",
  check_version = TRUE,
  overwrite = FALSE,
  ...
)

Arguments

Details

See SticsRFiles::get_stics_versions_compat() for listing versions

Value

None

Examples

dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")

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

Description

Upgrading _tec.xml file(s) to a newer version

Usage

upgrade_tec_xml(
  file,
  out_dir,
  param_newform_file,
  param_gen_file,
  stics_version = "V9.2",
  target_version = "V10.0",
  check_version = TRUE,
  overwrite = FALSE,
  ...
)

Arguments

Details

See get_stics_versions_compat() for listing versions

Value

None

Examples

dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")

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

Description

Upgrading a usms.xml file to a newer version

Usage

upgrade_usms_xml(
  file,
  out_dir,
  param_gen_file,
  obs_dir = NULL,
  stics_version = "V9.2",
  target_version = "V10.0",
  check_version = TRUE,
  overwrite = FALSE
)

Arguments

Details

See get_stics_versions_compat() for listing versions

Value

None

Examples

dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")

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

Description

Upgrading XML files of a JavaSTICS workspace directory to a newer STICS version format

Usage

upgrade_workspace_xml(
  workspace,
  javastics,
  out_dir,
  stics_version = "V9.2",
  target_version = "V10.0",
  plant = FALSE,
  overwrite = FALSE,
  ...
)

Arguments

Details

• See SticsRFiles::get_stics_versions_compat() for listing versions

• If general parameters files exist in workspace, they are also upgraded. In that case, residues parameters values are kept and might not be adapted to the target model version.

• Weather data and observations files are fully copied to out_dir

Value

None

Examples

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

## End(Not run)