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spadesCBM Manual: v. 0.1

1 CBM_defaults

This documentation is work in progress. Potential discrepancies and omissions may exist for the time being. If you find any regarding this module, contact us here.

1.1 Overview

CBM_defaults reads in default parameters for the managed forest of Canada. In SpaDES-speak, it has one event (init). On its own, this module provides R-based access to all defaults CBM parameters for the managed forests of Canada (run Usage section below to run this module independently). As part of spadesCBM, it provides simulations with default parameter values for the managed forests of Canada, akin to the Archive Index in the CBM-CFS3 documentation. Most parameters are read in from an SQLite database (link below), with some defaults, modified from CBM-CFS3 to accommodate a more flexible representation of vegetation dynamics enable by the libcbm Python functions used, available here. Defaults for the managed forests of Canada include disturbance data such as different disturbance types and their IDs, spinup parameters, pool names, fire return intervals for each ecozone and more. The outputs of this module are used by CBM_dataPrep_SK and CBM_core in spadesCBM simulations.

1.2 Background

This example uses default parameters that were created for use in CBM-CFS3 as described in Kurz et al. (2009). Few of these parameters have source references. The ones who do are outline in the Operational-scale Carbon Budget Model of the Canadian Forest Sector (CBM-CFS3) version 1.2: user’s guide. CBM_defaults brings the parameters to an R-environment, for easy user-access and modifications.

1.3 Inputs

Name Class Description Source
Archive Index SQL Database SQLite database file for CFS_CBM3 default tables GitHub
Disturbance Matrix Association Data table Default disturbance IDs GitHub
Disturbance Matrix Value Data table Default disturbance data GitHub
species.csv Data table Default species information GitHub
ecoLocator Shapefile Canada’s ecozone as polygon features Canadian Soil information Service
spuLocator Shapefile Canada’s spatial units as polygon features Google Drive

1.4 Module functioning

  • The SQLite database, and a selection of the cbm_exn resource files are downloaded and stored into the user’s Inputs folder from GitHub using the reproducible::prepInputs function, a useful tool in the SpaDES toolkit.
  • Parameters necessary for spadesCBM simulations are extracted from the downloaded files. Each of these are saved as objects in the simList (see list of output objects above).
  • The disturbanceMatrix and cTransfers objects help identify which carbon transfers matches the provided disturbances as it matches the transfer matrix IDs and the proportions transferred to disturbance names.
  • Parameters necessary for the spinup event in the CBM_core modules are assembled in the spinupSQL object.
  • pooldef gives the names of each carbon pool that exists in CBM.
  • species.csv is read in as the CBMspecies object.
  • cbmAdmin identifies all ecozones and spatial unit IDs combinations possible for each province and territory.

1.5 Outputs

Name Class Description
disturbanceMatrix Data table Default disturbance data
cTransfers Data table Default disturbance data
spinupSQL Data table Parameters for CBM_core spinup event
pooldef Character Vector of pools
CBMspecies Data table Default species data
cbmAdmin Data table Ecozone and spatial unit information for provincial boundaries

1.6 Usage

This module can run independently by running the global script below. Run independently, it provides transparent access to default parameters for all managed forests of Canada for spadesCBM simulations.

# project path and package install
projectPath <- "~/CBM_defaults"
repos <- c("predictiveecology.r-universe.dev", getOption("repos"))
if ((packageVersion("SpaDES.project") < "0.1.1" || packageVersion("Require") < "1.0.1.9002") |>
    tryCatch(error = function(x) TRUE))
  install.packages(c("SpaDES.project", "Require"), repos = repos)

# setup
out <- SpaDES.project::setupProject(
  paths = list(projectPath = projectPath),
  
  options = options(
    repos = c(repos = repos),
    reproducible.destinationPath = "inputs"
  ),
  modules =  c("PredictiveEcology/CBM_defaults@main"),
  require = c("SpaDES.core"),
)

# run
outDefaults <- SpaDES.core::simInitAndSpades2(out)