diff --git a/.github/workflows/R-CMD-check-macos.yaml b/.github/workflows/R-CMD-check-macos.yaml index 55811c9f..899764c6 100644 --- a/.github/workflows/R-CMD-check-macos.yaml +++ b/.github/workflows/R-CMD-check-macos.yaml @@ -71,7 +71,7 @@ jobs: install.packages("sf") install.packages("terra") install.packages("lwgeom") - remotes::install_github("dickoa/prepr") + remotes::install_github("prioritizr/prepr") remotes::install_github("r-spatial/link2GI") shell: Rscript {0} diff --git a/.github/workflows/R-CMD-check-ubuntu.yaml b/.github/workflows/R-CMD-check-ubuntu.yaml index 527e9a38..e5c946d0 100644 --- a/.github/workflows/R-CMD-check-ubuntu.yaml +++ b/.github/workflows/R-CMD-check-ubuntu.yaml @@ -83,7 +83,7 @@ jobs: install.packages("link2GI") install.packages("rgrass") install.packages("smoothr") - remotes::install_github("dickoa/prepr") + remotes::install_github("prioritizr/prepr") shell: Rscript {0} - name: Session information diff --git a/.github/workflows/R-CMD-check-windows.yaml b/.github/workflows/R-CMD-check-windows.yaml index 73659ba4..f61569a1 100644 --- a/.github/workflows/R-CMD-check-windows.yaml +++ b/.github/workflows/R-CMD-check-windows.yaml @@ -69,7 +69,7 @@ jobs: install.packages("sf") install.packages("terra") install.packages("lwgeom") - remotes::install_github("dickoa/prepr") + remotes::install_github("prioritizr/prepr") shell: Rscript {0} - name: Session information diff --git a/.github/workflows/documentation.yaml b/.github/workflows/documentation.yaml index 47b0fcc9..fa24ee2e 100644 --- a/.github/workflows/documentation.yaml +++ b/.github/workflows/documentation.yaml @@ -78,7 +78,7 @@ jobs: install.packages("lwgeom") install.packages("link2GI") install.packages("rgrass") - remotes::install_github("dickoa/prepr") + remotes::install_github("prioritizr/prepr") shell: Rscript {0} - name: Session information diff --git a/DESCRIPTION b/DESCRIPTION index 696a57a0..6defb911 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: aoh Type: Package -Version: 0.0.2.9 +Version: 0.0.2.10 Title: Create Area of Habitat Data Description: Create Area of Habitat data to characterize species distributions. Data are produced following procedures outlined by Brooks et al. (2019) @@ -15,7 +15,7 @@ Description: Create Area of Habitat data to characterize species distributions. processing time. To augment data cleaning procedures, users can also install the 'prepr' R package - (available at ). + (available at ). Authors@R: c(person(c('Jeffrey', 'O'), 'Hanson', email='jeffrey.hanson@uqconnect.edu.au', role = c('aut','cre'), @@ -51,7 +51,7 @@ Suggests: roxygen2 (>= 6.1.1), rmarkdown (>= 1.10), pingr (>= 1.1.2), - ggmap (>= 3.0.2.9002), + ggmap (>= 4.0.0), fields (>= 14.0), smoothr (>= 0.2.2), rnaturalearth (>= 0.3.3), @@ -59,7 +59,7 @@ Suggests: archive (>= 1.1.2), link2GI (>= 0.5-0), rgrass (>= 0.3-8), - prepr (>= 0.1.9000), + prepr (>= 0.3.0), vcr (>= 0.6.0) Depends: R (>= 4.1.0), @@ -73,7 +73,7 @@ SystemRequirements: GDAL (>= 3.0.2) (optional), PROJ (>= 7.2.0) (optional) URL: https://prioritizr.github.io/aoh/, https://github.com/prioritizr/aoh BugReports: https://github.com/prioritizr/aoh/issues VignetteBuilder: knitr -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 Collate: 'internal.R' 'calc_spp_frc_data.R' @@ -131,6 +131,5 @@ Collate: 'zzz.R' Roxygen: list(markdown = TRUE) Remotes: - dickoa/prepr, - r-spatial/link2GI, - dkahle/ggmap + prioritizr/prepr, + r-spatial/link2GI diff --git a/NEWS.md b/NEWS.md index b401753d..527bfc9b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# aoh 0.0.2.10 + +- Update _prepr_ and _ggmap_ package dependencies. + # aoh 0.0.2.9 - Remove _rgdal_ package dependency. diff --git a/README.Rmd b/README.Rmd index 4b6deec4..f3946610 100644 --- a/README.Rmd +++ b/README.Rmd @@ -50,7 +50,7 @@ The _aoh R_ package can leverage the _prepr R_ package to augment data cleaning ```{r, eval = FALSE} if (!require(remotes)) install.packages("remotes") -remotes::install_github("dickoa/prepr") +remotes::install_github("prioritizr/prepr") ``` The package can also leverage the [Geospatial Data Abstraction Library (GDAL)](https://gdal.org/) and [Geographic Resources Analysis Support System (GRASS)](https://grass.osgeo.org/) to help reduce processing time. Although use of these software is optional, they can help improve computational performance when processing data across large spatial extents. Below we provide platform-specific instructions to install dependencies for the _prepr R_ package, GDAL, and GRASS. diff --git a/README.md b/README.md index a83ec2de..dc4e00df 100644 --- a/README.md +++ b/README.md @@ -82,7 +82,7 @@ installed (see below for platform-specific instructions). ``` r if (!require(remotes)) install.packages("remotes") -remotes::install_github("dickoa/prepr") +remotes::install_github("prioritizr/prepr") ``` The package can also leverage the [Geospatial Data Abstraction Library @@ -349,11 +349,7 @@ map <- strip.text = element_text(color = "white"), strip.background = element_rect(fill = "black", color = "black") ) -``` - - ## |---------|---------|---------|---------|========================================= |---------|---------|---------|---------|========================================= -``` r # display maps print(map) ``` @@ -369,8 +365,8 @@ produce Area of Habitat data. 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. + Hanson JO (2024) aoh: Create Area of Habitat Data. R package version + 0.0.2.10. Available at 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/404.html b/docs/404.html index 60016eb7..7209253e 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ aoh - 0.0.2.9 + 0.0.2.10 diff --git a/docs/articles/aoh.html b/docs/articles/aoh.html index 3bc84937..79b31c5b 100644 --- a/docs/articles/aoh.html +++ b/docs/articles/aoh.html @@ -33,7 +33,7 @@ aoh - 0.0.2.9 + 0.0.2.10 @@ -83,7 +83,7 @@

Getting started

-

2023-11-02

+

2024-04-26

Source: vignettes/aoh.Rmd @@ -199,10 +199,10 @@

Tutorial## # A tibble: 4 × 5 ## id_no binomial seasonal path geometry ## <dbl> <chr> <int> <chr> <POLYGON [m]> -## 1 979 Alytes dickhilleni 1 /tmp/RtmpyhAIR… ((-105506.8 4465112, -10… -## 2 59448 Calotriton asper 1 /tmp/RtmpyhAIR… ((-238681 5029057, -2377… -## 3 4657 Chioglossa lusitanica 1 /tmp/RtmpyhAIR… ((-859201.6 4559278, -85… -## 4 58622 Rana iberica 1 /tmp/RtmpyhAIR… ((-849801.9 4614149, -84… +## 1 979 Alytes dickhilleni 1 /tmp/RtmpFuktG… ((-105506.8 4465112, -10… +## 2 59448 Calotriton asper 1 /tmp/RtmpFuktG… ((-238681 5029057, -2377… +## 3 4657 Chioglossa lusitanica 1 /tmp/RtmpFuktG… ((-859201.6 4559278, -85… +## 4 58622 Rana iberica 1 /tmp/RtmpFuktG… ((-849801.9 4614149, -84…

After generating the Area of Habitat data, we can import them.

 -
## 
-|---------|---------|---------|---------|
-=======
-                                          
-
-|---------|---------|---------|---------|
-=======
-                                          
-
-|---------|---------|---------|---------|
-=======
-                                          
-
-|---------|---------|---------|---------|
-=====================
-
+
## |---------|---------|---------|---------|=====                                          |---------|---------|---------|---------|=====                                          |---------|---------|---------|---------|=====                                          |---------|---------|---------|---------|=====================
-
## 
-|---------|---------|---------|---------|
-=========================================
-                                          
-
-|---------|---------|---------|---------|
-=========================================
-
+
## |---------|---------|---------|---------|=========================================                                          
 # display maps
 print(map)
@@ -385,7 +363,7 @@

Frequently asked questions

  • 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 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.

    • 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 f228346e..21180f77 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 6e4174f3..f795f9d5 100644 --- a/docs/articles/customization.html +++ b/docs/articles/customization.html @@ -33,7 +33,7 @@ aoh - 0.0.2.9 + 0.0.2.10 @@ -83,7 +83,7 @@

    Customization

    -

    2023-11-02

    +

    2024-04-26

    Source: vignettes/customization.Rmd @@ -264,7 +264,7 @@

    Tutorial) # import elevation data -elevation_data <- rast(elevation_path) +elevation_data <- rast(elevation_path) # preview data print(elevation_data)

    @@ -279,7 +279,7 @@

    Tutorial## max value : 3260 
     # visualize data
-plot(elevation_data, main = "Elevation data")
    +plot(elevation_data, main = "Elevation data")

    Next, we will import habitat classification data. Although such data would be automatically imported by default (using the get_lumb_cgls_habitat_data() function), here we will import example data distributed with the package.

    @@ -289,7 +289,7 @@ 
    Tutorial)
 
 # import habitat classification data
-habitat_data <- rast(habitat_path)
+habitat_data <- rast(habitat_path)
 
 # preview data
 print(habitat_data)
    @@ -304,7 +304,7 @@

    Tutorial## max value : 1405 
     # visualize data
-plot(habitat_data, main = "Habitat classification data")
    +plot(habitat_data, main = "Habitat classification data")

    Critically, the elevation data and habitat classification data must have exactly the same spatial properties. This means they must have the same coordinate reference system, resolution, and spatial extent. If you are using elevation or habitat classification data that you have previously prepared yourself (or manually download from online sources), you may need to resample (or reproject) your data to ensure both datasets have the same spatial properties using a geographic information system (GIS). For example, data could be resampled using ESRI ArcGIS, QGIS, terra R package, or the gdalUtilities R package. We can verify that both of the elevation and habitat classification datasets have the same spatial properties using the following code.

    +compareGeom(elevation_data, habitat_data) 
    ## [1] TRUE

    We will now import a crosswalk table for the habitat classification data. A crosswalk table specifies which pixel values in the habitat classification data correspond to which IUCN habitat classes. This table can specify one-to-one relationships (e.g., pixel value 12 corresponds to IUCN class 1.1), one-to-many relationships (e.g., pixel values 12 corresponds to IUCN classes 1.1 and 1.2), and many-to-many relationships (e.g., both pixel values 12 and 13 each correspond to IUCN classes 1.1 and 1.2). Although such data would be automatically imported by default (i.e., the crosswalk_lumb_cgls_data built-in dataset), here we will import example data distributed with the package. When using your own habitat classification data, please ensure that it follows the same format (i.e., same column names and data types).

    @@ -605,21 +605,21 @@ 
    Tutorial## 15 1.5|3.5|3.8|4.4|5.5|14.5    1.5|3.5|3.8|4.4|5.5|14.5                 32
 ##    elevation_upper    xmin    xmax    ymin    ymax path                      
 ##  *           <dbl>   <dbl>   <dbl>   <dbl>   <dbl> <chr>                     
-##  1             830 -896631  -61631 4373077 5070077 /tmp/RtmpNqzWup/932_1.tif 
-##  2             999 -902631  -60631 4303077 5070077 /tmp/RtmpNqzWup/3032_1.tif
-##  3             874 -707631  320369 4305077 5058077 /tmp/RtmpNqzWup/3046_1.tif
-##  4             874 -734631 -504631 4658077 5011077 /tmp/RtmpNqzWup/3046_3.tif
-##  5             874 -916631 -708631 4520077 5015077 /tmp/RtmpNqzWup/3046_4.tif
-##  6            1050 -620631  320369 4304077 5058077 /tmp/RtmpNqzWup/3255_1.tif
-##  7             933 -916631  116369 4304077 5044077 /tmp/RtmpNqzWup/4008_1.tif
-##  8             942 -916631  266369 4303077 5070077 /tmp/RtmpNqzWup/4785_1.tif
-##  9            1058 -910631   65369 4574077 5070077 /tmp/RtmpNqzWup/4973_1.tif
-## 10            1018 -565631  -96631 4304077 4587077 /tmp/RtmpNqzWup/5854_1.tif
-## 11            1052 -752631  -66631 4374077 5058077 /tmp/RtmpNqzWup/6068_1.tif
-## 12            1017 -284631  239369 4373077 4967077 /tmp/RtmpNqzWup/6678_1.tif
-## 13            1017 -794631 -396631 4901077 5070077 /tmp/RtmpNqzWup/6678_2.tif
-## 14            1017 -617631 -393631 4304077 4447077 /tmp/RtmpNqzWup/6678_3.tif
-## 15            1017 -868631 -654631 4404077 4576077 /tmp/RtmpNqzWup/6678_4.tif
+##  1             830 -896631  -61631 4373077 5070077 /tmp/Rtmpj0o7Xq/932_1.tif 
+##  2             999 -902631  -60631 4303077 5070077 /tmp/Rtmpj0o7Xq/3032_1.tif
+##  3             874 -707631  320369 4305077 5058077 /tmp/Rtmpj0o7Xq/3046_1.tif
+##  4             874 -734631 -504631 4658077 5011077 /tmp/Rtmpj0o7Xq/3046_3.tif
+##  5             874 -916631 -708631 4520077 5015077 /tmp/Rtmpj0o7Xq/3046_4.tif
+##  6            1050 -620631  320369 4304077 5058077 /tmp/Rtmpj0o7Xq/3255_1.tif
+##  7             933 -916631  116369 4304077 5044077 /tmp/Rtmpj0o7Xq/4008_1.tif
+##  8             942 -916631  266369 4303077 5070077 /tmp/Rtmpj0o7Xq/4785_1.tif
+##  9            1058 -910631   65369 4574077 5070077 /tmp/Rtmpj0o7Xq/4973_1.tif
+## 10            1018 -565631  -96631 4304077 4587077 /tmp/Rtmpj0o7Xq/5854_1.tif
+## 11            1052 -752631  -66631 4374077 5058077 /tmp/Rtmpj0o7Xq/6068_1.tif
+## 12            1017 -284631  239369 4373077 4967077 /tmp/Rtmpj0o7Xq/6678_1.tif
+## 13            1017 -794631 -396631 4901077 5070077 /tmp/Rtmpj0o7Xq/6678_2.tif
+## 14            1017 -617631 -393631 4304077 4447077 /tmp/Rtmpj0o7Xq/6678_3.tif
+## 15            1017 -868631 -654631 4404077 4576077 /tmp/Rtmpj0o7Xq/6678_4.tif
 ##                                                                         geometry
 ##  *                                                            <MULTIPOLYGON [m]>
 ##  1 (((-258785.9 4373975, -259388.9 4373961, -259722.7 4374219, -259763.3 437477…
diff --git a/docs/articles/customization_files/figure-html/unnamed-chunk-15-1.png b/docs/articles/customization_files/figure-html/unnamed-chunk-15-1.png
index 614d4368..4b8bab32 100644
Binary files a/docs/articles/customization_files/figure-html/unnamed-chunk-15-1.png and b/docs/articles/customization_files/figure-html/unnamed-chunk-15-1.png differ
diff --git a/docs/articles/index.html b/docs/articles/index.html
index ee318410..ff4640f0 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -17,7 +17,7 @@
       
       
         aoh
-        0.0.2.9
+        0.0.2.10
    diff --git a/docs/authors.html b/docs/authors.html index 0eb05228..d84fd453 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ aoh - 0.0.2.9 + 0.0.2.10 @@ -74,12 +74,12 @@

    Citation

    -

    Hanson JO (2023) aoh: Create Area of Habitat Data. R package version 0.0.2.9. Available at https://github.com/prioritizr/aoh.

    +

    Hanson JO (2024) aoh: Create Area of Habitat Data. R package version 0.0.2.10. 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 0.0.2.9},
+  year = {2024},
+  note = {R package version 0.0.2.10},
   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 4745d6cf..cd476441 100644 --- a/docs/index.html +++ b/docs/index.html @@ -25,7 +25,7 @@ processing time. To augment data cleaning procedures, users can also install the prepr' R package - (available at <https://github.com/dickoa/prepr>)."> + (available at <https://github.com/prioritizr/prepr>).">