CBM_core.Rmd

---
title: "CBM Spades Manual"
subtitle: "`r paste('v.', Sys.getenv('SpadesCBM_MAN_VERSION'))`"
author: "Céline Boisvenue"
date: "26 June 2024"
output: pdf_document
editor_options: 
  chunk_output_type: console
---

# CBM_core

## Overview

This is the core modules of Spades CBM.


### Notes on forest type
The SQligth (used in CBM_defaults) has has a column named `forest_type_id` that identifies a softwood forest (sw) as 1, a mixed forest as 2, and a hardwood forest (hw) as 3. This distinction is important because it determines how the root biomass will be calculated (sw differently than hw). The definition of `fotrest_type_id` is constant and is the same that is used in `canfi_species.csv` (species level identification of codes that is needed in the volumne to biomass translation in CBM_vol2biomass), in `gcMeta.csv` (SK specific growth curve metadata), and in `sim$growth_increments` because it built from `gcMeta` and `canfi_species`. The `sim$growth_increment$forest_type_id` is the one used to create the sw flag needed for input in the spinup event. After that, the sw_hw flag (1=sw, 0=hw) is stored in the `sim$cbm_vars$state$sw_hw` column.

## List of input objects

| Name              | Class      | Description                                                  | Source          |
|-----------------|-----------------|-----------------------|-----------------|
| growth_increments | Data table |                                                              | CBM_vol2biomass |
| forestTypeID      | Data table | Defines forest types and their respective IDs                | CM_defaults     |
| level3DT          | Data table | pixelGroup level table with all collapsed raster information |                 |
| spatialDT         | Data table | Pixel level table with all collapsed raster information      | CBM_dataPrep_x  |
| masterRaster      | SpatRaster |                                                              | CBM_dataPrep_x  |
| pooldel           | Character  | Vector of pools                                              | CBM_defaults    |
| spinupSQL         | Data table | Parameters for CBM_core spinup event                         | CBM_defaults    |
| disturbanceMatrix | Data table | Default disturbance data                                     | CBM_defaults    |

## List of output objects

| Name              | Class      | Description                                                     |
|------------------|------------------|-------------------------------------|
| spinup_input      | List       |                                                                 |
| cbm_vars          | List       |                                                                 |
| spinupResults     | Data frame | Pools post spinup in order of pixelGroup                        |
| pixelGroupC       | Data table | All vectors (pixelGroup columns) and pools for simulation year. |
| pixelKeep         | Data table | Tracking all pixels' pixel group through simulations            |
| cbmPools          | Data table | All pools and pixelGroups after each simulation                 |
| NPP               | Data table | Net primary production per pixel group                          |
| emissionsProducts | matrix     | Total emissions and products for study area per simulation year |

## Module flow (rename this section later)

1.  

2.  

3.  

4.  

## OLD VERSION

## Overview

NPP: Net primary productivity is for both above and below ground productivity. Provide an overview of what the module does / how to use the module.