spEcula

The goal of spEcula is to make it easier to use R for spatial prediction based on various spatial relationships (e.g. spatial dependence, spatial heterogeneity and geographical similarity).

Overview

Full document of the most recent release of spEcula is online: https://spatlyu.github.io/spEcula/

Current models and functions provided by spEcula are:

spatial prediction method	spEcula function	support status
Geographically Optimal Similarity	gos()	✔️
Sandwich Mapping Model	sandwich()	✔️

Installation

You can install the development version of spEcula from github:

# install.packages("devtools")
devtools::install_github("SpatLyu/spEcula",
                         build_vignettes = T,
                         dep = T)

or install spEcula from r-universe:

install.packages('spEcula',
                 repos = c("https://spatlyu.r-universe.dev",
                           "https://cran.rstudio.com/"),
                 dep = TRUE)

Example

Geographically Optimal Similarity (GOS) model

library(spEcula)
data(zn)
data(grid)

zn$Zn = log(zn$Zn)
tictoc::tic()
g1 = gos(Zn ~ Slope + Water + NDVI  + SOC + pH + Road + Mine,
         data = zn, newdata = grid, kappa = 0.08,cores = 6)
tictoc::toc()
## 6.6 sec elapsed

g1$pred = exp(g1$pred)
grid$pred = g1$pred
grid$uc99 = g1$`uncertainty99`
g1
## # A tibble: 13,132 × 7
##     pred uncertainty90 uncertainty95 uncertainty99 uncertainty99.5
##    <dbl>         <dbl>         <dbl>         <dbl>           <dbl>
##  1  21.8        0.0818        0.0523        0.0287         0.0243 
##  2  22.5        0.0529        0.0356        0.0102         0.00954
##  3  22.9        0.0693        0.0429        0.0224         0.0148 
##  4  22.6        0.0665        0.0572        0.0140         0.00799
##  5  21.9        0.0736        0.0460        0.0181         0.0139 
##  6  21.5        0.0728        0.0480        0.0200         0.0169 
##  7  23.2        0.0453        0.0345        0.0185         0.0178 
##  8  24.8        0.0488        0.0434        0.0227         0.0118 
##  9  25.0        0.0435        0.0432        0.0186         0.0103 
## 10  24.5        0.0217        0.0217        0.0182         0.0141 
## # ℹ 13,122 more rows
## # ℹ 2 more variables: uncertainty99.9 <dbl>, uncertainty100 <dbl>

library(ggplot2)
library(cowplot)
library(viridis)

f1 = ggplot(grid, aes(x = Lon, y = Lat, fill = pred)) +
  geom_tile() +
  scale_fill_viridis(option="magma", direction = -1) + 
  coord_equal() +
  labs(fill='Prediction') +
  theme_bw() 
f2 = ggplot(grid, aes(x = Lon, y = Lat, fill = uc99)) +
  geom_tile() +
  scale_fill_viridis(option="mako", direction = -1) + 
  coord_equal() +
  labs(fill=bquote(Uncertainty~(zeta==0.99))) +
  theme_bw() 

plot_grid(f1,f2,nrow = 1,label_fontfamily = 'serif',
          labels = paste0('(',letters[1:2],')'),
          label_fontface = 'plain',label_size = 10,
          hjust = -1.5,align = 'hv')  -> p
p

Sandwich Mapping Model

library(sf)
library(tidyverse)
library(spEcula)
simpath = system.file("extdata", "sim.gpkg", package="spEcula")
sampling = read_sf(simpath,layer = 'sim_sampling')
ssh = read_sf(simpath,layer = 'sim_ssh')
reporting = read_sf(simpath,layer = 'sim_reporting')

sampling_zone = sampling %>%
    st_join(ssh['X']) %>%
    st_drop_geometry()

library(ggpubr)

ggerrorplot(sampling_zone, x = "X", y = "Value",
            desc_stat = "mean_sd", color = "black",
            add = "violin", add.params = list(color = "darkgray")) +
  geom_text(data = summarise(sampling_zone,vmean = mean(Value),.by = X), 
            aes(x = X, y = vmean, label = round(vmean,2)), 
            vjust = -0.5, hjust = -0.15, color = "black",size = 3) +
  scale_x_discrete(labels = LETTERS[1:4]) +
  theme(axis.title.x = element_blank())

sim_est = sandwich(sampling = sampling,stratification = ssh,reporting = reporting,
                   sampling_attr = 'Value',ssh_zone = 'X',reporting_id = 'Y',
                   weight_type = 'area')
sim_est
## Simple feature collection with 7 features and 3 fields
## Geometry type: POLYGON
## Dimension:     XY
## Bounding box:  xmin: 5.684342e-14 ymin: 2 xmax: 4 ymax: 6
## Geodetic CRS:  WGS 84
## # A tibble: 7 × 4
##       Y sandwichest_mean sandwichest_standarderror                      geometry
##   <dbl>            <dbl>                     <dbl>                 <POLYGON [°]>
## 1     1             381.                      2.43 ((0.8 4, 0.8 4, 1 4, 1.2 4, …
## 2     2             262.                      2.10 ((2.8 6, 2.6 6, 2.4 6, 2.2 6…
## 3     3             298.                      2.49 ((2.4 3, 2.4 2.8, 2.2 2.8, 2…
## 4     4             401.                      2.88 ((4 3.6, 4 3.8, 4 4, 4 4.2, …
## 5     5             390.                      2.53 ((1 3.6, 1 3.4, 1.2 3.4, 1.4…
## 6     6             357.                      2.15 ((1.6 3, 1.6 2.8, 1.8 2.8, 2…
## 7     7             203.                      2.40 ((0.6 5, 0.6 5, 0.6 5.2, 0.6…

library(cowplot) 

f1 = ggplot(data = sim_est, aes(fill = sandwichest_mean), 
            color = "darkgray") +
  geom_sf() + 
  labs(fill='mean') +
  scale_fill_gradient(low = "#f0bc9c", high = "red",
                      breaks = range(sim_est$sandwichest_mean)) +
  theme_bw() +
  theme(
    axis.text = element_blank(),
    axis.ticks = element_blank(),
    axis.title = element_blank(),
    panel.grid = element_blank(),
    legend.position = 'right',
    legend.background = element_rect(fill = 'transparent',color = NA)
  )

f2 = ggplot(data = sim_est, aes(fill = sandwichest_standarderror), 
            color = "darkgray") +
  geom_sf() + 
  labs(fill='se') +
  scale_fill_gradient(low = "#b6edf0", high = "blue",
                      breaks = range(sim_est$sandwichest_standarderror)) +
  theme_bw() +
  theme(
    axis.text = element_blank(),
    axis.ticks = element_blank(),
    axis.title = element_blank(),
    panel.grid = element_blank(),
    legend.position = 'right',
    legend.background = element_rect(fill = 'transparent',color = NA)
  )

plot_grid(f1, f2, nrow = 1,label_fontfamily = 'serif',
          labels = paste0('(',letters[1:4],')'),
          label_fontface = 'plain',label_size = 10,
          hjust = 0.05,align = 'hv')  -> p
p