Package: growR 1.3.0.9001

Kevin Kramer

growR: Implementation of the Vegetation Model ModVege

Run grass growth simulations using a grass growth model based on ModVege (Jouven, M., P. Carrère, and R. Baumont "Model Predicting Dynamics of Biomass, Structure and Digestibility of Herbage in Managed Permanent Pastures. 1. Model Description." (2006) <doi:10.1111/j.1365-2494.2006.00515.x>). The implementation in this package contains a few additions to the above cited version of ModVege, such as simulations of management decisions, and influences of snow cover. As such, the model is fit to simulate grass growth in mountainous regions, such as the Swiss Alps. The package also contains routines for calibrating the model and helpful tools for analysing model outputs and performance.

Authors:Kevin Kramer [aut, cre, cph]

growR_1.3.0.9001.tar.gz
growR_1.3.0.9001.zip(r-4.7-any)growR_1.3.0.9001.zip(r-4.6-any)growR_1.3.0.9001.zip(r-4.5-any)
growR_1.3.0.9001.tgz(r-4.6-any)growR_1.3.0.9001.tgz(r-4.5-any)
growR_1.3.0.9001.tar.gz(r-4.7-any)growR_1.3.0.9001.tar.gz(r-4.6-any)
growR_1.3.0.9001.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
growR/json (API)

# Install 'growR' in R:
install.packages('growR', repos = c('https://kuadrat.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kuadrat/growr/issues

Pkgdown/docs site:https://kuadrat.github.io

Datasets:

On CRAN:

Conda:

agronomygrassgrasslandmodellingsimulation-modeling

4.98 score 4 stars 16 scripts 384 downloads 49 exports 4 dependencies

Last updated from:017ae9af01. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK122
source / vignettesOK168
linux-releaseOK123
macos-releaseOK211
macos-oldrelOK157
windows-develOK73
windows-releaseOK91
windows-oldrelOK85
wasm-releaseOK93

Exports:aCO2_inverseadd_linesanalyze_parameter_scanatmospheric_CO2Autocutbox_smoothbrowsebrowse_endbuild_functional_groupcreate_combinationscreate_example_environmentfCO2_growth_modfCO2_transpiration_modFG_AFG_BFG_CFG_DfPARfTFunctionalGroupfWget_biasgrowR_package_optionsgrowR_run_loopload_data_for_sitesload_matching_dataload_measured_dataloggerManagementDatamean_absolute_errormetric_mapModvegeEnvironmentModvegeParametersModvegeSitePetersenAutocutPhenologicalAutocutplot_parameter_scanPscanPlotterread_configroot_mean_squaredrun_parameter_scanSEAset_growR_verbositysetup_directorystart_of_growing_seasonstart_of_growing_season_mtdWeatherDataweighted_temperature_sumwillmott

Dependencies:R6rbibutilsRdpackrlang

Tutorial
Step 0: Goal of the tutorial | Step 1: Setting up all input files | 2. Run ModVege with the example configuration | 3. Have a look at the results | 4. Change inputs and run a different simulation
Rendered fromgrowR.Rmdusingknitr::rmarkdown

Last update: 2024-05-22
Started: 2023-10-13

Calibration
Prerequisites | The parameter scan loop | Running a parameter scan | Analyzing a parameter scan
Rendered fromcalibration.Rmdusingknitr::rmarkdown

Last update: 2023-11-21
Started: 2023-10-21

Parameter Descriptions
Parameters | State Variables | Initial conditions | Model parameters | Functional group parameters | Weather variables
Rendered fromparameter_descriptions.Rmdusingknitr::rmarkdown

Last update: 2023-10-15
Started: 2023-10-13

Readme and manuals

Help Manual

Help pageTopics
Concentration representative yearaCO2_inverse
Add data to a ggplotadd_lines
Analyze results of a parameter scananalyze_parameter_scan
Write *data* to supplied file in append mode without generating a warning message.append_to_table
Atmospheric CO2 concentrationatmospheric_CO2
AutocutAutocut
Endpoint smootherbox_smooth
Debugging utilitiesbrowse browse_end
Build the effective functional group as a weighted linear combination.build_functional_group
Check if *package* is availablecheck_for_package
CombinatorCombinator
Compare simulation resultscompare.R
Create Valid Combinationscreate_combinations
Provide an example ModvegeEnvironmentcreate_example_environment
Check if supplied table contains all *required* variables.ensure_table_columns
Replace given filename by a version that contains an incremental number in order to prevent overwriting existing files.ensure_unique_filename
CO2 growth modifierfCO2_growth_mod
CO2 transpiration modifierfCO2_transpiration_mod
Functional group AFG_A
Functional group BFG_B
Functional group CFG_C
Functional group DFG_D
Radiation limitationfPAR
Temperature limitationfT
Representation of a grassland plant populationFunctionalGroup
Water stressfW
Metric Functionsget_bias mean_absolute_error root_mean_squared
Extract the name of a site from a filenameget_site_name
Default options introduced by package growRgrowR_package_options
Run growR simulationsgrowR_run_loop
Load experimental dataload_data_for_sites load_matching_data load_measured_data
Primitive logger for debugging.logger
Create unique DOY + year identifiermake_yearDOY
Management practices for Swiss grasslandsmanagement_parameters
Management Data ClassManagementData
List of Performance Metricsmetric_map
growR environment dataModvegeEnvironment
Parameter Data ObjectModvegeParameters
ModvegeSiteModvegeSite
Example results of a parameter scanparameter_scan_example
Parse and generate lists of years.parse_year_strings
Petersen autocut algorithmPetersenAutocut
Autocut based on phenologyPhenologicalAutocut
Plot Parameter Scan Resultsplot_parameter_scan
Plot ModVege simulation result overviewplot.ModvegeSite
Example Weather Dataposieux_weather
Plot Parameter Scan ResultsPscanPlotter
Read simulation run configurations from fileread_config
Parameter Scanrun_parameter_scan
Seasonal effect on growthSEA
Set verbosity of growR output.set_growR_verbosity
Initialize growR directory structuresetup_directory
Determine start of growing seasonstart_of_growing_season
Multicriterial Thermal Definitionstart_of_growing_season_mtd
Weather Data ObjectWeatherData
Create a weighted temperature sumweighted_temperature_sum
Willmott Indexwillmott
Parameters for expected yields in Switzerlandyield_parameters