Merge pull request #7 from AAGI-AUS/devel

DESCRIPTION

@@ -4,25 +4,27 @@ Version: 0.0.0.9000
 Authors@R: c(
     person("Adam H.", "Sparks", , "[email protected]", role = "cre",
            comment = c(ORCID = "0000-0002-0061-8359")),
-    person("Russell", "Edson", , "[email protected]", role = "aut")
+    person("Russell", "Edson", , "[email protected]", role = "aut",
+           comment = c(ORCID = "0000-0002-4607-5396")),
+    person("Max", "Moldovan", , "[email protected]", role = "ctb")
   )
 Description: Provides access to Australia's TERN (Terrestrial Ecosystem
     Research Network) data through the API, <https://tern.org.au>.
 License: MIT + file LICENSE
-Suggests: 
-    roxyglobals,
-    testthat (>= 3.0.0)
-Config/testthat/edition: 3
-Encoding: UTF-8
-Roxygen: list(markdown = TRUE, roclets = c("collate", "namespace", "rd",
-    "roxyglobals::global_roclet"))
-RoxygenNote: 7.3.2
 Imports: 
     cli,
     data.table,
     lubridate,
     rlang,
     terra,
     utils
+Suggests: 
+    roxyglobals,
+    testthat (>= 3.0.0)
 Config/roxyglobals/filename: globals.R
 Config/roxyglobals/unique: FALSE
+Config/testthat/edition: 3
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE, roclets = c("collate", "namespace", "rd",
+    "roxyglobals::global_roclet"))
+RoxygenNote: 7.3.2

NAMESPACE

@@ -3,5 +3,4 @@
 export(get_key)
 export(plot)
 export(read_cog)
-export(read_cog_dt)
 importFrom(terra,plot)

R/read_cog.R

@@ -7,7 +7,7 @@
 #' Currently only Soil Moisture Integration and Prediction System
 #'   (\acronym{SMIPS}) v1.0 is supported.
 #'
-#' @param data A character vector of the data source to be queried, currently
+#' @param dataset A character vector of the data source to be queried, currently
 #'   only \dQuote{smips}.
 #' @param collection A character vector of the data collection to be queried,
 #'  currenly only \dQuote{smips} is supported with the following collections:
@@ -51,7 +51,7 @@
 #' @references <https://portal.tern.org.au/metadata/TERN/d1995ee8-53f0-4a7d-91c2-ad5e4a23e5e0https://geonetwork.tern.org.au/geonetwork/srv/eng/catalog.search#/metadata/d1995ee8-53f0-4a7d-91c2-ad5e4a23e5e0>
 #' @export
 
-read_cog <- function(data = "smips",
+read_cog <- function(dataset = "smips",
                      collection = "totalbucket",
                      day,
                      api_key = get_key(),
@@ -66,7 +66,7 @@ read_cog <- function(data = "smips",
   day <- .check_date(day)
   url_year <- lubridate::year(day)
 
-  if (data == "smips") {
+  if (dataset == "smips") {
     collection_url <- .make_smips_url(.collection = collection, .day = day)
 
     while (attempt <= max_tries && !success)
@@ -90,7 +90,8 @@ read_cog <- function(data = "smips",
       }, error = function(e) {
         if (attempt < max_tries) {
           delay <- initial_delay * 2 ^ (attempt - 1)
-          cli::cli_alert("Download failed on attempt { attempt }. Retrying in { delay } seconds...")
+          cli::cli_alert("Download failed on attempt { attempt }.
+                         Retrying in { delay } seconds...")
           Sys.sleep(delay)
           attempt <- attempt + 1
         } else {
@@ -120,7 +121,8 @@ read_cog <- function(data = "smips",
       "Ymd", "dmY", "mdY", "BdY", "Bdy", "bdY", "bdy"
     ), tz = Sys.timezone()),
     warning = function(c) {
-      cli::cli_abort("{ x } is not in a valid date format. Please enter a valid date format.")
+      cli::cli_abort("{ x } is not in a valid date format.
+                     Please enter a valid date format.")
     }
   )
   return(x)
@@ -168,7 +170,8 @@ read_cog <- function(data = "smips",
   if (.collection == "totalbucket" &&
       .url_year < 2005 ||
       .day > .last_week) {
-    cli::cli_abort("The data are not available before 2005 and past { .last_week }")
+    cli::cli_abort("The data are not available before 2005 and roughly
+                   much past { .last_week }")
   }
 }
 

README.Rmd

@@ -45,13 +45,22 @@ r <- read_cog(day = "2024-01-01")
 plot(r)
 ```
 
-## Example reading a COG as a data.table
+## Extract Values Given Lat/Lon Values
 
-This is a basic example which shows you how you can fetch one day's data from the SMIPS data as a data.table:
+Extract Soil Moisture for Corrigin and Merriden, WA and Tamworth, NSW given latitude and longitude values for each.
 
-```{r example_dt}
-library(nert)
-r <- read_cog_dt(day = "2024-01-01")
+```{r}
+df <- structure(list(
+  location = c("Corrigin", "Merredin", "Tamworth"),
+  x = c(117.87, 118.28, 150.84),
+  y = c(-32.33, -31.48, -31.07)
+),
+row.names = c(NA, -3L),
+class = "data.frame")
+
+cog_df <- terra::extract(x = r, y = df[, c("x", "y")], xy = TRUE)
 
-r
+cog_df <- cbind(df$location, cog_df)
+names(cog_df) <- c("location", "ID", "smips_totalbucket_mm_20240101", "x", "y")
+cog_df
 ```

README.md

@@ -49,27 +49,27 @@ plot(r)
 
 <img src="man/figures/README-example_cog-1.png" width="100%" />
 
-## Example reading a COG as a data.table
+## Extract Values Given Lat/Lon Values
 
-This is a basic example which shows you how you can fetch one day’s data
-from the SMIPS data as a data.table:
+Extract Soil Moisture for Corrigin and Merriden, WA and Tamworth, NSW
+given latitude and longitude values for each.
 
 ``` r
-library(nert)
-r <- read_cog_dt(day = "2024-01-01")
-
-r
-#>               lon       lat smips_totalbucket_mm_20240101
-#>             <num>     <num>                         <num>
-#>       1: 142.5328 -10.69951                      38.68500
-#>       2: 142.5228 -10.70951                      43.40917
-#>       3: 142.5328 -10.70951                      41.99442
-#>       4: 142.4428 -10.71951                      38.94186
-#>       5: 142.4928 -10.71951                      43.28778
-#>      ---                                                 
-#> 6873516: 146.8517 -43.62003                      40.96997
-#> 6873517: 146.8617 -43.62003                      38.49732
-#> 6873518: 146.8717 -43.62003                      48.08897
-#> 6873519: 146.8517 -43.63003                      33.92958
-#> 6873520: 146.8617 -43.63003                      32.85794
+df <- structure(list(
+  location = c("Corrigin", "Merredin", "Tamworth"),
+  x = c(117.87, 118.28, 150.84),
+  y = c(-32.33, -31.48, -31.07)
+),
+row.names = c(NA, -3L),
+class = "data.frame")
+
+cog_df <- terra::extract(x = r, y = df[, c("x", "y")], xy = TRUE)
+
+cog_df <- cbind(df$location, cog_df)
+names(cog_df) <- c("location", "ID", "smips_totalbucket_mm_20240101", "x", "y")
+cog_df
+#>   location ID smips_totalbucket_mm_20240101        x         y
+#> 1 Corrigin  1                    0.06715473 117.8688 -32.33328
+#> 2 Merredin  2                    0.22716530 118.2787 -31.48353
+#> 3 Tamworth  3                   93.44989014 150.8408 -31.07365
 ```

codemeta.json

@@ -17,7 +17,16 @@
       "@type": "Person",
       "givenName": "Russell",
       "familyName": "Edson",
-      "email": "[email protected]"
+      "email": "[email protected]",
+      "@id": "https://orcid.org/0000-0002-4607-5396"
+    }
+  ],
+  "contributor": [
+    {
+      "@type": "Person",
+      "givenName": "Max",
+      "familyName": "Moldovan",
+      "email": "[email protected]"
     }
   ],
   "maintainer": [
@@ -124,7 +133,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "174.876KB",
+  "fileSize": "171.536KB",
   "codeRepository": "https://github.com/AAGI-AUS/nert",
   "readme": "https://github.com/AAGI-AUS/nert/blob/main/README.md",
   "contIntegration": ["https://github.com/AAGI-AUS/nert/actions/workflows/R-CMD-check.yaml", "https://app.codecov.io/gh/AAGI-AUS/nert"]

inst/WORDLIST

@@ -0,0 +1,21 @@
+CMD
+COGs
+Codecov
+Corrigin
+Geotiff
+Merriden
+NSW
+ORCID
+Optimised
+Renviron
+Rprofile
+SMIPS
+SMindex
+bashrc
+config
+currenly
+deepD
+smips
+totalbucket
+visualise
+zshrc