foldExplorer: Explore the generated folds

In adamlilith/blockCV: Spatial and environmental blocking for k-fold cross-validation

Description

A function for visualising the generated folds on a map, and allowing interactive exploration of the data in the folds, using the RStudio Shiny app.

Usage

foldExplorer(blocks, rasterLayer, speciesData)

Arguments

blocks	An SpatialBlock, EnvironmentalBlock or BufferedBlock object.
rasterLayer	A RasterLayer, RasterBrick or RasterStack object as background map for visualisation.
speciesData	A SpatialPointsDataFrame, SpatialPoints or sf object containing species data.

Value

An interactive map showing folds and the species data, that can be used to explore folds. Note that this can also be opened in a web browser window. When you return to the R console, press “Esc” to return to the prompt.

See Also

spatialBlock, buffering and envBlock

Examples

## Not run: 

# load package data
awt <- raster::brick(system.file("extdata", "awt.grd", package = "blockCV"))
# import presence-absence species data
PA <- read.csv(system.file("extdata", "PA.csv", package = "blockCV"))
# make a SpatialPointsDataFrame object from data.frame
pa_data <- sp::SpatialPointsDataFrame(PA[,c("x", "y")], PA, proj4string=raster::crs(awt))

# spatial blocking by specified range and random assignment
sb <- spatialBlock(speciesData = pa_data,
                   species = "Species",
                   rasterLayer = awt,
                   theRange = 66000,
                   k = 5,
                   selection = 'random',
                   iteration = 250,
                   numLimit = NULL,
                   biomod2Format = TRUE)

foldExplorer(sb, awt, pa_data)

# buffering with presence-absence data
bf <- buffering(speciesData= pa_data,
                species= "Species", # to count the number of presences and absences
                theRange= 66500,
                spDataType = "PA",
                progress = T)

foldExplorer(bf, awt, pa_data)

# environmental clustering
eb <- envBlock(rasterLayer = awt,
               speciesData = pa_data,
               species = "Species",
               k = 5)

foldExplorer(eb, awt, pa_data)


## End(Not run)

adamlilith/blockCV documentation built on May 25, 2019, 12:41 a.m.