# Geographical Detector(GD)

This vignette explains how to run native geographic detector(GD) in gdverse package.

### Load package and pre-processing data.

    library(sf)
    library(tidyverse)
    library(gdverse)

See layers in `NTDs.gpkg`:

    ntdspath = system.file("extdata", "NTDs.gpkg",package = 'gdverse')
    st_layers(ntdspath)
    ## Driver: GPKG
    ## Available layers:
    ##   layer_name geometry_type features fields crs_name
    ## 1    disease       Polygon      189      2  unknown
    ## 2  watershed       Polygon        9      2  unknown
    ## 3  elevation Multi Polygon        7      2  unknown
    ## 4   soiltype Multi Polygon        6      2  unknown

In file `NTDs.gpkg`, `disease` layer is the dependent variable, which is a continuous numerical variable, while others are independent and discrete variables.

Now we need to combine these layers together:

    watershed = read_sf(ntdspath,layer = 'watershed')
    elevation = read_sf(ntdspath,layer = 'elevation')
    soiltype = read_sf(ntdspath,layer = 'soiltype')
    disease = read_sf(ntdspath,layer = 'disease')

Plot them together:

    library(cowplot)

    f1 = ggplot(data = disease) +
      geom_sf(aes(fill = incidence),lwd = .1,color = 'grey') +
      viridis::scale_fill_viridis(option="mako", direction = -1) +
      theme_bw() +
      theme(
        axis.text = element_blank(),
        axis.ticks = element_blank(),
        axis.title = element_blank(),
        panel.grid = element_blank(),
        legend.position = 'inside',
        legend.position.inside = c(.1,.25),
        legend.background = element_rect(fill = 'transparent',color = NA)
      )
    f2 = ggplot(data = watershed) +
      geom_sf(aes(fill = watershed),lwd = .1,color = 'grey') +
      tidyterra::scale_fill_whitebox_c() +
      coord_sf(crs = NULL) +
      theme_bw() +
      theme(
        axis.text = element_blank(),
        axis.ticks = element_blank(),
        axis.title = element_blank(),
        panel.grid = element_blank(),
        legend.position = 'inside',
        legend.position.inside = c(.1,.25),
        legend.background = element_rect(fill = 'transparent',color = NA)
      )
    f3 = ggplot(data = elevation) +
      geom_sf(aes(fill = elevation),lwd = .1,color = 'grey') +
      tidyterra::scale_fill_hypso_c() +
      theme_bw() +
      theme(
        axis.text = element_blank(),
        axis.ticks = element_blank(),
        axis.title = element_blank(),
        panel.grid = element_blank(),
        legend.position = 'inside',
        legend.position.inside = c(.1,.25),
        legend.background = element_rect(fill = 'transparent',color = NA)
      )
    f4 = ggplot(data = soiltype) +
      geom_sf(aes(fill = soiltype),lwd = .1,color = 'grey') +
      tidyterra::scale_fill_wiki_c() +
      theme_bw() +
      theme(
        axis.text = element_blank(),
        axis.ticks = element_blank(),
        axis.title = element_blank(),
        panel.grid = element_blank(),
        legend.position = 'inside',
        legend.position.inside = c(.1,.25),
        legend.background = element_rect(fill = 'transparent',color = NA)
      )

    plot_grid(f1,f2,f3,f4, nrow = 2,label_fontfamily = 'serif',
              labels = paste0('(',letters[1:4],')'),
              label_fontface = 'plain',label_size = 10,
              hjust = -1.5,align = 'hv')  -> p
    p

Attribute spatial join

    NTDs = disease %>%
      st_centroid() %>%
      st_join(watershed[,"watershed"]) %>%
      st_join(elevation[,"elevation"]) %>%
      st_join(soiltype[,"soiltype"])
    ## Warning: st_centroid assumes attributes are constant over geometries

Check whether has `NA` in `NTDs`:

    NTDs %>%
      dplyr::filter(if_any(everything(),~is.na(.x)))
    ## Simple feature collection with 4 features and 5 fields
    ## Geometry type: POINT
    ## Dimension:     XY
    ## Bounding box:  xmin: 301567.5 ymin: 3989433 xmax: 318763.3 ymax: 3991906
    ## Projected CRS: +proj=aea +lat_0=0 +lon_0=105 +lat_1=25 +lat_2=47 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs
    ## # A tibble: 4 × 6
    ##   SP_ID incidence               geom watershed elevation soiltype
    ## * <chr>     <dbl>        <POINT [m]>     <int>     <int>    <int>
    ## 1 141        6.48 (318763.3 3991847)         9        NA        3
    ## 2 165        6.53 (316574.1 3989433)         4        NA        2
    ## 3 166        6.43 (311439.1 3990674)         4        NA        2
    ## 4 188        6.26 (301567.5 3991906)        NA         2        3

Filter out all rows with no `NA` values:

    NTDs %>%
      dplyr::filter(if_all(everything(),~!is.na(.x))) -> NTDs
    NTDs
    ## Simple feature collection with 185 features and 5 fields
    ## Geometry type: POINT
    ## Dimension:     XY
    ## Bounding box:  xmin: 272784.9 ymin: 3982369 xmax: 333088.5 ymax: 4025117
    ## Projected CRS: +proj=aea +lat_0=0 +lon_0=105 +lat_1=25 +lat_2=47 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs
    ## # A tibble: 185 × 6
    ##    SP_ID incidence               geom watershed elevation soiltype
    ##  * <chr>     <dbl>        <POINT [m]>     <int>     <int>    <int>
    ##  1 0          5.94 (287216.1 4004408)         5         5        5
    ##  2 1          5.87 (284861.2 4001734)         5         5        4
    ##  3 2          5.88 (287731.3 4000289)         5         5        5
    ##  4 3          5.98 (290808.8 4000994)         5         5        5
    ##  5 4          5.96 (290924.8 4004432)         5         5        1
    ##  6 5          5.66 (272784.9 4007758)         5         5        4
    ##  7 6          5.74 (274308.9 4010571)         5         5        4
    ##  8 7          5.88 (279539.7 4003222)         5         5        4
    ##  9 8          6.1  (279032.9 4005677)         5         5        4
    ## 10 9          5.89 (282534.9 4004849)         5         5        4
    ## # ℹ 175 more rows

Remove unnecessary columns of data:

    NTDs = NTDs %>%
      st_drop_geometry() %>%
      dplyr::select(-SP_ID)
    NTDs
    ## # A tibble: 185 × 4
    ##    incidence watershed elevation soiltype
    ##        <dbl>     <int>     <int>    <int>
    ##  1      5.94         5         5        5
    ##  2      5.87         5         5        4
    ##  3      5.88         5         5        5
    ##  4      5.98         5         5        5
    ##  5      5.96         5         5        1
    ##  6      5.66         5         5        4
    ##  7      5.74         5         5        4
    ##  8      5.88         5         5        4
    ##  9      6.1          5         5        4
    ## 10      5.89         5         5        4
    ## # ℹ 175 more rows

### Factor detector

    fd = gd(incidence ~ watershed + elevation + soiltype,
            data = NTDs,type = 'factor')
    fd
    ##                 Factor Detector
    ##
    ## | variable  | Q-statistic |   P-value   |
    ## |:---------:|:-----------:|:-----------:|
    ## | watershed |  0.6377737  | 0.000128803 |
    ## | elevation |  0.6067087  | 0.043382244 |
    ## | soiltype  |  0.3857168  | 0.372145486 |
    plot(fd)

### Interaction detector

    id = gd(incidence ~ watershed + elevation + soiltype,
            data = NTDs,type = 'interaction')
    id
    ##                 Interaction Detector
    ##
    ## | Interactive variable  | Interaction  |
    ## |:---------------------:|:------------:|
    ## | watershed ∩ elevation | Enhance, bi- |
    ## | watershed ∩ soiltype  | Enhance, bi- |
    ## | elevation ∩ soiltype  | Enhance, bi- |
    plot(id)

### Risk detector

    rd = gd(incidence ~ watershed + elevation + soiltype,
            data = NTDs,type = 'risk')
    rd
    ##                 Risk Detector
    ##
    ##  Variable elevation:
    ##
    ## | zone  | zone1 | zone2 | zone3 | zone4 | zone5 | zone6 |
    ## |:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|
    ## | zone2 |  Yes  |  NA   |  NA   |  NA   |  NA   |  NA   |
    ## | zone3 |  Yes  |  No   |  NA   |  NA   |  NA   |  NA   |
    ## | zone4 |  Yes  |  Yes  |  Yes  |  NA   |  NA   |  NA   |
    ## | zone5 |  Yes  |  Yes  |  Yes  |  Yes  |  NA   |  NA   |
    ## | zone6 |  Yes  |  Yes  |  Yes  |  Yes  |  Yes  |  NA   |
    ## | zone7 |  Yes  |  Yes  |  Yes  |  Yes  |  Yes  |  Yes  |
    ##
    ##  Variable soiltype:
    ##
    ## | zone  | zone1 | zone2 | zone3 | zone4 |
    ## |:-----:|:-----:|:-----:|:-----:|:-----:|
    ## | zone2 |  Yes  |  NA   |  NA   |  NA   |
    ## | zone3 |  Yes  |  No   |  NA   |  NA   |
    ## | zone4 |  Yes  |  Yes  |  Yes  |  NA   |
    ## | zone5 |  No   |  Yes  |  Yes  |  Yes  |
    ##
    ##  Variable watershed:
    ##
    ## | zone  | zone1 | zone2 | zone3 | zone4 | zone5 | zone6 | zone7 | zone8 |
    ## |:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|
    ## | zone2 |  Yes  |  NA   |  NA   |  NA   |  NA   |  NA   |  NA   |  NA   |
    ## | zone3 |  Yes  |  Yes  |  NA   |  NA   |  NA   |  NA   |  NA   |  NA   |
    ## | zone4 |  Yes  |  No   |  Yes  |  NA   |  NA   |  NA   |  NA   |  NA   |
    ## | zone5 |  Yes  |  Yes  |  Yes  |  Yes  |  NA   |  NA   |  NA   |  NA   |
    ## | zone6 |  Yes  |  Yes  |  Yes  |  Yes  |  No   |  NA   |  NA   |  NA   |
    ## | zone7 |  Yes  |  Yes  |  No   |  Yes  |  Yes  |  Yes  |  NA   |  NA   |
    ## | zone8 |  Yes  |  Yes  |  No   |  Yes  |  Yes  |  Yes  |  No   |  NA   |
    ## | zone9 |  Yes  |  Yes  |  No   |  Yes  |  Yes  |  Yes  |  No   |  Yes  |
    plot(rd)

You can change the significant interval by assign `alpha` argument,the default value of `alpha` argument is `0.95`.

    rd99 = gd(incidence ~ watershed + elevation + soiltype,
              data = NTDs,type = 'risk',alpha = 0.99)
    rd99
    ##                 Risk Detector
    ##
    ##  Variable elevation:
    ##
    ## | zone  | zone1 | zone2 | zone3 | zone4 | zone5 | zone6 |
    ## |:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|
    ## | zone2 |  Yes  |  NA   |  NA   |  NA   |  NA   |  NA   |
    ## | zone3 |  Yes  |  No   |  NA   |  NA   |  NA   |  NA   |
    ## | zone4 |  Yes  |  Yes  |  Yes  |  NA   |  NA   |  NA   |
    ## | zone5 |  Yes  |  Yes  |  Yes  |  Yes  |  NA   |  NA   |
    ## | zone6 |  Yes  |  Yes  |  Yes  |  Yes  |  Yes  |  NA   |
    ## | zone7 |  Yes  |  Yes  |  Yes  |  Yes  |  Yes  |  Yes  |
    ##
    ##  Variable soiltype:
    ##
    ## | zone  | zone1 | zone2 | zone3 | zone4 |
    ## |:-----:|:-----:|:-----:|:-----:|:-----:|
    ## | zone2 |  Yes  |  NA   |  NA   |  NA   |
    ## | zone3 |  Yes  |  No   |  NA   |  NA   |
    ## | zone4 |  Yes  |  Yes  |  Yes  |  NA   |
    ## | zone5 |  No   |  Yes  |  Yes  |  Yes  |
    ##
    ##  Variable watershed:
    ##
    ## | zone  | zone1 | zone2 | zone3 | zone4 | zone5 | zone6 | zone7 | zone8 |
    ## |:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|
    ## | zone2 |  Yes  |  NA   |  NA   |  NA   |  NA   |  NA   |  NA   |  NA   |
    ## | zone3 |  Yes  |  Yes  |  NA   |  NA   |  NA   |  NA   |  NA   |  NA   |
    ## | zone4 |  Yes  |  No   |  Yes  |  NA   |  NA   |  NA   |  NA   |  NA   |
    ## | zone5 |  Yes  |  Yes  |  Yes  |  Yes  |  NA   |  NA   |  NA   |  NA   |
    ## | zone6 |  Yes  |  Yes  |  Yes  |  Yes  |  No   |  NA   |  NA   |  NA   |
    ## | zone7 |  Yes  |  Yes  |  No   |  Yes  |  Yes  |  Yes  |  NA   |  NA   |
    ## | zone8 |  Yes  |  Yes  |  No   |  Yes  |  Yes  |  Yes  |  No   |  NA   |
    ## | zone9 |  Yes  |  Yes  |  No   |  Yes  |  Yes  |  Yes  |  No   |  Yes  |

### Ecological detector

    ed = gd(incidence ~ watershed + elevation + soiltype,
            data = NTDs,type = 'ecological')
    ed
    ##                 Ecological Detector
    ##
    ## |          | elevation | soiltype |
    ## |:---------|:---------:|:--------:|
    ## |watershed |    No     |    No    |
    ## |elevation |    NA     |    No    |
    plot(ed)

You can also change the significant interval by assign `alpha` argument,the default value of `alpha` argument is `0.95`.

    ed99 = gd(incidence ~ watershed + elevation + soiltype,
              data = NTDs,type = 'ecological',alpha = 0.99)
    ed99
    ##                 Ecological Detector
    ##
    ## |          | elevation | soiltype |
    ## |:---------|:---------:|:--------:|
    ## |watershed |    No     |    No    |
    ## |elevation |    NA     |    No    |

### Running four basic geodetectors simultaneously

    g = gd(incidence ~ watershed + elevation + soiltype,
           data = NTDs,
           type = c("factor", "interaction", "risk", "ecological"))
    g
    ##                 Factor Detector
    ##
    ## | variable  | Q-statistic |   P-value   |
    ## |:---------:|:-----------:|:-----------:|
    ## | watershed |  0.6377737  | 0.000128803 |
    ## | elevation |  0.6067087  | 0.043382244 |
    ## | soiltype  |  0.3857168  | 0.372145486 |
    ##
    ##                 Interaction Detector
    ##
    ## | Interactive variable  | Interaction  |
    ## |:---------------------:|:------------:|
    ## | watershed ∩ elevation | Enhance, bi- |
    ## | watershed ∩ soiltype  | Enhance, bi- |
    ## | elevation ∩ soiltype  | Enhance, bi- |
    ##
    ##                 Risk Detector
    ##
    ##  Variable elevation:
    ##
    ## | zone  | zone1 | zone2 | zone3 | zone4 | zone5 | zone6 |
    ## |:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|
    ## | zone2 |  Yes  |  NA   |  NA   |  NA   |  NA   |  NA   |
    ## | zone3 |  Yes  |  No   |  NA   |  NA   |  NA   |  NA   |
    ## | zone4 |  Yes  |  Yes  |  Yes  |  NA   |  NA   |  NA   |
    ## | zone5 |  Yes  |  Yes  |  Yes  |  Yes  |  NA   |  NA   |
    ## | zone6 |  Yes  |  Yes  |  Yes  |  Yes  |  Yes  |  NA   |
    ## | zone7 |  Yes  |  Yes  |  Yes  |  Yes  |  Yes  |  Yes  |
    ##
    ##  Variable soiltype:
    ##
    ## | zone  | zone1 | zone2 | zone3 | zone4 |
    ## |:-----:|:-----:|:-----:|:-----:|:-----:|
    ## | zone2 |  Yes  |  NA   |  NA   |  NA   |
    ## | zone3 |  Yes  |  No   |  NA   |  NA   |
    ## | zone4 |  Yes  |  Yes  |  Yes  |  NA   |
    ## | zone5 |  No   |  Yes  |  Yes  |  Yes  |
    ##
    ##  Variable watershed:
    ##
    ## | zone  | zone1 | zone2 | zone3 | zone4 | zone5 | zone6 | zone7 | zone8 |
    ## |:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|
    ## | zone2 |  Yes  |  NA   |  NA   |  NA   |  NA   |  NA   |  NA   |  NA   |
    ## | zone3 |  Yes  |  Yes  |  NA   |  NA   |  NA   |  NA   |  NA   |  NA   |
    ## | zone4 |  Yes  |  No   |  Yes  |  NA   |  NA   |  NA   |  NA   |  NA   |
    ## | zone5 |  Yes  |  Yes  |  Yes  |  Yes  |  NA   |  NA   |  NA   |  NA   |
    ## | zone6 |  Yes  |  Yes  |  Yes  |  Yes  |  No   |  NA   |  NA   |  NA   |
    ## | zone7 |  Yes  |  Yes  |  No   |  Yes  |  Yes  |  Yes  |  NA   |  NA   |
    ## | zone8 |  Yes  |  Yes  |  No   |  Yes  |  Yes  |  Yes  |  No   |  NA   |
    ## | zone9 |  Yes  |  Yes  |  No   |  Yes  |  Yes  |  Yes  |  No   |  Yes  |
    ##
    ##                 Ecological Detector
    ##
    ## |          | elevation | soiltype |
    ## |:---------|:---------:|:--------:|
    ## |watershed |    No     |    No    |
    ## |elevation |    NA     |    No    |
    plot(g)