Package: rsofun 5.1.0.9000

Benjamin Stocker

rsofun: The P-Model and BiomeE Modelling Framework

Implements the Simulating Optimal FUNctioning framework for site-scale simulations of ecosystem processes, including model calibration. It contains 'Fortran 90' modules for the P-model (Stocker et al. (2020) <doi:10.5194/gmd-13-1545-2020>), SPLASH (Davis et al. (2017) <doi:10.5194/gmd-10-689-2017>) and BiomeE (Weng et al. (2015) <doi:10.5194/bg-12-2655-2015>).

Authors:Benjamin Stocker [aut, cre], Koen Hufkens [aut], Josefa Arán Paredes [aut], Laura Marqués [ctb], Mayeul Marcadella [ctb], Ensheng Weng [ctb], Fabian Bernhard [aut], Geocomputation and Earth Observation, University of Bern [cph, fnd]

rsofun_5.1.0.9000.tar.gz
rsofun_5.1.0.9000.zip(r-4.7)rsofun_5.1.0.9000.zip(r-4.6)rsofun_5.1.0.9000.zip(r-4.5)
rsofun_5.1.0.9000.tgz(r-4.6-x86_64)rsofun_5.1.0.9000.tgz(r-4.6-arm64)rsofun_5.1.0.9000.tgz(r-4.5-x86_64)rsofun_5.1.0.9000.tgz(r-4.5-arm64)
rsofun_5.1.0.9000.tar.gz(r-4.7-arm64)rsofun_5.1.0.9000.tar.gz(r-4.7-x86_64)rsofun_5.1.0.9000.tar.gz(r-4.6-arm64)rsofun_5.1.0.9000.tar.gz(r-4.6-x86_64)
rsofun_5.1.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
rsofun/json (API)

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

Bug tracker:https://github.com/geco-bern/rsofun/issues

Pkgdown/docs site:https://geco-bern.github.io

Uses libs:
  • fortran– Runtime library for GNU Fortran applications
Datasets:

On CRAN:

Conda:

dgvmgrowthmodelingp-modelsimulationvegetation-dynamicsfortran

9.06 score 33 stars 183 scripts 178 downloads 11 exports 120 dependencies

Last updated from:c5da46b203. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK208
linux-devel-x86_64OK263
source / vignettesOK352
linux-release-arm64OK210
linux-release-x86_64OK215
macos-release-arm64OK234
macos-release-x86_64OK319
macos-oldrel-arm64OK178
macos-oldrel-x86_64OK394
windows-develOK222
windows-releaseOK240
windows-oldrelOK172
wasm-releaseOK161

Exports:build_luc_matrixcalib_sofuncost_likelihood_biomeecost_likelihood_pmodelcost_rmse_biomeecost_rmse_pmodelrun_biomee_f_bysiterun_pmodel_f_bysiterun_pmodel_onestep_f_bysiterunread_biomee_frunread_pmodel_f

Dependencies:apeaskpassbase64encBayesianToolsbootbridgesamplingBrobdingnagbslibcachemcallrclicodacodetoolscommonmarkcpp11crayoncrosstalkcurldata.tableDHARMadigestdoParalleldplyrellipseemulatorevaluateexpmfarverfastmapfontawesomeforeachfsgapgap.datasetsgenericsGenSAggplot2gluegmmgtablehighrhtmltoolshtmlwidgetshttpuvhttrIDPmiscisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelme4lmtestlubridatemagrittrMASSMatrixmemoisemgcvmimeminqamsmmultidplyrmvtnormnlmenloptrnumDerivopensslotelpillarpkgconfigplotlyplyrprocessxpromisespspurrrqgamqs2R6rappdirsrbibutilsRColorBrewerRcppRcppEigenRcppParallelRdpackreformulasrlangrmarkdownS7sandwichsassscalesshinysourcetoolsstringfishstringistringrsurvivalsystibbletidyrtidyselecttimechangetinytextmvtnormutf8vctrsviridisLitewithrxfunxtableyamlzoo

BiomeE usage
Demo data | Two model approaches | Running the BiomeE model with standard photosynthesis | Plotting output | Running the BiomeEP model | Calibrating model parameters | Validating model output
Rendered frombiomee_use.Rmdusingknitr::rmarkdown

Last update: 2026-02-16
Started: 2022-11-25

Parameter calibration and cost functions
Calibration to GPP using RMSE and GenSA optimizer | Calibration to GPP using a simple likelihood function and BayesianTools | Calibration to GPP and Vcmax25 using the joint log-likelihood and BayesianTools | Write your custom cost function
Rendered fromnew_cost_function.Rmdusingknitr::rmarkdown

Last update: 2026-02-16
Started: 2022-11-24

Sensitivity analysis and calibration interpretation
Morris sensitivity analysis | Interpretation of Bayesian calibration routine | Plotting P-model output after calibration
Rendered fromsensitivity_analysis.Rmdusingknitr::rmarkdown

Last update: 2026-02-16
Started: 2023-05-26

BiomeE LULUC
Overview | Fractional tiles | LU transitions | Clear-cut and wood harvest | Other land management practices | Output | Getting started | Setup | Simulation | Wood harvest and urbanism | Crop rotation and land management | LUH2 integration
Rendered frombiomee_luluc.Rmdusingknitr::rmarkdown

Last update: 2025-10-06
Started: 2025-06-11

P-model usage
Demo data | Running model | Plotting output | Calibrating model parameters | One-step P-model call
Rendered frompmodel_use.Rmdusingknitr::rmarkdown

Last update: 2025-07-28
Started: 2021-09-29

Data format
Philosophy | Drivers data (inputs) | Specific data for each model | Forcing data | Output data | P-model | BiomeE
Rendered fromdata_format.Rmdusingknitr::rmarkdown

Last update: 2024-11-25
Started: 2023-07-25

Readme and manuals

Help Manual

Help pageTopics
rsofun BiomeE driver data (Leuning photosynthesis model)biomee_gs_leuning_drivers
rsofun BiomeE (gs_leuning) output databiomee_gs_leuning_output
rsofun BiomeE driver data (P-model photosynthesis model)biomee_p_model_drivers
rsofun BiomeE driver data (P-model photosynthesis model) with LULUCbiomee_p_model_luluc_drivers
rsofun BiomeE (P-model) output databiomee_p_model_luluc_output
rsofun BiomeE (P-model) output databiomee_p_model_output
rsofun BiomeE targets validation databiomee_validation
Build LUC matrixbuild_luc_matrix
Calibrates SOFUN model parameterscalib_sofun
Log-likelihood cost function for BiomeE with different targetscost_likelihood_biomee
Cost function computing a log-likelihood for calibration of P-model parameterscost_likelihood_pmodel
RMSE cost function for BiomeEcost_rmse_biomee
Cost function computing RMSE for calibration of P-model parameterscost_rmse_pmodel
Initialises a tibble with datesinit_dates_dataframe
rsofun P-model driver datap_model_drivers
rsofun P-model driver data (for leaf traits)p_model_drivers_vcmax25
rsofun P-model output datap_model_output
rsofun P-model output data (using vcmax25 drivers)p_model_output_vcmax25
rsofun P-model GPP validation datap_model_validation
rsofun P-model Vcmax25 validation datap_model_validation_vcmax25
Run BiomeE (R wrapper)run_biomee_f_bysite
Run P-model (time series)run_pmodel_f_bysite
Run P-model (single time step)run_pmodel_onestep_f_bysite
Run BiomeErunread_biomee_f
Run P-modelrunread_pmodel_f