{ "_id": "6a4e0df7e691af43f13dfbfd", "Package": "rsofun", "Title": "The P-Model and BiomeE Modelling Framework", "Version": "5.1.0", "Authors@R": "c(\nperson(\nfamily = \"Stocker\",\ngiven = \"Benjamin\",\nemail = \"benjamin.stocker@gmail.com\",\ncomment = c(ORCID = \"0000-0003-2697-9096\"),\nrole = c(\"aut\", \"cre\")),\nperson(\nfamily = \"Hufkens\",\ngiven = \"Koen\",\nemail = \"koen.hufkens@gmail.com\",\ncomment = c(ORCID = \"0000-0002-5070-8109\"),\nrole = c(\"aut\")),\nperson(\nfamily = \"Arán Paredes\",\ngiven = \"Josefa\",\nemail = \"pepa.aran@gmail.com\",\ncomment = c(ORCID = \"0009-0006-7176-2311\"),\nrole = c(\"aut\")),\nperson(\nfamily = \"Marqués\",\ngiven = \"Laura\",\nemail = \"lauramarqueslopez@gmail.com\",\ncomment = c(ORCID = \"0000-0002-3593-5557\"),\nrole = c(\"ctb\")),\nperson(\nfamily = \"Marcadella\",\ngiven = \"Mayeul\",\nemail = \"mayeul.marcadella@gmail.com\",\ncomment = c(ORCID = \"0000-0001-8555-3808\"),\nrole = c(\"ctb\")),\nperson(\nfamily = \"Weng\",\ngiven = \"Ensheng\",\nemail = \"wengensheng@gmail.com\",\ncomment = c(ORCID = \"0000-0002-1858-4847\"),\nrole = c(\"ctb\")),\nperson(\nfamily = \"Bernhard\",\ngiven = \"Fabian\",\nemail = \"fabian.bernhard@alumni.epfl.ch\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-0338-0961\")),\nperson(given = \"Geocomputation and Earth Observation, University of Bern\",\nrole = c(\"cph\", \"fnd\"))\n)", "Description": "Implements the Simulating Optimal FUNctioning framework\nfor site-scale simulations of ecosystem processes, including\nmodel calibration. It contains 'Fortran 90' modules for the\nP-model (Stocker et al. (2020) ),\nSPLASH (Davis et al. (2017) ) and\nBiomeE (Weng et al. (2015) ).", "URL": "https://github.com/geco-bern/rsofun", "BugReports": "https://github.com/geco-bern/rsofun/issues", "License": "GPL-3", "LazyData": "true", "LazyDataCompression": "xz", "ByteCompile": "true", "NeedsCompilation": "yes", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Config/testthat/edition": "3", "Packaged": { "Date": "2026-07-08 08:40:00 UTC", "User": "root" }, "Author": "Benjamin Stocker [aut, cre] (ORCID:\n), Koen Hufkens [aut]\n(ORCID: ), Josefa Arán\nParedes [aut] (ORCID: ),\nLaura Marqués [ctb] (ORCID:\n), Mayeul Marcadella\n[ctb] (ORCID: ), Ensheng\nWeng [ctb] (ORCID: ),\nFabian Bernhard [aut] (ORCID:\n), Geocomputation and\nEarth Observation, University of Bern [cph, fnd]", "Maintainer": "Benjamin Stocker ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2025-10-09 14:43:31 UTC", "RemoteUrl": "https://github.com/cran/rsofun", "RemoteRef": "HEAD", "RemoteSha": "38e6f6b93a3b67772e867bdb9d09f5bfa75add4e", "_user": "cran", "_type": "src", "_file": "rsofun_5.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/0d08d1845ce478cdadf6d827274d9d793aa6a51ee035b8db2808e6ed6f09aa1f", "_filesize": 5115657, "_sha256": "0d08d1845ce478cdadf6d827274d9d793aa6a51ee035b8db2808e6ed6f09aa1f", "_expires": "2026-10-16T08:44:36.000Z", "_created": "2026-07-08T08:40:00.000Z", "_published": "2026-07-08T08:44:38.936Z", "_jobs": [ { "job": 85824708552, "time": 221, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8162835601" }, { "job": 85824708605, "time": 204, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8162827325" }, { "job": 85824708894, "time": 193, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8162824123" }, { "job": 85824708598, "time": 210, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8162830091" }, { "job": 85823649032, "time": 335, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8162746599" }, { "job": 85824708494, "time": 183, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8162818807" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/cran/actions/runs/28929104948", "_status": "success", "_upstream": "https://github.com/cran/rsofun", "_commit": { "id": "38e6f6b93a3b67772e867bdb9d09f5bfa75add4e", "author": "Benjamin Stocker ", "committer": "cran-robot ", "message": "version 5.1.0\n", "time": 1760021011 }, "_maintainer": { "name": "Benjamin Stocker", "email": "benjamin.stocker@gmail.com", "login": "stineb", "description": "", "uuid": 6704682, "orcid": "0000-0003-2697-9096" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "GenSA", "role": "Imports" }, { "package": "BayesianTools", "role": "Imports" }, { "package": "lubridate", "role": "Imports" }, { "package": "multidplyr", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "covr", "role": "Suggests" }, { "package": "constructive", "role": "Suggests" }, { "package": "cowplot", "role": "Suggests" }, { "package": "rcmdcheck", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "sensitivity", "role": "Suggests" }, { "package": "rpmodel", "role": "Suggests" }, { "package": "rlang", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-41", "n": 1 } ], "_tags": [ { "name": "5.1.0", "date": "2025-10-09" } ], "_stars": 0, "_contributors": [ { "user": "stineb", "count": 3, "uuid": 6704682 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 617, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 308, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rsofun" }, "_devurl": "https://github.com/geco-bern/rsofun", "_searchresults": 183, "_topics": [ "fortran", "glibc" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/rsofun.html", "manual.pdf" ], "_homeurl": "https://github.com/geco-bern/rsofun", "_realowner": "geco-bern", "_cranurl": false, "_releases": [ { "version": "4.4", "date": "2023-10-30" }, { "version": "5.0.0", "date": "2024-11-28" }, { "version": "5.1.0", "date": "2025-10-09" } ], "_exports": [ "build_luc_matrix", "calib_sofun", "cost_likelihood_biomee", "cost_likelihood_pmodel", "cost_rmse_biomee", "cost_rmse_pmodel", "run_biomee_f_bysite", "run_pmodel_f_bysite", "run_pmodel_onestep_f_bysite", "runread_biomee_f", "runread_pmodel_f" ], "_datasets": [ { "name": "biomee_gs_leuning_drivers", "title": "rsofun BiomeE driver data (Leuning photosynthesis model)", "object": "biomee_gs_leuning_drivers", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "sitename", "site_info", "params_siml", "params_tile", "params_species", "init_cohort", "init_soil", "forcing" ], "rows": 1, "table": false, "tojson": true }, { "name": "biomee_gs_leuning_output", "title": "rsofun BiomeE (gs_leuning) output data", "object": "biomee_gs_leuning_output", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "sitename", "data" ], "rows": 1, "table": false, "tojson": true }, { "name": "biomee_p_model_drivers", "title": "rsofun BiomeE driver data (P-model photosynthesis model)", "object": "biomee_p_model_drivers", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "sitename", "site_info", "params_siml", "params_tile", "params_species", "init_cohort", "init_soil", "forcing" ], "rows": 1, "table": false, "tojson": true }, { "name": "biomee_p_model_luluc_drivers", "title": "rsofun BiomeE driver data (P-model photosynthesis model) with LULUC", "object": "biomee_p_model_luluc_drivers", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "sitename", "site_info", "params_siml", "params_tile", "params_species", "init_cohort", "init_soil", "forcing", "init_lu", "luc_forcing" ], "rows": 1, "table": false, "tojson": true }, { "name": "biomee_p_model_luluc_output", "title": "rsofun BiomeE (P-model) output data", "object": "biomee_p_model_luluc_output", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "sitename", "aggregated", "primary", "secondary" ], "rows": 1, "table": false, "tojson": true }, { "name": "biomee_p_model_output", "title": "rsofun BiomeE (P-model) output data", "object": "biomee_p_model_output", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "sitename", "data" ], "rows": 1, "table": false, "tojson": true }, { "name": "biomee_validation", "title": "rsofun BiomeE targets validation data", "object": "biomee_validation", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "sitename", "data" ], "rows": 1, "table": false, "tojson": true }, { "name": "p_model_drivers", "title": "rsofun P-model driver data", "object": "p_model_drivers", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "sitename", "params_siml", "site_info", "forcing" ], "rows": 1, "table": false, "tojson": true }, { "name": "p_model_drivers_vcmax25", "title": "rsofun P-model driver data (for leaf traits)", "object": "p_model_drivers_vcmax25", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "sitename", "params_siml", "site_info", "forcing" ], "rows": 4, "table": false, "tojson": true }, { "name": "p_model_output", "title": "rsofun P-model output data", "object": "p_model_output", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "sitename", "site_info", "data" ], "rows": 1, "table": false, "tojson": true }, { "name": "p_model_output_vcmax25", "title": "rsofun P-model output data (using vcmax25 drivers)", "object": "p_model_output_vcmax25", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "sitename", "site_info", "data" ], "rows": 4, "table": false, "tojson": true }, { "name": "p_model_validation", "title": "rsofun P-model GPP validation data", "object": "p_model_validation", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "sitename", "data" ], "rows": 1, "table": false, "tojson": true }, { "name": "p_model_validation_vcmax25", "title": "rsofun P-model Vcmax25 validation data", "object": "p_model_validation_vcmax25", "class": [ "grouped_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "sitename", "data" ], "rows": 4, "table": false, "tojson": true } ], "_help": [ { "page": "biomee_gs_leuning_drivers", "title": "rsofun BiomeE driver data (Leuning photosynthesis model)", "topics": [ "biomee_gs_leuning_drivers" ] }, { "page": "biomee_gs_leuning_output", "title": "rsofun BiomeE (gs_leuning) output data", "topics": [ "biomee_gs_leuning_output" ] }, { "page": "biomee_p_model_drivers", "title": "rsofun BiomeE driver data (P-model photosynthesis model)", "topics": [ "biomee_p_model_drivers" ] }, { "page": "biomee_p_model_luluc_drivers", "title": "rsofun BiomeE driver data (P-model photosynthesis model) with LULUC", "topics": [ "biomee_p_model_luluc_drivers" ] }, { "page": "biomee_p_model_luluc_output", "title": "rsofun BiomeE (P-model) output data", "topics": [ "biomee_p_model_luluc_output" ] }, { "page": "biomee_p_model_output", "title": "rsofun BiomeE (P-model) output data", "topics": [ "biomee_p_model_output" ] }, { "page": "biomee_validation", "title": "rsofun BiomeE targets validation data", "topics": [ "biomee_validation" ] }, { "page": "build_luc_matrix", "title": "Build LUC matrix", "topics": [ "build_luc_matrix" ] }, { "page": "calib_sofun", "title": "Calibrates SOFUN model parameters", "topics": [ "calib_sofun" ] }, { "page": "cost_likelihood_biomee", "title": "Log-likelihood cost function for BiomeE with different targets", "topics": [ "cost_likelihood_biomee" ] }, { "page": "cost_likelihood_pmodel", "title": "Cost function computing a log-likelihood for calibration of P-model parameters", "topics": [ "cost_likelihood_pmodel" ] }, { "page": "cost_rmse_biomee", "title": "RMSE cost function for BiomeE", "topics": [ "cost_rmse_biomee" ] }, { "page": "cost_rmse_pmodel", "title": "Cost function computing RMSE for calibration of P-model parameters", "topics": [ "cost_rmse_pmodel" ] }, { "page": "init_dates_dataframe", "title": "Initialises a tibble with dates", "topics": [ "init_dates_dataframe" ] }, { "page": "p_model_drivers", "title": "rsofun P-model driver data", "topics": [ "p_model_drivers" ] }, { "page": "p_model_drivers_vcmax25", "title": "rsofun P-model driver data (for leaf traits)", "topics": [ "p_model_drivers_vcmax25" ] }, { "page": "p_model_output", "title": "rsofun P-model output data", "topics": [ "p_model_output" ] }, { "page": "p_model_output_vcmax25", "title": "rsofun P-model output data (using vcmax25 drivers)", "topics": [ "p_model_output_vcmax25" ] }, { "page": "p_model_validation", "title": "rsofun P-model GPP validation data", "topics": [ "p_model_validation" ] }, { "page": "p_model_validation_vcmax25", "title": "rsofun P-model Vcmax25 validation data", "topics": [ "p_model_validation_vcmax25" ] }, { "page": "run_biomee_f_bysite", "title": "Run BiomeE (R wrapper)", "topics": [ "run_biomee_f_bysite" ] }, { "page": "run_pmodel_f_bysite", "title": "Run P-model (time series)", "topics": [ "run_pmodel_f_bysite" ] }, { "page": "run_pmodel_onestep_f_bysite", "title": "Run P-model (single time step)", "topics": [ "run_pmodel_onestep_f_bysite" ] }, { "page": "runread_biomee_f", "title": "Run BiomeE", "topics": [ "runread_biomee_f" ] }, { "page": "runread_pmodel_f", "title": "Run P-model", "topics": [ "runread_pmodel_f" ] } ], "_rundeps": [ "ape", "askpass", "base64enc", "BayesianTools", "boot", "bridgesampling", "Brobdingnag", "bslib", "cachem", "callr", "cli", "coda", "codetools", "commonmark", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DHARMa", "digest", "doParallel", "dplyr", "ellipse", "emulator", "evaluate", "expm", "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", "lubridate", "magrittr", "MASS", "Matrix", "memoise", "mgcv", "mime", "minqa", "msm", "multidplyr", "mvtnorm", "nlme", "nloptr", "numDeriv", "openssl", "otel", "pillar", "pkgconfig", "plotly", "plyr", "processx", "promises", "ps", "purrr", "qgam", "qs2", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppEigen", "RcppParallel", "Rdpack", "reformulas", "rlang", "rmarkdown", "S7", "sandwich", "sass", "scales", "shiny", "sourcetools", "stringfish", "stringi", "stringr", "survival", "sys", "tibble", "tidyr", "tidyselect", "timechange", "tinytex", "tmvtnorm", "utf8", "vctrs", "viridisLite", "withr", "xfun", "xtable", "yaml", "zoo" ], "_sysdeps": [ { "shlib": "libgfortran", "package": "libgfortran5", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "fortran", "homepage": "http://gcc.gnu.org/", "description": "Runtime library for GNU Fortran applications" }, { "shlib": "libmvec", "package": "libc6", "headers": "libc6-dev", "source": "glibc", "version": "2.43-2ubuntu2", "name": "glibc", "homepage": "https://www.gnu.org/software/libc/libc.html", "description": "GNU C Library: Shared libraries" } ], "_vignettes": [ { "source": "biomee_luluc.Rmd", "filename": "biomee_luluc.html", "title": "BiomeE LULUC", "author": "Mayeul Marcadella", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2025-10-09 14:43:31", "modified": "2025-10-09 14:43:31", "commits": 1 }, { "source": "biomee_use.Rmd", "filename": "biomee_use.html", "title": "BiomeE usage", "author": "Koen Hufkens, Josefa Arán, Fabian Bernhard", "engine": "knitr::rmarkdown", "headings": [ "Demo data", "Two model approaches", "Running the BiomeE model with standard photosynthesis", "Plotting output", "Running the BiomeEP model", "Calibrating model parameters", "Validating model output" ], "created": "2023-10-30 14:31:46", "modified": "2025-10-09 14:43:31", "commits": 3 }, { "source": "data_format.Rmd", "filename": "data_format.html", "title": "Data format", "author": "Koen Hufkens, Josefa Arán", "engine": "knitr::rmarkdown", "headings": [ "Philosophy", "Drivers data (inputs)", "Specific data for each model", "Forcing data", "Output data", "P-model", "BiomeE" ], "created": "2023-10-30 14:31:46", "modified": "2024-11-28 23:10:02", "commits": 2 }, { "source": "pmodel_use.Rmd", "filename": "pmodel_use.html", "title": "P-model usage", "author": "Koen Hufkens, Josefa Arán, Benjamin Stocker", "engine": "knitr::rmarkdown", "headings": [ "Demo data", "Running model", "Plotting output", "Calibrating model parameters", "One-step P-model call" ], "created": "2023-10-30 14:31:46", "modified": "2025-10-09 14:43:31", "commits": 3 }, { "source": "new_cost_function.Rmd", "filename": "new_cost_function.html", "title": "Parameter calibration and cost functions", "author": "Josefa Arán", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2023-10-30 14:31:46", "modified": "2025-10-09 14:43:31", "commits": 2 }, { "source": "sensitivity_analysis.Rmd", "filename": "sensitivity_analysis.html", "title": "Sensitivity analysis and calibration interpretation", "author": "Josefa Arán", "engine": "knitr::rmarkdown", "headings": [ "Morris sensitivity analysis", "Interpretation of Bayesian calibration routine", "Plotting P-model output after calibration" ], "created": "2023-10-30 14:31:46", "modified": "2025-10-09 14:43:31", "commits": 3 } ], "_score": 4.040602340114074, "_indexed": false, "_nocasepkg": "rsofun", "_universes": [ "cran" ], "_indexurl": "https://geco-bern.r-universe.dev/rsofun", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "5.1.0", "date": "2026-07-08T08:43:21.000Z", "distro": "resolute", "arch": "aarch64", "commit": "38e6f6b93a3b67772e867bdb9d09f5bfa75add4e", "fileid": "https://r2.ropensci.org/bec24169bac58454fac9391ed4d5c844e06645f2d35f8dc14bbc65158990a881", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/28929104948" }, { "r": "4.7.0", "os": "linux", "version": "5.1.0", "date": "2026-07-08T08:42:48.000Z", "distro": "resolute", "arch": "x86_64", "commit": "38e6f6b93a3b67772e867bdb9d09f5bfa75add4e", "fileid": "https://r2.ropensci.org/06a0f244e5ace6537853969a5b6b59bf0c599f0a59a98b9d7ad9e2a4efa40f52", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/28929104948" }, { "r": "4.6.1", "os": "linux", "version": "5.1.0", "date": "2026-07-08T08:42:56.000Z", "distro": "resolute", "arch": "aarch64", "commit": "38e6f6b93a3b67772e867bdb9d09f5bfa75add4e", "fileid": "https://r2.ropensci.org/eb3493fdee78fe3c78770ce919f7de845af4021c07b3ac8d5dc8c97e4525ea62", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/28929104948" }, { "r": "4.6.1", "os": "linux", "version": "5.1.0", "date": "2026-07-08T08:42:54.000Z", "distro": "resolute", "arch": "x86_64", "commit": "38e6f6b93a3b67772e867bdb9d09f5bfa75add4e", "fileid": "https://r2.ropensci.org/5b45cef80f39c9fa6eded74da8a4802932700b1653b7983aa866c8712d7d36ff", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/28929104948" }, { "r": "4.6.0", "os": "wasm", "version": "5.1.0", "date": "2026-07-08T08:43:18.000Z", "arch": "emscripten", "commit": "38e6f6b93a3b67772e867bdb9d09f5bfa75add4e", "fileid": "https://r2.ropensci.org/1d3d9e8655ae3667b85b1ad541aac0e30ec11b42b547f11fa324f8e4d35d77f5", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/28929104948" } ] }