title	BiomeBGC_core Manual
subtitle	v.0.0.0.9000
date	Last updated: 2025-11-18
output	bookdown::html_document2 toc toc_float theme number_sections df_print keep_md true true sandstone false paged true
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BiomeBGC_core Module

(ref:BiomeBGC-core) BiomeBGC_core

Authors:

Dominique Caron dominique.caron@nrcan-rncan.gc.ca [aut, cre]

Module Overview

Module summary

Provide a brief summary of what the module does / how to use the module.

Module documentation should be written so that others can use your module. This is a template for module documentation, and should be changed to reflect your module.

Module inputs and parameters

Describe input data required by the module and how to obtain it (e.g., directly from online sources or supplied by other modules) If sourceURL is specified, downloadData("BiomeBGC_core", "C:/Users/docaron/Documents/repos") may be sufficient.

Table @ref(tab:moduleInputs-BiomeBGC-core) shows the full list of module inputs.

(\#tab:moduleInputs-BiomeBGC-core)(\#tab:moduleInputs-BiomeBGC-core)List of (ref:BiomeBGC-core) input objects and their description.

objectName	objectClass	desc	sourceURL
bbgcSpinup.ini	character	Biome-BGC initialization files for the spinup. Path to the .ini files (one path per site/scenario).	NA
bbgc.ini	character	Biome-BGC initialization files. Path to the .ini files (one path per site/scenario).	NA

Summary of user-visible parameters (Table @ref(tab:moduleParams-BiomeBGC-core))

(\#tab:moduleParams-BiomeBGC-core)(\#tab:moduleParams-BiomeBGC-core)List of (ref:BiomeBGC-core) parameters and their description.

paramName	paramClass	default	min	max	paramDesc
argv	character	-a	NA	NA	Arguments for the BiomeBGC library (same as 'bgc' commandline application)
bbgcPath	character	C:\Users....	NA	NA	Path to base directory to use for simulations.
bbgcInputPath	character	C:\Users....	NA	NA	Path to the Biome-BGC input directory.
.plots	character	screen	NA	NA	Used by Plots function, which can be optionally used here
.plotInitialTime	numeric	0	NA	NA	Describes the simulation time at which the first plot event should occur.
.plotInterval	numeric	NA	NA	NA	Describes the simulation time interval between plot events.
.saveInitialTime	numeric	NA	NA	NA	Describes the simulation time at which the first save event should occur.
.saveInterval	numeric	NA	NA	NA	This describes the simulation time interval between save events.
.studyAreaName	character	NA	NA	NA	Human-readable name for the study area used - e.g., a hash of the studyarea obtained using `reproducible::studyAreaName()`
.seed	list		NA	NA	Named list of seeds to use for each event (names).
.useCache	logical	FALSE	NA	NA	Should caching of events or module be used?

Events

Describe what happens for each event type.

Plotting

Write what is plotted.

Saving

Write what is saved.

Module outputs

Description of the module outputs (Table @ref(tab:moduleOutputs-BiomeBGC-core)).

(\#tab:moduleOutputs-BiomeBGC-core)(\#tab:moduleOutputs-BiomeBGC-core)List of (ref:BiomeBGC-core) outputs and their description.

objectName	objectClass	desc
outputControl	data.frame	NA
dailyOutput	data.frame	NA
annualOutput	data.frame	NA

Links to other modules

Describe any anticipated linkages to other modules, such as modules that supply input data or do post-hoc analysis.

Getting help

• provide a way for people to obtain help (e.g., module repository issues page)

References