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Vign GRTSmh: update wrt default terra usage
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florisvdh committed Nov 24, 2023
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---
title: "Using the GRTS data sources"
author: "Floris Vanderhaeghe"
date: "2019-05-29"
date: "2023-11-24"
bibliography: references.bib
output:
rmarkdown::html_vignette:
Expand All @@ -18,19 +18,20 @@ vignette: >
options(stringsAsFactors = FALSE)
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
comment = "#>",
eval = FALSE
)
library(n2khab)
library(magrittr)
library(knitr)
```

_General note: the below vignette contains frozen output of 29 May 2019._
_General note: the below vignette contains frozen output of 24 November 2023._
_This makes it possible to build the package with vignettes without access to the data sources._

## Intro

With this vignette, you get acquainted with three functions that usually return a RasterLayer or a RasterBrick:
With this vignette, you get acquainted with three functions that usually return a SpatRaster object from the {terra} package:

- `read_GRTSmh()`
- `read_GRTSmh_base4frac()`
Expand Down Expand Up @@ -67,44 +68,50 @@ See the `vignette("v020_datastorage")` for more information.

`read_GRTSmh()` by default returns the `GRTSmaster_habitats` dataset:

```{r eval=FALSE}
```{r}
read_GRTSmh()
#> class : RasterLayer
#> dimensions : 2843, 7401, 21041043 (nrow, ncol, ncell)
#> resolution : 32, 32 (x, y)
#> extent : 22029.59, 258861.6, 153054.1, 244030.1 (xmin, xmax, ymin, ymax)
#> crs : +proj=lcc +lat_1=51.16666723333333 +lat_2=49.8333339 +lat_0=90 +lon_0=4.367486666666666 +x_0=150000.013 +y_0=5400088.438 +ellps=intl +towgs84=-106.8686,52.2978,-103.7239,0.3366,-0.457,1.8422,-1.2747 +units=m +no_defs
#> source : [...]/n2khab_data/10_raw/GRTSmaster_habitats/GRTSmaster_habitats.tif
#> names : GRTSmaster_habitats
#> values : 1, 67108857 (min, max)
#> class : SpatRaster
#> dimensions : 2843, 7401, 1 (nrow, ncol, nlyr)
#> resolution : 32, 32 (x, y)
#> extent : 22029.59, 258861.6, 153054.1, 244030.1 (xmin, xmax, ymin, ymax)
#> coord. ref. : BD72 / Belgian Lambert 72 (EPSG:31370)
#> source : GRTSmaster_habitats.tif
#> name : GRTSmaster_habitats
#> min value : 1
#> max value : 67108857
```

With the argument `brick = TRUE` however, you will get the `GRTSmh_brick` data source, i.e. `GRTSmaster_habitats` plus 9 extra layers:

```{r eval=FALSE}
read_GRTSmh(brick = TRUE)
#> class : RasterBrick
#> dimensions : 2843, 7401, 21041043, 10 (nrow, ncol, ncell, nlayers)
#> resolution : 32, 32 (x, y)
#> extent : 22029.59, 258861.6, 153054.1, 244030.1 (xmin, xmax, ymin, ymax)
#> crs : +proj=lcc +lat_1=51.16666723333333 +lat_2=49.8333339 +lat_0=90 +lon_0=4.367486666666666 +x_0=150000.013 +y_0=5400088.438 +ellps=intl +towgs84=-106.8686,52.2978,-103.7239,0.3366,-0.457,1.8422,-1.2747 +units=m +no_defs
#> source : [...]/n2khab_data/20_processed/GRTSmh_brick/GRTSmh_brick.tif
#> names : level0, level1, level2, level3, level4, level5, level6, level7, level8, level9
#> min values : 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
#> max values : 67108857, 16777209, 4194297, 1048569, 262137, 65529, 16377, 4089, 1017, 253
```{r}
r10 <- read_GRTSmh(brick = TRUE)
r10
#> class : SpatRaster
#> dimensions : 2843, 7401, 10 (nrow, ncol, nlyr)
#> resolution : 32, 32 (x, y)
#> extent : 22029.59, 258861.6, 153054.1, 244030.1 (xmin, xmax, ymin, ymax)
#> coord. ref. : BD72 / Belgian Lambert 72 (EPSG:31370)
#> source : GRTSmh_brick.tif
#> names : level0, level1, level2, level3, level4, level5, ...
#> min values : 1, 1, 1, 1, 1, 1, ...
#> max values : 67108857, 16777209, 4194297, 1048569, 262137, 65529, ...
terra::minmax(r10)
#> level0 level1 level2 level3 level4 level5 level6 level7 level8 level9
#> min 1 1 1 1 1 1 1 1 1 1
#> max 67108857 16777209 4194297 1048569 262137 65529 16377 4089 1017 253
```

The higher-level ranking numbers of the RasterBrick allow spatially balanced samples at lower spatial resolution than that of 32 m, and can also be used for aggregation purposes.
The provided hierarchical levels correspond to the resolution vector `32 * 2^(0:9)` (minimum: 32 meters, maximum: 16384 meters), with the corresponding RasterBrick layers named as `level0` to `level9`.
The layers with higher-level ranking numbers allow spatially balanced samples at lower spatial resolution than that of 32 m, and can also be used for aggregation purposes.
The provided hierarchical levels correspond to the resolution vector `32 * 2^(0:9)` (minimum: 32 meters, maximum: 16384 meters), with the corresponding layers named as `level0` to `level9`.

### read_GRTSmh_diffres()

`read_GRTSmh_diffres()` by default returns one RasterLayer from the `GRTSmh_diffres` data source, i.e. with the GRTS ranking numbers of the user-specified hierarchical level.
`read_GRTSmh_diffres()` by default returns one raster layer from the `GRTSmh_diffres` data source, i.e. with the GRTS ranking numbers of the user-specified hierarchical level.
This is done _at the corresponding spatial resolution_ of the GRTS algorithm, which is the fundamental distinction from `read_GRTSmh(brick = TRUE)`.

The resolutions of each level are the following (in meters):

```{r warning = FALSE, echo = FALSE}
```{r warning = FALSE, echo = FALSE, eval = TRUE}
data.frame(
level = 1:9,
resolution = 32 * 2^(1:9)
Expand All @@ -114,59 +121,62 @@ data.frame(

An example with level 5:

```{r eval=FALSE}
```{r}
read_GRTSmh_diffres(level = 5)
#> class : RasterLayer
#> dimensions : 89, 232, 20648 (nrow, ncol, ncell)
#> resolution : 1024, 1024 (x, y)
#> extent : 22030, 259598, 153054, 244190 (xmin, xmax, ymin, ymax)
#> crs : +proj=lcc +lat_1=51.16666723333333 +lat_2=49.8333339 +lat_0=90 +lon_0=4.367486666666666 +x_0=150000.013 +y_0=5400088.438 +ellps=intl +towgs84=-106.8686,52.2978,-103.7239,0.3366,-0.457,1.8422,-1.2747 +units=m +no_defs
#> source : [...]/n2khab_data/20_processed/GRTSmh_diffres/GRTSmh_diffres.5.tif
#> names : level5
#> values : 1, 65529 (min, max)
#> class : SpatRaster
#> dimensions : 89, 232, 1 (nrow, ncol, nlyr)
#> resolution : 1024, 1024 (x, y)
#> extent : 22030, 259598, 153054, 244190 (xmin, xmax, ymin, ymax)
#> coord. ref. : BD72 / Belgian Lambert 72 (EPSG:31370)
#> source : GRTSmh_diffres.5.tif
#> name : level5
#> min value : 1
#> max value : 65529
```

Alternatively, a dissolved, polygonized variant of the corresponding `GRTSmh_brick` level can be returned as an `sf` object.
In order not to inflate the data source, this was only made available for levels 4 to 9.

```{r eval=FALSE}
```{r}
read_GRTSmh_diffres(level = 5, polygon = TRUE)
#> Simple feature collection with 13791 features and 1 field
#> geometry type: POLYGON
#> dimension: XY
#> bbox: xmin: 22029.59 ymin: 153054.1 xmax: 258861.6 ymax: 244030.1
#> epsg (SRID): 31370
#> proj4string: +proj=lcc +lat_1=51.16666723333333 +lat_2=49.8333339 +lat_0=90 +lon_0=4.367486666666666 +x_0=150000.013 +y_0=5400088.438 +ellps=intl +towgs84=-106.8686,52.2978,-103.7239,0.3366,-0.457,1.8422,-1.2747 +units=m +no_defs
#> First 10 features:
#> value geom
#> 1 23390 POLYGON ((178093.6 244030.1...
#> 2 56158 POLYGON ((178701.6 243646.1...
#> 3 23134 POLYGON ((177581.6 243870.1...
#> 4 60254 POLYGON ((179757.6 243454.1...
#> 5 6750 POLYGON ((176621.6 243390.1...
#> 6 60254 POLYGON ((180333.6 243230.1...
#> 7 58718 POLYGON ((176653.6 243166.1...
#> 8 52318 POLYGON ((177677.6 243166.1...
#> 9 3166 POLYGON ((178701.6 243166.1...
#> 10 15454 POLYGON ((179725.6 243166.1...
#> Geometry type: POLYGON
#> Dimension: XY
#> Bounding box: xmin: 22029.59 ymin: 153054.1 xmax: 258861.6 ymax: 244030.1
#> Projected CRS: BD72 / Belgian Lambert 72
#> # A tibble: 13,791 × 2
#> value geom
#> * <int> <POLYGON [m]>
#> 1 23390 ((178093.6 244030.1, 178093.6 243998.1, 178061.6 243998.1, 177997.6 24…
#> 2 56158 ((178701.6 243646.1, 178701.6 243166.1, 179725.6 243166.1, 179725.6 24…
#> 3 23134 ((177581.6 243870.1, 177581.6 243838.1, 177549.6 243838.1, 177485.6 24…
#> 4 60254 ((179757.6 243454.1, 179757.6 243422.1, 179725.6 243422.1, 179725.6 24…
#> 5 6750 ((176621.6 243390.1, 176621.6 243358.1, 176589.6 243358.1, 176589.6 24…
#> 6 60254 ((180333.6 243230.1, 180333.6 243198.1, 180365.6 243198.1, 180365.6 24…
#> 7 58718 ((176653.6 243166.1, 176653.6 242142.1, 177677.6 242142.1, 177677.6 24…
#> 8 52318 ((177677.6 243166.1, 177677.6 242142.1, 178701.6 242142.1, 178701.6 24…
#> 9 3166 ((178701.6 243166.1, 178701.6 242142.1, 179725.6 242142.1, 179725.6 24…
#> 10 15454 ((179725.6 243166.1, 179725.6 242142.1, 180749.6 242142.1, 180749.6 24…
#> # ℹ 13,781 more rows
```


### read_GRTSmh_base4frac()

Its use is just to return the base-4-fraction-converted `GRTSmaster_habitats` as a RasterLayer:
Its use is just to return the base-4-fraction-converted `GRTSmaster_habitats` as a SpatRaster object:

```{r eval=FALSE}
```{r}
options(scipen = 999, digits = 15)
read_GRTSmh_base4frac()
#> class : RasterLayer
#> dimensions : 2843, 7401, 21041043 (nrow, ncol, ncell)
#> resolution : 32, 32 (x, y)
#> extent : 22029.591973471, 258861.591973471, 153054.113583292, 244030.113583292 (xmin, xmax, ymin, ymax)
#> crs : +proj=lcc +lat_1=51.16666723333333 +lat_2=49.8333339 +lat_0=90 +lon_0=4.367486666666666 +x_0=150000.013 +y_0=5400088.438 +ellps=intl +towgs84=-106.8686,52.2978,-103.7239,0.3366,-0.457,1.8422,-1.2747 +units=m +no_defs
#> source : [...]/n2khab_data/20_processed/GRTSmh_base4frac/GRTSmh_base4frac.tif
#> names : GRTSmh_base4frac
#> values : 0.0000000000001, 0.3333333333321 (min, max)
#> class : SpatRaster
#> dimensions : 2843, 7401, 1 (nrow, ncol, nlyr)
#> resolution : 32, 32 (x, y)
#> extent : 22029.591973471, 258861.591973471, 153054.113583292, 244030.113583292 (xmin, xmax, ymin, ymax)
#> coord. ref. : BD72 / Belgian Lambert 72 (EPSG:31370)
#> source : GRTSmh_base4frac.tif
#> name : GRTSmh_base4frac
#> min value : 0.0000000000001
#> max value : 0.3333333333321
```

Note that the used options are necessary when treating these base-4-fraction GRTS addresses as characters; otherwise scientific notations will be used.
Expand Down

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