install.packages('dsmextraLite',
repos=c('https://pifsc-protected-species-division.r-universe.dev','https://cloud.r-project.org')
)
install.packages('dsmextraLite', type='source',
repos=c('https://pifsc-protected-species-division.r-universe.dev','https://cloud.r-project.org')
)
remotes::install_github('pifsc-protected-species-division/dsmextraLite')
library(sf)
library(terra)
library(mapview)
library(concaveman)
library(rmapshaper)
library(mapview)
library(ggplot2)
library(ggspatial)
library(rnaturalearth)
library(ggnewscale)
library(paletteer)
library(RColorBrewer)
library(dsmextraLite)
#' -----------------------------------------------------------------------------
#' Load sperm whale example data
#' -----------------------------------------------------------------------------
load(system.file("example_data", "spermwhales.rda", package = "dsmextraLite"))
#' -----------------------------------------------------------------------------
#' Create a raster prediction grid for demonstration
#' -----------------------------------------------------------------------------
study_area <- concaveman::concaveman(predgrid) %>%
ms_simplify(keep=0.15) %>% st_buffer(10000)
predgrid <- dsmextraLite::sf_to_rast(predgrid)
#' -----------------------------------------------------------------------------
#' Compute extrapolation
#' -----------------------------------------------------------------------------
spermwhale.extrapolation <- compute_extrapolation(
samples = segments,
covariate.names = c("Depth", "SST", "NPP", "DistToCAS", "EKE"),
prediction.grid = predgrid
)
summary(spermwhale.extrapolation)
#>
#>
#> Table: Extrapolation
#>
#> Type Count Percentage
#> -------------- ------------ ------------
#> Univariate 65 1.23
#> Combinatorial 45 0.85
#> ----------- ----------- -----------
#> Sub-total 110 2.08
#> ----------- ----------- -----------
#> Analogue 5175 97.92
#> ----------- ----------- -----------
#> Total 5285 100
#>
#>
#> Table: Most influential covariates (MIC)
#>
#> Type Covariate Count Percentage
#> -------------- ------------ ------------ ------------
#> Univariate EKE 24 0.45
#> Univariate SST 17 0.32
#> Univariate Depth 16 0.3
#> Univariate NPP 6 0.11
#> Univariate DistToCAS 2 0.038
#> ----------- ----------- ----------- -----------
#> Sub-total 65 1.2
#> ----------- ----------- ----------- -----------
#> Combinatorial NPP 39 0.74
#> Combinatorial Depth 6 0.11
#> ----------- ----------- ----------- -----------
#> Sub-total 45 0.85
#> ----------- ----------- ----------- -----------
#> Total 110 2.1
#' -----------------------------------------------------------------------------
#' High definition fixed plot for export
#' -----------------------------------------------------------------------------
land <- st_geometry(ne_countries(scale=10))
## ExDet plot
ggplot() + theme_bw() +
annotation_spatial(land, fill="grey30") +
#layer_spatial(study_area, fill=NA) +
layer_spatial(spermwhale.extrapolation$rasters$ExDet$combinatorial) +
scale_fill_distiller(palette = "Purples", direction = 2, na.value=NA) +
guides(fill=guide_legend(title="Combinatorial")) +
new_scale_fill() +
layer_spatial(spermwhale.extrapolation$rasters$ExDet$univariate) +
scale_fill_distiller(palette = "Oranges", na.value=NA) +
guides(fill=guide_legend(title="Univariate")) +
new_scale_fill() +
layer_spatial(spermwhale.extrapolation$rasters$ExDet$analogue) +
scale_fill_distiller(palette = "Greens", direction = 2, na.value=NA) +
guides(fill=guide_legend(title="Analogue")) +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())
#> Warning: Removed 21254 rows containing missing values or values outside the scale range
#> (`geom_raster()`).
#> Warning: Removed 21237 rows containing missing values or values outside the scale range
#> (`geom_raster()`).
#> Warning: Removed 16117 rows containing missing values or values outside the scale range
#> (`geom_raster()`).
## MIC plot
disc_pal <- c("gray90", paletteer_d("ggthemes::calc", 5))
ggplot() + theme_bw() +
annotation_spatial(land, fill="gray30") +
layer_spatial(spermwhale.extrapolation$rasters$mic$all) +
scale_fill_manual(values=disc_pal, na.translate=FALSE) +
guides(fill=guide_legend(title="MIC")) +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())
#> Warning: Removed 15996 rows containing missing values or values outside the scale range
#> (`geom_raster()`).
#' -----------------------------------------------------------------------------
#' Interactive plot using the {mapview} package
#' -----------------------------------------------------------------------------
# library(mapview)
## ExDet
# mapview(spermwhale.extrapolation$rasters$ExDet$combinatorial,
# layer.name="Combinatorial", na.color=NA, col.regions=brewer.pal(9, "Purples")) +
# mapview(spermwhale.extrapolation$rasters$ExDet$univariate,
# layer.name="Univariate", na.color=NA, col.regions=rev(brewer.pal(9, "Oranges"))) +
# mapview(spermwhale.extrapolation$rasters$ExDet$analogue,
# layer.name="Analogue", na.color=NA, col.regions=brewer.pal(9, "Greens"))
## MIC -- currently doesn't work, legend is wrong
# mapview(spermwhale.extrapolation$rasters$mic$all, layer.name="MIC", na.color=NA)
This software package is developed and maintained by scientists at the NOAA Fisheries Pacific Islands Fisheries Science Center and should be considered a fundamental research communication. The recommendations and conclusions presented here are those of the authors and this software should not be construed as official communication by NMFS, NOAA, or the U.S. Dept. of Commerce. In addition, reference to trade names does not imply endorsement by the National Marine Fisheries Service, NOAA. While the best efforts have been made to insure the highest quality, tools such as this are under constant development and are subject to change.