| title | author | date | output | editor_options | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
fireSense_dataPrepFit |
|
September 2020; updated February 2022 |
|
|
Prepare data required by fireSense_IginitionFit, fireSense_EscapeFit, and fireSense_SpreadFit.
Provide a summary of user-visible parameters.
| paramName | paramClass | default | min | max | paramDesc |
|---|---|---|---|---|---|
| .plotInitialTime | numeric | NA | 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 | studyArea name that will be appended to file-backed rasters | |
| .useCache | logical | FALSE | NA | NA | Should this entire module be run with caching activated? This is intended for data-type modules, where stochasticity and time are not relevant |
| areaMultiplier | numeric,.... | fireSens.... | NA | NA | Either a scalar that will buffer areaMultiplier fireSize or a function of fireSize. Default is 2. See fireSenseUtils::bufferToArea for help |
| cutoffForYoungAge | numeric | 15 | NA | NA | Age at and below which pixels are considered 'young' --> young <- age <= cutoffForYoungAge |
| fireYears | integer | 2001, 20.... | NA | NA | A numeric vector indicating which years should be extracted from the fire databases to use for fitting |
| forestedLCC | numeric | 1, 2, 3,.... | NA | NA | Forested land cover classes. These classes will be excluded from the PCA. |
| igAggFactor | numeric | 40 | 1 | NA | aggregation factor for rasters during ignition prep. |
| ignitionFuelClassCol | character | FuelClass | NA | NA | the column in sppEquiv that defines unique fuel classes for ignition |
| minBufferSize | numeric | 5000 | NA | NA | Minimum size of buffer and nonbuffer. This is imposed after multiplier on the bufferToArea fn |
| missingLCCgroup | character | nonFores.... | NA | NA | if a pixel is forested but is absent from cohortData, it will be grouped in this class. Must be one of the names in sim$nonForestedLCCGroups |
| nonflammableLCC | numeric | 13, 16, .... | NA | NA | non-flammable LCC in sim$rstLCC. |
| PCAcomponentsForClimate | numeric | 1 | 1 | NA | number of PCA components to include from climate variables |
| PCAcomponentsForTerrain | numeric | 1 | 1 | NA | currently unused - may be needed if using separate terrain and veg PCAs |
| PCAcomponentsForVeg | numeric | 10 | 1 | NA | number of veg and terrain components to include in GLM |
| PCAcomponentsFromGLM | numeric | 5 | 0 | NA | the number of components to select from GLM model of burn ~ PCAcomponents |
| plotPCA | logical | TRUE | NA | NA | plot the PCA components with a heat map. |
| sppEquivCol | character | LandR | NA | NA | column name in sppEquiv object that defines unique species in cohortData |
| spreadFuelClassCol | character | FuelClass | NA | NA | if using fuel classes for spread, the column in sppEquiv that defines unique fuel classes |
| useCentroids | logical | TRUE | NA | NA | Should fire ignitions start at the sim$firePolygons centroids (TRUE) or at the ignition points in sim$firePoints? |
| usePCA | logical | TRUE | NA | NA | use PCA approach to covariates, as opposed to fuel class approach |
| whichModulesToPrepare | character | fireSens.... | NA | NA | Which fireSense fit modules to prep? defaults to all 3 |
Describe what happens for each event type.
Write what is plotted.
Write what is saved.
How to obtain input data, and a description of the data required by the module.
If sourceURL is specified, downloadData("fireSense_dataPrepFit", "..") may be sufficient.
| objectName | objectClass | desc | sourceURL |
|---|---|---|---|
| cohortData2001 | data.table | Table that defines the cohorts by pixelGroup in 2001 | NA |
| cohortData2011 | data.table | Table that defines the cohorts by pixelGroup in 2011 | NA |
| spreadFirePoints | list | list of spatialPointsDataFrame for each fire yearwith each point denoting an ignition location | NA |
| firePolys | list | List of SpatialPolygonsDataFrames representing annual fire polygons.List must be named with followign convention: 'year' | NA |
| firePolysForAge | list | firePolys used to classify timeSinceDisturbance in nonforest LCC | NA |
| flammableRTM | RasterLayer | RTM without ice/rocks/urban/water. Flammable map with 0 and 1. | NA |
| historicalClimateRasters | list | list of historical climate variables in raster stack form, name according to variable | NA |
| ignitionFirePoints | list | list of spatialPolygonDataFrame objects representing annual ignition locations. This includes all fires regardless of size | NA |
| nonForestedLCCGroups | list | a named list of non-forested landcover groups e.g. list('wetland' = c(19, 23, 32)) These will become covariates in fireSense_IgnitionFit | NA |
| pixelGroupMap2001 | RasterLayer | RasterLayer that defines the pixelGroups for cohortData table in 2001 | NA |
| pixelGroupMap2011 | RasterLayer | RasterLayer that defines the pixelGroups for cohortData table in 2011 | NA |
| rasterToMatch | RasterLayer | template raster for study area. Assumes some buffering of core area to limit edge effect of fire. | NA |
| rstLCC | RasterLayer | Raster of land cover. Defaults to LCC05. | NA |
| sppEquiv | data.table | table of LandR species equivalencies | NA |
| standAgeMap2001 | RasterLayer | map of stand age in 2001 used to create cohortData2001 | NA |
| standAgeMap2011 | RasterLayer | map of stand age in 2011 used to create cohortData2011 | NA |
| studyArea | SpatialPolygonsDataFrame | studyArea that determines spatial boundaries of all data | NA |
| terrainCovariates | RasterStack | a raster stack of terrain covariates; defaults are elev, aspect, slope, TRI, TWI | NA |
Description of the module outputs.
| objectName | objectClass | desc |
|---|---|---|
| climateComponentsToUse | character | names of the climate components or variables needed for FS models |
| coefficientPrintOut | data.table | Coefficients from the logit model |
| componentPrintOut | data.table | A data.table showing the PCA axes and their loadings with the different covariates, e.g., fuel, TPI, HLI, etc. |
| fireBufferedListDT | list | list of data.tables with fire id, pixelID, and buffer status |
| firePolys | list | list of spatialPolygonDataFrame objects representing annual fires |
| fireSense_annualSpreadFitCovariates | list | list of tables with climate PCA components, burn status, polyID, and pixelID |
| fireSense_escapeCovariates | data.table | ignition covariates with added column of escapes |
| fireSense_escapeFormula | character | formula for escape, using fuel classes and landcover, as character |
| fireSense_ignitionCovariates | data.table | table of aggregated ignition covariates with annual ignitions |
| fireSense_ignitionFormula | character | formula for ignition, using fuel classes and landcover, as character |
| fireSense_nonAnnualSpreadFitCovariates | list | list of two tables with veg PCA components, burn status, polyID, and pixelID |
| fireSense_spreadFormula | character | formula for spread, using climate and terrain components, as character |
| ignitionFitRTM | RasterLayer | A (template) raster with information with regards to the spatial resolution and geographical extent of fireSense_ignitionCovariates. Used to pass this information onto fireSense_ignitionFitted Needs to have number of non-NA cells as attribute (ignitionFitRTM@data@attributes$nonNAs). |
| landcoverDT | data.table | data.table with pixelID and relevant landcover classes that is used by predict functions. |
| nonForest_timeSinceDisturbance2001 | RasterLayer | time since burn for non-forested pixels in 2001 |
| nonForest_timeSinceDisturbance2011 | RasterLayer | time since burn for non-forested pixels in 2011 |
| PCAclimate | prcomp | PCA model for climate covariates, needed for fireSensePredict |
| PCAcoeffPlot | gglot | ggplot with PCA loadings for axes used to predict spread |
| PCAveg | prcomp | PCA model for veg and LCC covariates, needed for FS models |
| spreadFirePoints | list | list of spatialPolygonDataFrame objects representing annual fire centroids. This only includes fires that escaped (e.g. size > res(flammableRTM). |
| terrainDT | data.table | data.table with pixelID and relevant terrain variables used by predict models |
| vegComponentsToUse | character | names of the veg components to use in ignition, escape, and spread predict models |
Outputs used by fireSense_IginitionFit, fireSense_EscapeFit, and fireSense_SpreadFit.