Skip to content

achubaty/mpbPine

Repository files navigation

title author date output bibliography editor_options
mpbPine
Alex M. Chubaty
Barry J. Cooke
Eliot J. B. McIntire
May 25, 2021
html_document
keep_md toc toc_depth toc_float
true
true
3
true
bibliography.bib
chunk_output_type
console

Overview

Download and use proportion pine data, based on provincial forest inventory data and prepared for the updated MPB Risk Assessment [@Bleiker:2019]. These data cover most of the managed boreal forests in Alberta and Saskatchewan.

In the current model, we calculate the number of available jack pine and lodgepole pine trees from the proportion pine for each species, by multiplying by the average stem density of 1125 mature stems per hectare, which is typical for beetle-prone lodgepole pine stands [@Whitehead:2004rz; @Cooke:2017fem].

A more sophisticated estimate of pine stem density for each species is currently under development for future versions of this module.

Usage

library(SpaDES.core)

setPaths(modulePath = file.path(".."))
getPaths() # shows where the 4 relevant paths are

times <- list(start = 0, end = 10)

parameters <- list(
  #.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("mpbPine")
objects <- list()
inputs <- list()
outputs <- list()

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

mySimOut <- spades(mySim)

Parameters

Provide a summary of user-visible parameters.

## defineParameter: '.plotInitialTime' is not of specified type 'numeric'.
paramName paramClass default min max paramDesc
lowMemory logical FALSE NA NA Should high memory-usage steps be skipped? Useful for running on laptops.
sppEquivCol character Boreal NA NA The column in sim$specieEquivalency data.table to use as a naming convention
simplifyPines logical TRUE NA NA A test evaluating whether one of the pines represents > 90% of the abundance. If it does, and this parameter is TRUE, then the two pines will be collapsed into one species, labelled with the dominmant species name.
.maxMemory numeric 1e+09 NA NA Used to set the 'maxmemory' raster option. See '?rasterOptions'.
.plotInitialTime numeric start(sim) 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
.tempdir character NA NA Temporary (scratch) directory to use for transient files (e.g., GIS intermediates).
.useCache logical FALSE NA NA Should this entire module be run with caching activated?

Events

Describe what happens for each event type.

Plotting

Write what is plotted.

Saving

Write what is saved.

Data dependencies

Input data

How to obtain input data, and a description of the data required by the module. If sourceURL is specified, downloadData("mpbPine", "..") may be sufficient.

## defineParameter: '.plotInitialTime' is not of specified type 'numeric'.
objectName objectClass desc sourceURL
mpbGrowthDT data.table Current MPB attack map (number of red attacked trees). NA
pineMap RasterStack Pine percent cover maps (lodgepole and jack pine).
rasterToMatch RasterLayer if not supplied, will default to standAgeMap NA
sppColors character A named vector of colors to use for plotting. The names must be in sim$speciesEquivalency[[sim$sppEquivCol]], and should also contain a color for 'Mixed' NA
sppEquiv data.table table of species equivalencies. See LandR::sppEquivalencies_CA.
standAgeMap RasterLayer stand age map in study area, default is Canada national stand age map http://ftp.maps.canada.ca/pub/nrcan_rncan/Forests_Foret/canada-forests-attributes_attributs-forests-canada/2001-attributes_attributs-2001/NFI_MODIS250m_2001_kNN_Structure_Stand_Age_v1.tif
studyArea SpatialPolygons The study area to which all maps will be cropped and reprojected. NA
studyAreaLarge SpatialPolygons The larger study area to use for spread parameter estimation. NA

Output data

Description of the module outputs.

## defineParameter: '.plotInitialTime' is not of specified type 'numeric'.
objectName objectClass desc
pineDT data.table Proportion cover etc. by species (lodgepole and jack pine).
pineMap RasterLayer Percent cover maps by species (lodgepole and jack pine).

Links to other modules

Part of the LandR_MPB Mountain Pine Beetle Red Top Model, which evaluates short-run potential for MPB establishment, eruption, and spread.

  • mpbClimateData
  • mpbMassAttacksData
  • mpbPine
  • mpbRedTopSpread

Future linkages include the LandR Biomass suite of modules to simulate/forecast forest vegetation dynamics, and the fireSense wildfire simulation model.

References

About

No description, website, or topics provided.

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published