vignettes/Manipulating_Stics_XML_files.Rmd
Manipulating_Stics_XML_files.Rmd
The purpose of this document is to provide starting information about:
Simple reproducible use cases based on 3 essential functions get_param_info, get_param_xml and set_param_xml are described in this document.
For the moment, queries for selecting information among
usms
, soils
are limited. For example, getting
soil parameters for a list of soils is possible, as getting usms
informations using a usms list.
Queries inspecting elements downwards are not available yet; as for
example, getting soil names/parameters using a criterion like
argi
values > 20.
Exploring files content for files sets are also possible, but not replacing parameters values.
This document has been generated using the latest STICS version V10.1.0.
XML files are self documented files and hierarchically structured. Syntaxic rules are based on what we call nodes (i.e. nodes names, similar to html tags) and attributes (nodes attributes values).
STICS XML files are filled with different kinds of parameters description structures according to their type/role in the model formalisms.
As we can see in the above XML file extract from a general parameter file:
Parameters are grouped according to formalisms (in a
xml <formalisme>...</formalisme>
block)
Parameters may be defined by single values This kind of
definition is common for all files types and the parameter name is
stored in the nom
attribute of a param
XML
node. So the first parameter name in the example is beta
and its value is 1.40000
(inside param
tags).
Option parameters (with or without attached parameters,
eventually with sub-option) The corresponding parameter name for an
option node is stored in an attribute named
nomParam
and the corresponding value is given in the
attribute choix
of the option node. For example, the value
of the parameter codesymbiose
is 2
in the
example (choix=“2”).
<formalisme nom="Water absorption and nitrogen content of the plant">
<param format="real" max="2.0" min="1.0" nom="beta">1.40000</param>
<param format="real" max="1.0" min="0.2" nom="lvopt">0.50000</param>
<param format="real" max="0.1" min="0.01" nom="difN">0.04500</param>
<param format="real" max="30.0" min="5.0" nom="plNmin">10.00000</param>
<param format="real" max="50.0" min="0.0" nom="irrlev">20.00000</param>
<param format="real" max="50.0" min="0.0" nom="QNpltminINN">0.00000</param>
<option choix="2" nom="Nitrogen fixation by legumes" nomParam="codesymbiose">
<choix code="1" nom="critical nitrogen"/>
<choix code="2" nom="nodule activity">
<option choix="2" nom="mineral nitrogen inhibition" nomParam="codefxn">
<choix code="1" nom="no effect"/>
<choix code="2" nom="nitrogen amount"/>
<choix code="3" nom="nitrogen concentration"/>
</option>
</choix>
</option>
</formalisme>
Parameters with several values (for soil layers, technical operations,…) Several values may be defined for example relatively to soil parameters (different layers) or for crop management operations (with time repetitions).
Example from soil files In the above file extract for soil
parameters, each set of parameters (included in tableau
nodes) is repeated for each soil layer (layers names are set in the
nom
attributes from layer 1 to layer 5).
The parameters names are defined in a nom
attribute in each
colonne
XML tag.
<sol nom="solcanne">
...
</tableau_entete>
<tableau nb_colonnes="8" nom="layer 1">
<colonne nom="epc">20.00</colonne>
<colonne nom="HCCF">46.80</colonne>
<colonne nom="HMINF">26.20</colonne>
<colonne nom="DAF">1.08</colonne>
<colonne nom="cailloux">0.00</colonne>
<colonne nom="typecailloux">1</colonne>
<colonne nom="infil">50.00</colonne>
<colonne nom="epd">10</colonne>
...
</tableau>
<tableau nb_colonnes="8" nom="layer 5">
<colonne nom="epc">20.00</colonne>
<colonne nom="HCCF">50.10</colonne>
<colonne nom="HMINF">25.50</colonne>
<colonne nom="DAF">0.99</colonne>
<colonne nom="cailloux">0.00</colonne>
<colonne nom="typecailloux">1</colonne>
<colonne nom="infil">50.00</colonne>
<colonne nom="epd">10</colonne>
...
intervention
node .
Inside each intervention
node, parameters names are defined
in a nom
attribute for each colonne
XML
tag. <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">112</colonne>
<colonne nom="coderes">1</colonne>
<colonne nom="qres">1.00</colonne>
<colonne nom="Crespc">42.00</colonne>
<colonne nom="CsurNres">60.00</colonne>
<colonne nom="Nminres">0.00</colonne>
<colonne nom="eaures">0.00</colonne>
</intervention>
...
<intervention nb_colonnes="7">
<colonne nom="julres">220</colonne>
<colonne nom="coderes">1</colonne>
<colonne nom="qres">1.00</colonne>
<colonne nom="Crespc">42.00</colonne>
<colonne nom="CsurNres">60.00</colonne>
<colonne nom="Nminres">0.00</colonne>
<colonne nom="eaures">0.00</colonne>
</intervention>
...
Rules have been defined to easily search and extract information from XML files in order to simplify the way of using functions dedicated to XML files manipulations.
In some cases, information relative to upward dependence are needed for extracting parameters values, but in most cases only the parameters names are mandatory in functions arguments.
SticsRFiles
library
Several XML examples files have bee included in the package in order
to use them in reproducible
manipulations
and results described in this document. These examples
files are extracted from the JavaSTICS standard distribution (some of
them have been renamed).
In xml_dir, we store the directory path of the XML files available in the SticsRFiles installation directory.
xml_dir <- get_examples_path(file_type = "xml", stics_version = stics_version)
# For linux > '/path/to/user/R/x86_64-pc-linux-gnu-library/3.6/SticsRFiles/ >
# extdata/xml/examples/V10.0'
# For windows > 'C:/Users/username/Documents/R/win-lib/3.6/SticsRFiles/ >
# extdata/xml/examples/V10.0'
xml_files <- list.files(path = xml_dir, pattern = ".xml$", full.names = TRUE)
# Listing only the first three files of the entire list
# For linux > [1]
# '/path/to/user/R/x86_64-pc-linux-gnu-library/3.6/SticsRFiles/extdata/xml >
# /examples/V10.0/file_ini.xml' > [2]
# '/path/to/user/R/x86_64-pc-linux-gnu-library/3.6/SticsRFiles/extdata/xml >
# /examples/V10.0/file_plt.xml' > [3]
# '/path/to/user/R/x86_64-pc-linux-gnu-library/3.6/SticsRFiles/extdata/xml >
# /examples/V10.0/file_sta.xml'
# For windows > [1]
# 'C:/Users/username/Documents/R/win-lib/3.6/SticsRFiles/extdata/xml/ >
# examples/V10.0/file_ini.xml' > [2]
# 'C:/Users/username/Documents/R/win-lib/3.6/SticsRFiles/extdata/xml/ >
# examples/V10.0/file_plt.xml' > [3]
# 'C:/Users/username/Documents/R/win-lib/3.6/SticsRFiles/extdata/xml/ >
# examples/V10.0/file_sta.xml'
The corresponding files types to file names is given in the above table:
files | groups |
---|---|
file_ini.xml | initializations |
file_plt.xml | plant |
file_sta.xml | station |
file_tec.xml | crop management |
param_gen.xml | general |
param_newform.xml | general (new formalisms) |
sols.xml | soils |
usms.xml | usms |
file.copy(from = xml_files, to = xml_loc_dir)
#> [1] TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE
The get_param_info
function search is performed in a
parameter table stored internally in the SticsRFiles library with
respect to the model version (V10.1.0 as default one).
This function uses 2 optional arguments i.e.: * param
a
name or a part of a parameter name (or a vector of) for searching in
parameters names * and/or keyword
for searching in the
parameters description information.
The information columns in the returned tibble are:
name
: parameter namefile
: file type of the parameter (keyword), see above
table for correspondence with fileskeyword | xml file | parameter kind |
---|---|---|
STATION | _sta.xml | wheather station |
PARPLT | _plt.xml | plant |
PARAM | param_gen.xml | general |
PARSOL | sols.xml | soil |
PARTEC | _tec.xml | crop management |
PARAMV6 | param_newform.xml | general parameters |
USMXML | usms.xml | usm |
USM/USMXML | usms.xml | usm |
INIT | _ini.xml | initialisation |
PARSOL/USM | sols.xml/usms.xml | soil or usm |
min
: minimal boundmax
: maximal bounddefinition
: parameter descriptionWhatever the arguments list is when calling the function, the returned tibble always contains all of these columns.
Information about bounds
may be missing according to
parameters kind.
For example, for initialization or usm parameters and/or character type parameters (files names, residues type,…), bounds dont make any sense and
NA
is used as missing values.
Using the get_param_info
function without any argument,
or with specifying the desired STICS
version, allows to get
a table containing all input parameters.
In the above code block, an extract of the returned information table is shown:
param_names <- get_param_info()
head(param_names)
#> name file min max
#> 1 aangst STATION 0 0.9
#> 2 abscission PARPLT 0 1
#> 3 aclim STATION 4 25
#> 4 adens PARPLT -2 0
#> 5 adfol PARPLT -10 10
#> 6 adil PARPLT 1 7
#> definition
#> 1 coefficient of the Angstrom relationship for extraterrestrial radiation
#> 2 fraction of senescent leaves falling to the soil
#> 3 climatic component to calculate actual soil evaporation (Brisson & Perrier, 1991)
#> 4 Interplant competition parameter
#> 5 parameter determining the leaf density evolution within the chosen shape
#> 6 parameter of the critical dilution curve [Nplante]=adil MS^(-bdil)
The full parameters data.frame content is presented in the above paged table.
If parameters names are known and are given with the right syntax, information can be retrieved as follows
get_param_info(param = "albedo")
get_param_info(param = c("albedo", "latitude", "humcapil"))
#> name file min max definition
#> 55 albedo PARSOL 0.05 0.6 albedo of the bare dry soil
#> 56 albedomulchplastique PARTEC 0.05 0.8 albedo of plastic cover
#> 57 albedomulchresidus PARAM 0.05 0.8 albedo of plant mulch
#> 58 albedomulchresidus(1) PARAM 0.05 0.8 albedo of plant mulch
#> 59 albedomulchresidus(10) PARAM 0.05 0.8 albedo of plant mulch
#> 60 albedomulchresidus(11) PARAM 0.05 0.8 albedo of plant mulch
#> 61 albedomulchresidus(12) PARAM 0.05 0.8 albedo of plant mulch
#> 62 albedomulchresidus(13) PARAM 0.05 0.8 albedo of plant mulch
#> 63 albedomulchresidus(14) PARAM 0.05 0.8 albedo of plant mulch
#> 64 albedomulchresidus(15) PARAM 0.05 0.8 albedo of plant mulch
#> 65 albedomulchresidus(16) PARAM 0.05 0.8 albedo of plant mulch
#> 66 albedomulchresidus(17) PARAM 0.05 0.8 albedo of plant mulch
#> 67 albedomulchresidus(18) PARAM 0.05 0.8 albedo of plant mulch
#> 68 albedomulchresidus(19) PARAM 0.05 0.8 albedo of plant mulch
#> 69 albedomulchresidus(2) PARAM 0.05 0.8 albedo of plant mulch
#> 70 albedomulchresidus(20) PARAM 0.05 0.8 albedo of plant mulch
#> 71 albedomulchresidus(21) PARAM 0.05 0.8 albedo of plant mulch
#> 72 albedomulchresidus(3) PARAM 0.05 0.8 albedo of plant mulch
#> 73 albedomulchresidus(4) PARAM 0.05 0.8 albedo of plant mulch
#> 74 albedomulchresidus(5) PARAM 0.05 0.8 albedo of plant mulch
#> 75 albedomulchresidus(6) PARAM 0.05 0.8 albedo of plant mulch
#> 76 albedomulchresidus(7) PARAM 0.05 0.8 albedo of plant mulch
#> 77 albedomulchresidus(8) PARAM 0.05 0.8 albedo of plant mulch
#> 78 albedomulchresidus(9) PARAM 0.05 0.8 albedo of plant mulch
#> name file min max
#> 55 albedo PARSOL 0.05 0.6
#> 56 albedomulchplastique PARTEC 0.05 0.8
#> 57 albedomulchresidus PARAM 0.05 0.8
#> 58 albedomulchresidus(1) PARAM 0.05 0.8
#> 59 albedomulchresidus(10) PARAM 0.05 0.8
#> 60 albedomulchresidus(11) PARAM 0.05 0.8
#> 61 albedomulchresidus(12) PARAM 0.05 0.8
#> 62 albedomulchresidus(13) PARAM 0.05 0.8
#> 63 albedomulchresidus(14) PARAM 0.05 0.8
#> 64 albedomulchresidus(15) PARAM 0.05 0.8
#> 65 albedomulchresidus(16) PARAM 0.05 0.8
#> 66 albedomulchresidus(17) PARAM 0.05 0.8
#> 67 albedomulchresidus(18) PARAM 0.05 0.8
#> 68 albedomulchresidus(19) PARAM 0.05 0.8
#> 69 albedomulchresidus(2) PARAM 0.05 0.8
#> 70 albedomulchresidus(20) PARAM 0.05 0.8
#> 71 albedomulchresidus(21) PARAM 0.05 0.8
#> 72 albedomulchresidus(3) PARAM 0.05 0.8
#> 73 albedomulchresidus(4) PARAM 0.05 0.8
#> 74 albedomulchresidus(5) PARAM 0.05 0.8
#> 75 albedomulchresidus(6) PARAM 0.05 0.8
#> 76 albedomulchresidus(7) PARAM 0.05 0.8
#> 77 albedomulchresidus(8) PARAM 0.05 0.8
#> 78 albedomulchresidus(9) PARAM 0.05 0.8
#> 803 humcapil PARSOL 2 10
#> 1050 latitude STATION -90 90
#> definition
#> 55 albedo of the bare dry soil
#> 56 albedo of plastic cover
#> 57 albedo of plant mulch
#> 58 albedo of plant mulch
#> 59 albedo of plant mulch
#> 60 albedo of plant mulch
#> 61 albedo of plant mulch
#> 62 albedo of plant mulch
#> 63 albedo of plant mulch
#> 64 albedo of plant mulch
#> 65 albedo of plant mulch
#> 66 albedo of plant mulch
#> 67 albedo of plant mulch
#> 68 albedo of plant mulch
#> 69 albedo of plant mulch
#> 70 albedo of plant mulch
#> 71 albedo of plant mulch
#> 72 albedo of plant mulch
#> 73 albedo of plant mulch
#> 74 albedo of plant mulch
#> 75 albedo of plant mulch
#> 76 albedo of plant mulch
#> 77 albedo of plant mulch
#> 78 albedo of plant mulch
#> 803 threshold of soil gravimetric water content under which capillary rise occurs (dry soil)
#> 1050 latitude of the site
A search with incomplete names may be done as follows
get_param_info(param = "hum")
#> name file min max
#> 392 codetesthumN PARAMV6 1 2
#> 803 humcapil PARSOL 2 10
#> 804 humirac PARAMV6 0 2
#> 805 humirac_decisemis PARTEC 0 1
#> 1249 profhum PARSOL 10 150
#> 1250 profhumrecolteuse PARTEC 0 100
#> 1251 profhumsemoir PARTEC 0 100
#> 1282 prophumtassrec PARAM 0.8 1.8
#> 1283 prophumtasssem PARAM 0.8 1.8
#> 1293 psihumin PARAM -5 -0.1
#> definition
#> 392 option to define automatic N fertilisation calculation: 1 = based on rainfall, 2 = based on soil water content
#> 803 threshold of soil gravimetric water content under which capillary rise occurs (dry soil)
#> 804 A revoir: 1 = la fonction F_humirac atteint un plateau (ancien code) / 2 = la fonction n atteint pas de plateau (identique a la phase germination-levee)
#> 805 relative soil moisture threshold above which sowing is possible (0 = no sensitivity to drought, 1 = highly sensitive)
#> 1249 maximum soil depth with an active biological activity
#> 1250 soil depth at which moisture is considered to allow harvesting (if soil compaction is activated)
#> 1251 soil depth at which moisture is considered to allow sowing (if soil compaction is activated)
#> 1282 soil moisture content (fraction of field capacity) above which compaction may occur and delay harvest
#> 1283 soil moisture content (fraction of field capacity) above which compaction may occur and delay sowing
#> 1293 soil water potential corresponding to wilting point
param_names <- get_param_info(param = c("alb", "hum"))
The found parameters data.frame content is presented in the above paged table.
The keyword
argument (one or several possible strings)
may be used to search in all textual columns as name
or
description
.
get_param_info(keyword = "hum")
param_names <- get_param_info(keyword = c("alb", "hum"))
The found parameters data.frame content is presented in the above paged table.
The get_param_xml
function is used for extracting
parameters values in XML files (for one file or a list of), optionally
providing it a parameter name or a names list.
The result of the function call is a named list (with files names), and each element of the list contains a named list of the parameters values (see examples below).
For usms or soils parameter, a conditional selection may be used to filter parameter values respectively through a list of usms or soils.
Among STICS parameters files types, XML structure may be different, and they can contain either one/several occurrence(s) of parameters with scalar values (soils or usms description), or one/several occurrence(s) of parameters with vector values (along soil depth, crop management operations,…).
So parameters values extraction with the get_param_xml
requires different input arguments combination to do so.
# Fixing files paths
sols <- file.path(xml_loc_dir, "sols.xml")
par_gen <- file.path(xml_loc_dir, "param_gen.xml")
# A option parameter
get_param_xml(par_gen, param = "codeactimulch")
#> $param_gen.xml
#> $param_gen.xml$codeactimulch
#> [1] 1
# A simple parameter
get_param_xml(par_gen, param = "tnitopt")
#> $param_gen.xml
#> $param_gen.xml$tnitopt
#> [1] 30
# Using a conditional selection
get_param_xml(sols, param = "argi", select = "sol", select_value = "solcanne")
#> $sols.xml
#> $sols.xml$argi
#> [1] 30.2
# For all soils
get_param_xml(sols, param = "argi")
#> $sols.xml
#> $sols.xml$argi
#> [1] 30.2 21.0 27.0 39.0 1.0 12.2 70.0 22.0 9.9 10.2 10.2 17.0 23.1 22.0 27.0
#> [16] 30.7 0.1 27.3 25.0 10.2 25.0 28.6 36.0 29.0 10.2 21.2 22.2 13.0 17.0 15.0
#> [31] 26.0 28.2 20.0
# For all soils
get_param_xml(sols, param = c("argi", "pH"))
#> $sols.xml
#> $sols.xml$argi
#> [1] 30.2 21.0 27.0 39.0 1.0 12.2 70.0 22.0 9.9 10.2 10.2 17.0 23.1 22.0 27.0
#> [16] 30.7 0.1 27.3 25.0 10.2 25.0 28.6 36.0 29.0 10.2 21.2 22.2 13.0 17.0 15.0
#> [31] 26.0 28.2 20.0
#>
#> $sols.xml$pH
#> [1] 7.00 7.00 7.00 7.00 5.36 8.10 7.00 7.00 6.10 8.40 8.30 7.00 7.00 7.00 7.00
#> [16] 7.00 7.00 7.00 7.00 8.30 7.00 7.00 7.00 7.00 7.00 7.95 7.00 7.00 6.50 7.00
#> [31] 7.86 7.84 5.00
# For one soil
get_param_xml(sols, param = c("argi", "pH"), select = "sol", select_value = "solcanne")
#> $sols.xml
#> $sols.xml$argi
#> [1] 30.2
#>
#> $sols.xml$pH
#> [1] 7
Vectors parameters are typically present in soils file or crop management files.
# For all soil layers
get_param_xml(sols, param = c("epc", "infil"))
#> $sols.xml
#> $sols.xml$epc
#> [1] 20 20 20 20 20 30 30 30 30 30 30 30 30 30 0 20 20 20
#> [19] 0 0 5 10 15 15 15 30 30 30 30 30 10 10 10 10 40 25
#> [37] 30 35 30 0 10 20 20 20 0 30 30 30 30 0 30 30 30 30
#> [55] 0 10 30 20 40 80 15 15 30 30 30 25 30 35 30 0 5 15
#> [73] 20 50 80 20 20 20 0 0 50 0 0 0 0 22 33 7 0 0
#> [91] 25 20 40 35 0 30 30 30 30 0 25 20 40 35 0 30 20 20
#> [109] 20 110 10 20 40 60 70 10 50 50 0 0 30 30 30 30 0 10
#> [127] 30 30 30 15 25 25 25 45 0 10 40 70 40 40 20 20 60 0
#> [145] 0 20 30 30 20 20 10 20 30 30 30 10 20 30 30 30 20 5
#> [163] 0 0 0
#>
#> $sols.xml$infil
#> [1] 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00
#> [13] 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 0.00 0.00 0.00 0.00
#> [25] 0.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00
#> [37] 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00
#> [49] 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00
#> [61] 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 10.00 20.00
#> [73] 2.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 0.00 0.00 0.00 0.00
#> [85] 0.00 0.00 0.00 0.00 0.00 0.00 50.00 50.00 50.00 50.00 50.00 50.00
#> [97] 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 0.00 0.00 0.00
#> [109] 0.00 0.00 50.00 50.00 50.00 50.00 20.00 50.00 50.00 50.00 50.00 50.00
#> [121] 50.00 50.00 50.00 50.00 50.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> [133] 0.00 0.00 0.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00 50.00
#> [145] 50.00 0.00 0.00 0.00 0.00 0.00 30.00 30.00 30.00 30.00 30.00 15.00
#> [157] 15.00 15.00 15.00 15.00 10.00 0.01 50.00 50.00 50.00
# For all soil layers
get_param_xml(sols, param = c("epc", "infil"), select = "sol", value = "solcanne")
#> Warning: The `value` argument of `get_param_xml()` is deprecated as of SticsRFiles
#> 1.0.0.
#> ℹ Please use the `select_value` argument instead.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> $sols.xml
#> $sols.xml$epc
#> [1] 20 20 20 20 20
#>
#> $sols.xml$infil
#> [1] 50 50 50 50 50
# For all irrigation supplies
tec <- file.path(xml_loc_dir, "file_tec.xml")
get_param_xml(tec, param = c("julapI_or_sum_upvt", "amount"))
#> $file_tec.xml
#> $file_tec.xml$julapI_or_sum_upvt
#> [1] 178 185 193 198 200 204 207 211 214 218 221 232 239 249 257 264
#>
#> $file_tec.xml$amount
#> [1] 20 24 29 29 28 31 21 21 23 18 22 16 16 30 29 20
# For soil layers 1 to 3
get_param_xml(sols, param = c("epc", "infil"), select = "sol", select_value = "solcanne",
ids = 1:3)
#> $sols.xml
#> $sols.xml$epc
#> [1] 20 20 20 20 20
#>
#> $sols.xml$infil
#> [1] 50 50 50 50 50
# For irrigation operations 1 to 5
get_param_xml(tec, param = c("julapI_or_sum_upvt", "amount"), ids = 1:5)
#> $file_tec.xml
#> $file_tec.xml$julapI_or_sum_upvt
#> [1] 178 185 193 198 200 204 207 211 214 218 221 232 239 249 257 264
#>
#> $file_tec.xml$amount
#> [1] 20 24 29 29 28 31 21 21 23 18 22 16 16 30 29 20
Using the function without any argument produces a list of all parameters values of a file.
tec_param_values <- get_param_xml(tec)[[1]]
# Displaying only a subset of the list
head(tec_param_values, n = 10)
#> $julres
#> [1] 112
#>
#> $coderes
#> [1] 1
#>
#> $qres
#> [1] 1
#>
#> $Crespc
#> [1] 42
#>
#> $CsurNres
#> [1] 60
#>
#> $Nminres
#> [1] 0
#>
#> $eaures
#> [1] 0
#>
#> $code_auto_profres
#> [1] 1
#>
#> $resk
#> [1] 0.14
#>
#> $resz
#> [1] 5
A files list may be used also to get all parameters as follows in the same list
param_values <- get_param_xml(c(tec, sols))
# Files list names
names(param_values)
#> [1] "file_tec.xml" "sols.xml"
# param_values extract of 5 elements from each file sub-list
head(param_values$file_tec.xml, n = 5)
#> $julres
#> [1] 112
#>
#> $coderes
#> [1] 1
#>
#> $qres
#> [1] 1
#>
#> $Crespc
#> [1] 42
#>
#> $CsurNres
#> [1] 60
head(param_values$sols.xml, n = 5)
#> $argi
#> [1] 30.2 21.0 27.0 39.0 1.0 12.2 70.0 22.0 9.9 10.2 10.2 17.0 23.1 22.0 27.0
#> [16] 30.7 0.1 27.3 25.0 10.2 25.0 28.6 36.0 29.0 10.2 21.2 22.2 13.0 17.0 15.0
#> [31] 26.0 28.2 20.0
#>
#> $norg
#> [1] 0.270 0.100 0.210 0.150 0.700 0.110 0.200 0.120 0.070 0.160 0.180 0.210
#> [13] 0.140 0.120 0.140 0.140 0.070 0.080 0.200 0.180 0.100 0.120 0.150 0.120
#> [25] 0.140 0.070 0.110 0.100 0.150 0.080 0.088 0.088 0.100
#>
#> $profhum
#> [1] 40.0 31.0 27.0 27.0 40.0 30.0 50.0 35.0 50.0 30.0 30.0 27.0 22.0 35.0 30.0
#> [16] 30.0 30.0 30.0 30.0 28.0 30.0 40.0 40.0 30.0 31.5 30.0 30.0 30.0 15.0 35.0
#> [31] 25.0 25.0 20.0
#>
#> $calc
#> [1] 0.00 0.70 3.70 0.00 0.82 0.60 0.00 1.00 9.00 65.30 64.10 3.00
#> [13] 0.60 1.00 5.50 0.00 0.00 0.10 6.50 64.10 6.50 0.00 0.95 1.00
#> [25] 64.10 13.00 0.10 7.60 1.00 0.00 1.67 11.10 32.50
#>
#> $pH
#> [1] 7.00 7.00 7.00 7.00 5.36 8.10 7.00 7.00 6.10 8.40 8.30 7.00 7.00 7.00 7.00
#> [16] 7.00 7.00 7.00 7.00 8.30 7.00 7.00 7.00 7.00 7.00 7.95 7.00 7.00 6.50 7.00
#> [31] 7.86 7.84 5.00
The set_param_xml function allows to set the output file with the following optional arguments as follows:
For overwriting the existing file: use
overwrite = TRUE
For specifying a new file name and directory: use
save_as
for giving the new xml file path (including the
.xml extension)
In the following examples, the original file is always overwritten.
Before and after each set_param_xml
call, the original and
new written values are checked with a get_param_xml
call.
## An option parameter
# Initial value
get_param_xml(par_gen, param = "codeactimulch")
#> $param_gen.xml
#> $param_gen.xml$codeactimulch
#> [1] 1
# Setting a new one
set_param_xml(par_gen, param = "codeactimulch", values = 2, overwrite = TRUE)
# Controlling the written value
get_param_xml(par_gen, param = "codeactimulch")
#> $param_gen.xml
#> $param_gen.xml$codeactimulch
#> [1] 2
## A simple parameter
# Initial value
get_param_xml(par_gen, param = "tnitopt")
#> $param_gen.xml
#> $param_gen.xml$tnitopt
#> [1] 30
# Setting a new one
set_param_xml(par_gen, param = "tnitopt", values = 29.5, overwrite = TRUE)
# Controlling written value
get_param_xml(par_gen, param = "tnitopt")
#> $param_gen.xml
#> $param_gen.xml$tnitopt
#> [1] 29.5
## Using a conditional selection
# Initial value
get_param_xml(sols, param = "argi", select = "sol", select_value = "solcanne")
#> $sols.xml
#> $sols.xml$argi
#> [1] 30.2
# Setting a new one
set_param_xml(sols, param = "argi", values = 33, select = "sol", select_value = "solcanne",
overwrite = TRUE)
# Controlling written value
get_param_xml(sols, param = "argi", select = "sol", select_value = "solcanne")
#> $sols.xml
#> $sols.xml$argi
#> [1] 33
For passing several parameters values (for one or more parameters) or
single values for several parameters, the param_value
argument must contain a list of vectors of values with the same length
as param
vector.
## For all soils
soils_number <- length(get_soils_list(sols))
# Initial values
get_param_xml(sols, param = "argi")
#> $sols.xml
#> $sols.xml$argi
#> [1] 33.0 21.0 27.0 39.0 1.0 12.2 70.0 22.0 9.9 10.2 10.2 17.0 23.1 22.0 27.0
#> [16] 30.7 0.1 27.3 25.0 10.2 25.0 28.6 36.0 29.0 10.2 21.2 22.2 13.0 17.0 15.0
#> [31] 26.0 28.2 20.0
# One value per occurence
set_param_xml(sols, param = "argi", values = list(1:soils_number), overwrite = TRUE)
# Controlling written values
get_param_xml(sols, param = "argi")
#> $sols.xml
#> $sols.xml$argi
#> [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
#> [26] 26 27 28 29 30 31 32 33
# Setting the same value for all occurences
set_param_xml(sols, param = "argi", values = 40, overwrite = TRUE)
# Controlling written values
get_param_xml(sols, param = "argi")
#> $sols.xml
#> $sols.xml$argi
#> [1] 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
#> [26] 40 40 40 40 40 40 40 40
## For all soils
soils_number <- length(get_soils_list(sols))
# Initial values
# Setting one value per parameters occurence
set_param_xml(sols, param = list("argi", "pH"), values = list(1:soils_number, soils_number:1),
overwrite = TRUE)
# Controlling written values
get_param_xml(sols, param = c("argi", "pH"))
#> $sols.xml
#> $sols.xml$argi
#> [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
#> [26] 26 27 28 29 30 31 32 33
#>
#> $sols.xml$pH
#> [1] 33 32 31 30 29 28 27 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 9
#> [26] 8 7 6 5 4 3 2 1
# Setting the same value for all occurences
set_param_xml(sols, param = c("argi", "pH"), values = list(50, 8), overwrite = TRUE)
# Controlling written values
get_param_xml(sols, param = c("argi", "pH"))
#> $sols.xml
#> $sols.xml$argi
#> [1] 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50
#> [26] 50 50 50 50 50 50 50 50
#>
#> $sols.xml$pH
#> [1] 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8
## For one soil
# Initial values
get_param_xml(sols, param = c("argi", "pH"), select = "sol", select_value = "solcanne")
#> $sols.xml
#> $sols.xml$argi
#> [1] 50
#>
#> $sols.xml$pH
#> [1] 8
# Setting new values
set_param_xml(sols, param = c("argi", "pH"), values = list(50, 8), select = "sol",
select_value = "solcanne", overwrite = TRUE)
# Controlling written values
get_param_xml(sols, param = c("argi", "pH"), select = "sol", select_value = "solcanne")
#> $sols.xml
#> $sols.xml$argi
#> [1] 50
#>
#> $sols.xml$pH
#> [1] 8
## For all soil layers
# Initial values
get_param_xml(sols, param = c("epc", "infil"), select = "sol", select_value = "solcanne")
#> $sols.xml
#> $sols.xml$epc
#> [1] 20 20 20 20 20
#>
#> $sols.xml$infil
#> [1] 50 50 50 50 50
# Setting new values
set_param_xml(sols, param = c("epc", "infil"), values = list(18:22, 48:52), select = "sol",
select_value = "solcanne", overwrite = TRUE)
# Controlling written values
get_param_xml(sols, param = c("epc", "infil"), select = "sol", select_value = "solcanne")
#> $sols.xml
#> $sols.xml$epc
#> [1] 18 19 20 21 22
#>
#> $sols.xml$infil
#> [1] 48 49 50 51 52
## For all irrigation operations
tec <- file.path(xml_loc_dir, "file_tec.xml")
# Initial values
get_param_xml(tec, param = c("julapI_or_sum_upvt", "amount"))
#> $file_tec.xml
#> $file_tec.xml$julapI_or_sum_upvt
#> [1] 178 185 193 198 200 204 207 211 214 218 221 232 239 249 257 264
#>
#> $file_tec.xml$amount
#> [1] 20 24 29 29 28 31 21 21 23 18 22 16 16 30 29 20
# Setting new values
set_param_xml(tec, param = c("julapI_or_sum_upvt", "amount"), values = list(200:215,
20:35), overwrite = TRUE)
# Controlling written values
get_param_xml(tec, param = c("julapI_or_sum_upvt", "amount"))
#> $file_tec.xml
#> $file_tec.xml$julapI_or_sum_upvt
#> [1] 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215
#>
#> $file_tec.xml$amount
#> [1] 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35
In the examples below, ids
contains the position of the
parameters values in the vector, for a given soil (5 layers) name or for
irrigation supplies operations amounts. In that case, used values in
ids
are contiguous, but they do not need to be.
A vector of logical values may be used instead of position values for queries or replacement.
## For soil layers 1 to 3
# Initial values
get_param_xml(sols, param = c("epc", "infil"), select = "sol", select_value = "solcanne",
ids = 1:3)
#> $sols.xml
#> $sols.xml$epc
#> [1] 18 19 20 21 22
#>
#> $sols.xml$infil
#> [1] 48 49 50 51 52
# Setting new values
set_param_xml(sols, param = c("epc", "infil"), values = list(20:18, 50:48), select = "sol",
select_value = "solcanne", overwrite = TRUE, ids = 1:3)
#> Warning in set_param_value(xml_doc, param_name = param_name[p], param_value =
#> param_value[[p]], : epcreplacement values are not consistent with parameters
#> number !
#> Warning in set_param_value(xml_doc, param_name = param_name[p], param_value =
#> param_value[[p]], : infilreplacement values are not consistent with parameters
#> number !
# Controlling written values
get_param_xml(sols, param = c("epc", "infil"), select = "sol", select_value = "solcanne",
ids = 1:3)
#> $sols.xml
#> $sols.xml$epc
#> [1] 18 19 20 21 22
#>
#> $sols.xml$infil
#> [1] 48 49 50 51 52
## For irrigation operations 1 to 5 (same indices for all parameters)
# Initial values
get_param_xml(tec, param = c("julapI_or_sum_upvt", "amount"))
#> $file_tec.xml
#> $file_tec.xml$julapI_or_sum_upvt
#> [1] 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215
#>
#> $file_tec.xml$amount
#> [1] 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35
# Setting new values
set_param_xml(tec, param = c("julapI_or_sum_upvt", "amount"), values = list(204:200,
24:20), overwrite = TRUE, ids = 1:5)
#> Warning in set_param_value(xml_doc, param_name = param_name[p], param_value =
#> param_value[[p]], : julapI_or_sum_upvtreplacement values are not consistent
#> with parameters number !
#> Warning in set_param_value(xml_doc, param_name = param_name[p], param_value =
#> param_value[[p]], : amountreplacement values are not consistent with parameters
#> number !
# Controlling written values
get_param_xml(tec, param = c("julapI_or_sum_upvt", "amount"))
#> $file_tec.xml
#> $file_tec.xml$julapI_or_sum_upvt
#> [1] 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215
#>
#> $file_tec.xml$amount
#> [1] 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35