Package 'usefulFuns'

Title: Useful functions for my modules and packages
Description: A few functions and wrappers around useful code.
Authors: Tati Micheletti
Maintainer: Tati Micheletti <[email protected]>
License: GPL (>=2)
Version: 0.1.1
Built: 2024-12-25 06:16:13 UTC
Source: https://github.com/PredictiveEcology/usefulFuns

Help Index

usefulFuns package

Description

A few functions and wrappers around useful code.

Compare two or more scenarios for averages through time

Description

Compare two or more scenarios for averages through time

Usage

avrgTimeComparison(
  ...,
  upload,
  outputFolder,
  comparisonID,
  folderID,
  plotCI = TRUE
)

Arguments

...

List or tables of results coming from meanValuesTime to be compared.
upload

logical. Should the raster be uploaded to Google Drive? Only works if the raster exists OR is set to be written.
outputFolder

character. Path to the folder where it should be saved.
comparisonID

character. Name to identify the comparison (for file name)
folderID

character. Google folder id to upload to. Only needs to be provided if upload == TRUE. Default is 'NULL“
plotCI

logical. Should the plot have confidence interval?

Value

list of significant species or scenarios with indication of increasing or decreasing

Author(s)

Tati Micheletti

Creates a GIF of biomass change

Description

Creates a GIF of biomass change

Usage

biomassPerSpeciesYearGIF(dataPath, years = NULL, uploadTo)

Arguments

dataPath

character. Path to data
years

numeric. Years available/intended to be used for the animated gif.
uploadTo

character. Google drive folder id. (i.e. "1ZqPVs33HxnnmjLUW94i7AuwAS-nloPGH")

Value

list of plots

Author(s)

Tati Micheletti

Creates a GIF of total biomass change

Description

Creates a GIF of total biomass change

Usage

biomassYearGIF(dataPath, years = NULL, uploadTo)

Arguments

dataPath

character. Path to data.
years

numeric. Years available/intended to be used for the animated gif.
uploadTo

character. Google drive folder id. (i.e. "1ZqPVs33HxnnmjLUW94i7AuwAS-nloPGH")

Value

RasterStack

Author(s)

Tati Micheletti

Bootstrap rasters for testing significance on comparable rasters of different species or scenarios

Description

Bootstrap rasters for testing significance on comparable rasters of different species or scenarios

Usage

bootstrapPercentChanges(
  dataPath,
  years = c(2001, 2100),
  sampleSize = "auto",
  n = 100,
  shp = NULL,
  species = NULL,
  useFuture = FALSE
)

Arguments

dataPath

character. Path to raster data.
years

numeric. Years to compare. Currently this function only compares 2 years.
sampleSize

numeric or "auto" (default). What is the sample size (i.e. number of pixels) we want to use on the bootstrapping? If "auto" it calculates internally Cohen's D And Hedges G Effect Size.
n

numeric. Default is 100. How many iterations (random selection of sampleSize pixels) should be done?
shp

character or shapefile. If you wish to calculate these metrics for separate areas. Needs to match the rasters. Default is NULL (i.e. the whole raster is only one area)
species

character. Default is NULL. Which species should this function be ran ?
useFuture

logical. Should use future to parallelize? Requires future and future_apply packages.

Value

list of significant species or scenarios with indication of increasing or decreasing

Author(s)

Tati Micheletti

Bring objects that represent time series into a list

Description

Bring objects that represent time series into a list

Usage

bringObjectTS(path, rastersNamePattern)

Arguments

path

path to the directory containing the files to be brought as list.
rastersNamePattern

Character vector of the name pattern to be used for the search.

Value

A list of the objects that were read from disk. Currently the function only works with .tif (i.e. raster) and .rds objects.

Author(s)

Tati Micheletti

Calculate pixels in a rule

Description

Uses a set of rules to calculate how many non-NA pixels in a raster follow those rules, using a shapefile to subset those of interest

Usage

calculatePixelsInaRule(ras, rule, pol, shp, ...)

Arguments

ras

RasterLayer to calculate the number of pixels that follow a given rule
rule

character string of rule to determine which pixels should be computed
pol

numeric. Representation of the polygon of interest in pol for the calculation
shp

shapefile indicating the different areas to subset the pixels to consider in the calculation
...

Additional arguments

Value

A list of the percent disturbance, total pixels not NA and how many pixels are disturbed according to the rules.

Author(s)

Tati Micheletti

Column binds a list of data.frames or data.tables

Description

Column binds a list of data.frames or data.tables

Usage

cbindFromList(lst)

Arguments

lst

List of data.tables or data.frames to column bind.

Value

Returns a merged data.table with unique columns

Author(s)

Tati Micheletti

Provides an easy way of modifying species traits table in LandR by multiplication of original traits by a specified factor

Description

Provides an easy way of modifying species traits table in LandR by multiplication of original traits by a specified factor

Usage

changeTraits(speciesTable, param, facMult, species)

Arguments

speciesTable

speciesTable object (data.table) from LandR. Contains different traits in columns and a row for each species.
param

Character vector of the trait to be modified.
facMult

numeric. Factor by which the specified trait should be multiplied.
species

character string of the Species for which the trait should be modified

Value

A data.table updated with the new parameters.

Author(s)

Tati Micheletti

All packages' versioning

Description

Returns a data.table of versions of all packages attached to your current R session, or used in a simulation - including git commit if a package was installed from e.g., GitHub.

Usage

checkPackagesVersions(simList = NULL, filePath = NULL)

Arguments

simList

simList object resulting from a SpaDES.core::spades() call. Default NULL.
filePath

Character string. If passed, the table is written to the specified file path, as an RDS file. Default NULL.

Details

If you don't provide it, the function will return the information regarding your current R session's information. When running a simulation, it is automatically be created by the spades() and attached as the invisible object .packagesVersions.

Author(s)

Tati Micheletti

Classify wetlands (really!) using the wetlands layer set as input and a either LCC05 or LCC2010

Description

Classify wetlands (really!) using the wetlands layer set as input and a either LCC05 or LCC2010

Usage

classifyWetlands(
  LCC,
  wetLayerInput,
  pathData,
  studyArea = NULL,
  RasterToMatch = NULL
)

Arguments

LCC

numeric. 2005 (250 m resolution) or 2010 (30 m resolution) landcover rasters.
wetLayerInput

Which wetland should be used as input (raster with projection). It was originally designed to work with the DUCKS Unlimited Waterland layer (30 m) but can work with any water layers that have the following code: possibleLakes == 0, ⁠water bodies == 1⁠, wetlands == 2, uplands > 2.
pathData

Where the layers are stored and/or should be saved to
studyArea

If the layer should be cropped and masked after classification. Optional.
RasterToMatch

raster to match the new layer after classification to. Optional.

Value

As with archivist::cache, returns the value of the function call or the cached version (i.e., the result from a previous call to this same cached function with identical arguments).

Author(s)

Tati Micheletti

Create the necessary layers for predictive caribou RSF module.

Description

Intended for use within a SpaDES module.

Usage

createDynamicLayersRSF(
  ageMap,
  biomassMap,
  biomassMapName,
  oldBurnTime,
  oldBurnName,
  newBurnName,
  roadDensity,
  roadDensityName,
  waterRaster,
  waterRasterName,
  RTM
)

createStaticLayersRSF(
  elevation,
  vrug,
  LCC,
  shrubName,
  herbName,
  elevationName,
  vrugName,
  reclassLCC05,
  dynamicLayers,
  RTM,
  destinationPath
)

Arguments

ageMap

RasterLayer of forest age.
biomassMap

RasterLayerof forest biomass.
biomassMapName

character. Name of the forest biomass layer.
oldBurnTime

numeric. Definition of the initial interval considered to be old burn. The end of this time is 20 years later (i.e. 40-60 years).
oldBurnName

character. Name of the old burn layer in the model.
newBurnName

character. Name of the new burn layer in the model.
roadDensity

Anthropogenic disturbance (raster) layer. Currently, road density layer used for both RSF and demographic models.
roadDensityName

character. Name of the road Density layer in the model.
waterRaster

RasterLayer indicating water bodies.
waterRasterName

character. Name of the water layer in the model.
RTM

RasterLayer template for these layers to match.
elevation

RasterLayer of elevation
vrug

RasterLayer of ruggedness
LCC

RasterLayer of landcover classes 2005
shrubName

character. Name of the shrub layer in the model.
herbName

character. Name of the herb layer in the model.
elevationName

character. Name of the elevation layer in the model.
vrugName

character. Name of the vrug layer in the model.
reclassLCC05

List with reclassification for LCC05 values (i.e. LCC05 classes that should be classified as shrub or herbs)
dynamicLayers

RasterStack to be stacked with the staticLayers created in the current function to be passed for the model prediction.
destinationPath

TODO

Value

RasterStack of layers

RasterStack

Author(s)

Tati Micheletti

Write an equation based on a data.frame (or data.table), bootstrapping a set of covariates around the standard error present in the table.

Description

Write an equation based on a data.frame (or data.table), bootstrapping a set of covariates around the standard error present in the table.

Usage

createEquation(model, replicates = 100)

Arguments

model

data.framewith columns Coefficient, and Value and StdErr for a given parameter. The model table NEEDS to have at least two rows, one being the Intercept as Coefficient. If Intercept is not found, it enters browser() mode.
replicates

numeric. Number of repetitions to be added to the bootstrapping.

Value

As with archivist::cache, returns the value of the function call or the cached version (i.e., the result from a previous call to this same cached function with identical arguments).

Author(s)

Tati Micheletti

Create caribou models based on 2011 ECCC report on population demographics and RSF.

Description

Uses createEquation internally.

Usage

createModels(caribouCoefTable = NULL, modelsToUse = "M3")

Arguments

caribouCoefTable

data.table of the coefficient values for all models available. If not provided, will use as default the one from ECCC 2011 for population demographics.
modelsToUse

Character string of the model to be used. Currently only "M3" and "M7" (demographics) and "TaigaPlains" (RSF) have been implemented. Default "M3".

Value

named list of the quote of the model that can be parsed to generate the simulated data bootstrapped using the model coefficients.

Author(s)

Tati Micheletti

Create a simulation model object

Description

Check a simList for a specific object at a specific time, or searches for it in an input folder (i.e. saved outputs). Simulates the existence of a simList with specific objects in time t.

Usage

createModObject(data, sim = NULL, pathInput, currentTime, fun = readRDS)

Arguments

data

character string of the object or file name to be searched for
sim

simList object. Default NULL.
pathInput

path to the directory containing the files to be searched for.
currentTime

Numeric. Current time to be used to search for the object.
fun

function to be used to recover the file. Default is readRDS

Value

A list of the objects that were read from disk. Currently the function only works with .tif (i.e. raster) and .rds objects.

Author(s)

Tati Micheletti

Creates the necessary shrub or herb layers for predictive caribou RSF module.

Description

Creates the necessary shrub or herb layers for predictive caribou RSF module.

Usage

createShrubHerbLayers(
  landCoverECCC,
  reclassLCC05,
  layerName,
  includeCrops = FALSE
)

Arguments

landCoverECCC

RasterLayer LCC2005 reclassified to ECCC landcover.
reclassLCC05

List with reclassification for LCC05 values (i.e. LCC05 classes that should be classified as shrub or herbs)
layerName

character. Name of the shrub layer in the model.
includeCrops

Logical. Should this layer include crops?

Value

RasterLayer of herbs or shrubs

Author(s)

Tati Micheletti

Preparing study area for Canadian projects

Description

Downloads, reprojects, crops and masks to specific areas in Canada such as: boreal, random areas, provinces and territories, or any of the last in the boreal.

Usage

defineStudyArea(
  testArea = NULL,
  specificTestArea = NULL,
  mapSubset = NULL,
  destinationFolder = tempdir()
)

Arguments

testArea

Logical. Indicates if the test area should be anything other than NULL. Default is NULL.
specificTestArea

A character string with a province or territory name, or 'boreal'. (following Brandt et al., 2013). Default is NULL.
mapSubset

If specificTestArea is supplied as 'boreal', this can be set as a character string with a province or territory that is contained in the boreal or 'Canada' if the whole Canadian boreal is wanted. Default is NULL.
destinationFolder

Path to where to save downloaded files. Default is tempdir().

Author(s)

Tati Micheletti

Examples

## rp is the whole North American boreal region
rp <- defineStudyArea(testArea = TRUE, specificTestArea = "boreal", mapSubset = NULL)

## Alberta
rp <- defineStudyArea(testArea = TRUE, specificTestArea = "Alberta", mapSubset = NULL)

## Alberta inside boreal extension
rp <- defineStudyArea(testArea = TRUE, specificTestArea = "boreal", mapSubset = "Alberta")

Extract disturbance of anthropogenic and fire

Description

Extract disturbance of anthropogenic and fire

Usage

extractDisturbanceFast(
  ageMap,
  caribouShapefile,
  recoveryTime = 40,
  anthropogenicLayer = NULL,
  waterRaster,
  rasterToMatch,
  destinationPath
)

Arguments

ageMap

RasterLayer. Map with forest age.
caribouShapefile

Shapefile with polygons for which we want to calculate lambda for the caribou demographic model.
recoveryTime

numeric. Recovery time in years that the forest needs to support Caribou. Default = 40.
anthropogenicLayer

Anthropogenic disturbance (raster) layer. Currently, road density layer used for both RSF and demographic models.
waterRaster

RasterLayer indicating water bodies.
rasterToMatch

RasterLayer template for these layers to match.
destinationPath

TODO

Value

A list of the anthropogenic and fire disturbances as percent (0-100)

Author(s)

Tati Micheletti

Plots of forest age

Description

Plots of forest age

Usage

forestAgePlot(
  dataPath,
  typeSim,
  addCaribousuitability = FALSE,
  overwrite = FALSE
)

Arguments

dataPath

character. Path to data
typeSim

character. Which simulation is it? i.e., 'LandR_SCFM' or 'LandR.CS_fS'
addCaribousuitability

logical. Should the plot show which forest ages are better or worse for Caribou in a colour-coded way?
overwrite

logical.

Value

plot

Author(s)

Tati Micheletti

Get the necessary layers for predictive modules such as caribouPopGrowth and caribouRSF.

Description

Get the necessary layers for predictive modules such as caribouPopGrowth and caribouRSF.

Usage

getLayers(
  currentTime,
  cohortData,
  pixelGroupMap,
  startTime,
  endTime,
  recoveryTime = 40,
  listSACaribou,
  anthropogenicLayer,
  roadDensity,
  waterRaster,
  isRSF = FALSE,
  decidousSp = NULL,
  oldBurnTime = NULL,
  elevation = NULL,
  vrug = NULL,
  LCC05 = NULL,
  reclassLCC05 = NULL,
  rasterToMatch = NULL,
  destinationPath
)

Arguments

currentTime

numeric. Current time being used (i.e. time(sim)).
cohortData

data.table. Output from LandR_Biomass module.
pixelGroupMap

raster to identify the cohortData.
startTime

numeric. start time of the simulation. Needed to verify and potentially adjust relative simulation times.
endTime

numeric. end time of the simulation. Needed to verify and potentially adjust relative simulation times.
recoveryTime

numeric. Recovery time in years that the forest needs to support Caribou. Default = 40.
listSACaribou

list of shapefiles with polygons for which we want to calculate lambda for the caribou demographic model.
anthropogenicLayer

Anthropogenic disturbance (raster) layer. Currently, 500 m buffered anthropogenic disturbance for demographic models.
roadDensity

Anthropogenic disturbance (raster) layer. Currently, road density layer used for RSF models.
waterRaster

RasterLayer indicating water bodies.
isRSF

logical. Identify if it should get the layers for the RSF or demographic model.
decidousSp

binary raster layer indicating if the dominant biomass in a pixel belongs to a deciduous species.
oldBurnTime

numeric. Definition of the initial interval considered to be old burn. The end of this time is 20 years later (i.e. 40-60 years).
elevation

RasterLayer of elevation
vrug

RasterLayer of ruggedness
LCC05

RasterLayer of landcover classes 2005
reclassLCC05

List with reclassification for LCC05 values (i.e. LCC05 classes that should be classified as shrub or herbs)
rasterToMatch

RasterLayer template for these layers to match.
destinationPath

TODO

Value

TODO

Author(s)

Tati Micheletti

Grep using multiple patterns

Description

Works similarly to grepl, but for multiple patterns and returning the object.

Usage

grepMulti(x, patterns, unwanted = NULL)

Arguments

x

object where to look for patterns.
patterns

Character vector of patterns to look for objects.
unwanted

Character vector of patterns to exclude from search.

Value

The objects with specified patterns combined

Author(s)

Tati Micheletti

Create a matrix to use for reclassification of rasters

Description

Create a matrix to use for reclassification of rasters

Usage

makeReclassifyMatrix(table, originalCol, reclassifiedTo)

Arguments

table

data.frame or data.table that has the original classification and the desired classification to replace the first.
originalCol

character. Column in the table that identifies the original classification.
reclassifiedTo

character. Column in the table that identifies the desired classification.

Value

Matrix to use for reclassification of rasters

Author(s)

Tati Micheletti

Calculates the mean value of rasters through time

Description

Calculates the mean value of rasters through time

Usage

meanValuesTime(ras, scenario, initialTime)

Arguments

ras

RasterStack. Time series used to calculate the mean value through time.
scenario

character. Which scenario are you running i.e., LandR.CS_fS Needs to match the rasters. Default is NULL (i.e., the whole raster is only one area)
initialTime

numeric. Format of the first year of analysis.

Value

table with average, SD and ⁠CI95%⁠

Author(s)

Tati Micheletti

Show the modules that have stickers available

Description

Show the modules that have stickers available

Usage

modulesAvailable()

Value

A character vector of all modules that have stickers available.

Author(s)

Tati Micheletti

Function to create stickers for SpaDES modules

Description

Function to create stickers for SpaDES modules

Usage

moduleSticker(
  moduleTable = NULL,
  moduleName,
  directory = getwd(),
  useCache = NULL,
  savedSticker = NULL,
  ...
)

Arguments

moduleTable

Table with the information to generate the sticker (i.e. figure name, height, colours, etc)
moduleName

character string of the module's name.
directory

character string of the directory where the sticker should be saved
useCache

logical. Should the process of downloading and loading the table be cached?
savedSticker

Character string. Name of the file to be saved. If not provided, saves with the name of the figure. Useful if more than one stickers have the same figure
...

Other parameters for ggplot2 (i.e. fontface, lineheight)

Value

This function returns the location where the sticker is available

Author(s)

Tati Micheletti

Name a raster, postProcess it using RTM, and brings it to memory

Description

Name a raster, postProcess it using RTM, and brings it to memory

Usage

nameAndBringOn(ras, name, RTM = NULL)

Arguments

ras

RasterLayer.
name

character. Name of the raster layer.
RTM

RasterLayer template. If a RTM is passed, the function masks the raster to it, converting non-NA to 0.

Value

RasterStack

Author(s)

Tati Micheletti

Plots summary of burns

Description

Plots summary of burns

Usage

plotBurnSummary(
  dataPath,
  typeSim,
  lastYear,
  theObject = NULL,
  overwrite = FALSE
)

Arguments

dataPath

character. Path to data
typeSim

character. Which simulation is it? i.e., 'LandR_SCFM' or 'LandR.CS_fS'
lastYear

TODO
theObject

TODO
overwrite

logical. Default FALSE

Value

plot

Author(s)

Tati Micheletti

Plots Leading Vegetation Type using cohortData and pixelGroupMap

Description

Plots Leading Vegetation Type using cohortData and pixelGroupMap

Usage

plotLeadingVegetationType(
  dataPath,
  typeSim,
  colNA = "grey85",
  saveRAS = TRUE,
  overwrite = FALSE
)

Arguments

dataPath

character. Path to data
typeSim

character. Which simulation is it? i.e. 'LandR_SCFM' or 'LandR.CS_fS'.
colNA

character. The colour to use for NA.
saveRAS

logical. Save the raster for posterior use?
overwrite

logical.

Value

plot

Author(s)

Tati Micheletti

Plots vegetation biomass type using cohortData and pixelGroupMap

Description

Plots vegetation biomass type using cohortData and pixelGroupMap

Usage

plotVegetationBiomass(
  years = c(2011, 2100),
  dataPath,
  typeSim,
  colNA = "grey85",
  saveRAS = TRUE,
  overwrite = FALSE
)

Arguments

years

numeric. Years available/intended to be used.
dataPath

character. Path to data.
typeSim

character. Which simulation is it? i.e., 'LandR_SCFM' or 'LandR.CS_fS'.
colNA

character. The colour to use for NA.
saveRAS

logical. Save the raster for posterior use?
overwrite

logical.

Value

plot

Author(s)

Tati Micheletti

Create raster stack for climate sensitive models

Description

Designed primarily for NWT project, but somewhat flexible.

Usage

prepareClimateLayers(
  pathInputs = NULL,
  variables = NULL,
  years = NULL,
  GDriveFolder = NULL,
  climateFilePath = NULL,
  fileResolution = NULL,
  authEmail = NULL,
  RCP = NULL,
  climateModel = NULL,
  ensemble = NULL,
  rasterToMatch = NULL,
  studyArea = NULL,
  model = NULL,
  droughtMonths = 4:9,
  returnCalculatedLayersForFireSense = FALSE,
  yearsWithClimateProjections = 2011:2100,
  overwrite = FALSE,
  overwriteOriginalData = FALSE
)

Arguments

pathInputs

Default NULL (TODO: description needed)
variables

Character string of the variables to be used, i.e. c("PPT", "Tmax").
years

Character string of the years to use. i.e. c(2011:20100).
GDriveFolder

Character string of the folder in Google Drive to upload the layers to. Handy for shared projects.
climateFilePath

Character string of the path to the climate file in google drive (i.e. "https://drive.google.com/open?id=1wcgytGJmfZGaapZZ9M9blfGa-45eLVWE" for Canada3ArcMinute.7z)
fileResolution

Character string of the for naming purposes (i.e. ⁠3ArcMinute⁠)
authEmail

Character string of Google email for authentication for non-interactive use.
RCP

Character string of RCP to be used (i.e. 45)
climateModel

Character string of climate mode to be used (i.e. CanESM2)
ensemble

Character string of climate ensemble to be used (i.e. r11i1p1)
rasterToMatch

RasterLayer template for these layers to match
studyArea

shapefile of study area
model

For naming and shortcut for variables: i.e., "birds" or "fireSense". If providing the variables to be produced, don't use "birds" nor "fireSense" here.
droughtMonths

Numeric. Months to calculate Monthly Drought Code (MDC) i.e. 4:9.
returnCalculatedLayersForFireSense

Logical. Should it calculate MDC (TRUE) or return the original variables (FALSE)? Default is FALSE.
yearsWithClimateProjections

Numeric. The user can pass the years that have climate projection in the data. Default to 2011:2100.
overwrite

logical. Default FALSE. Should the layers be overwritten if exist?
overwriteOriginalData

logical. Default FALSE. If changes happen in the original layer (the one provided in climateFilePath), set this to TRUE to overwrite the zip files downloaded and return the calculated MDC layers already, not the original stack with Tmax and PPT.

Value

A list of all years, with each year being the local path for the raster stack that contains all variables.

Author(s)

Tati Micheletti

Prepare DUCKS layer

Description

Intended to prepare the DUCKS Unlimited Hybrid Wetland v. 2.1 layer for different purposes. The output is a RasterLayer cropped and reprojected to the studyArea, and resampled to the rasterToMatch if any of these are provided.

Usage

prepInputsLayers_DUCKS(
  destinationPath,
  lccLayer = "2005",
  url = NULL,
  archive = NULL,
  targetFile = NULL,
  studyArea = NULL,
  rasterToMatch = NULL,
  overwrite = TRUE
)

Arguments

destinationPath

Path where to save the downloaded file.
lccLayer

Which year should be used as a base for the vegetation layer? Default to 2005
url

The url from where the layer should be downloaded from. If NULL, the default is used.
archive

TODO
targetFile

TODO
studyArea

Study area for which the layer should be cropped to
rasterToMatch

TODO
overwrite

Logical indicating whether to overwrite the previously processed file.

Value

RasterLayer

Simple wrapper around prepInputs for a stack of raster layers

Description

Simple wrapper around prepInputs for a stack of raster layers

Usage

prepInputStack(...)

Arguments

...

Arguments passed to fun (i.e,. user supplied), postProcess and Cache. Since ... is passed to postProcess, these will also be passed into the inner functions, e.g., cropInputs. User should supply several named arguments here, including: targetFile, archive, url, alsoExtract, destinationPath, fun, quick, purge, overwrite, and useCache. See details and examples.

Value

RasterStack

Author(s)

Tati Micheletti

Preparing study area based on BCR and Canadian or American provinces or states.

Description

Downloads, reprojects, crops and masks to specific areas in Canada such as: BCR6, random areas, provinces and territories, or any of the last in the BCR6.

Usage

provinceBCRStudyArea(bcr = NULL, province = NULL, country, ...)

Arguments

bcr

Numeric. Bird Conservation Region in North America that you want to crop for. Default is NULL. If 'NULL“, it returns only the shapefile of the province.
province

Character string. Province or territory. Default is NULL. If null, returns the map of ??.
country

Character string. 3 letter ISO for a specific country. The complete list of countries can be seen by calling raster::getData('ISO3').
...

Arguments to be passed to prepInputs or Cache (i.e. targetFile, cacheId, destinationPath, overwrite, etc.).

Details

If you provide a BCR that is outside of a province area, the object returned is NULL.

Author(s)

Tati Micheletti

Bootstraps rasters for testing significance on comparable rasters of different species or scenarios

Description

Bootstraps rasters for testing significance on comparable rasters of different species or scenarios

Usage

reviseSpeciesTraits(
  speciesTable = NULL,
  updatedTable = NULL,
  destinationPath = tempdir(),
  returnTable = FALSE,
  species = c("BETU.PAP", "LARI.LAR", "PICE.GLA", "PICE.MAR", "PINU.BAN", "POPU.TRE",
    "PINU.CON")
)

Arguments

speciesTable

data.table. Table to be updated. If returnTable == TRUE this can be NULL. In this case, the function will use the ORIGINAL species table traits (from LANDIS-II).
updatedTable

data.table. Table used to update speciesTable. If NULL, the function uses a default.
destinationPath

character. Where to save the table. Default is tempdir().
returnTable

logical. If TRUE, it uses the ORIGINAL species table traits from LANDIS-II. If FALSE, you have to supply your own table.
species

character. Species to update the table for.

Value

Table of updated tree species traits to be used in LandR biomass simulation

Author(s)

Tati Micheletti

ECCC's RSF plot style

Description

ECCC's RSF plot style

Usage

RSFplot(
  ras,
  upload = FALSE,
  writeReclasRas = FALSE,
  outputFolder = tempdir(),
  rasName,
  folderID = NULL
)

Arguments

ras

RasterLayer. Layer to generate 10 binned green to red (caribou RSF) map.
upload

logical. Should the raster be uploaded to Google Drive? Only works if the raster exists OR is set to be written.
writeReclasRas

logical. Default is FALSE. Should the raster be written to disk?
outputFolder

character. Path to the folder where it should be saved.
rasName

character. Name of the raster to be saved.
folderID

character. Google folder id to upload to. Only needs to be provided if upload == TRUE. Default is 'NULL“

Value

Used for side effects of generating plots that have similar binning system to ECCC's 2011 Caribou RSF, and optionally uploading them to Google Drive.

Author(s)

Tati Micheletti

Get all the values of a raster and remove the NA's, keeping pixel ID.

Description

Get all the values of a raster and remove the NA's, keeping pixel ID.

Usage

subsetNonNARas(ras, N = NULL)

Arguments

ras

RasterLayer.
N

numeric. If passed, subsets N pixels from the raster. If NULL, returns the whole non-NA raster values. Default is NULL.

Value

data.table of pixel values and pixel ID

Author(s)

Tati Micheletti

Get a sub-string based on the number of characters and the side to start

Description

Get a sub-string based on the number of characters and the side to start

Usage

substrBoth(strng, howManyCharacters, fromEnd = TRUE)

Arguments

strng

String from which to grab a subset
howManyCharacters

numeric. How many characters should be returned in the sub-string?
fromEnd

logical. Default is TRUE. Should the subset start in the end of the string?

Value

character string of the subset.

Author(s)

Tati Micheletti

Plots biomass per species: proportional or absolute, and total or just overstory

Description

Plots biomass per species: proportional or absolute, and total or just overstory

Usage

totalBiomassPerSpecies(
  dataPath,
  typeSim,
  proportional = FALSE,
  columnsType = FALSE,
  overstory = FALSE,
  overwrite = FALSE,
  maxVal = 2e+10
)

Arguments

dataPath

character. Path to data
typeSim

character. Which type of simulation is it? i.e., 'LandR_SCFM' or 'LandR.CS_fS'
proportional

logical. Should the plot be of the proportional biomass?
columnsType

logical. Should the plot be continuous (lines) or columns?
overstory

logical. Should the plot be of the overstory biomass?
overwrite

logical.
maxVal

numeric. Max value for y axis. Passing this ensures that both overstory and all biomass plots are comparable Default to 1e10.

Value

plot

Author(s)

Tati Micheletti