vignettes/aoh.Rmd
aoh.RmdAfter generating the Area of Habitat data, we can import them.
# import the Area of Habitat data
@@ -288,10 +288,14 @@ Tutorial## resolution : 100, 100 (x, y)
## extent : -914731, 318669, 4364377, 5066777 (xmin, xmax, ymin, ymax)
## coord. ref. : World_Behrmann
-## sources : spat_pN3mxv1FCLTOgNL_55031.tif
-## spat_vXSxz0rfRIU1cl4_55031.tif
-## spat_oKUh2besnzKiIvj_55031.tif
-## spat_uFag2xakMQdtk9u_55031.tif
+## sources : spat_s5FSk0PawCzA9Hn_751859.tif
+## spat_afzRH2jBAHmqqD7_751859.tif
+## spat_3us8VucBA4OYU4Q_751859.tif
+## spat_O3tavtYKMg3ocTw_751859.tif
+## varnames : 979_1
+## 59448_1
+## 4657_1
+## ...
## names : AOH_979_1, AOH_59448_1, AOH_4657_1, AOH_58622_1
## min values : 0, 0, 0, 0
## max values : 1, 1, 1, 1
@@ -300,7 +304,11 @@ Can I use habitat classification data from other data sources?
-Yes, you can use habitat classification data from a variety of sources. For example, the habitat classification data could be derived from Copernicus Corine Land Cover, and MODIS Land Cover data (MCD12Q1)). To use such data, you will also need to develop a crosswalk table to specify which land cover (or habitat) classes correspond to which habitat classes as defined by the IUCN Red List Habitat Classification Scheme (e.g., see Tracewski et al. 2016; Lumbierres et al. 2021). After preparing the habitat classification data and the crosswalk table, they can be used to create Area of Habitat data (via create_spp_aoh_data()). For more information, see the Customization vignette.
Yes, you can use habitat classification data from a variety of sources. For example, the habitat classification data could be derived from Copernicus Corine Land Cover, and MODIS Land Cover data (MCD12Q1)). To use such data, you will also need to develop a crosswalk table to specify which land cover (or habitat) classes correspond to which habitat classes as defined by the IUCN Red List Habitat Classification Scheme (e.g., see Tracewski et al. 2016; Lumbierres et al. 2021). After preparing the habitat classification data and the crosswalk table, they can be used to create Area of Habitat data (via create_spp_aoh_data()). For more information, see the Customization vignette.
The output Area of Habitat data have different spatial extents, how can I combine them together?
diff --git a/docs/articles/aoh_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/aoh_files/figure-html/unnamed-chunk-10-1.png index 7ce507c2..f228346e 100644 Binary files a/docs/articles/aoh_files/figure-html/unnamed-chunk-10-1.png and b/docs/articles/aoh_files/figure-html/unnamed-chunk-10-1.png differ diff --git a/docs/articles/customization.html b/docs/articles/customization.html index b8d3c3ad..6e4174f3 100644 --- a/docs/articles/customization.html +++ b/docs/articles/customization.html @@ -33,7 +33,7 @@vignettes/customization.Rmd
customization.RmdThe aoh R package provides a flexible framework for generating Area of Habitat data. By default, it will use elevation data derived from Robinson et al. (2014) and habitat classification data derived from Lumbierres et al. (2021). Its defaults also include using species’ elevational limit and habitat preference data from the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. In addition to these defaults, it provides built-in functions to use habitat classification derived from other data sources (e.g., from Jung et al. 2020). The package can also be used to generate Area of Habitat data using other datasets that have been manually created by the user. For example, it could be used to produce Area of Habitat data using habitat classification data derived from Copernicus Corine Land Cover data or species’ elevational limit data from the BirdLife Data Zone.
+The aoh R package provides a flexible framework for generating Area of Habitat data. By default, it will use elevation data derived from Robinson et al. (2014) and habitat classification data derived from Lumbierres et al. (2021). Its defaults also include using species’ elevational limit and habitat preference data from the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. In addition to these defaults, it provides built-in functions to use habitat classification derived from other data sources (e.g., from Jung et al. 2020). The package can also be used to generate Area of Habitat data using other datasets that have been manually created by the user. For example, it could be used to produce Area of Habitat data using habitat classification data derived from Copernicus Corine Land Cover data or species’ elevational limit data from the BirdLife Data Zone.
Hanson JO (2023) aoh: Create Area of Habitat Data. R package version 0.0.2.8. Available at https://github.com/prioritizr/aoh.
+Hanson JO (2023) aoh: Create Area of Habitat Data. R package version 0.0.2.9. Available at https://github.com/prioritizr/aoh.
@Manual{,
author = {Jeffrey O Hanson},
title = {aoh: Create Area of Habitat Data},
year = {2023},
- note = {R package version 0.0.2.8},
+ note = {R package version 0.0.2.9},
url = {https://github.com/prioritizr/aoh},
}
IUCN [insert year] IUCN Red List of Threatened Species. Version [insert version]. Available at www.iucnredlist.org.
diff --git a/docs/index.html b/docs/index.html index 0b841587..4745d6cf 100644 --- a/docs/index.html +++ b/docs/index.html @@ -46,7 +46,7 @@ @@ -293,7 +293,11 @@# create maps
## N.B. you might need to install the ggmap package
map <-
- plot_spp_aoh_data(spp_aoh_data, zoom = 6, maptype = "toner-background") +
+ plot_spp_aoh_data(
+ spp_aoh_data,
+ zoom = 6,
+ maptype = "stamen_toner_background"
+ ) +
scale_fill_viridis_d() +
scale_color_manual(values = c("range" = "red")) +
scale_size_manual(values = c("range" = 0.5)) +
@@ -302,9 +306,10 @@ Usage
axis.text = element_text(size = 6),
strip.text = element_text(color = "white"),
strip.background = element_rect(fill = "black", color = "black")
- )
-
-# display maps
+ )
+## |---------|---------|---------|---------|========================================= |---------|---------|---------|---------|=========================================
+# display maps
print(map)
Please cite the aoh R package and the underlying datasets used to produce Area of Habitat data.
-Area of Habitat data are created using a range of different datasets.
-Depending on which datasets are used, please cite the aoh package and
-relevant data using:
-
- Hanson JO (2023) aoh: Create Area of Habitat Data. R package version
- 0.0.2.8. Available at https://github.com/prioritizr/aoh.
-
- IUCN [insert year] IUCN Red List of Threatened Species. Version
- [insert version]. Available at www.iucnredlist.org.
-
- BirdLife International and Handbook of the Birds of the World
- ([insert year]) Bird species distribution maps of the world. Version
- [insert version]. Available at
- http://datazone.birdlife.org/species/requestdis.
-
- Jung M, Dahal PR, Butchart SHM, Donald PF, De Lamo X, Lesiv M, Kapos
- V, Rondinini C, Visconti P (2020). "A global map of terrestrial
- habitat types." _Scientific Data_, *7*(1), 256.
- doi:10.1038/s41597-020-00599-8
- <https://doi.org/10.1038/s41597-020-00599-8>.
-
- Jung M, Dahal PR, Butchart SHM, Donald PF, De Lamo X, Lesiv M, Kapos
- V, Rondinini C, and Visconti P (2020b) A global map of terrestrial
- habitat types (insert version) [Data set]. Zenodo. Available at
- https://doi.org/10.5281/zenodo.4058819.
-
- Lumbierres M, Dahal PR, Di Marco M, Butchart SHM, Donald PF,
- Rondinini C (2021). "Translating habitat class to land cover to map
- area of habitat of terrestrial vertebrates." _Conservation Biology_,
- *36*(3), e13851. doi:10.1111/cobi.13851
- <https://doi.org/10.1111/cobi.13851>.
-
- Robinson N, Regetz J, Guralnick RP (2014). "EarthEnv-DEM90: A
- nearly-global, void-free, multi-scale smoothed 90m digital elevation
- model from fused ASTER and SRTM data." _ISPRS Journal of
- Photogrammetry and Remote Sensing_, *87*(1), 57-67.
- doi:10.1016/j.isprsjprs.2013.11.002
- <https://doi.org/10.1016/j.isprsjprs.2013.11.002>.
-
-To see these entries in BibTeX format, use 'print(<citation>,
-bibtex=TRUE)', 'toBibtex(.)', or set
-'options(citation.bibtex.max=999)'.Area of Habitat data are created using a range of different datasets.
+Depending on which datasets are used, please cite the aoh package and
+relevant data using:
+
+ Hanson JO (2023) aoh: Create Area of Habitat Data. R package version
+ 0.0.2.9. Available at https://github.com/prioritizr/aoh.
+
+ IUCN [insert year] IUCN Red List of Threatened Species. Version
+ [insert version]. Available at www.iucnredlist.org.
+
+ BirdLife International and Handbook of the Birds of the World
+ ([insert year]) Bird species distribution maps of the world. Version
+ [insert version]. Available at
+ http://datazone.birdlife.org/species/requestdis.
+
+ Jung M, Dahal PR, Butchart SHM, Donald PF, De Lamo X, Lesiv M, Kapos
+ V, Rondinini C, Visconti P (2020). "A global map of terrestrial
+ habitat types." _Scientific Data_, *7*(1), 256.
+ doi:10.1038/s41597-020-00599-8
+ <https://doi.org/10.1038/s41597-020-00599-8>.
+
+ Jung M, Dahal PR, Butchart SHM, Donald PF, De Lamo X, Lesiv M, Kapos
+ V, Rondinini C, and Visconti P (2020b) A global map of terrestrial
+ habitat types (insert version) [Data set]. Zenodo. Available at
+ https://doi.org/10.5281/zenodo.4058819.
+
+ Lumbierres M, Dahal PR, Di Marco M, Butchart SHM, Donald PF,
+ Rondinini C (2021). "Translating habitat class to land cover to map
+ area of habitat of terrestrial vertebrates." _Conservation Biology_,
+ *36*(3), e13851. doi:10.1111/cobi.13851
+ <https://doi.org/10.1111/cobi.13851>.
+
+ Robinson N, Regetz J, Guralnick RP (2014). "EarthEnv-DEM90: A
+ nearly-global, void-free, multi-scale smoothed 90m digital elevation
+ model from fused ASTER and SRTM data." _ISPRS Journal of
+ Photogrammetry and Remote Sensing_, *87*(1), 57-67.
+ doi:10.1016/j.isprsjprs.2013.11.002
+ <https://doi.org/10.1016/j.isprsjprs.2013.11.002>.
+
+To see these entries in BibTeX format, use 'print(<citation>,
+bibtex=TRUE)', 'toBibtex(.)', or set
+'options(citation.bibtex.max=999)'.NEWS.md
+ plot_spp_aoh_data() and plot_spp_frc_data() to be compatible with changes to the ggmap package for creating maps with a basemap.numeric Value indicating the zoom level for the basemap.
-See documentation for the zoom parameter in the ggmap::get_stamenmap()
+See documentation for the zoom parameter in the ggmap::get_stadiamap()
function for details.
Defaults to NULL such that no basemap is shown.
character Value indicating the name of the
the basemap to use for the plot.
See documentation for the maptype parameter in the
-ggmap::get_stamenmap()
+ggmap::get_stadiamap()
function for details.
Defaults to NULL such that no basemap is shown.
Note that the ggmap package must be installed to show a basemap.
Additional arguments passed to ggmap::get_stamenmap().
Additional arguments passed to ggmap::get_stadiamap().
diff --git a/docs/reference/plot_spp_frc_data-3.png b/docs/reference/plot_spp_frc_data-3.png
index 1e10d3ae..0c056782 100644
Binary files a/docs/reference/plot_spp_frc_data-3.png and b/docs/reference/plot_spp_frc_data-3.png differ
diff --git a/docs/reference/plot_spp_frc_data.html b/docs/reference/plot_spp_frc_data.html
index 05339f6b..10f14729 100644
--- a/docs/reference/plot_spp_frc_data.html
+++ b/docs/reference/plot_spp_frc_data.html
@@ -18,7 +18,7 @@
numeric Value indicating the zoom level for the basemap.
-See documentation for the zoom parameter in the ggmap::get_stamenmap()
+See documentation for the zoom parameter in the ggmap::get_stadiamap()
function for details.
Defaults to NULL such that no basemap is shown.
character Value indicating the name of the
the basemap to use for the plot.
See documentation for the maptype parameter in the
-ggmap::get_stamenmap()
+ggmap::get_stadiamap()
function for details.
Defaults to NULL such that no basemap is shown.
Note that the ggmap package must be installed to show a basemap.
Additional arguments passed to ggmap::get_stamenmap().
Additional arguments passed to ggmap::get_stadiamap().
diff --git a/docs/reference/read_spp_range_data.html b/docs/reference/read_spp_range_data.html
index 821d9b27..e88ecfcf 100644
--- a/docs/reference/read_spp_range_data.html
+++ b/docs/reference/read_spp_range_data.html
@@ -19,7 +19,7 @@
After generating the Area of Habitat data, we can import them.
# import the Area of Habitat data
## since the data for each species have a different spatial extent
@@ -342,19 +342,19 @@ Tutorial
spp_aoh_rasters <- terra_combine(spp_aoh_rasters)##
|---------|---------|---------|---------|
-==========
+========
|---------|---------|---------|---------|
-==========
+========
|---------|---------|---------|---------|
-==========
+========
|---------|---------|---------|---------|
-=====================
+=========================
# assign identifiers to layer names
names(spp_aoh_rasters) <- paste0(
@@ -368,10 +368,14 @@ Tutorial
## resolution : 100, 100 (x, y)
## extent : -914731, 318669, 4364377, 5066777 (xmin, xmax, ymin, ymax)
## coord. ref. : World_Behrmann
-## sources : spat_xr9LNoI3lw6sGAS_55478.tif
-## spat_rl2INSwBzo3Bpiq_55478.tif
-## spat_r513KMZWKhupFt8_55478.tif
-## spat_29FAKr7VjmetEyo_55478.tif
+## sources : spat_HPn6UMuggEKqVTn_752309.tif
+## spat_AMY34IdEb9yBKOZ_752309.tif
+## spat_raTJr8EPKYYg6V5_752309.tif
+## spat_ITOzWXlpPYsO0Z1_752309.tif
+## varnames : 979_1
+## 59448_1
+## 4657_1
+## ...
## names : AOH_979_1, AOH_59448_1, AOH_4657_1, AOH_58622_1
## min values : 0, 0, 0, 0
## max values : 1, 1, 1, 1# create maps
## N.B. you might need to install the ggmap package to create the maps
map <-
- plot_spp_aoh_data(spp_aoh_data, zoom = 6, maptype = "toner-background") +
- scale_fill_viridis_d() +
- scale_color_manual(values = c("range" = "red")) +
- scale_size_manual(values = c("range" = 0.5)) +
- theme(
- axis.title = element_blank(),
- axis.text = element_text(size = 6),
- strip.text = element_text(color = "white"),
- strip.background = element_rect(fill = "black", color = "black")
- )##
-|---------|---------|---------|---------|
-=========================================
- # display maps
-print(map)
Please open the .Renviron file on your computer (e.g., using usethis::edit_r_environ()). Next, please add the following text to the file (replacing the string with the token) and save the file:
IUCN_REDLIST_KEY="your_actual_token_not_this_string"Please restart your R session. You should now be able to access the IUCN Red List API. To verify this, please try running the following R code and – assuming everything works correctly – you should see the current version of the IUCN Red List:
-# verify access to IUCN Red List API
-rredlist::rl_version()# verify access to IUCN Red List API
+rredlist::rl_version()If these instructions did not work, please consult the documentation for the rredlist R package for further details.
Where can I find species range data for generating Area of Habitat data?
Species range data can be obtained from the IUCN Red List (see Spatial Data Download resources). They can also be obtained from other data sources (see the question below for details).
Can I use elevation data from other data sources?
Yes, you can use elevation data from a variety of sources. For example, elevation data could be derived from NASA’s Shuttle Radar Topography Mission (SRTM). After preparing the elevation data, they can be used to create Area of Habitat data (via create_spp_aoh_data()). For more information, see the Customization vignette.
Can I use habitat classification data from other data sources?
-Yes, you can use habitat classification data from a variety of sources. For example, the habitat classification data could be derived from Copernicus Corine Land Cover, and MODIS Land Cover data (MCD12Q1)). To use such data, you will also need to develop a crosswalk table to specify which land cover (or habitat) classes correspond to which habitat classes as defined by the IUCN Red List Habitat Classification Scheme (e.g., see Tracewski et al. 2016; Lumbierres et al. 2021). After preparing the habitat classification data and the crosswalk table, they can be used to create Area of Habitat data (via create_spp_aoh_data()). For more information, see the Customization vignette.
Yes, you can use habitat classification data from a variety of sources. For example, the habitat classification data could be derived from Copernicus Corine Land Cover, and MODIS Land Cover data (MCD12Q1)). To use such data, you will also need to develop a crosswalk table to specify which land cover (or habitat) classes correspond to which habitat classes as defined by the IUCN Red List Habitat Classification Scheme (e.g., see Tracewski et al. 2016; Lumbierres et al. 2021). After preparing the habitat classification data and the crosswalk table, they can be used to create Area of Habitat data (via create_spp_aoh_data()). For more information, see the Customization vignette.
The output Area of Habitat data have different spatial extents, how can I combine them together?
The terra_combine() function can be used to align and combine a list of raster terra::rast() objects into a single object. Note that this procedure is only recommended when all species occur in the same geographic region. Please see the tutorial above for an example of using this function to combine Area of Habitat data for multiple species into a single object.
The aoh R package provides a flexible framework for generating Area of Habitat data. By default, it will use elevation data derived from Robinson et al. (2014) and habitat classification data derived from Lumbierres et al. (2021). Its defaults also include using species’ elevational limit and habitat preference data from the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. In addition to these defaults, it provides built-in functions to use habitat classification derived from other data sources (e.g., from Jung et al. 2020). The package can also be used to generate Area of Habitat data using other datasets that have been manually created by the user. For example, it could be used to produce Area of Habitat data using habitat classification data derived from Copernicus Corine Land Cover data or species’ elevational limit data from the BirdLife Data Zone.
+The aoh R package provides a flexible framework for generating Area of Habitat data. By default, it will use elevation data derived from Robinson et al. (2014) and habitat classification data derived from Lumbierres et al. (2021). Its defaults also include using species’ elevational limit and habitat preference data from the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. In addition to these defaults, it provides built-in functions to use habitat classification derived from other data sources (e.g., from Jung et al. 2020). The package can also be used to generate Area of Habitat data using other datasets that have been manually created by the user. For example, it could be used to produce Area of Habitat data using habitat classification data derived from Copernicus Corine Land Cover data or species’ elevational limit data from the BirdLife Data Zone.
