hydricsoils v0.1.2

.gitignore

@@ -4,3 +4,4 @@
 .Ruserdata
 docs
 inst/doc
+FIHS.pdf

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: hydricsoils
 Type: Package
 Title: Tools for 'Field Indicators of Hydric Soils in the United States' 
-Version: 0.1.1
+Version: 0.1.2
 Author: Andrew G. Brown
 Maintainer: Andrew G. Brown <brown.andrewg@gmail.com>
 Description: The goal of 'hydricsoils' is to provide easy access to definitions, criteria, and area of applicability for 'Field Indicators of Hydric Soils in the United States' and also to provide tools which assist in evaluating associated soil morphology.
@@ -10,7 +10,7 @@ Encoding: UTF-8
 LazyData: false
 Depends: R (>= 4.0.0)
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 URL: https://github.com/brownag/hydricsoils/, https://humus.rocks/hydricsoils/
 BugReports: https://github.com/brownag/hydricsoils/issues/
 Imports: 

NAMESPACE

@@ -3,11 +3,13 @@
 export(cache_lrrmlra_geometry)
 export(clear_lrrmlra_geometry)
 export(fihs_match)
+export(hydricsoils_data_dir)
 export(indicator_to_name)
 export(indicator_to_usesym)
 export(lrr_to_lrrname)
 export(lrr_to_mlra)
 export(lrrmlra_geometry)
+export(lrrmlra_geometry_dsn)
 export(lrrmlra_match)
 export(lrrname_to_lrr)
 export(mlra_to_lrr)

NEWS.md

@@ -1,3 +1,17 @@
+# Changes in version 0.1.2
+
+## Improvements
+
+ - Update `fihs` dataset for Field Indicators of Hydric Soils v9.0
+
+   - Adds new "All Soils" indicator: "A18" _Iron Monosulfide_
+
+ - Updated `lrrmlra` geometry source URL
+
+## Additions
+
+ - Added `lrrmlra_geometry_dsn()` and `hydricsoils_data_dir()` functions for getting data sources and paths
+
 # Changes in version 0.1.1
 
 ## Improvements

R/cache_lrrmlra_geometry.R

@@ -29,17 +29,16 @@
 #' }
 #'
 cache_lrrmlra_geometry <- function(overwrite = FALSE,
-                                   dsn = "/vsizip//vsicurl/https://www.nrcs.usda.gov/sites/default/files/2022-10/MLRA_52_2022.zip/MLRA_52_2022") {
+                                   dsn = lrrmlra_geometry_dsn()) {
 
   if (is.null(dsn)) {
-    dsn <- "/vsizip//vsicurl/https://www.nrcs.usda.gov/sites/default/files/2022-10/MLRA_52_2022.zip/MLRA_52_2022"
+    dsn <- lrrmlra_geometry_dsn()
   }
 
-  fp <- file.path(tools::R_user_dir("hydricsoils", which = "data"),
-                  "lrrmlra.gpkg")
+  fp <- file.path(hydricsoils_data_dir(), "lrrmlra.gpkg")
 
   if (!requireNamespace("terra")) {
-    stop("package 'terra' is required to cache the LRR/MLRA spatial dataset")
+    stop("package 'terra' is required to create local MLRA Geographic Database cache")
   }
 
   if (!dir.exists(dirname(fp))) {
@@ -58,21 +57,29 @@ cache_lrrmlra_geometry <- function(overwrite = FALSE,
 #' @rdname lrrmlra-geometry
 #' @return `clear_lrrmlra_geometry()`: logical. Called for the side-effect of removing the MLRA geometry file from the cache. Returns `TRUE` if `"lrrmlra.gpkg"` is successfully removed from user data cache.
 clear_lrrmlra_geometry <- function() {
-  invisible(file.remove(file.path(
-    tools::R_user_dir("hydricsoils", which = "data"),
-    "lrrmlra.gpkg"
-  )))
+  invisible(
+    file.remove(
+      file.path(hydricsoils_data_dir(), "lrrmlra.gpkg")
+    )
+  )
 }
 
 #' @export
 #' @rdname lrrmlra-geometry
 #' @return `lrrmlra_geometry()`: A terra _SpatVector_ object containing `lrrmlra` attributes and geometry.
 lrrmlra_geometry <- function(overwrite = FALSE,
-                             dsn = "/vsizip//vsicurl/https://www.nrcs.usda.gov/sites/default/files/2022-10/MLRA_52_2022.zip/MLRA_52_2022") {
+                             dsn = lrrmlra_geometry_dsn()) {
   if (cache_lrrmlra_geometry(overwrite = overwrite, dsn = dsn)) {
-    return(terra::vect(file.path(
-      tools::R_user_dir("hydricsoils", which = "data"),
-      "lrrmlra.gpkg"
-    )))
+    return(terra::vect(
+      file.path(hydricsoils_data_dir(), "lrrmlra.gpkg")
+    ))
   }
 }
+
+#' @export
+#' @rdname lrrmlra-geometry
+#' @return `lrrmlra_geometry_dsn()`: character. Path to MLRA Geographic Database source.
+lrrmlra_geometry_dsn <- function() {
+  # "https://www.nrcs.usda.gov/sites/default/files/2022-10/MLRA_52_2022.zip/MLRA_52_2022"
+  "/vsizip//vsicurl/https://s3-fpac-nrcs-dshub-public.s3.us-gov-west-1.amazonaws.com/MLRA_52_2022.zip"
+}

R/hydricsoils-package.R

@@ -4,3 +4,4 @@
 ## usethis namespace: start
 ## usethis namespace: end
 NULL
+

R/hydricsoils.R

@@ -15,3 +15,15 @@
 #' @keywords datasets
 #' @references United States Department of Agriculture, Natural Resources Conservation Service. 2022. Land resource regions and major land resource areas of the United States, the Caribbean, and the Pacific Basin. U.S. Department of Agriculture, Agriculture Handbook 296. Available online: <https://www.nrcs.usda.gov/resources/data-and-reports/major-land-resource-area-mlra>
 "lrrmlra"
+
+#' hydricsoils Data Directory
+#' @returns `hydricsoils_data_dir()`: character. Path to hydricsoil package user
+#'   data directory. Default: `tools::R_user_dir("hydricsoils", which = "data")`
+#' @export
+#' @examples
+#'
+#' hydricsoils_data_dir()
+#'
+hydricsoils_data_dir <- function() {
+  tools::R_user_dir("hydricsoils", which = "data")
+}

data-raw/fihs.R

@@ -1,16 +1,22 @@
 ## code to prepare `fihs` dataset goes here
-# download.file("https://www.nrcs.usda.gov/sites/default/files/2022-09/Field_Indicators_of_Hydric_Soils.pdf",
+# download.file("https://www.nrcs.usda.gov/sites/default/files/2024-09/Field-Indicators-of-Hydric-Soils.pdf",
 #               destfile = "FIHS.pdf", mode = "wb")
 # system("pdftotext -raw -nodiag FIHS.pdf FIHS.txt")
 
 # # remove figure captions manually
 x <- readLines("inst/extdata/FIHS.txt", warn = FALSE)
 f <- readLines("inst/extdata/FIGS.txt", warn = FALSE)
 
+# clean FIGS
+cat(trimws(strsplit(paste0(f, collapse = " "), "—")[[1]]), file = "inst/extdata/FIGS.txt", sep = "\n")
+
+f <- readLines("inst/extdata/FIGS.txt", warn = FALSE)
+
+
 ## metadata, added as attributes
-VERSION <- "8.2"
-VERSION_YEAR <- "2018"
-REFERENCE <- "United States Department of Agriculture, Natural Resources Conservation Service. 2018. Field Indicators of Hydric Soils in the United States, Version 8.2. L.M. Vasilas, G.W. Hurt, and J.F. Berkowitz (eds.). USDA, NRCS, in cooperation with the National Technical Committee for Hydric Soils. Available online: <https://www.nrcs.usda.gov/resources/guides-and-instructions/field-indicators-of-hydric-soils>"
+VERSION <- "9.0"
+VERSION_YEAR <- "2024"
+REFERENCE <- "United States Department of Agriculture, Natural Resources Conservation Service. 2024. Field Indicators of Hydric Soils in the United States, Version 9.0. Available online: <https://www.nrcs.usda.gov/resources/guides-and-instructions/field-indicators-of-hydric-soils>"
 
 #
 ##
@@ -22,7 +28,8 @@ REFERENCE <- "United States Department of Agriculture, Natural Resources Conserv
 ##
 ## somehow rebuild suitable text vector from `fd` ...
 ##
-idx <- grep("^All Soils$|^Sandy Soils$|^Loamy and Clayey Soils$|Test Indicators of Hydric Soils$|^\\f\\fAccessibility Statement$", x)
+idx <- grep("^Introduction$|^All Soils$|^Sandy Soils$|^Loamy and Clayey Soils$|Test Indicators of Hydric Soils$|^References$", x)
+idx <- idx[4:8]
 x <- gsub("(for use in all LRRs) or Histel (for", "or Histel. ", x, fixed = TRUE)
 x <- gsub("use in LRRs with permafrost). ", "", x, fixed = TRUE)
 x <- gsub("from12 to18 percent", "from 12 to 18 percent", x)
@@ -34,16 +41,18 @@ x[grep("A1.\u2014", x) + 1]
 sec.idx <- c(idx - 1, length(x))
 sec.len <- diff(c(0, sec.idx))
 sec.lbl <- c("Field Indicators of Hydric Soils",
+             "Front Matter",
              "All Soils", "Sandy Soils", "Loamy and Clayey Soils",
-             "Test Indicators", "All Soils (Test)", "Sandy Soils (Test)",
-             "Loamy and Clayey Soils (Test)", "End Matter")
+             # "Test Indicators",
+             # "All Soils (Test)", "Sandy Soils (Test)", "Loamy and Clayey Soils (Test)",
+             "End Matter")
 page.idx <- grep("^\\f+", x)
 page.len <- diff(c(0, page.idx))
 page.num <- gsub("^\\f+([0-9iv]+).*(Hydric Soils|Field Indicators of)?", "\\1", x[page.idx])
 page.idx <- page.idx - 1
 page.num[1] <- "i"
-page.num[49] <- page.num[48]
-page.num[48] <- "46"
+page.num[40] <- "36"
+page.num[55] <- "52"
 page.num <- gsub("\\f", "", page.num)
 
 # break out page numbers and sections for each line of content
@@ -219,10 +228,12 @@ fihs <- fihs[c("section", "indicator", "indicator_name", "page",
 
 if (interactive())
   View(fihs)
-
+fihs <- fihs[-1,]
+rownames(fihs) <- NULL
 attr(fihs, 'version') <- VERSION
 attr(fihs, 'version_year') <- VERSION_YEAR
 attr(fihs, 'reference') <- REFERENCE
+fihs90 <- fihs
 usethis::use_data(fihs, overwrite = TRUE)
 
 ## TODO: fihs_test dataset; need to confirm where they are being tested