Rory Landcover Functions

.Rbuildignore

@@ -12,3 +12,5 @@
 ^misc$
 ^\.vscode$
 ^[.]?air[.]toml$
+^\.positai$
+^\.claude$

.gitignore

@@ -7,4 +7,13 @@ docs
 misc
 cache
 rosm.cache
-*.zip
+*.zip
+testdir
+.positai
+vignettes/articles/modis
+vignettes/articles/TerrainTiles
+vignettes/articles/worldclim
+vignettes/articles/daymet
+modis
+scanfi
+daymet

CODE_DESIGN.md

@@ -1,51 +1,59 @@
 # naturecounts design principles
 
 ## Non-cloud data
+
 - Put data required to precompile vignettes in the `misc` folder
 - This isn't uploaded to GitHub
 
 ## Locations
+
 - API urls
   - are stored in `meta_info`, a tibble created in `data-raw/data_creation.R`
   - This is where you can change from main to sandbox versions
-  - https://naturecounts.ca/api vs. https://sandbox.naturecounts.ca/api
-  - To apply this you must **re-run** `data-raw/data_creation.R` and then
-    **re-load** the functions/package
+  - <https://naturecounts.ca/api> vs. <https://sandbox.naturecounts.ca/api>
+  - To apply this you must **re-run** `data-raw/data_creation.R` and then **re-load** the functions/package
 
 ## Fields returned by the API
 
 #### Desired behaviour
+
 Required and extra fields returned by the API are expected and treated, respectively, as follows:
 
-Function           | API Entry Point           | Required fields            | Extra fields
------------------- |-------------------------- | -------------------------- | ------------
-`nc_count()`       | `data/list_collections`   |  `collection`, `nrecords`  | Ignored
-`nc_count()`       | `data/list_permissions`   |  `collection`, `akn_level` | Ignored
-`nc_count()`       | `metadata/collections`    |  `collection`, `akn_level` | Ignored
-`nc_permissions()` | `data/list_permissions`   |  `collection`, `akn_level` | Ignored
-`srv_auth()`       | `data/authenticate`       |  `token`                   | Ignored
-`nc_data_dl()`     | `data/release_request_id` |  None (close request only) | Ignored
-`nc_data_dl()`     | `data/get_data`           |  Any                       | Added
-`meta_XXX()`       | `metadata/XXX`            |  Any                       | Added
+| Function | API Entry Point | Required fields | Extra fields |
+|----|----|----|----|
+| `nc_count()` | `data/list_collections` | `collection`, `nrecords` | Ignored |
+| `nc_count()` | `data/list_permissions` | `collection`, `akn_level` | Ignored |
+| `nc_count()` | `metadata/collections` | `collection`, `akn_level` | Ignored |
+| `nc_permissions()` | `data/list_permissions` | `collection`, `akn_level` | Ignored |
+| `srv_auth()` | `data/authenticate` | `token` | Ignored |
+| `nc_data_dl()` | `data/release_request_id` | None (close request only) | Ignored |
+| `nc_data_dl()` | `data/get_data` | Any | Added |
+| `meta_XXX()` | `metadata/XXX` | Any | Added |
 
 #### What will break the package
-- Missing "Required fields" 
-- Missing/renamed "container"  
-  Some API entry points return data in a container, for example, 
-
-  - `data/get_data` -> `results` (holds main data)
-  - `data/list_collections` -> `results` (holds counts); `request_id` (holds request id)
-  - `data/list_requests` -> `requests` (holds details on individual requests)
+
+- Missing "Required fields"
+
+- Missing/renamed "container"\
+  Some API entry points return data in a container, for example,
+
+  - `data/get_data` -\> `results` (holds main data)
+  - `data/list_collections` -\> `results` (holds counts); `request_id` (holds request id)
+  - `data/list_requests` -\> `requests` (holds details on individual requests)
 
   If these "containers" change names, the package will break.
 
 #### Coding Principles
-- In package, after accessing the API, explictly `select()` the fields/columns expected. This way extra fields won't break existing code 
+
+- In package, after accessing the API, explictly `select()` the fields/columns expected. This way extra fields won't break existing code
   - Missing fields **will** break the code, but at least they will break the code early!
   - Do **not** do this for data downloads (i.e. `nc_single_dl()` under `nc_data_dl()`) or metadata downloads (i.e. `meta_XXX()`)
   - **Unless**, using a `meta_XXX()` download internally. Then always `select()` the fields required
 
 ## Testing
+
 - Tests are run using the user "testuser"
   - Locally password can be stored in .Renviron as naturecounts_testuser = PASSWORD
   - For remote testing, password is supplied as encrypted values
+- Tests for covariate download and extraction functions are run using the EarthData user with email `[email protected]` and username `rdjmacklin_bc`. If Rory Macklin can't be contacted to access credentials, a new user can be made with necessary changes to `ed_email` argument in tests for `landcover_download()` and `vegetation_download()` and to `ed_username` argument in tests for `daymet_download()` , `daymet_request()` and `daymet_check()`.
+  - Locally, password can be stored in .Renviron as EarthData_password = PASSWORD or supplied via `askpass::askpass()` built into functions.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: naturecounts
 Type: Package
 Title: Access and download data on plant and animal populations from NatureCounts
-Version: 0.5.0
+Version: 0.5.0.9000
 Authors@R: c(
     person("Steffi", "LaZerte", email = "[email protected]", role = "aut"),
     person("Denis", "Lepage", email = "[email protected]", role = c("aut", "cre")))
@@ -35,19 +35,31 @@ Imports:
     units (>= 0.8.1),
     wk (>= 0.7.1)
 Suggests:
+    appeears,
+    elevatr,
+    exactextractr,
+    geodata,
     ggspatial (>= 1.1.10),
     here,
     knitr,
+    landscapemetrics,
+    luna (>= 0.4-1),
     mapview,
+    measurements,
     patchwork,
     prettymapr (>= 0.2.5),
     rmarkdown,
     rnaturalearth,
     rnaturalearthhires,
+    readr,
     rosm,
     roxygen2,
     sf (>= 1.0-9),
+    spData,
     spelling,
+    stats,
+    tidyterra,
+    terra,
     testthat,
     vdiffr
 Language: en-US
@@ -58,6 +70,6 @@ URL: https://github.com/BirdsCanada/naturecounts,
     https://birdscanada.github.io/naturecounts/
 VignetteBuilder: knitr
 Config/testthat/edition: 3
-Remotes:  
-    ropensci/rnaturalearthhires,
-    wranglezone/tibblify
+Remotes: ropensci/rnaturalearthhires,
+         rspatial/luna,
+         wranglezone/tibblify

NAMESPACE

@@ -4,9 +4,19 @@ export("%>%")
 export(.data)
 export(cosewic_plot)
 export(cosewic_ranges)
+export(data_buff)
+export(data_fmt)
+export(daymet_check)
+export(daymet_download)
+export(daymet_extract)
+export(daymet_request)
+export(elevation_download)
+export(elevation_extract)
 export(format_dates)
 export(format_zero_fill)
 export(grid_canada)
+export(landcover_download)
+export(landcover_extract)
 export(map_canada)
 export(meta_bcr_codes)
 export(meta_bmde_fields)
@@ -25,6 +35,7 @@ export(meta_statprov_codes)
 export(meta_subnational2_codes)
 export(meta_utm_squares)
 export(nc_count)
+export(nc_covariates_merge)
 export(nc_data_dl)
 export(nc_metadata)
 export(nc_metadata_version)
@@ -33,11 +44,17 @@ export(nc_query_table)
 export(nc_remove_cache)
 export(nc_requests)
 export(region_search)
+export(scanfi_download)
+export(scanfi_extract)
 export(search_region)
 export(search_species)
 export(search_species_code)
 export(species_code_search)
 export(species_search)
+export(vegetation_download)
+export(vegetation_extract)
+export(worldclim_download)
+export(worldclim_extract)
 importFrom(dbplyr,sql)
 importFrom(magrittr,"%>%")
 importFrom(magrittr,"%T>%")