PaleoRegion: R6 class representing a paleontological region.

In paleopop: Pattern-Oriented Modeling Framework for Coupled Niche-Population Paleo-Climatic Models

R6 class representing a paleontological region.

Description

R6 class representing a study region of temporally changing spatial grid cells, defined via a RasterLayer object (see raster) and a temporal mask indicating which cells are included at each time step.

Super classes

poems::GenericClass -> poems::Region -> PaleoRegion

Public fields

attached

A list of dynamically attached attributes (name-value pairs).

Active bindings

coordinates

Data frame (or matrix) of X-Y population (WGS84) coordinates in longitude (degrees West) and latitude (degrees North) (get and set), or distance-based coordinates dynamically returned by region raster (get only).

region_raster

A RasterLayer object (see raster) defining the region with finite values (NAs elsewhere).

use_raster

Boolean to indicate that a raster is to be used to define the region (default TRUE).

strict_consistency

Boolean to indicate that, as well as resolution, extent and CRS, consistency checks also ensure that a raster's finite/occupiable cells are the same or a subset of those defined by the region (default TRUE).

temporal_mask

Matrix of booleans indicating which region cells are included at each time step.

region_cells

Dynamically calculated number of region coordinates or raster cells with finite/non-NA values.

region_indices

Dynamically calculated region indices for raster cells with finite/non-NA values (all if not a raster).

Methods

Public methods

• PaleoRegion$new()

• PaleoRegion$raster_from_values()

• PaleoRegion$temporal_mask_raster()

• PaleoRegion$clone()

Inherited methods

• poems::GenericClass$new_clone()
• poems::Region$raster_is_consistent()

---

Method new()

Initialization method sets temporally changing raster layers for paleontological region.

Usage

PaleoRegion$new(template_raster = NULL, remove_zeros = FALSE, ...)

Arguments

template_raster

A RasterLayer, RasterBrick, or RasterStack object (see raster) defining the paleontological region with example finite values (NAs elsewhere)

remove_zeros

Boolean to indicate that cells that are zero across all layers (times) are to be removed, i.e. set to NA (default is FALSE).

...

Additional parameters passed individually.

---

Method raster_from_values()

Converts an array (or matrix) of values into a raster (or stack) consistent with the region raster (matching extent, resolution, and finite/NA cells), and with the temporal mask (if any) applied.

Usage

PaleoRegion$raster_from_values(values)

Arguments

values

An array (or matrix) of values to be placed in the raster (or stack) having dimensions consistent with the region cell number.

Returns

A RasterLayer (or RasterStack/Brick) object consistent with the region raster with temporal mask (if any) applied.

---

Method temporal_mask_raster()

Returns the temporal mask as a raster stack/brick object consistent with the region raster.

Usage

PaleoRegion$temporal_mask_raster()

Returns

A RasterStack/Brick) object with temporal mask values of 1 (true) and NA elsewhere.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

PaleoRegion$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

library(poems)
library(raster)
# Ring Island example region
coordinates <- data.frame(x = rep(seq(-178.02, -178.06, -0.01), 5),
                          y = rep(seq(19.02, 19.06, 0.01), each = 5))
template_raster <- Region$new(coordinates = coordinates)$region_raster # full extent
sealevel_raster <- template_raster
template_raster[][c(7:9, 12:14, 17:19)] <- NA # make Ring Island
sealevel_raster[][c(7:9, 12:14, 17:18)] <- NA
raster_stack <- raster::stack(x = append(replicate(9, template_raster), sealevel_raster))
region <- PaleoRegion$new(template_raster = raster_stack)
raster::plot(region$temporal_mask_raster()[[1]], main = "Ring Island (first timestep)",
             xlab = "Longitude (degrees)", ylab = "Latitude (degrees)",
             colNA = "blue", legend = FALSE)
raster::plot(region$temporal_mask_raster()[[10]], main = "Ring Island (last timestep)",
             xlab = "Longitude (degrees)", ylab = "Latitude (degrees)",
             colNA = "blue", legend = FALSE)

paleopop documentation built on April 12, 2025, 1:38 a.m.