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update readme
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@SpatLyu
SpatLyu committed Jun 4, 2024
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44 changes: 32 additions & 12 deletions README.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,9 @@ knitr::opts_chunk$set(
collapse = TRUE,
comment = "##",
fig.path = "man/figures/README-",
out.width = "100%"
out.width = "100%",
warning = FALSE,
message = FALSE
)
```

Expand Down Expand Up @@ -51,11 +53,14 @@ grid$uc99 = g1$`uncertainty99`
g1
```

```{r fig.width=9.5,fig.height=3.5}
```{r}
library(ggplot2)
library(cowplot)
library(viridis)
```


```{r fig.width=9.5,fig.height=3.5}
f1 = ggplot(grid, aes(x = Lon, y = Lat, fill = pred)) +
geom_tile() +
scale_fill_viridis(option="magma", direction = -1) +
Expand All @@ -76,6 +81,31 @@ plot_grid(f1,f2,nrow = 1,label_fontfamily = 'serif',
p
```

### Geographic detectors(geodetector) model

```{r example_gd}
library(sf)
library(terra)
library(tidyverse)
library(spEcula)
fvcpath = system.file("extdata", "FVC.zip",package = 'spEcula')
fvc = terra::rast(paste0("/vsizip/",fvcpath))
fvc = as_tibble(terra::as.data.frame(fvc,na.rm = T))
head(fvc)
```

```{r}
tictoc::tic()
g = gd_bestunidisc(fvc ~ .,data = select(fvc,-lulc),discnum = 2:15,cores = 6)
tictoc::toc()
```

```{r}
new.fvc = bind_cols(select(fvc,fvc,lulc),g$disv)
ssh.test(fvc ~ .,data = new.fvc,type = 'factor')
ssh.test(fvc ~ .,data = new.fvc,type = 'interaction')
```

### Spatially-aware Self-Organizing Maps(GeoSOM) model

```{r example_geosom}
Expand Down Expand Up @@ -122,13 +152,3 @@ pmc %>%
theme(axis.text = element_blank(),
axis.ticks = element_blank())
```

### Geographic detectors(geodetector) model

```{r example_gd}
data(NTDs)
ssh.test(incidence ~ watershed + elevation + soiltype,
data = NTDs,type = 'factor')
```

172 changes: 133 additions & 39 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ tictoc::tic()
g1 = gos(Zn ~ Slope + Water + NDVI + SOC + pH + Road + Mine,
data = zn, newdata = grid, kappa = 0.08,cores = 6)
tictoc::toc()
## 10.18 sec elapsed
## 11.03 sec elapsed
```

``` r
Expand Down Expand Up @@ -69,11 +69,9 @@ g1
library(ggplot2)
library(cowplot)
library(viridis)
## Loading required package: viridisLite
```

``` r

f1 = ggplot(grid, aes(x = Lon, y = Lat, fill = pred)) +
geom_tile() +
scale_fill_viridis(option="magma", direction = -1) +
Expand All @@ -94,7 +92,136 @@ plot_grid(f1,f2,nrow = 1,label_fontfamily = 'serif',
p
```

<img src="man/figures/README-unnamed-chunk-2-1.png" width="100%" />
<img src="man/figures/README-unnamed-chunk-3-1.png" width="100%" />

### Geographic detectors(geodetector) model

``` r
library(sf)
library(terra)
library(tidyverse)
library(spEcula)
fvcpath = system.file("extdata", "FVC.zip",package = 'spEcula')
fvc = terra::rast(paste0("/vsizip/",fvcpath))
fvc = as_tibble(terra::as.data.frame(fvc,na.rm = T))
head(fvc)
## # A tibble: 6 × 13
## fvc premax premin presum tmpmax tmpmin tmpavg pop ntl lulc elev slope
## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 0.198 163. 7.95 3956. 20.8 -7.53 8.05 1.90 6.60 10 1758. 2.65
## 2 0.193 161. 6.80 3892. 20.7 -7.55 8.02 1.20 4.91 10 1754. 3.45
## 3 0.192 160. 5.24 3842. 20.9 -7.48 8.15 0.547 3.75 10 1722. 3.96
## 4 0.189 159. 5 3808. 21.1 -7.39 8.35 0.542 3.99 10 1672. 2.90
## 5 0.208 164. 9.98 4051. 20.6 -7.59 7.97 10.4 7.10 10 1780. 1.94
## 6 0.196 163. 8.15 3973. 20.7 -7.53 8.03 9.31 6.56 10 1755. 3.01
## # ℹ 1 more variable: aspect <dbl>
```

``` r
tictoc::tic()
g = gd_bestunidisc(fvc ~ .,data = select(fvc,-lulc),discnum = 2:15,cores = 6)
tictoc::toc()
## 18.45 sec elapsed
```

``` r
new.fvc = bind_cols(select(fvc,fvc,lulc),g$disv)
ssh.test(fvc ~ .,data = new.fvc,type = 'factor')
## Spatial Stratified Heterogeneity Test
##
## Factor detector
```

| variable | Q-statistic | P-value |
|:--------:|:-----------:|:---------:|
| presum | 0.6401 | 9.029e-10 |
| lulc | 0.5533 | 9.106e-10 |
| premin | 0.4432 | 4.286e-10 |
| tmpmin | 0.4059 | 6.318e-10 |
| tmpmax | 0.2227 | 5.586e-10 |
| elev | 0.209 | 1.5e-10 |
| tmpavg | 0.1951 | 6.666e-10 |
| slope | 0.1943 | 7.057e-10 |
| pop | 0.1856 | 3.221e-10 |
| premax | 0.1341 | 6.351e-10 |
| ntl | 0.02156 | 8.297e-10 |
| aspect | 0.00741 | 5.448e-10 |

``` r
ssh.test(fvc ~ .,data = new.fvc,type = 'interaction')
## Spatial Stratified Heterogeneity Test
##
## Interaction detector
```

| Interactive variable | Interaction |
|:--------------------:|:------------------:|
| lulc ∩ aspect | Enhance, nonlinear |
| lulc ∩ elev | Enhance, bi- |
| lulc ∩ ntl | Enhance, nonlinear |
| lulc ∩ pop | Enhance, bi- |
| lulc ∩ premax | Enhance, bi- |
| lulc ∩ premin | Enhance, bi- |
| lulc ∩ presum | Enhance, bi- |
| lulc ∩ slope | Enhance, bi- |
| lulc ∩ tmpavg | Enhance, bi- |
| lulc ∩ tmpmax | Enhance, bi- |
| lulc ∩ tmpmin | Enhance, bi- |
| aspect ∩ elev | Enhance, nonlinear |
| aspect ∩ ntl | Enhance, nonlinear |
| aspect ∩ pop | Enhance, nonlinear |
| aspect ∩ premax | Enhance, nonlinear |
| aspect ∩ premin | Enhance, nonlinear |
| aspect ∩ presum | Weaken, uni- |
| aspect ∩ slope | Enhance, nonlinear |
| aspect ∩ tmpavg | Enhance, nonlinear |
| aspect ∩ tmpmax | Enhance, nonlinear |
| aspect ∩ tmpmin | Enhance, nonlinear |
| elev ∩ ntl | Enhance, nonlinear |
| elev ∩ pop | Enhance, bi- |
| elev ∩ premax | Enhance, nonlinear |
| elev ∩ premin | Weaken, uni- |
| elev ∩ presum | Enhance, bi- |
| elev ∩ slope | Enhance, bi- |
| elev ∩ tmpavg | Enhance, bi- |
| elev ∩ tmpmax | Enhance, nonlinear |
| elev ∩ tmpmin | Enhance, bi- |
| ntl ∩ pop | Enhance, nonlinear |
| ntl ∩ premax | Enhance, nonlinear |
| ntl ∩ premin | Enhance, nonlinear |
| ntl ∩ presum | Enhance, nonlinear |
| ntl ∩ slope | Enhance, nonlinear |
| ntl ∩ tmpavg | Enhance, nonlinear |
| ntl ∩ tmpmax | Enhance, nonlinear |
| ntl ∩ tmpmin | Enhance, nonlinear |
| pop ∩ premax | Enhance, nonlinear |
| pop ∩ premin | Enhance, bi- |
| pop ∩ presum | Enhance, bi- |
| pop ∩ slope | Enhance, bi- |
| pop ∩ tmpavg | Enhance, nonlinear |
| pop ∩ tmpmax | Enhance, nonlinear |
| pop ∩ tmpmin | Enhance, bi- |
| premax ∩ premin | Enhance, nonlinear |
| premax ∩ presum | Enhance, bi- |
| premax ∩ slope | Enhance, nonlinear |
| premax ∩ tmpavg | Enhance, nonlinear |
| premax ∩ tmpmax | Enhance, nonlinear |
| premax ∩ tmpmin | Enhance, nonlinear |
| premin ∩ presum | Enhance, bi- |
| premin ∩ slope | Enhance, bi- |
| premin ∩ tmpavg | Enhance, bi- |
| premin ∩ tmpmax | Enhance, bi- |
| premin ∩ tmpmin | Enhance, bi- |
| presum ∩ slope | Enhance, bi- |
| presum ∩ tmpavg | Enhance, bi- |
| presum ∩ tmpmax | Enhance, bi- |
| presum ∩ tmpmin | Enhance, bi- |
| slope ∩ tmpavg | Enhance, bi- |
| slope ∩ tmpmax | Enhance, bi- |
| slope ∩ tmpmin | Enhance, bi- |
| tmpavg ∩ tmpmax | Enhance, nonlinear |
| tmpavg ∩ tmpmin | Enhance, nonlinear |
| tmpmax ∩ tmpmin | Enhance, nonlinear |

### Spatially-aware Self-Organizing Maps(GeoSOM) model

Expand All @@ -108,7 +235,7 @@ geosom_bestparam(data = pmc,
wt = c(seq(0.1,1,by = 0.1),2:5),
xdim = 4:10, ydim = 4:10,cores = 6) -> g_bestparam
tictoc::toc()
## 44.37 sec elapsed
## 44.63 sec elapsed
```

build geosom model
Expand Down Expand Up @@ -140,22 +267,7 @@ g_label

``` r
library(sf)
## Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.3.1; sf_use_s2() is TRUE
```

``` r
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
```

``` r

pmc %>%
mutate(zone = as.factor(g_label)) %>%
Expand All @@ -168,22 +280,4 @@ pmc %>%
axis.ticks = element_blank())
```

<img src="man/figures/README-unnamed-chunk-5-1.png" width="100%" />

### Geographic detectors(geodetector) model

``` r
data(NTDs)

ssh.test(incidence ~ watershed + elevation + soiltype,
data = NTDs,type = 'factor')
## Spatial Stratified Heterogeneity Test
##
## Factor detector
```

| variable | Q-statistic | P-value |
|:---------:|:-----------:|:---------:|
| watershed | 0.6378 | 0.0001288 |
| elevation | 0.6067 | 0.04338 |
| soiltype | 0.3857 | 0.3721 |
<img src="man/figures/README-unnamed-chunk-8-1.png" width="100%" />
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