# Generating STICS XML files from tabulated data

    library(SticsRFiles)
    library(dplyr)

# Introduction

- In this part information are focusing on functionalities related to STICS XML files generation capabilities based on parameterization for lists of simulations (USMs) stored in tabulated data files; as Excel or CSV files.

- The functions operate on data loaded as data.frames from Excel sheets or CSV files

- Specialized functions for producing XML files are taking into account: initialization files, stations files, crop management files, usms file and soils files. General parameters files generation are not available, but will be eventually included in future developments.

- Observations data files generation have been included even if they are not in XML format.

- The generation of weather files is not included yet in the package, but will be included in a future version. One can use the tool provided by JavaSTICS GUI to perform these files generation.

This document has been generated using the latest STICS version V10.1.0.

# Package functions to be used

There is not at the moment an integrated function which is able to produce all needed parameters files. Individual functions are dedicated to each parameter file kind and may be called individually or gathered in a single script for doing all tasks at once. Use examples are given in next parts below.

- gen_usms_xml: for generating a `usms.xml` file
- gen_sols_xml: for generating a `sols.xml` file
- gen_ini_xml: for generating simulations initialization files (`*_ini.xml`)
- gen_tec_xml: for generating crop management files (`*_tec.xml`)
- gen_sta_xml: for generating weather stations files (`*_sta.xml`)

# Getting a table file example

## 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

# Description of tables expected content and use

As told in the previous section, parameters data may be stored either in Excel files containing several sheets or in several equivalent individual CSV files.

Sheets content and CSV files content is the same, only their use is different. But, CSV files are easily traced under version control systems and they also can be generated programmatically with the help of functions dedicated for example to generating crop management parameters like irrigation, fertilization (interventions and doses calculations).

## 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, initializations (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.

usm_name | datedebut | datefin | finit | nomsol | fstation | fclim1 | fclim2 | culturean | nbplantes | codesimul | fplt_1 | ftec_1 | flai_1 | fobs_1 | fplt_2 | ftec_2 | flai_2 | fobs_2
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
USM_2017_T1_CI | 199 | 263 | USM_2017_T1_ini.xml | USM_T1 | climatex_sta.xml | climatex.2017 | climatex.2017 | 1 | 1 | 0 | rapeseed_plt.xml | USM_2017_T1_CI_tec.xml | NA | USM_2017_T1_CI.obs | NA | NA | NA | NA
USM_2018_T1 | 264 | 570 | USM_2017_T1_ini.xml | USM_T1 | climatex_sta.xml | climatex.2017 | climatex.2018 | 2 | 1 | 0 | wheat_plt.xml | USM_2018_T1_tec.xml | NA | USM_2018_T1.obs | NA | NA | NA | NA
BIN_CAN_05_SEC_220-0-0_34K_CANPC05T3_Q | 199 | 263 | Vill11_ini.xml | LF1 | climatex_sta.xml | climatex.2017 | climatex.2017 | 2 | 1 | 0 | proto_potato_plt.xml | BIN_CAN_05_SEC_220-0-0_34K_CANPC05T3_Q_tec.xml | NA | NA | NA | NA | NA | NA
BIN_AGT_04_IRR_220-0-0_33K_AGT04T2_Q | 264 | 570 | Vill11_ini.xml | LF1 | climatex_sta.xml | climatex.2017 | climatex.2018 | 2 | 1 | 0 | proto_potato_plt.xml | BIN_AGT_04_IRR_220-0-0_33K_AGT04T2_Q_tec.xml | NA | NA | NA | NA | NA | NA
AGA_ARB_13_IRR_220-0-0_37K_ARB13_C | 199 | 263 | Vill11_ini.xml | LF1 | climatex_sta.xml | climatex.2017 | climatex.2017 | 2 | 1 | 0 | proto_potato_plt.xml | AGA_ARB_13_IRR_220-0-0_37K_ARB13_C_tec.xml | NA | NA | NA | NA | NA | NA
AGA_ARB_13_SEC_220-0-0_37K_ARB13_C | 264 | 570 | Vill11_ini.xml | LF1 | climatex_sta.xml | climatex.2017 | climatex.2018 | 2 | 1 | 0 | proto_potato_plt.xml | AGA_ARB_13_SEC_220-0-0_37K_ARB13_C_tec.xml | NA | NA | NA | NA | NA | NA
FRA_ARB_11_SEC_220-0-0_38K_E | 199 | 263 | Vill11_ini.xml | LF1 | climatex_sta.xml | climatex.2017 | climatex.2017 | 2 | 1 | 0 | proto_potato_plt.xml | FRA_ARB_11_SEC_220-0-0_38K_E_tec.xml | NA | NA | NA | NA | NA | NA
MAG_ARB_09_SEC_220-0-0_38K_E | 264 | 570 | Vill11_ini.xml | LF1 | climatex_sta.xml | climatex.2017 | climatex.2018 | 2 | 1 | 0 | proto_potato_plt.xml | MAG_ARB_09_SEC_220-0-0_38K_E_tec.xml | NA | NA | NA | NA | NA | NA
MAG_ARV_12_IRR_220-0-0_36K_ARV12_C | 199 | 263 | Vill11_ini.xml | LF1 | climatex_sta.xml | climatex.2017 | climatex.2017 | 2 | 1 | 0 | proto_potato_plt.xml | MAG_ARV_12_IRR_220-0-0_36K_ARV12_C_tec.xml | NA | NA | NA | NA | NA | NA
MAG_ARV_12_SEC_220-0-0_36K_ARV12_C | 264 | 570 | Vill11_ini.xml | LF1 | climatex_sta.xml | climatex.2017 | climatex.2018 | 2 | 1 | 0 | proto_potato_plt.xml | MAG_ARV_12_SEC_220-0-0_36K_ARV12_C_tec.xml | NA | NA | NA | NA | NA | NA
FRA_ARB_12_SEC_220-0-0_31K_ARB12_C | 199 | 263 | Vill11_ini.xml | LF1 | climatex_sta.xml | climatex.2017 | climatex.2017 | 2 | 1 | 0 | proto_potato_plt.xml | FRA_ARB_12_SEC_220-0-0_31K_ARB12_C_tec.xml | NA | NA | NA | NA | NA | NA
FRA_ARB_13_SEC_220-0-0_37K_ARB13_C | 264 | 570 | Vill11_ini.xml | LF1 | climatex_sta.xml | climatex.2017 | climatex.2018 | 2 | 1 | 0 | proto_potato_plt.xml | FRA_ARB_13_SEC_220-0-0_37K_ARB13_C_tec.xml | NA | NA | NA | NA | NA | NA

# Generating the `usms` XML file (usms.xml)

The gen_usms_xml function is working on a data.frame object that can be loaded either from an Excel file sheet or from a csv file. Here after code shows how to get data from the downloaded examples Excel and CSV files.

## 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>

# Generating the `sols` XML file (sols.xml)

As for `gen_usms_xml`, `gen_sols_xml` function is working on a data.frame object loaded from an Excel file sheet. The following code only shows here after the `sols.xml` file generation section.

## 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>

# Generating multiple crop management XML files (*_tec.xml)

## 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>

# Generating multiple initialization XML files (*_ini.xml)

## 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>

# Generating multiple meteorological station XML files (*_sta.xml)

## 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"/>
    #>     <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>