Getting inputs Excel example file from the SticsRFiles package

In the following example /path/to/target/dir must be replaced with a real path depending on the operating system (i.e. starting with c:/ for windows for example)

# Getting the file in the current directory
usm_xl_file <- download_usm_xl()

# Getting the file in a specic directory
xl_dir <- "/path/to/xl/dir" # or something like C:/path/to/xl/dir" for Windows

usm_xl_file <- download_usm_xl(out_dir = xl_dir)

#> [1] "inputs_stics_example.xlsx  has been copied in directory
#> "/path/to/xl/dir

Getting an USMs inputs CSV example file from the SticsRFiles package

# Getting the file in the current directory
usm_csv_file <- download_usm_csv(file = "inputs_stics_example_USMs.csv")

# Getting the file in a specific directory
csv_dir <- "/path/to/csv/dir" # or something like C:/path/to/xl/dir" for Windows

usm_csv_file <- download_usm_csv(
  file = "inputs_stics_example_USMs.csv",
  out_dir = csv_dir
)

#> [1] inputs_stics_example_USMs.csv  has been copied in directory
#> "/path/to/csv/dir

Important information

The USMs data which are necessary for generating the usms.xml must be all provided either through an Excel sheet or a CSV file; as shown in the USMs sheet example.

Other data stored in Excel or CSV files must be adapted to the use cases here after:

• For generating new files, containing parameters with different values for each USM, tables must contain values for all the files parameters.

• For generating files with a common set of parameter values and only a part of them must be overloaded with values coming from parameters tables, one must give an existing file as a template for files generation to functions gen_*_xml (listed here).

Specificities of Excel sheets

Excel sheet names are completely free, but must be meaningful regarding the kind of parameters set they contain.

In the example, useful sheets for generating XML parameters files are named: USMs, Ini, Soils, Tec, Station

Common tables specifications

The first column is used for storing identifiers or files names (or prefix) and the USMs table contains identifiers of the other linked tables in columns names finit, nomsol, fstation, ftec_1, ftec_2 with respect to initialization files, soil name, station files and crop management files (for main crops and optionally associated crops).

The first column names of data tables are automatically detected and must contain keywords prefix to do so as listed: usm_, ini_, soil_, sta_, tec_

These first columns may contain either names identifiers or files names according to data type:

• USMs or soil data: usm name or soil name
• Initialization, station or crop management data: files names either with or without suffix and XML extension (_ini.xml, _tec.xml, or _sta.xml)

Other columns of tables are named with parameters names according to the following rules:

• Scalar parameters used parameter names must match the exact parameter names (checking it syntax with the help of the get_param_info function)
• Vector parameters used parameter names must also match real parameter names with adding a suffix indicating their index; for example jultrav_1, jultrav_2, and so on…
• Exceptions in some cases used parameters names in tables may be different from real parameter names

Here is the actual correspondence table of keywords to be used in parameters tables (i.e excel files for example) in replacement of real names in XML files:

As an example, looking in the Tec sheet of the previously downloaded Excel file, irrigation parameters for setting days and amount of water supplied, are respectively named julapI_1, julapI_2,… and doseI_1, doseI_2,… instead of using absolute_value/% and amount.

Data consistency checks in tables

For the moment, no consistency checks (between Excel sheets or CSV equivalents files) functionalities have been included in the package in order to prevent missing generated files or misspelled file names or identifiers.

So, one must take care of links between xml files names for example files names defined for usms related to names declared for example in Excel sheets Tec, Station, and so on.

In future developments, checks will be included to run be run prior to files generations, for preventing errors.

USMs table example

The Excel file which contains parameters values to take into account for STICS inputs may contain specific sheets for each kind of parameters groups, i.e. USMs, crop management, soil, weather station, initialization (except plant parameters and general parameters).

The following table contains data extracted from a sheet named USMs containing a list of USMS parameters or from his equivalent CSV example file.

Getting data

# Reading the Excel file
usms_param <- read_params_table(usm_xl_file, sheet_name = "USMs")
# Or
# Reading the CSV file
usms_param <- read_params_table(usm_csv_file)

Generating the file

# Output file path
out_file <- "/path/to/file/usms.xml"
# or something like C:/path/to/file/usms.xml" for Windows

# Generating a new usms.xml file, for all xl_param lines
gen_usms_xml(file = out_file, param_df = usms_param)

usms.xml file content

Example of the first usm parameters:

#> <?xml version="1.0" encoding="UTF-8" standalone="no"?>
#> <usms version="10.1.0">
#>   <usm nom="USM_2017_T1_CI">
#>     <datedebut>199</datedebut>
#>     <datefin>263</datefin>
#>     <finit>USM_2017_T1_ini.xml</finit>
#>     <nomsol>USM_T1</nomsol>
#>     <fstation>climatex_sta.xml</fstation>
#>     <fclim1>climatex.2017</fclim1>
#>     <fclim2>climatex.2017</fclim2>
#>     <culturean>1</culturean>
#>     <nbplantes>1</nbplantes>
#>     <codesimul>0</codesimul>
#>     <plante dominance="1">
#>       <fplt>rapeseed_plt.xml</fplt>
#>       <ftec>USM_2017_T1_CI_tec.xml</ftec>
#>       <flai>NA</flai>
#>       <fobs>USM_2017_T1_CI.obs</fobs>
#>     </plante>
#>     <plante dominance="2">
#>       <fplt>NA</fplt>
#>       <ftec>NA</ftec>
#>       <flai>NA</flai>
#>       <fobs>NA</fobs>
#> ...
#> </usms>

Getting data

# Reading the Excel file
soils_param <- read_params_table(usm_xl_file, sheet_name = "Soils")

Generating the file

# Output file path
out_file <- "/path/to/file/sols.xml"
# or something like C:/path/to/file/usms.xml" for Windows

# Generating a new sols.xml file, for all xl_param lines
gen_sols_xml(file = out_file, param_df = soils_param)

sols.xml file content

Example of the first sol parameters sub-list:

#> <?xml version="1.0" encoding="UTF-8"?>
#> <sols version="10.1.0">
#>   <sol nom="USM_T1">
#>     <param format="real" max="60.0" min="0.0" nom="argi">20.35</param>
#>     <param format="real" max="0.5" min="0.05" nom="norg">0.1</param>
#>     <param format="real" max="60.0" min="10.0" nom="profhum">40</param>
#>     <param format="real" max="100.0" min="0.0" nom="calc">0.52</param>
#>     <param format="real" max="9.0" min="4.0" nom="pH">8.23</param>
#>     <param format="real" max="0.5" min="0.0" nom="concseuil">0.2</param>
#>     <param format="real" max="0.6" min="0.05" nom="albedo">0.22</param>
#>     <param format="real" max="50.0" min="0.0" nom="q0">9.63</param>
#>     <param format="real" max="1.0" min="0.0" nom="ruisolnu">0</param>
#>     <param format="real" max="1000.0" min="10.0" nom="obstarac">200</param>
#>     <param format="real" max="100.0" min="5.0" nom="pluiebat">50</param>
#>     <param format="real" max="2.0" min="0.0" nom="mulchbat">0.5</param>
#>     <param format="real" max="150.0" min="10.0" nom="zesx">60</param>
#>     <param format="real" max="10.0" min="-10.0" nom="cfes">5</param>
#>     <param format="real" max="0.2" min="0.01" nom="z0solnu">0.01</param>
#>     <param format="real" max="20.0" min="8.0" nom="CsurNsol">0</param>
#>     <param nom="finert">0.65</param>
#>     <param format="real" max="5.0" min="0.0" nom="penterui">0.33</param>
#>     <option choix="2" nom="pebbles" nomParam="codecailloux">
#>       <choix code="1" nom="yes"/>
#>       <choix code="2" nom="no"/>
#>     </option>
#>     <option choix="1" nom="macroporosity" nomParam="codemacropor">
#>       <choix code="1" nom="yes"/>
#>       <choix code="2" nom="no"/>
#>     </option>
#>     <option choix="2" nom="cracks (case of swelling clay soils)" nomParam="codefente">
#> ...
#>     </tableau>
#> ...
#> </sols>

Getting data

# Reading the Excel file
tec_param <- read_params_table(usm_xl_file, sheet_name = "Tec")

Generating files

# *_tec.xml files, one for each xl_param line
gen_tec_xml(param_df = tec_param, out_dir = workspace_path)

Example of a tec parameters file content sub-list:

#> <?xml version="1.0" encoding="UTF-8" standalone="no"?>
#> <fichiertec version="10.1.0">
#>   <formalisme nom="supply of organic residus">
#>     <ta nb_interventions="1" nom="interventions">
#>       <ta_entete nb_colonnes="7">
#>         <colonne nom="julres"/>
#>         <colonne nom="coderes"/>
#>         <colonne nom="qres"/>
#>         <colonne nom="Crespc"/>
#>         <colonne nom="CsurNres"/>
#>         <colonne nom="Nminres"/>
#>         <colonne nom="eaures"/>
#>       </ta_entete>
#>       <intervention nb_colonnes="7">
#>         <colonne nom="julres">110</colonne>
#>         <colonne nom="coderes">1</colonne>
#>         <colonne nom="qres">9</colonne>
#>         <colonne nom="Crespc">42</colonne>
#>         <colonne nom="CsurNres">90</colonne>
#>         <colonne nom="Nminres">0</colonne>
#>         <colonne nom="eaures">7</colonne>
#>       </intervention>
#>     </ta>
#>   </formalisme>
#>   <formalisme nom="soil tillage">
#>     <option choix="2" nom="Automatic calculation of the depth of residues incorporation in function of proftrav" nomParam="code_auto_profres">
#>       <choix code="1" nom="yes">
#>         <param format="real" max="0.0" min="1.0" nom="resk">-999</param>
#>         <param format="real" max="0.0" min="10.0" nom="resz">-999</param>
#>       </choix>
#> ...
#> </fichiertec>

Getting data

# Reading the Excel file
ini_param <- read_params_table(usm_xl_file, sheet_name = "Ini")

Generating files

# *_ini.xml files, one for each xl_param line
gen_ini_xml(param_df = ini_param, out_dir = workspace_path)

XML file content

Example of a ini parameters file content sub-list:

#> <?xml version="1.0" encoding="UTF-8"?>
#> <initialisations version="10.1.0">
#>   <nbplantes>1</nbplantes>
#>   <plante dominance="1">
#>     <stade0>snu</stade0>
#>     <lai0>0</lai0>
#>     <magrain0>0</magrain0>
#>     <zrac0>0</zrac0>
#>     <option choix="2" nom="Simulation of Nitrogen and Carbon reserves" nomParam="code_acti_reserve">
#>       <choix code="1" nom="yes">
#>         <maperenne0>0</maperenne0>
#>         <QNperenne0>0</QNperenne0>
#>         <masecnp0>0</masecnp0>
#>         <QNplantenp0>0</QNplantenp0>
#>       </choix>
#>       <choix code="2" nom="no">
#>         <masec0>0</masec0>
#>         <QNplante0>0</QNplante0>
#>         <restemp0>0</restemp0>
#> ...
#> </initialisations>

Getting data

# Reading the Excel file
sta_param <- read_params_table(usm_xl_file, sheet_name = "Station")

Generating files

# *_sta.xml files, one for each xl_param line
gen_sta_xml(param_df = sta_param, out_dir = workspace_path)

XML file content

Example of a sta parameters file content sub-list:

#> <?xml version="1.0" encoding="UTF-8" standalone="no"?>
#> <fichiersta version="10.1.0">
#>   <formalisme nom="Weather station">
#>     <param format="real" max="10.0" min="2.0" nom="zr">2.5</param>
#>     <param format="real" max="10.0" min="0.0" nom="NH3ref">0</param>
#>     <param format="real" max="3.0" min="0.0" nom="concrr">0.02</param>
#>     <param format="real" max="90.0" min="-90.0" nom="latitude">49</param>
#>     <param format="real" max="1200.0" min="800.0" nom="patm">1000</param>
#>     <param format="real" max="25.0" min="4.0" nom="aclim">20</param>
#>   </formalisme>
#>   <formalisme nom="climate">
#>     <option choix="1" nom="reading OR calculation of PET" nomParam="codeetp">
#>       <choix code="1" nom="PET-Penman_reading"/>
#>       <choix code="2" nom="PET-Penman_calculation"/>
#>       <choix code="3" nom="PET-Shuttleworth-Wallace_calculation"/>
#>       <choix code="4" nom="PET-Priestley-Taylor_calculation">
#>         <param format="real" max="2.0" min="1.0" nom="alphapt">1.25</param>
#>       </choix>
#>     </option>
#>     <option choix="1" nom="climate change" nomParam="codeclichange">
#>       <choix code="1" nom="no"/>
#>       <choix code="2" nom="yes"/>
#>     </option>
#>     <option choix="1" nom="climate in altitude" nomParam="codaltitude">
#>       <choix code="1" nom="no"/>
#>       <choix code="2" nom="yes">
#>         <param format="real" max="2000.0" min="0.0" nom="altistation">440</param>
#>         <param format="real" max="2000.0" min="0.0" nom="altisimul">800</param>
#>         <param format="real" max="3.0" min="0.1" nom="gradtn">-0.5</param>
#>         <param format="real" max="3.0" min="0.1" nom="gradtx">-0.55</param>
#>         <param format="real" max="2000.0" min="0.0" nom="altinversion">500</param>
#>         <param format="real" max="3.0" min="0.1" nom="gradtninv">1.3</param>
#>         <param format="real" max="1.0" min="0.0" nom="cielclair">0.8</param>
#>         <option choix="1" nom="option.adret.or.ubac" nomParam="codadret">
#>           <choix code="1" nom="adret(south)"/>
#>           <choix code="2" nom="ubac(north)">
#>             <param format="real" max="5.0" min="-5.0" nom="ombragetx">-1.4</param>
#>           </choix>
#>         </option>
#>       </choix>
#>     </option>
#> ...
#> </fichiersta>