https://github.com/predictiveecology/biomebgc_core

https://github.com/predictiveecology/biomebgc_core

Last synced: 4 months ago
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• Host: GitHub
• URL: https://github.com/predictiveecology/biomebgc_core
• Owner: PredictiveEcology
• License: other
• Created: 2025-11-17T22:47:27.000Z (8 months ago)
• Default Branch: main
• Last Pushed: 2026-03-13T20:32:55.000Z (5 months ago)
• Last Synced: 2026-03-14T08:46:38.418Z (5 months ago)
• Language: HTML
• Size: 510 KB
• Stars: 1
• Watchers: 0
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS.md
  • License: LICENSE.md
  • Citation: citation.bib

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README

          
---

title: "BiomeBGC_core Manual"

subtitle: "v.0.0.0.9000"

date: "Last updated: 2025-11-18"

output:

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    theme: sandstone

    number_sections: false

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    keep_md: yes

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---

# BiomeBGC_core Module

(ref:BiomeBGC-core) *BiomeBGC_core*

[![made-with-Markdown](figures/markdownBadge.png)](https://commonmark.org)

#### Authors:

Dominique Caron  [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