The goal of SticsRFiles is to perform manipulations of all types of files related to the input and outputs of the STICS model.
This article presents the design of the package and its basic features, i.e. the main functions to deal with the XML files. For a complete introduction to SticsRPacks (managing files, running simulations, plotting, optimization…), see the tutorial from the SticsRPacks package.
The executable of the STICS model reads text files with standard names and format to import the inputs describing a single unit of simulation (USM), e.g. one crop for one year.
Here’s a typical list of the input files for the STICS executable (without the optional files):
workspace
│
├── 📜climat.txt # The meteorological data for the USM
├── 📜ficini.txt # The initialization
├── 📜ficplt1.txt # Parameters for the plant to be simulated
├── 📜fictec1.txt # The management applied to the soil and crop
├── 📜new_travail.usm # The general configuration parameters for the USM
├── 📜param.sol # Soil parameters
├── 📜station.txt # The site parameters (*e.g.* altitude, latitude)
├── 📜tempopar.sti # More general parameters not in the other files
├── 📜tempoparv6.sti # Parameters for the custom versions of STICS
└── 📜var.mod # Variables to write in the outputsBecause these files only describe one USM at a time and can be tedious to explore and parameterize, we usually don’t interact with them directly, but through another program: JavaSTICS.
JavaSTICS is a graphical user interface used to easily create input text files for the STICS executable according to the user’s choices, and for managing STICS simulations. JavaSTICS saves the parameter values and options choices in XML files.
The XML files store more information than the text files: not only do they store the parameter values but also their description, maximum and minimum boundary values, all existing formalisms, the different choices allowed, and more importantly they allow for the management of several USMs in the same folder (called workspace), and can help make successive USMs.
It is important to note that only JavaSTICS interact with the XML files, not the STICS executable. The STICS input text files are then automatically created by JavaSTICS when running a simulation, just before calling the STICS executable.
SticsRFiles is an R package that uses JavaSTICS from the command line to manage the XML and the text files. We can generate XML or text files, get and set parameter values, import simulations outputs, and manage observation files.
Advanced features also include:
Here’s a simple example usage of SticsRFiles using an example workspace.
All the example data used in this article are available from the data
repository in the SticsRPacks organization.
SticsRFiles provides a function to download it from the command line. Please execute the following command in R:
library(SticsRFiles)
example_data <- SticsRFiles::download_data(example_dirs = "study_case_1",
"V10.0")The example data is downloaded by default in a temporary folder.
For the sake of readability, we’ll declare the workspace path and the path to the plant file here. But remember the functions can be applied to any XML files or workspaces.
get_var_info() helps to get any STICS variable name by
doing a fuzzy search. For example to get all variables with
lai in their names, you would do:
SticsRFiles::get_var_info("lai")
#> name
#> 5 albedolai
#> 242 exolai
#> 338 innlai
#> 353 lai(n)
#> 354 lai_mx_av_cut
#> 355 laimax
#> 356 laisen(n)
#> 742 splai
#> 805 ulai(n)
#> definition
#> 5 albedo of the crop including soil and vegetation
#> 242 reduction factor on leaf growth due to water excess
#> 338 reduction factor on leaf growth due to NNI (nitrogen deficiency)
#> 353 leaf area index (table)
#> 354 LAI before cut (for cut crops , for others = lai(n) )
#> 355 maximum leaf area index
#> 356 leaf area index of senescent leaves (table)
#> 742 source to sink ratio of assimilates in the leaves
#> 805 relative development unit for LAI
#> unit type
#> 5 SD real
#> 242 0-1 real
#> 338 innmin to 1 real
#> 353 m2.m-2 real
#> 354 SD real
#> 355 m2.m-2 real
#> 356 m2.m-2 real
#> 742 SD real
#> 805 0-3 realSometimes it is also useful to search in the variable definition
instead of its name. To do so, you can use the keyword
argument like so:
SticsRFiles::get_var_info(keyword = "lai")
#> name
#> 5 albedolai
#> 171 diftemp1intercoupe
#> 172 diftemp2intercoupe
#> 242 exolai
#> 334 inn1intercoupe
#> 336 inn2intercoupe
#> 338 innlai
#> 353 lai(n)
#> 354 lai_mx_av_cut
#> 355 laimax
#> 356 laisen(n)
#> 360 leai
#> 742 splai
#> 745 str1intercoupe
#> 746 str2intercoupe
#> 747 stu1intercoupe
#> 748 stu2intercoupe
#> 801 tustress
#> 805 ulai(n)
#> definition
#> 5 albedo of the crop including soil and vegetation
#> 171 mean difference between crop and air temperatures during the vegetative phase (emergence - maximum LAI)
#> 172 mean difference between crop and air temperatures during the reproductive phase (maximum LAI - maturity)
#> 242 reduction factor on leaf growth due to water excess
#> 334 average NNI during the cut (cut crop vegetative phase: emergence to maximum LAI)
#> 336 average NNI during the cut (cut crop reproductive phase: maximum LAI to maturity)
#> 338 reduction factor on leaf growth due to NNI (nitrogen deficiency)
#> 353 leaf area index (table)
#> 354 LAI before cut (for cut crops , for others = lai(n) )
#> 355 maximum leaf area index
#> 356 leaf area index of senescent leaves (table)
#> 360 Leaf+ear area index = lai +eai
#> 742 source to sink ratio of assimilates in the leaves
#> 745 average stomatal water stress index during the vegetative phase (emergence - maximum LAI) of forage crops
#> 746 average stomatal water stress index during the reproductive phase (maximum LAI - maturity) of forage crops
#> 747 average turgescence water stress index during the vegetative phase (emergence - maximum LAI) of forage crops
#> 748 average turgescence water stress index during the reproductive phase (maximum LAI - maturity) of forage crops
#> 801 reduction factor on leaf growth due to the effective water stress (= min(turfac,innlai))
#> 805 relative development unit for LAI
#> unit type
#> 5 SD real
#> 171 degreeC real
#> 172 degreeC real
#> 242 0-1 real
#> 334 0-2 real
#> 336 0-2 real
#> 338 innmin to 1 real
#> 353 m2.m-2 real
#> 354 SD real
#> 355 m2.m-2 real
#> 356 m2.m-2 real
#> 360 m2.m-2 real
#> 742 SD real
#> 745 0-1 real
#> 746 0-1 real
#> 747 0-1 real
#> 748 0-1 real
#> 801 0-1 real
#> 805 0-3 realget_param_info() can be used giving a part of parameters
names :
get_param_info(param = "lai")
#> name file min max
#> 225 cielclair STATION 0 1
#> 305 codeclaircie PARTEC 1 2
#> 339 codelaitr PARPLT 1 2
#> 408 codlainet PARPLT 1 2
#> 556 dlaimax PARPLT 5e-06 0.5
#> 557 dlaimaxbrut PARPLT 5e-06 0.5
#> 558 dlaimin PARPLT 0 1
#> 699 flai USM/USMXML 0 0
#> 827 inilai PARPLT 0 1
#> 899 juleclair PARTEC 1 731
#> 900 juleclair(1) PARTEC 1 731
#> 901 juleclair(10) PARTEC 1 731
#> 902 juleclair(2) PARTEC 1 731
#> 903 juleclair(3) PARTEC 1 731
#> 904 juleclair(4) PARTEC 1 731
#> 905 juleclair(5) PARTEC 1 731
#> 906 juleclair(6) PARTEC 1 731
#> 907 juleclair(7) PARTEC 1 731
#> 908 juleclair(8) PARTEC 1 731
#> 909 juleclair(9) PARTEC 1 731
#> 1021 lai INIT 0 10
#> 1022 lai0 INIT 0 10
#> 1023 laicomp PARPLT 0 1
#> 1024 laidebeff PARTEC 1 10
#> 1025 laieffeuil PARTEC 0.05 10
#> 1026 laiplantule PARPLT 0 8
#> 1027 lairesiduel PARTEC 0 2
#> 1028 lairesiduel(1) PARTEC 0 2
#> 1029 lairesiduel(10) PARTEC 0 2
#> 1030 lairesiduel(11) PARTEC 0 2
#> 1031 lairesiduel(12) PARTEC 0 2
#> 1032 lairesiduel(13) PARTEC 0 2
#> 1033 lairesiduel(14) PARTEC 0 2
#> 1034 lairesiduel(15) PARTEC 0 2
#> 1035 lairesiduel(16) PARTEC 0 2
#> 1036 lairesiduel(17) PARTEC 0 2
#> 1037 lairesiduel(18) PARTEC 0 2
#> 1038 lairesiduel(19) PARTEC 0 2
#> 1039 lairesiduel(2) PARTEC 0 2
#> 1040 lairesiduel(20) PARTEC 0 2
#> 1041 lairesiduel(3) PARTEC 0 2
#> 1042 lairesiduel(4) PARTEC 0 2
#> 1043 lairesiduel(5) PARTEC 0 2
#> 1044 lairesiduel(6) PARTEC 0 2
#> 1045 lairesiduel(7) PARTEC 0 2
#> 1046 lairesiduel(8) PARTEC 0 2
#> 1047 lairesiduel(9) PARTEC 0 2
#> 1221 pentlaimax PARPLT 0 10
#> 1425 seuilLAIapex PARPLT 0 10
#> 1433 splaimax PARPLT 0.7 2
#> 1434 splaimin PARPLT 0.01 1
#> 1581 udlaimax PARPLT 1 3
#> 1645 vlaimax PARPLT 1.5 2.5
#> definition
#> 225 fraction of sunny hours allowing the inversion of thermal gradient with altitude
#> 305 option to simulate fruit removal: 1 = no, 2 = yes (for smallest fruits)
#> 339 option to calculate the intercepted radiation according to: 1 = LAI, 2 = soil cover
#> 408 option to calculate the LAI: 1 = net LAI, 2 = difference between gross LAI and senescent LAI
#> 556 maximum rate of net daily increase of LAI
#> 557 maximum rate of gross daily increase of LAI
#> 558 accelerating parameter for the lai growth rate
#> 699 name of the LAI file
#> 827 initial value of lai for cotyledons
#> 899 day of fruits removal
#> 900 day of fruits removal
#> 901 day of fruits removal
#> 902 day of fruits removal
#> 903 day of fruits removal
#> 904 day of fruits removal
#> 905 day of fruits removal
#> 906 day of fruits removal
#> 907 day of fruits removal
#> 908 day of fruits removal
#> 909 day of fruits removal
#> 1021 initial leaf area index
#> 1022 initial leaf area index
#> 1023 LAI above which competition between plants starts
#> 1024 LAI at the beginning of leaf removal
#> 1025 LAI removed from the crop at day juleffeuil
#> 1026 LAI of plantlet at the plantation
#> 1027 residual LAI after each cut of forage crop
#> 1028 residual LAI after each cut of forage crop
#> 1029 residual LAI after each cut of forage crop
#> 1030 residual LAI after each cut of forage crop
#> 1031 residual LAI after each cut of forage crop
#> 1032 residual LAI after each cut of forage crop
#> 1033 residual LAI after each cut of forage crop
#> 1034 residual LAI after each cut of forage crop
#> 1035 residual LAI after each cut of forage crop
#> 1036 residual LAI after each cut of forage crop
#> 1037 residual LAI after each cut of forage crop
#> 1038 residual LAI after each cut of forage crop
#> 1039 residual LAI after each cut of forage crop
#> 1040 residual LAI after each cut of forage crop
#> 1041 residual LAI after each cut of forage crop
#> 1042 residual LAI after each cut of forage crop
#> 1043 residual LAI after each cut of forage crop
#> 1044 residual LAI after each cut of forage crop
#> 1045 residual LAI after each cut of forage crop
#> 1046 residual LAI after each cut of forage crop
#> 1047 residual LAI after each cut of forage crop
#> 1221 parameter of the logistic curve of LAI growth
#> 1425 maximal value of LAI+LAIapex when LAIapex is > 0
#> 1433 maximal sources/sinks value allowing the trophic stress calculation for leaf growing
#> 1434 minimal value of ratio sources/sinks for the leaf growth
#> 1581 ulai from which the rate of leaf growth decreases
#> 1645 ulai at the inflexion point of the function DELTAI=f(ULAI)it can also be used by giving a keyword that will be searched in the parameters names and definitions:
get_param_info(keyword = "plant")
#> name file min max
#> 4 adens PARPLT -2 0
#> 6 adil PARPLT 1 7
#> 7 adilmax PARPLT 3 10
#> 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
#> 135 bdens PARPLT 1 200
#> 136 bdil PARPLT 0.01 0.8
#> 137 bdilmax PARPLT 0.01 0.8
#> 219 celong PARPLT 1 10
#> 276 codazofruit PARPLT 1 2
#> 322 codeffeuil PARTEC 1 2
#> 323 codefixpot PARPLT 1 3
#> 331 codehypo PARPLT 1 2
#> 346 codemonocot PARPLT 1 2
#> 354 codepalissage PARTEC 1 3
#> 356 codephot PARPLT 1 2
#> 358 codeplante PARPLT 0 0
#> 359 codeplisoleN PARPLT 1 2
#> 389 codetemp PARPLT 1 2
#> 404 codgellev PARPLT 1 2
#> 547 densitesem PARTEC 0.05 2000
#> 617 draclong PARPLT 1 1000
#> 620 durviesupmax PARPLT 0 1
#> 640 effeuil PARTEC 0 1
#> 705 fplt USM/USMXML 0 0
#> 767 hautmaxtec PARTEC 0.5 3
#> 768 hautrogne PARTEC 0.2 2
#> 825 inflomax PARPLT 0 100
#> 946 julrogne PARTEC 1 731
#> 986 kcouvmlch PARAM 0 1
#> 987 kcouvmlch(1) PARAM 0 1
#> 988 kcouvmlch(10) PARAM 0 1
#> 989 kcouvmlch(11) PARAM 0 1
#> 990 kcouvmlch(12) PARAM 0 1
#> 991 kcouvmlch(13) PARAM 0 1
#> 992 kcouvmlch(14) PARAM 0 1
#> 993 kcouvmlch(15) PARAM 0 1
#> 994 kcouvmlch(16) PARAM 0 1
#> 995 kcouvmlch(17) PARAM 0 1
#> 996 kcouvmlch(18) PARAM 0 1
#> 997 kcouvmlch(19) PARAM 0 1
#> 998 kcouvmlch(2) PARAM 0 1
#> 999 kcouvmlch(20) PARAM 0 1
#> 1000 kcouvmlch(21) PARAM 0 1
#> 1001 kcouvmlch(3) PARAM 0 1
#> 1002 kcouvmlch(4) PARAM 0 1
#> 1003 kcouvmlch(5) PARAM 0 1
#> 1004 kcouvmlch(6) PARAM 0 1
#> 1005 kcouvmlch(7) PARAM 0 1
#> 1006 kcouvmlch(8) PARAM 0 1
#> 1007 kcouvmlch(9) PARAM 0 1
#> 1023 laicomp PARPLT 0 1
#> 1026 laiplantule PARPLT 0 8
#> 1061 margerogne PARTEC 0.01 1
#> 1062 masec INIT 0 10
#> 1063 masec0 INIT 0 10
#> 1064 masecmeta PARPLT 0.1 1
#> 1068 masecplantule PARPLT 0.002 4
#> 1138 nbfeuilplant PARPLT 0 10
#> 1142 nbinflo PARPLT 1 1000
#> 1164 nbplantes USM/USMXML 1 2
#> 1173 nlevlim1 PARPLT 1 100
#> 1174 nlevlim2 PARPLT 1 100
#> 1175 Nmeta PARPLT 0 100
#> 1198 Nreserve PARPLT 0 100
#> 1219 penterui PARSOL 0 5
#> 1346 QNplante INIT 0 10
#> 1347 QNplante0 INIT 0 10
#> 1348 QNplantenp INIT 0 200
#> 1349 QNplantenp0 INIT 0 200
#> 1350 QNpltminINN PARAM 0 50
#> 1502 tauxrecouvkmax PARPLT 0.5 2
#> 1503 tauxrecouvmax PARPLT 0.5 2
#> 1507 tdebgel PARPLT -5 5
#> 1514 temax PARPLT 15 40
#> 1542 teopt PARPLT 10 30
#> 1543 teoptbis PARPLT 10 30
#> 1549 tgellev10 PARPLT -25 0
#> 1550 tgellev90 PARPLT -25 0
#> 1556 tletale PARPLT -30 -1
#> 1636 variete PARTEC 1 200
#> 1637 vigueurbat PARPLT 1e-04 1
#> 1695 zracplantule PARPLT 0 200
#> definition
#> 4 Interplant competition parameter
#> 6 parameter of the critical dilution curve [Nplante]=adil MS^(-bdil)
#> 7 parameter of the maximum dilution curve [Nplante]=adilmax MS^(-bdilmax)
#> 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
#> 135 minimal plant density above which interplant competition starts
#> 136 parameter of the critical dilution curve [Nplante]=adil MS^(-bdil)
#> 137 parameter of the maximum dilution curve [Nplante]=adilmax MS^(-bdilmax)
#> 219 parameter of the plantlet elongation curve
#> 276 option to activate the direct effect of N plant status on the fruit/grain number: 1 = no, 2 = yes
#> 322 option to activate plant thinning: 1 = no, 2 = yes
#> 323 option to calculate the maximal symbiotic fixation: 1 = fixed value read in the plant file, 2 = depends on growth rate
#> 331 option to simulate plant emergency: 1 = phase of hypocotyl growth (sown crops), 2 = plantation of plantlets
#> 346 option to define the type of plant: 1 = monocot, 2 =dicot
#> 354 option to define if the plant is fixed onto a vertical support: 1 = no, 2 =yes
#> 356 option to define plant photoperiodism: 1 = yes, 2 = no
#> 358 option to define the coding name of the plant (3 characters)
#> 359 option to define N requirements at the beginning of the cycle: 1 = dense plant population, 2 = isolated plants
#> 389 option to calculate thermal time for plant growth: 1 = based on air temperature, 2 = based on crop temperature
#> 404 option to activate the frost effect on plantlet growth: 1 = no, 2 = yes
#> 547 plant sowing density
#> 617 maximum rate of root length production per plant
#> 620 relative additional lifespan due to N excess in plant (INN > 1)
#> 640 fraction of leaf removed by plant thinning
#> 705 name of the plant file
#> 767 maximal height of the plant allowed by the management
#> 768 cutting height for trimmed plants
#> 825 maximal number of inflorescences per plant
#> 946 day of plant trimming
#> 986 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 987 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 988 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 989 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 990 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 991 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 992 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 993 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 994 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 995 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 996 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 997 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 998 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 999 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 1000 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 1001 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 1002 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 1003 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 1004 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 1005 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 1006 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 1007 extinction coefficient connecting the soil cover to the amount of plant mulch
#> 1023 LAI above which competition between plants starts
#> 1026 LAI of plantlet at the plantation
#> 1061 topping occurs when plant height exceeds (hautrogne+margerogne) when automatic trimming is activated
#> 1062 initial plant biomass (if the option to simulate N and C reserves is not activated)
#> 1063 initial plant biomass (if the option to simulate N and C reserves is not activated)
#> 1064 biomass of the plantlet supposed to be composed of metabolic N
#> 1068 initial shoot biomass of plantlet
#> 1138 leaf number per plant when planting
#> 1142 imposed number of inflorescences per plant
#> 1164 number of simulated plants
#> 1173 number of days after germination after which plant emergence is reduced
#> 1174 number of days after germination after which plant emergence is impossible
#> 1175 proportion of metabolic N in the plantlet
#> 1198 maximal proportion of N in plant reserves (difference between the maximal and critical dilution curves)
#> 1219 runoff coefficient taking into account the plant mulch
#> 1346 initial N amount in the plant (if the option to simulate N and C reserves is not activated)
#> 1347 initial N amount in the plant (if the option to simulate N and C reserves is not activated)
#> 1348 initial N amount in non-perennial organs of the plant
#> 1349 initial N amount in non-perennial organs of the plant
#> 1350 minimal amount of N in the plant required to compute INN
#> 1502 soil cover rate corresponding to the maximal crop coefficient for water requirement (plant surface / soil surface)
#> 1503 maximal soil cover rate (plant surface / soil surface)
#> 1507 temperature below which frost affects plant growth
#> 1514 maximal temperature above which plant growth stops
#> 1542 optimal temperature (1/2) for plant growth
#> 1543 optimal temperature (2/2) for plant growth
#> 1549 temperature resulting in 10% of frost damages on plantlet
#> 1550 temperature resulting in 90% of frost damages on plantlet
#> 1556 lethal temperature for the plant
#> 1636 cultivar number corresponding to the cultivar name in the plant file
#> 1637 plant vigor index allowing to emerge through a soil crust
#> 1695 initial depth of root apex of the plantletget_param_xml() is used to get the values of a parameter
in an XML file. For example if we want to get dlaimax, we
would do:
dlaimax <- get_param_xml(plant_file, "dlaimax")
dlaimax
#> $maisopti_plt.xml
#> $maisopti_plt.xml$dlaimax
#> [1] 0.00321 0.00321 0.00321 0.00321 0.00321But this function is way more powerful than just that. You can also
get the values for all parameters in a given formalism
(formalisme in French, yes some variables are still written
in French in STICS). To do so, use the select argument like
so:
values <- get_param_xml(plant_file, select = "formalisme",
select_value = "radiation interception")
unlist(values) # For pretty-printing
#> maisopti_plt.xml.codetransrad maisopti_plt.xml.forme
#> 1 1
#> maisopti_plt.xml.rapforme maisopti_plt.xml.adfol
#> 4 1
#> maisopti_plt.xml.dfolbas maisopti_plt.xml.dfolhaut
#> 5 5We can also change the value of a parameter programmatically using
set_param_xml(). It is used similarly to
get_param_xml(). For example if we want to increase
dlaimax by 30%:
set_param_xml(plant_file, "dlaimax", unlist(dlaimax) * 1.3, overwrite = TRUE)Don’t forget to use the overwrite argument and set it to
TRUE. It is FALSE by default to avoid any
mishandling.
New values written in the file can be checked:
dlaimax <- get_param_xml(plant_file, "dlaimax")
dlaimax
#> $maisopti_plt.xml
#> $maisopti_plt.xml$dlaimax
#> [1] 0.004173 0.004173 0.004173 0.004173 0.004173We can generate observation files from a data.frame
using gen_obs().
Lets create some dummy data.frame first:
obs_df <- data.frame(usm_name = "Test", ian = 2021, mo = 3:10, jo = 1,
`masec(n)` = 0.1 * 3:10)Then we can write the data to a file using
gen_obs():
gen_obs(df = obs_df, out_dir = "/path/to/dest/dir")We can read the observation files in a workspace using
get_obs(). Note that all observation files should be named
after the USM they are linked to. See the help page for more details,
e.g. about intercrops.
obs <- get_obs(workspace)
#> bo96iN+.obs
#> bou00t1.obs
#> bou00t3.obs
#> bou99t1.obs
#> bou99t3.obs
#> lu96iN+.obs
#> lu96iN6.obs
#> lu97iN+.obsLikewise, we can read the observation files in a workspace using
get_sim():
sim <- get_sim(workspace)
#> Warning in get_file_(workspace = x, usm_name = usm_name, usms_filepath =
#> usms_path, : Not any sim file detected in
#> workspace/tmp/RtmpjkDYAq/data-master/
#> study_case_1/V10.0/XmlFilesBut as there aren’t any simulations yet in the workspace, the function will return an error. To make a simulation, head to SticsOnR. Then to plot both observations and simulations, you can use CroPlotR.