Package: rsofun 5.1.0.9001

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]

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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-dynamicsfortranglibc

8.88 score 34 stars 198 scripts 266 downloads 13 exports 121 dependencies

Last updated from:0bf91fc97d. Checks:10 OK, 4 NOTE, 1 WARNING. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK196
linux-devel-x86_64OK235
source / vignettesOK562
linux-release-arm64OK187
linux-release-x86_64OK216
macos-release-arm64NOTE281
macos-release-x86_64NOTE280
macos-oldrel-arm64NOTE274
macos-oldrel-x86_64NOTE472
windows-devel-arm64OK578
windows-devel-x86_64OK183
windows-release-arm64WARNING577
windows-release-x86_64OK255
windows-oldrel-x86_64OK221
wasm-releaseOK153

Exports:build_luc_matrixcalib_sofuncalib_sofun_legacycost_likelihood_biomeecost_likelihood_pmodelcost_likelihood_pmodel_legacycost_rmse_biomeecost_rmse_pmodelrun_biomee_f_bysiterun_pmodel_f_bysiterun_pmodel_onestep_f_bysiterunread_biomee_frunread_pmodel_f

Dependencies:apeaskpassbase64encBayesianToolsbootbridgesamplingBrobdingnagbslibcachemcallrclicodacodetoolscommonmarkcpp11crayoncrosstalkcurldata.tableDHARMadigestdoParalleldplyrellipseemulatorevaluateexpmfarverfastmapfontawesomeforeachfsgapgap.datasetsgenericsGenSAggplot2gluegmmgtablehighrhtmltoolshtmlwidgetshttpuvhttrIDPmiscisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelme4lmtestlubridatemagrittrMASSMatrixmemoisemgcvmimeminqamsmmultidplyrmvtnormnlmenloptrnumDerivopensslotelpillarpkgconfigplotlyplyrprocessxpromisespspurrrqgamqs2quadformR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRcppParallelRdpackreformulasrlangrmarkdownS7sandwichsassscalesshinysourcetoolsstringfishstringistringrsurvivalsystibbletidyrtidyselecttimechangetinytextmvtnormutf8vctrsviridisLitewithrxfunxtableyamlzoo

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: 2026-09-25
Started: 2022-11-25

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: 2026-07-10
Started: 2025-06-11

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: 2026-07-10
Started: 2023-07-25

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

Last update: 2026-07-10
Started: 2021-09-29

Parameter calibration (P-Model) and cost functions
Calibration to GPP using RMSE and GenSA optimizer | Calibration to GPP using a simple likelihood function and BayesianTools | Write your custom cost function
Rendered fromnew_cost_function.Rmdusingknitr::rmarkdown

Last update: 2026-07-10
Started: 2022-11-24

Parameter calibration (P-Model) to multiple targets (GPP, bigD13C)
Calibrating one GPP and one D13C site | Calibrating multiple GPP and D13C sites | Some helper functions for calibration | Run calibration | Analyze model calibration | Compare predictions of the calibrated model with observations
Rendered fromparam_calib_multitarget.Rmdusingknitr::rmarkdown

Last update: 2026-07-10
Started: 2026-07-10

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: 2026-07-10
Started: 2023-05-26

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 validation databiomee_validation
Build LUC matrixbuild_luc_matrix
Calibrates SOFUN model parameters (for parallelized applications)calib_sofun
Calibrates SOFUN model parameterscalib_sofun_legacy
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
Cost function computing a log-likelihood for calibration of P-model parameterscost_likelihood_pmodel_legacy
RMSE cost function for BiomeEcost_rmse_biomee
Cost function computing RMSE for calibration of P-model parameterscost_rmse_pmodel
Internal convenience function to create a mixed prior distributioncreateMixedPrior
Function running P-model and combining model and observationsget_mod_obs_pmodel
Initialises a tibble with datesinit_dates_dataframe
Checks if provided parameter list describes a beta distributionis_beta_prior
Checks if provided parameter list describes a lognormal distributionis_lognormal_prior
Checks if provided parameter list describes a normal distributionis_normal_prior
Checks if provided parameter list describes a truncated lognormal distributionis_trunclognormal_prior
Checks if provided parameter list describes a truncated normal distributionis_truncnormal_prior
Checks if provided parameter list describes a uniform distributionis_uniform_prior
rsofun P-model driver datap_model_oldformat_drivers
rsofun P-model GPP validation datap_model_oldformat_validation
rsofun P-model driver datapmodel_drivers
rsofun P-model output datapmodel_output
rsofun P-model GPP and leaf D13C validation datapmodel_validation
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