title	birds_BRT Manual
subtitle	v.2.0.0
date	Last updated: 2025-02-20
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editor_options	chunk_output_type bibliography console citations/references_birds_BRT.bib
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birds_BRT Module

(ref:birds-BRT) birds_BRT

Authors:

Tati Micheletti tati.micheletti@gmail.com [aut], Diana Stralberg dstralberg@gmail.com [aut], Alex M Chubaty achubaty@or-cast.ca [aut, cre]

Module Overview

Module summary

The birds module for loads an existing glm object for each species located in
https://drive.google.com/open?id=1obSvU4ml8xa8WMQhQprd6heRrN47buvI. The model uses dynamic (vegetation: biomass of tree species) and static layers (Non-veg: WAT = water (1/0), URBAG = urban/agriculture (1/0), lLED25 = lake edge density with 5x5 moving window (continuous), DEV25 = development proportion within 5x5 moving window (continuous), and landform (categorical).

North American landcover 2005 (MODIS) is source for all but landform (from AdaptWest land facet datset). Vector ruggedness (already available - https://drive.google.com/open?id=1dgIw70mDpDYrBExA52SkPoS1TFaZdLE9) and road density (that should be available from the Anthropogenic module) will be added to the next version of these models. The birds' prediction is masked to uplands as we do not have data for lowlands.

Module inputs and parameters

Table @ref(tab:moduleInputs-birds-BRT) shows the full list of module inputs.

(\#tab:moduleInputs-birds-BRT)(\#tab:moduleInputs-birds-BRT)List of (ref:birds-BRT) input objects and their description.

objectName	objectClass	desc	sourceURL
usrEmail	character	User's e.mail to automatic authentication of GoogleDriveNA	NA
waterRaster	RasterLayer	Wetland raster for excluding water from final bird layers. Water == 1	NA
wetlandRaster	RasterLayer	Wetland raster for creating upland raster. wetlands == 1	NA
uplandsRaster	RasterLayer	Upland raster for excluding wetlands and water from bird's predictions. LandR has NOT been tested for wetlands. Uplands == 1.	NA
birdsList	character	Bird species to be predicted	NA
cloudFolderID	character	Folder ID for cloud caching	NA
urlModels	character	Url for the GDrive folder that has all models (used for flat structures) objects. Alternatively, it might be a `data.table` object with the following columns: `Species`, `folderID`, `modelUsed`, which will contain the individual species models inside each of the species folders (`folderID`).	NA
urlStaticLayers	RasterLayer	Static Layers (WET, VRUG, WAT, URBAG, lLED25, DEV25 and landform) url	https://drive.google.com/drive/u/0/folders/1G1VIR3bHZ_HztDToJnMwALuZqZ2ef38Q
studyArea	SpatialPolygonDataFrame	Study area for the prediction. Currently only available for NWT	https://drive.google.com/open?id=1P4grDYDffVyVXvMjM-RwzpuH1deZuvL3
rasterToMatch	RasterLayer	All spatial outputs will be reprojected and resampled to it	https://drive.google.com/open?id=1P4grDYDffVyVXvMjM-RwzpuH1deZuvL3
forestOnly	RasterLayer	Raster to match but NA'ed for non-forest pixels	NA
climateLayersBirds	list	List of raster stacks of climate variables for birds such as: AHM, bFFP, CMD, DD_0, DD_18, DD18, DD5, eFFP, EMT, EXT, FFP, MAP, MAT, MCMT, MSP, MWMT, NFFD, PAS, PPT_sm, PPT_wt, SHM, Tave_sm, Tave_wt, TD,	NA
climateDataFolder	character	Folder where to look for the climate data. If not provided, set as inputPath(sim).	NA
zipClimateDataFilesFolder	character	Folder where to look for the climate data '.zip' files if these have not been extracted.	NA
sppEquiv	data.table	table of species equivalencies. See LandR::sppEquivalencies_CA.	NA
sppEquivCol	character	The column in the specie Equivalency table to use as a naming convention	NA

Provide a summary of user-visible parameters (Table @ref(tab:moduleParams-birds-BRT))

(\#tab:moduleParams-birds-BRT)(\#tab:moduleParams-birds-BRT)List of (ref:birds-BRT) parameters and their description.

paramName	paramClass	default	min	max	paramDesc
scenario	character	NA	NA	NA	Are these predictions from a specific scenario? If not, leave it as NA.
rastersShowingNA	logical	FALSE	NA	NA	Should the raster present `NA` where wetlands are? This is because LandR doesn't predict for wetlands.
predictLastYear	logical	TRUE	NA	NA	Should it schedule events for the last year of simulation if this is not a multiple of interval?
useStaticPredictionsForNonForest	logical	TRUE	NA	NA	If `TRUE`, it will use the original kNN data to fill up the `NA`s back after if we don't want to leave `NA` pixels in the predictions, independently of having the `pixelGroupMap` being masked to uplands or not.
useOnlyUplandsForPrediction	logical	TRUE	NA	NA	Should the bird layers be masked to forest uplands only? masks `pixelGroupMap` with uplands as quality of DUCKS layer is better than `rstLCC` to ID the wetlands. We currently have succession happening in some wetlands because of the low quality of LCC05. This should not be happening. But as the layer is proprietary, we can't use it in LandR.
.useCache	logical	FALSE	NA	NA	Should this entire module be run with caching?
version	character	6a	NA	NA	Number of the bird module version to be used
useParallel	logical	FALSE	NA	NA	Should bird prediction be parallelized?
useTestSpeciesLayers	logical	TRUE	NA	NA	Use testing layers if forest succesion is not available?
predictionInterval	numeric	10	NA	NA	Time between predictions
nCores	characte....	auto	NA	NA	If parallelizing, how many cores to use? Use 'auto' (90% of available), or numeric.
baseLayer	numeric	2005	NA	NA	Which layer should be used? LCC05 or LCC10?
overwritePredictions	logical	FALSE	NA	NA	Should overwrite bird predictions thta might be available?
lowMem	logical	FALSE	NA	NA	Should the bird predictions return the final rasters (FALSE) or path to these (TRUE).
vegetationStatic	logical	FALSE	NA	NA	Should the bird predictions keep vegetation static through time?
climateStatic	logical	FALSE	NA	NA	Should the bird predictions keep climate layers static through time?
RCP	character	85	NA	NA	Which RCP should be used? Default to 85.
climateModel	character	CCSM4	NA	NA	Which climate model should be used? Default to CCSM4.
ensemble	character		NA	NA	Which ensemble model should be used? Default to ''. CCSM4 doesn't have ensemble, just CanESM2 (r11i1p1).
climateResolution	character		NA	NA	Which DEM resolution was used for generating the climate layers? Default to '3ArcMin'.
climateFilePath	character	https://....	NA	NA	URL to zipped climate file coming from ClimateNA, containing all climate variables for all years of simulation.
staticLayersNames	character	dev750, ....	NA	NA	This is the vector of layer names to indicate which ones are static. Defaults to the ones used in models from BAM.
onlyLoadModels	logical	FALSE	NA	NA	If set to TRUE, the module will only download the models that can be used.

Events

Describe what happens for each event type.

Plotting

Write what is plotted.

Saving

Write what is saved.

Module outputs

Description of the module outputs (Table @ref(tab:moduleOutputs-birds-BRT)).

(\#tab:moduleOutputs-birds-BRT)(\#tab:moduleOutputs-birds-BRT)List of (ref:birds-BRT) outputs and their description.

objectName	objectClass	desc
birdPrediction	list	List per year of the bird species predicted rasters
birdModels	list	List of the bird models for prediction
staticLayers	RasterStack	Raster stack of all static layers (WAT, URBAG, lLED25, DEV25 and landform) for the bird models
successionLayers	RasterStack	Raster stack of all succession layers (species) and total biomass for the bird models
unavailableModels	character	Character vector with all missing models
biomassMap	RasterLayer	Total biomass map
cohortData	data.table	Table with cohort information (biomass per species per pixelGroup)
pixelGroupMap	RasterLayer	Mapping raster to pixelGroup
allVariables	character	Vector of all variables that compose all models for each of the species.

Links to other modules

Describe any anticipated linkages to other modules, such as modules that supply input data or do post-hoc analysis.

Getting help

GitHub repository: https://github.com/FOR-CAST/birds_BRT