Make drop_na.SpatRaster internal (#13)

* Remove examples on drop_na * Update docs with pkgdev * Fix docs * Update docs with pkgdev Co-authored-by: dieghernan <[email protected]>
dieghernan · May 19, 2022 · 99bdddd · 99bdddd
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diff --git a/CITATION.cff b/CITATION.cff
@@ -69,6 +69,7 @@ references:
     given-names: Gábor
     email: [email protected]
   year: '2022'
+  url: https://CRAN.R-project.org/package=cli
   version: '>= 3.0.0'
 - type: software
   title: crayon
@@ -79,7 +80,7 @@ references:
     given-names: Gábor
     email: [email protected]
   year: '2022'
-  url: https://github.com/r-lib/crayon#readme
+  url: https://CRAN.R-project.org/package=crayon
 - type: software
   title: dplyr
   abstract: 'dplyr: A Grammar of Data Manipulation'
@@ -98,6 +99,7 @@ references:
     given-names: Kirill
     orcid: https://orcid.org/0000-0002-1416-3412
   year: '2022'
+  url: https://CRAN.R-project.org/package=dplyr
 - type: software
   title: ggplot2
   abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
@@ -131,6 +133,7 @@ references:
     given-names: Dewey
     orcid: https://orcid.org/0000-0002-9415-4582
   year: '2022'
+  url: https://CRAN.R-project.org/package=ggplot2
   version: '>= 3.1.0'
 - type: software
   title: magrittr
@@ -144,6 +147,7 @@ references:
     given-names: Hadley
     email: [email protected]
   year: '2022'
+  url: https://CRAN.R-project.org/package=magrittr
 - type: software
   title: rlang
   abstract: 'rlang: Functions for Base Types and Core R and ''Tidyverse'' Features'
@@ -156,6 +160,7 @@ references:
     given-names: Hadley
     email: [email protected]
   year: '2022'
+  url: https://CRAN.R-project.org/package=rlang
 - type: software
   title: scales
   abstract: 'scales: Scale Functions for Visualization'
@@ -167,6 +172,7 @@ references:
   - family-names: Seidel
     given-names: Dana
   year: '2022'
+  url: https://CRAN.R-project.org/package=scales
 - type: software
   title: sf
   abstract: 'sf: Simple Features for R'
@@ -177,6 +183,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0001-8049-7069
   year: '2022'
+  url: https://CRAN.R-project.org/package=sf
   version: '>= 1.0.0'
 - type: software
   title: terra
@@ -188,7 +195,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0001-5872-2872
   year: '2022'
-  url: https://rspatial.org/terra/
+  url: https://CRAN.R-project.org/package=terra
   version: '>= 1.5.0'
 - type: software
   title: tibble
@@ -202,6 +209,7 @@ references:
     given-names: Hadley
     email: [email protected]
   year: '2022'
+  url: https://CRAN.R-project.org/package=tibble
 - type: software
   title: tidyr
   abstract: 'tidyr: Tidy Messy Data'
@@ -213,6 +221,7 @@ references:
   - family-names: Girlich
     given-names: Maximilian
   year: '2022'
+  url: https://CRAN.R-project.org/package=tidyr
 - type: software
   title: isoband
   abstract: 'isoband: Generate Isolines and Isobands from Regularly Spaced Elevation
@@ -228,7 +237,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0002-5147-4711
   year: '2022'
-  url: https://wilkelab.org/isoband/
+  url: https://CRAN.R-project.org/package=isoband
 - type: software
   title: knitr
   abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
@@ -239,7 +248,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0003-0645-5666
   year: '2022'
-  url: https://yihui.org/knitr/
+  url: https://CRAN.R-project.org/package=knitr
 - type: software
   title: lifecycle
   abstract: 'lifecycle: Manage the Life Cycle of your Package Functions'
@@ -253,6 +262,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0003-4757-117X
   year: '2022'
+  url: https://CRAN.R-project.org/package=lifecycle
 - type: software
   title: maptiles
   abstract: 'maptiles: Download and Display Map Tiles'
@@ -263,7 +273,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0002-1932-3323
   year: '2022'
-  url: https://github.com/riatelab/maptiles/
+  url: https://CRAN.R-project.org/package=maptiles
 - type: software
   title: rmarkdown
   abstract: 'rmarkdown: Dynamic Documents for R'
@@ -302,6 +312,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0003-3925-190X
   year: '2022'
+  url: https://CRAN.R-project.org/package=rmarkdown
 - type: software
   title: testthat
   abstract: 'testthat: Unit Testing for R'
@@ -311,6 +322,7 @@ references:
     given-names: Hadley
     email: [email protected]
   year: '2022'
+  url: https://CRAN.R-project.org/package=testthat
   version: '>= 3.0.0'
 - type: software
   title: vdiffr
@@ -334,3 +346,4 @@ references:
     given-names: Vaudor
     email: [email protected]
   year: '2022'
+  url: https://CRAN.R-project.org/package=vdiffr
diff --git a/R/drop_na.Spat.R b/R/drop_na.Spat.R
@@ -1,18 +1,15 @@
-#' Drop cells and attributes of  Spat* objects containing missing values
+#' Drop attributes of SpatVector objects containing missing values
 #'
 #' @description
-#' `r lifecycle::badge('questioning')`
-#'
-#' `drop_na()` method drops cells and attributes where any layer or column
-#' specified by ... contains a missing value.
+#' `drop_na()` method drops geometries where any attribute specified by `...`
+#'  contains a missing value.
 #'
 #'
 #' @return A Spat* object  of the same class than `.data`. See **Methods**.
 #'
-#' @param data A SpatRaster created with [terra::rast()] or a SpatVector
-#'   created with [terra::vect()].
-#' @param ... [`tidy-select`][tidyr::drop_na()]  Columns or layers to inspect
-#'   for missing values. If empty, all columns/layers are used.
+#' @param data A SpatVector created with [terra::vect()].
+#' @param ... [`tidy-select`][tidyr::drop_na()]  Attributes to inspect for
+#'   missing values. If empty, all attributes are used.
 #'
 #' @export
 #'
@@ -21,7 +18,72 @@
 #'
 #' @importFrom tidyr drop_na
 #'
-#' @seealso [tidyr::drop_na()]
+#' @seealso
+#' [tidyr::drop_na()]. `r lifecycle::badge('questioning')` A method for
+#' SpatRaster is also available, see [drop_na.SpatRaster()].
+#'
+#' @family tidyr.methods
+#'
+#'
+#' @section Methods:
+#'
+#' Implementation of the **generic** [tidyr::drop_na()] function.
+#'
+#' ## SpatVector
+#'
+#' The implementation of this method is performed on a `by-attribute` basis,
+#' meaning that `NAs` are assessed on the attributes (columns) of each vector
+#' (rows). The result is a SpatVector with potentially less geometries than the
+#' input
+#'
+#' @examples
+#'
+#' library(terra)
+#'
+#' f <- system.file("extdata/cyl.gpkg", package = "tidyterra")
+#'
+#' v <- terra::vect(f)
+#'
+#' # Add NAs
+#' v <- v %>% mutate(iso2 = ifelse(cpro <= "09", NA, cpro))
+#'
+#' # Init
+#' plot(v, col = "red")
+#'
+#' # Mask with lyr.1
+#' v %>%
+#'   drop_na(iso2) %>%
+#'   plot(col = "red")
+drop_na.SpatVector <- function(data, ...) {
+
+  # Use sf method
+  sf_obj <- sf::st_as_sf(data)
+  dropped <- tidyr::drop_na(sf_obj, ...)
+
+  return(terra::vect(dropped))
+}
+
+#' Drop cells of SpatRaster objects containing missing values
+#'
+#' @description
+#' `r lifecycle::badge('questioning')`. See **Methods**.
+#'
+#' `drop_na()` method drops cells where any layer specified by `...` contains
+#' a missing value.
+#'
+#' @return A Spat* object  of the same class than `.data`. See **Methods**.
+#'
+#' @param data A SpatRaster created with [terra::rast()].
+#' @param ... [`tidy-select`][tidyr::drop_na()]  Layers to inspect
+#'   for missing values. If empty, all layers are used.
+#'
+#' @export
+#' @keywords internal
+#' @rdname drop_na.SpatRaster
+#'
+#' @seealso
+#'
+#' [tidyr::drop_na()], [drop_na()].
 #'
 #' @family tidyr.methods
 #'
@@ -56,13 +118,6 @@
 #'
 #' Check the **Examples** to have a better understanding of this method.
 #'
-#' ## SpatVector
-#'
-#' The implementation of this method is performed on a `by-attribute` basis,
-#' meaning that `NAs` are assessed on the attributes (columns) of each vector
-#' (rows). The result is a SpatVector with potentially less geometries than the
-#' input
-#'
 #' @examples
 #'
 #' library(terra)
@@ -136,14 +191,3 @@ drop_na.SpatRaster <- function(data, ...) {
 
   return(newrast)
 }
-
-#' @export
-#' @rdname drop_na
-drop_na.SpatVector <- function(data, ...) {
-
-  # Use sf method
-  sf_obj <- sf::st_as_sf(data)
-  dropped <- tidyr::drop_na(sf_obj, ...)
-
-  return(terra::vect(dropped))
-}
diff --git a/R/replace_na.Spat.R b/R/replace_na.Spat.R
@@ -5,7 +5,8 @@
 #' Replace `NAs` on layers/attributes with specified values
 #'
 #'
-#' @inheritParams drop_na
+#' @param data A SpatRaster created with [terra::rast()] or a SpatVector
+#'   created with [terra::vect()].
 #' @param replace list of values, with one value for each layer/attribute that
 #'   has `NA` values to be replaced.
 #' @param ... Ignored

diff --git a/codemeta.json b/codemeta.json
@@ -282,7 +282,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "1431.952KB",
+  "fileSize": "1433.921KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",