title	author	date	output	editor_options
CBM_dataPrep_RIA	Celine Boisvenue Alex Chubaty	September 2020	html_document keep_md true	chunk_output_type console

Overview

This module runs independently with the global script below. Its main task is to read-in user-provided information or provide defaults. It reads-in rasters (ageRaster, ecoRaster, gcIndexRaster, spuRaster, and masterRaster) from either defaults of provided by the user. From the rasters is creates pixelGroup which are unique combinations of the rasters values. pixelGroup is a main processing unit in SpaDS CBM simulations. In a first step, a spatialDT which is a data.table listing all pixels with their respective values of raster, pixelIndex and pixelGroup is created (sim$spatialDT). From the spatialDT, a reduced data.table is create (sim$level3DT) which is the data.table from which processing will start in CBM_core. The number of records in this data.table (sim$level3DT) should equal the number of pixel groups that will be processed in the spinup event of the CBM_core module. This present module also creates variables of the same length as the rows in level3DT for use in other events of the CBM_core module. These are: returnIntervals, maxRotations, minRotations, lastPassDMIDs, historicDMIDs, and delays all stored in the simList.

Another important object created in this module is mySpuDmids. This data.table links the user-defined disturbances ($userDist) with a spatial unit and a disturbance matrix. This will be used to apply disturbances to pixel groups in the annual event of the CBM_core module. The mySpuDmids object is created starting from a user provided list of disturbances (userDist) that matches the rasterId of the disturbance raster to the disturbance name. That name and the location of the disturbance (spatial unit id) is used to associate a disturbance matrix identification number to the disturbed pixelGroup. Disturbance Matrices (DM) determine what proportion of a carbon pool gets transferred to another because of disturbance. There are 426 matrix IDs in the present default data (outDefaults$processes$disturbanceMatrices). DMIDs (Disturbance Matrix IDs) are part of the default data that come with CBM-CFS3. DMs are specific to spatial units which are a numbering (48 of them outDefaults$cbmData@spatialUnitIds) of the overlay of the administrative boundaries and ecozones in Canada. Spatial units are central units in CBM-CFS3, as are ecozones because both determining various ecological and other parameters that will be used in simulations via the CBM_core module. The proportion of carbon transferred by a specific DMID can be found here outDefaults$cbmData@disturbanceMatrixValues. A series of R-functions were built to help users associate the correct disturbance matrices (spuDist(), mySpu(), seeDist(), simDist()) and are searchable in this package.

Note:

• CBM_defaults objects are recreated in the .inputObject of this module
• nothing is in carbon or carbon increments at this point. This module feeds into the CBM_core module as does the CBM_vol2biomass.R module.

Usage

library(igraph)
library(SpaDES.core)

moduleDir <- getwd()
inputDir <- file.path(moduleDir, "inputs") %>% reproducible::checkPath(create = TRUE)
outputDir <- file.path(moduleDir, "outputs")
cacheDir <- file.path(outputDir, "cache")
times <- list(start = 0, end = 10)
parameters <- list(
  #CBM_dataPrep = list(.useCache = ".inputObjects")
 #.progress = list(type = "text", interval = 1), # for a progress bar
 ## If there are further modules, each can have its own set of parameters:
 #module1 = list(param1 = value1, param2 = value2),
 #module2 = list(param1 = value1, param2 = value2)
 )
modules <- list("CBM_dataPrep")
objects <- list(
  userDistFile = file.path(moduleDir,"CBM_dataPrep","data","userDist.csv")
)
paths <- list(
 cachePath = cacheDir,
 modulePath = moduleDir,
 inputPath = inputDir,
 outputPath = outputDir
 )

myInputs <- simInit(times = times, params = parameters, modules = modules,
                 objects = objects, paths = paths)

outInputs <- spades(myInputs)

Events

Describe what happens for each event type.

Plotting

Write what is plotted.

Saving

Write what is saved.

Data dependencies

Module parameters

## Loading required package: dplyr

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

paramName	paramClass	default	min	max	paramDesc
.plotInitialTime	numeric	NA	NA	NA	This describes the simulation time at which the first plot event should occur
.plotInterval	numeric	NA	NA	NA	This describes the simulation time interval between plot events
.saveInitialTime	numeric	NA	NA	NA	This 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
.useCache	logical	FALSE	NA	NA	Should this entire module be run with caching activated? This is generally intended for data-type modules, where stochasticity and time are not relevant

Input data

objectName	objectClass	desc	sourceURL
cbmData	dataset	S4 object created from selective reading in of cbm_default.db in CBM_efaults module	NA
pooldef	character	Vector of names (characters) for each of the carbon pools, with Input being the first one	NA
PoolCount	numeric	count of the length of the Vector of names (characters) for each of the carbon pools, with Input being the first one	NA
dbPath	character	NA	NA
sqlDir	character	NA	NA
userDistFile	character	User provided file name that identifies disturbances for simulation (key words for searching CBM files, if not there the userDist will be created with defaults	NA
userDist	data.table	User provided file that identifies disturbances for simulation, if not there it will use userDistFile	https://drive.google.com/file/d/1YMg0zf8pqBPii0REvBvnj8Yh9CQ3HhRD
ageRasterURL	character	URL for ageRaster - optional, need this or a ageRaster	NA
ageRaster	raster	Raster ages for each pixel	https://drive.google.com/file/d/1hylk0D1vO19Dpg4zFtnSNhnyYP4j-bEA
gcIndexRasterURL	character	URL for ageRaster - optional, need this or a ageRaster	NA
gcIndexRaster	raster	Raster ages for each pixel	https://drive.google.com/file/d/1yunkaYCV2LIdqej45C4F9ir5j1An0KKr/view?usp=sharing
spuRaster	raster	Raster has spatial units for each pixel	NA
ecoRaster	raster	Raster has ecozones for each pixel	NA
userGcM3File	character	User file name for the files containing: GrowthCurveComponentID,Age,MerchVolume. Default name userGcM3	NA
userGcM3	dataframe	User file containing: GrowthCurveComponentID,Age,MerchVolume. Default name userGcM3	https://drive.google.com/file/d/1u7o2BzPZ2Bo7hNcC8nEctNpDmp7ce84m
disturbanceRasters	vector	Character vector of the disturbance rasters for use in simulations - defaults are the Wulder and White rasters for SK.	https://drive.google.com/file/d/12YnuQYytjcBej0_kdodLchPg7z9LygCt
masterRasterURL	character	URL for masterRaster - optional, need this or a masterRaster	NA
masterRaster	raster	Raster has NAs where there are no species and the pixel groupID where the pixels were simulated. It is used to map results	https://drive.google.com/file/d/1zUyFH8k6Ef4c_GiWMInKbwAl6m6gvLJW

Output data

objectName	objectClass	desc
pools	matrix	NA
ages	numeric	Ages of the stands from the inventory in 1990
nStands	numeric	not really the number of stands, but the number of pixel groups
gcids	numeric	The identification of which growth curves to use on the specific stands provided by...
historicDMIDs	numeric	Vector, one for each stand, indicating historical disturbance type, linked to the S4 table called cbmData. Only Spinup.
lastPassDMIDS	numeric	Vector, one for each stand, indicating final disturbance type, linked to the S4 table called cbmData. Only Spinup.
delays	numeric	Vector, one for each stand, indicating regeneration delay post disturbance. Only Spinup.
minRotations	numeric	Vector, one for each stand, indicating minimum number of rotations. Only Spinup.
maxRotations	numeric	Vector, one for each stand, indicating maximum number of rotations. Only Spinup.
returnIntervals	numeric	Vector, one for each stand, indicating the fixed fire return interval. Only Spinup.
spatialUnits	numeric	The id given to the intersection of province and ecozones across Canada, linked to the S4 table called cbmData
ecozones	numeric	Vector, one for each stand, indicating the numeric represenation of the Canadian ecozones, as used in CBM-CFS3
level3DT	data.table	the table linking the spu id, with the disturbance_matrix_id and the events. The events are the possible raster values from the disturbance rasters of Wulder and White.
spatialDT	data.table	the table containing one line per pixel
mySpuDmids	data.frame	the table containing one line per pixel

Links to other modules

• CBM_core
• CBM_defaults
• CBM_vol2biomass