This package is considered a duplicate. The official version of this package is found at:https://geco-bern.r-universe.dev/rsofun

Package: rsofun 5.0.0

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_5.0.0.tar.gz
rsofun_5.0.0.tar.gz(r-4.5-noble)rsofun_5.0.0.tar.gz(r-4.4-noble)
rsofun.pdf |rsofun.html✨
rsofun/json (API)

# Install 'rsofun' in R:

install.packages('rsofun', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

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

Uses libs:

fortran– Runtime library for GNU Fortran applications

Datasets:

biomee_gs_leuning_drivers - Rsofun BiomeE driver data
biomee_gs_leuning_output - Rsofun BiomeE (gs_leuning) output data
biomee_p_model_drivers - Rsofun BiomeE driver data
biomee_p_model_output - Rsofun BiomeE (P-model) output data
biomee_validation - Rsofun BiomeE targets validation data
p_model_drivers - Rsofun P-model driver data
p_model_drivers_vcmax25 - Rsofun P-model driver data
p_model_output - Rsofun P-model output data
p_model_output_vcmax25 - Rsofun P-model output data
p_model_validation - Rsofun P-model GPP validation data
p_model_validation_vcmax25 - Rsofun P-model Vcmax25 validation data

fortran

3.77 score 118 scripts 10 downloads 9 exports 120 dependencies

Last updated 28 days agofrom:50f98ab226. Checks:OK: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-linux-x86_64	OK	Nov 29 2024

Exports:calib_sofun cost_likelihood_biomee cost_likelihood_pmodel cost_rmse_biomee cost_rmse_pmodel run_biomee_f_bysite run_pmodel_f_bysite runread_biomee_f runread_pmodel_f

Dependencies:ape askpass base64enc BayesianTools BH boot bridgesampling Brobdingnag bslib cachem callr cli coda codetools colorspace commonmark cpp11 crayon crosstalk curl data.table DHARMa digest doParallel dplyr ellipse emulator evaluate expm fansi farver fastmap fontawesome foreach fs gap gap.datasets generics GenSA ggplot2 glue gmm gtable highr htmltools htmlwidgets httpuv httr IDPmisc isoband iterators jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle lme4 lmtest magrittr MASS Matrix memoise mgcv mime minqa msm multidplyr munsell mvtnorm nlme nloptr numDeriv openssl pillar pkgconfig plotly plyr processx promises ps purrr qgam qs R6 RApiSerialize rappdirs rbibutils RColorBrewer Rcpp RcppEigen RcppParallel Rdpack rlang rmarkdown sandwich sass scales shiny sourcetools stringfish stringi stringr survival sys tibble tidyr tidyselect tinytex tmvtnorm utf8 vctrs viridisLite withr xfun xtable yaml zoo

BiomeE usage

Koen Hufkens, Josefa Arán

Rendered frombiomee_use.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-11-28
Started: 2023-10-30

Data format

Koen Hufkens, Josefa Arán

Rendered fromdata_format.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-11-28
Started: 2023-10-30

P-model usage

Koen Hufkens, Josefa Arán

Rendered frompmodel_use.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-11-28
Started: 2023-10-30

Parameter calibration and cost functions

Josefa Arán

Rendered fromnew_cost_function.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2023-10-30
Started: 2023-10-30

Sensitivity analysis and calibration interpretation

Josefa Arán

Rendered fromsensitivity_analysis.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-11-28
Started: 2023-10-30

Citation

Readme and manuals

Help Manual

Help page	Topics
rsofun BiomeE driver data (Leuning photosynthesis model)	biomee_gs_leuning_drivers
rsofun BiomeE (gs_leuning) output data	biomee_gs_leuning_output
rsofun BiomeE driver data (P-model photosynthesis model)	biomee_p_model_drivers
rsofun BiomeE (P-model) output data	biomee_p_model_output
rsofun BiomeE targets validation data	biomee_validation
Calibrates SOFUN model parameters	calib_sofun
Log-likelihood cost function for BiomeE with different targets	cost_likelihood_biomee
Cost function computing a log-likelihood for calibration of P-model parameters	cost_likelihood_pmodel
RMSE cost function for BiomeE	cost_rmse_biomee
Cost function computing RMSE for calibration of P-model parameters	cost_rmse_pmodel
Initialises a tibble with dates	init_dates_dataframe
rsofun P-model driver data	p_model_drivers
rsofun P-model driver data (for leaf traits)	p_model_drivers_vcmax25
rsofun P-model output data	p_model_output
rsofun P-model output data (using vcmax25 drivers)	p_model_output_vcmax25
rsofun P-model GPP validation data	p_model_validation
rsofun P-model Vcmax25 validation data	p_model_validation_vcmax25
Run BiomeE (R wrapper)	run_biomee_f_bysite
R wrapper for SOFUN P-model	run_pmodel_f_bysite
Run BiomeE	runread_biomee_f
Run the P-model	runread_pmodel_f

Package: rsofun 5.0.0

rsofun: The P-Model and BiomeE Modelling Framework

BiomeE usage

Data format

P-model usage

Parameter calibration and cost functions

Sensitivity analysis and calibration interpretation

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)