Merge pull request #27 from MikkoVihtakari/sf-version

Sf version

DESCRIPTION

@@ -1,18 +1,14 @@
 Package: ggOceanMaps
 Type: Package
 Title: Plot Data on Oceanographic Maps using 'ggplot2'
-Version: 1.3.7
-Date: 2022-11-24
+Version: 2.0.0
+Date: 2023-07-04
 Authors@R: c(person("Mikko", "Vihtakari", email = "mikko.vihtakari@hi.no",
                   role = c("aut", "cre"), 
                   comment = c(affiliation = "Institute of Marine Research", 
                   ORCID = "0000-0003-0371-4319")),
-             person("Yves", "Reecht", role = "ctb",
-                  comment = c(affiliation = "Institute of Marine Research", 
-                  ORCID = "0000-0003-3583-1843")),
-             person("Hadley", "Wickham", role = "ctb"),
-             person("Simon", "O'Hanlon", role = "ctb"),
-             person("Roger", "Bivand", role = "ctb")
+             person("Roger", "Bivand", role = "ctb"),
+             person("Hadley", "Wickham", role = "ctb")
             )
 URL: https://mikkovihtakari.github.io/ggOceanMaps/
 BugReports: https://github.com/MikkoVihtakari/ggOceanMaps/issues
@@ -21,16 +17,17 @@ Description: Allows plotting data on bathymetric maps using 'ggplot2'. Plotting
   for custom modifications. Data that contain geographic information from 
   anywhere around the globe can be plotted on maps generated by the basemap()
   or qmap() functions using 'ggplot2' layers separated by the '+' operator. The 
-  package uses spatial shapefiles stored in the 'ggOceanMapsData' package, 
-  geospatial packages for R to manipulate, and the 'ggspatial' package to help 
-  to plot these shapefiles. High-resolution shapefiles for detailed maps are 
-  stored on GitHub and downloaded automatically when needed. 
-Depends: R (>= 3.5.0), ggplot2, ggspatial
-Imports: sp, raster, sf, rgeos, methods, utils, stars, smoothr, units, dplyr, parallel
-Suggests: ggOceanMapsData, cowplot, knitr, rmarkdown, scales, rgdal, ggnewscale
-Additional_repositories: https://mikkovihtakari.github.io/drat
+  package uses spatial shape- ('sf') and raster ('stars') files, geospatial 
+  packages for R to manipulate, and the 'ggplot2' package to plot these 
+  files. The package ships with low-resolution spatial data files and 
+  higher resolution files for detailed maps are stored in the 
+  'ggOceanMapsLargeData' repository on GitHub and downloaded automatically 
+  when needed. 
+Depends: R (>= 3.5.0), ggplot2
+Imports: sf, stars, methods, utils, smoothr, units
+Suggests: ggspatial, cowplot, knitr, rmarkdown, scales, ggnewscale
 License: GPL-3
 Encoding: UTF-8
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 LazyData: true
-
+LazyDataCompression: xz

NAMESPACE

@@ -6,13 +6,13 @@ export(auto_limits)
 export(basemap)
 export(basemap_data)
 export(clip_shapefile)
-export(convert_crs)
+export(dd_clip_boundary)
 export(dd_to_deg)
+export(define_bathy_style)
 export(define_shapefiles)
 export(deg_to_dd)
 export(dist2land)
 export(geonorge_bathymetry)
-export(getCores)
 export(guess_coordinate_columns)
 export(is_decimal_limit)
 export(load_map_data)
@@ -21,32 +21,18 @@ export(qmap)
 export(quiet)
 export(raster_bathymetry)
 export(reorder_layers)
+export(rotate_crs)
 export(round_any)
 export(select_element)
 export(shapefile_list)
 export(theme_map)
 export(transform_coord)
 export(vector_bathymetry)
 import(ggplot2)
-import(ggspatial)
-import(raster)
-import(rgeos)
-import(sf)
-import(sp)
 importFrom(grDevices,chull)
 importFrom(methods,"slot<-")
 importFrom(methods,slot)
-importFrom(parallel,detectCores)
-importFrom(parallel,makeCluster)
-importFrom(parallel,mclapply)
-importFrom(parallel,parLapply)
-importFrom(parallel,stopCluster)
-importFrom(rgeos,createSPComment)
-importFrom(rgeos,gDistance)
-importFrom(rgeos,gIntersection)
-importFrom(rgeos,gIntersects)
-importFrom(rgeos,gSimplify)
+importFrom(sf,st_sf)
+importFrom(stars,read_stars)
 importFrom(utils,download.file)
 importFrom(utils,menu)
-importFrom(utils,setTxtProgressBar)
-importFrom(utils,txtProgressBar)

NEWS.md

@@ -1,11 +1,17 @@
-# ggOceanMaps 1.4 (development version)
-
+# ggOceanMaps 2.0 
+
+* Full [sf](https://r-spatial.github.io/sf/) integration. Old GIS packages for R and ggspatial dependencies removed. Since this change required rewriting of most functions, new bugs have almost certainly been introduced.
+* Bathymetry system redesigned (see [this](https://mikkovihtakari.github.io/ggOceanMaps/articles/new-features.html))
+* Decimal degree maps can now be plotted across the antimeridian.
+* Added spatial data to ggOceanMaps making the ggOceanMapsData package not needed any longer.
+* `dist2land()` now uses great circle distances on a spherical Earth ([s2](https://r-spatial.github.io/s2/)) by default and should be able to calculate distances to land anywhere around the globe.
+* qmap points turned red. Addressed a long-standing issue with `shapefiles` and `shape` getting mixed. 
 * Fixed a bug with shapefiles argument shortcut.
 * Fixed a bug in ices_data
-* Add sf support for clip_shapefile
-* Add sf support for shapefiles (converts to sp, needs to be refined)
-* Fix a bug with expanded limits in decimal degree projection
-* Fix a bug where shapefile_list("all") would retunr multiple rows per shapefile name.
+* Added sf support for clip_shapefile
+* Added sf support for shapefiles (converts to sp, needs to be refined)
+* Fixed a bug with expanded limits in decimal degree projection
+* Fixed a bug where shapefile_list("all") would return multiple rows per shapefile name.
 
 # ggOceanMaps 1.3.4
 

R/auto_limits.R

@@ -1,53 +1,33 @@
 #' @title Automatic limits for basemap
 #' @description Find limits for a \code{\link{basemap}} from a data frame.
-#' @param data Data frame containing data for which the limits should be calculated.
+#' @param data Data frame or a spatial object containing data for which the limits should be calculated.
 #' @param proj.in Original \code{\link[sf:st_crs]{CRS}} projection. Must be defined as character argument.
 #' @param proj.out Resulting map projection. See \code{\link{transform_coord}}.
 #' @param lon,lat Names of longitude and latitude columns in \code{data} as character or integer index. If \code{NULL}, the column names are \link[=guess_coordinate_columns]{guessed}.
 #' @param expand.factor Expansion factor for map limits. Set to \code{NULL} to ignore.
 #' @param rotate Logical indicating whether the limits should be rotated to point towards the pole relative to mid-longitude limit.
 #' @param verbose Logical indicating whether information about the projection and guessed column names should be returned as message. Set to \code{FALSE} to make the function silent.
-#' @param output.sf Logical indicating whether an \code{\link[sf:st_polygon]{sf}} (\code{TRUE}) or \code{sp} (\code{FALSE}) polygon should be returned.
 #' @details This is an internal function, which is automatically run by the \code{\link{basemap}} function.
 #' @return A list of limits and projections in \code{proj.in} and \code{proj.out} formats.
 #' @keywords internal
 #' @author Mikko Vihtakari
 #' @family customize shapefiles
 #' @examples
-#' if(requireNamespace("ggOceanMapsData")) {
 #' auto_limits(data = expand.grid(lon = c(-120, 180, 120),
 #'    lat = c(60, 60, 80)))
-#' }
 #' @export
 
-# data = expand.grid(lon = c(-120, 180, 120), lat = c(60, 60, 80)); lon = NULL; lat = NULL; proj.in = 4326; proj.out = NULL; expand.factor = NULL; verbose = FALSE; output.sf = FALSE
-auto_limits <- function(data, lon = NULL, lat = NULL, proj.in = 4326, proj.out = NULL, expand.factor = NULL, verbose = FALSE, output.sf = FALSE) {
+# lon = NULL; lat = NULL; proj.in = 4326; proj.out = NULL; expand.factor = NULL; verbose = FALSE
+auto_limits <- function(data, lon = NULL, lat = NULL, proj.in = 4326, proj.out = NULL, expand.factor = NULL, verbose = FALSE) {
 
-  # Get limits from spatial polygons ####
+  # Get coordinates from spatial objects
 
-  if(any(inherits(data, c("SpatialPolygonsDataFrame", "SpatialPolygons")))) {
-    proj.in <- raster::crs(data)
-
-    # if(!sf::st_is_longlat(proj.in)) {
-    #   data <- sp::spTransform(data, sp::CRS(convert_crs(4326)))
-    #   proj.in <- convert_crs(4326)
-    #   message("The data argument is a spatial polygons object, which is not given as decimal degrees. Converted to decimal degrees.")
-    # }
-
-    data <- suppressMessages(ggplot2::fortify(data)[c("long", "lat")])
-    names(data) <- c("lon", "lat")
-  }
-
-  # Get limits from sf objects
-
-  if(any(inherits(data, "sf"))) {
-    proj.in <- sf::st_crs(data)
-
-    tmp <- sf::st_bbox(data)
+  if(any(inherits(data, c("sf", "sfc", "SpatialPolygonsDataFrame", "SpatialPolygons")))) {
+    tmp <- sf::st_bbox(sf::st_transform(sf::st_as_sfc(sf::st_bbox(data)), proj.in))
 
     data <- expand.grid(data.frame(
-      lon = tmp[c(1,3)],
-      lat = tmp[c(2,4)])
+      lon = tmp[c("xmin", "xmax")],
+      lat = tmp[c("ymin", "ymax")])
     )
   }
 
@@ -125,18 +105,15 @@ auto_limits <- function(data, lon = NULL, lat = NULL, proj.in = 4326, proj.out =
 
   }
 
-  # Projected boundaries
+  projLims <- stats::setNames(projLims, c("xmin", "xmax", "ymin", "ymax"))
 
+  # Projected boundaries
 
-  ## Old sp way, to be removed when the sf way is tested
-  # projBound <- sp::Polygon(matrix(c(projLims[1], projLims[3], projLims[1], projLims[4], projLims[2], projLims[4], projLims[2], projLims[3], projLims[1], projLims[3]), ncol = 2, byrow = TRUE))
-  # projBound <- sp::SpatialPolygons(list(sp::Polygons(list(projBound), ID = "clip_boundary")),
-  #                                   proj4string = if(class(proj.crs) == "CRS") {proj.crs} else {sp::CRS(proj.crs)})
-  # tmp <- as.data.frame(t(sp::bbox(projBound)))
-  # projBoundNodes <- sp::SpatialPoints(expand.grid(lon = tmp$x, lat = tmp$y), 
-  #                                     proj4string = if(class(proj.crs) == "CRS") {proj.crs} else {sp::CRS(convert_crs(proj.crs))})
+  projBound <- sf::st_polygon(
+    list(matrix(c(projLims[1], projLims[3], projLims[1], projLims[4], projLims[2], 
+                  projLims[4], projLims[2], projLims[3], projLims[1], projLims[3]), 
+                ncol = 2, byrow = TRUE)))
 
-  projBound <- sf::st_polygon(list(matrix(c(projLims[1], projLims[3], projLims[1], projLims[4], projLims[2], projLims[4], projLims[2], projLims[3], projLims[1], projLims[3]), ncol = 2, byrow = TRUE)))
   projBound <- sf::st_sfc(projBound, crs = sf::st_crs(proj.crs))
 
   tmp <- sf::st_bbox(projBound)
@@ -148,20 +125,18 @@ auto_limits <- function(data, lon = NULL, lat = NULL, proj.in = 4326, proj.out =
 
   decBoundNodes <- sf::st_transform(projBoundNodes, 4326)
 
-  # decBoundNodes <- sp::spTransform(projBoundNodes, sp::CRS(convert_crs(4326))) # proj.in
-
   if(!identical(sign(projLims[3]), sign(projLims[4]))) { # Spans across the pole
-    decLims <- unname(sf::st_bbox(decBoundNodes)[c(1,3,2,4)]) # old: c(raster::extent(decBoundNodes)[1:3], 90)
+    decLims <- c(unname(sf::st_bbox(decBoundNodes)[c(1,3,2)]), 90) # old: c(raster::extent(decBoundNodes)[1:3], 90)
     decLims <- c(decLims[1:3], sign(decLims[4]) * 90)
   } else if(sign(decLims[1]) != sign(decLims[2]) & decLims[1] < decLims[2]) { # Antimeridian correction
     decLims <-  unname(sf::st_bbox(decBoundNodes)[c(1,3,2,4)]) # old: c(raster::extent(decBoundNodes)[1:4])
   }
 
+  names(decLims) <- c("xmin", "xmax", "ymin", "ymax")
+
   # Return
 
-  if(output.sf) {
-    list(ddLimits = decLims, projLimits = projLims, projBound = projBound, proj.in = attributes(x)$proj.in, proj.out = proj.out)
-  } else {
-    list(ddLimits = decLims, projLimits = projLims, projBound = sf::as_Spatial(projBound), proj.in = attributes(x)$proj.in, proj.out = proj.out)
-  }
+  list(ddLimits = decLims, projLimits = projLims, projBound = projBound, 
+       proj.in = attributes(x)$proj.in, proj.out = proj.out)
+
 }