{"id":47748259,"url":"https://github.com/predictiveecology/biomebgc_core","last_synced_at":"2026-04-04T04:31:48.722Z","repository":{"id":324927151,"uuid":"1098600136","full_name":"PredictiveEcology/BiomeBGC_core","owner":"PredictiveEcology","description":null,"archived":false,"fork":false,"pushed_at":"2026-03-13T20:32:55.000Z","size":522,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-03-14T08:46:38.418Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/PredictiveEcology.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"citation.bib","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-11-17T22:47:27.000Z","updated_at":"2026-03-13T20:32:59.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/PredictiveEcology/BiomeBGC_core","commit_stats":null,"previous_names":["dominiquecaron/biomebgc_core","predictiveecology/biomebgc_core"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/PredictiveEcology/BiomeBGC_core","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PredictiveEcology%2FBiomeBGC_core","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PredictiveEcology%2FBiomeBGC_core/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PredictiveEcology%2FBiomeBGC_core/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PredictiveEcology%2FBiomeBGC_core/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/PredictiveEcology","download_url":"https://codeload.github.com/PredictiveEcology/BiomeBGC_core/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PredictiveEcology%2FBiomeBGC_core/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31326844,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-03T01:42:14.489Z","status":"online","status_checked_at":"2026-04-03T02:00:06.642Z","response_time":107,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2026-04-03T02:01:24.509Z","updated_at":"2026-04-03T02:01:34.797Z","avatar_url":"https://github.com/PredictiveEcology.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\ntitle: \"BiomeBGC_core Manual\"\nsubtitle: \"v.0.0.0.9000\"\ndate: \"Last updated: 2025-11-18\"\noutput:\n  bookdown::html_document2:\n    toc: true\n    toc_float: true\n    theme: sandstone\n    number_sections: false\n    df_print: paged\n    keep_md: yes\neditor_options:\n  chunk_output_type: console\nlink-citations: true\nalways_allow_html: true\n---\n\n# BiomeBGC_core Module\n\n\u003c!-- the following are text references used in captions for LaTeX compatibility --\u003e\n(ref:BiomeBGC-core) *BiomeBGC_core*\n\n\n\n[![made-with-Markdown](figures/markdownBadge.png)](https://commonmark.org)\n\n\u003c!-- if knitting to pdf remember to add the pandoc_args: [\"--extract-media\", \".\"] option to yml in order to get the badge images --\u003e\n\n#### Authors:\n\nDominique Caron \u003cdominique.caron@nrcan-rncan.gc.ca\u003e [aut, cre]\n\u003c!-- ideally separate authors with new lines, '\\n' not working --\u003e\n\n## Module Overview\n\n### Module summary\n\nProvide a brief summary of what the module does / how to use the module.\n\nModule documentation should be written so that others can use your module.\nThis is a template for module documentation, and should be changed to reflect your module.\n\n### Module inputs and parameters\n\nDescribe input data required by the module and how to obtain it (e.g., directly from online sources or supplied by other modules)\nIf `sourceURL` is specified, `downloadData(\"BiomeBGC_core\", \"C:/Users/docaron/Documents/repos\")` may be sufficient.\n\nTable \\@ref(tab:moduleInputs-BiomeBGC-core) shows the full list of module inputs.\n\n\u003ctable class=\"table\" style=\"color: black; margin-left: auto; margin-right: auto;\"\u003e\n\u003ccaption\u003e(\\#tab:moduleInputs-BiomeBGC-core)(\\#tab:moduleInputs-BiomeBGC-core)List of (ref:BiomeBGC-core) input objects and their description.\u003c/caption\u003e\n \u003cthead\u003e\n  \u003ctr\u003e\n   \u003cth style=\"text-align:left;\"\u003e objectName \u003c/th\u003e\n   \u003cth style=\"text-align:left;\"\u003e objectClass \u003c/th\u003e\n   \u003cth style=\"text-align:left;\"\u003e desc \u003c/th\u003e\n   \u003cth style=\"text-align:left;\"\u003e sourceURL \u003c/th\u003e\n  \u003c/tr\u003e\n \u003c/thead\u003e\n\u003ctbody\u003e\n  \u003ctr\u003e\n   \u003ctd style=\"text-align:left;\"\u003e bbgcSpinup.ini \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e character \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e Biome-BGC initialization files for the spinup. Path to the .ini files (one path per site/scenario). \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n  \u003c/tr\u003e\n  \u003ctr\u003e\n   \u003ctd style=\"text-align:left;\"\u003e bbgc.ini \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e character \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e Biome-BGC initialization files. Path to the .ini files (one path per site/scenario). \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n  \u003c/tr\u003e\n\u003c/tbody\u003e\n\u003c/table\u003e\n\nSummary of user-visible parameters (Table \\@ref(tab:moduleParams-BiomeBGC-core))\n\n\n\u003ctable class=\"table\" style=\"color: black; margin-left: auto; margin-right: auto;\"\u003e\n\u003ccaption\u003e(\\#tab:moduleParams-BiomeBGC-core)(\\#tab:moduleParams-BiomeBGC-core)List of (ref:BiomeBGC-core) parameters and their description.\u003c/caption\u003e\n \u003cthead\u003e\n  \u003ctr\u003e\n   \u003cth style=\"text-align:left;\"\u003e paramName \u003c/th\u003e\n   \u003cth style=\"text-align:left;\"\u003e paramClass \u003c/th\u003e\n   \u003cth style=\"text-align:left;\"\u003e default \u003c/th\u003e\n   \u003cth style=\"text-align:left;\"\u003e min \u003c/th\u003e\n   \u003cth style=\"text-align:left;\"\u003e max \u003c/th\u003e\n   \u003cth style=\"text-align:left;\"\u003e paramDesc \u003c/th\u003e\n  \u003c/tr\u003e\n \u003c/thead\u003e\n\u003ctbody\u003e\n  \u003ctr\u003e\n   \u003ctd style=\"text-align:left;\"\u003e argv \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e character \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e -a \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e Arguments for the BiomeBGC library (same as 'bgc' commandline application) \u003c/td\u003e\n  \u003c/tr\u003e\n  \u003ctr\u003e\n   \u003ctd style=\"text-align:left;\"\u003e bbgcPath \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e character \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e C:\\Users.... \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e Path to base directory to use for simulations. \u003c/td\u003e\n  \u003c/tr\u003e\n  \u003ctr\u003e\n   \u003ctd style=\"text-align:left;\"\u003e bbgcInputPath \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e character \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e C:\\Users.... \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e Path to the Biome-BGC input directory. \u003c/td\u003e\n  \u003c/tr\u003e\n  \u003ctr\u003e\n   \u003ctd style=\"text-align:left;\"\u003e .plots \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e character \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e screen \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e Used by Plots function, which can be optionally used here \u003c/td\u003e\n  \u003c/tr\u003e\n  \u003ctr\u003e\n   \u003ctd style=\"text-align:left;\"\u003e .plotInitialTime \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e numeric \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e 0 \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e Describes the simulation time at which the first plot event should occur. \u003c/td\u003e\n  \u003c/tr\u003e\n  \u003ctr\u003e\n   \u003ctd style=\"text-align:left;\"\u003e .plotInterval \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e numeric \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e Describes the simulation time interval between plot events. \u003c/td\u003e\n  \u003c/tr\u003e\n  \u003ctr\u003e\n   \u003ctd style=\"text-align:left;\"\u003e .saveInitialTime \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e numeric \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e Describes the simulation time at which the first save event should occur. \u003c/td\u003e\n  \u003c/tr\u003e\n  \u003ctr\u003e\n   \u003ctd style=\"text-align:left;\"\u003e .saveInterval \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e numeric \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e This describes the simulation time interval between save events. \u003c/td\u003e\n  \u003c/tr\u003e\n  \u003ctr\u003e\n   \u003ctd style=\"text-align:left;\"\u003e .studyAreaName \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e character \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e Human-readable name for the study area used - e.g., a hash of the studyarea obtained using `reproducible::studyAreaName()` \u003c/td\u003e\n  \u003c/tr\u003e\n  \u003ctr\u003e\n   \u003ctd style=\"text-align:left;\"\u003e .seed \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e list \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e  \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e Named list of seeds to use for each event (names). \u003c/td\u003e\n  \u003c/tr\u003e\n  \u003ctr\u003e\n   \u003ctd style=\"text-align:left;\"\u003e .useCache \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e logical \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e FALSE \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e Should caching of events or module be used? \u003c/td\u003e\n  \u003c/tr\u003e\n\u003c/tbody\u003e\n\u003c/table\u003e\n\n### Events\n\nDescribe what happens for each event type.\n\n### Plotting\n\nWrite what is plotted.\n\n### Saving\n\nWrite what is saved.\n\n### Module outputs\n\nDescription of the module outputs (Table \\@ref(tab:moduleOutputs-BiomeBGC-core)).\n\n\u003ctable class=\"table\" style=\"color: black; margin-left: auto; margin-right: auto;\"\u003e\n\u003ccaption\u003e(\\#tab:moduleOutputs-BiomeBGC-core)(\\#tab:moduleOutputs-BiomeBGC-core)List of (ref:BiomeBGC-core) outputs and their description.\u003c/caption\u003e\n \u003cthead\u003e\n  \u003ctr\u003e\n   \u003cth style=\"text-align:left;\"\u003e objectName \u003c/th\u003e\n   \u003cth style=\"text-align:left;\"\u003e objectClass \u003c/th\u003e\n   \u003cth style=\"text-align:left;\"\u003e desc \u003c/th\u003e\n  \u003c/tr\u003e\n \u003c/thead\u003e\n\u003ctbody\u003e\n  \u003ctr\u003e\n   \u003ctd style=\"text-align:left;\"\u003e outputControl \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e data.frame \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n  \u003c/tr\u003e\n  \u003ctr\u003e\n   \u003ctd style=\"text-align:left;\"\u003e dailyOutput \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e data.frame \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n  \u003c/tr\u003e\n  \u003ctr\u003e\n   \u003ctd style=\"text-align:left;\"\u003e annualOutput \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e data.frame \u003c/td\u003e\n   \u003ctd style=\"text-align:left;\"\u003e NA \u003c/td\u003e\n  \u003c/tr\u003e\n\u003c/tbody\u003e\n\u003c/table\u003e\n\n### Links to other modules\n\nDescribe any anticipated linkages to other modules, such as modules that supply input data or do post-hoc analysis.\n\n### Getting help\n\n-   provide a way for people to obtain help (e.g., module repository issues page)\n\n## References\n\n\u003c!-- autogenerated from bibligraphy --\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpredictiveecology%2Fbiomebgc_core","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpredictiveecology%2Fbiomebgc_core","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpredictiveecology%2Fbiomebgc_core/lists"}