Add anchors to links + fix typos

Author: olivroy

NEWS.md

@@ -76,15 +76,15 @@ new features:
 
   * new function removeMapJunk to remove control elements from a map (e.g. the zoom control).
   * added tentative support for platform 'leafgl'.
-  * stars method now uses leafem::addGeoRaster. https://github.com/r-spatial/leafem/issues/25
-  * leafem::addCopyExtent now included in all methods.
-  * sf(c) methods now use leafem::addFgb if GDAL >= 3.1.
+  * stars method now uses `leafem::addGeoRaster()`. https://github.com/r-spatial/leafem/issues/25
+  * `leafem::addCopyExtent()` now included in all methods.
+  * sf(c) methods now use `leafem::addFgb()` if GDAL >= 3.1.
   * new | operator to compare two maps side-by-side.
 
 miscellaneous:
 
   * all deprecated functions are now defunct. See ?`mapview-defunct`.
-  * drop viridisLite dependency and use base::hcl.colors instead. We now depend on R >= 3.6.
+  * drop viridisLite dependency and use `base::hcl.colors()` instead. We now depend on R >= 3.6.
 
 ## mapview 2.7.8
 
@@ -112,7 +112,7 @@ miscellaneous:
 
   * addMouseCoordinates now also displays native coordinates for leaflet maps. #205 - now moved to package leafem.
   * deprecated slideview, cubeview, latticeview & sync, plainview, popup* functions.
-  * deprecated addFeatures, garnishMap, addHomeButton, addImageQuery, addLogo, addMouseCoordinates.
+  * deprecated `addFeatures`, `garnishMap`, `addHomeButton`, `addImageQuery`, `addLogo`, `addMouseCoordinates`.
 
 bugfixes:
 
@@ -139,7 +139,7 @@ bugfixes:
   * isFALSE (caused errors on R < 3.5) is now handled properly.
   * mapshot does not unintentionally delete url anymore if saving to png with same name.
   * mapshot now properly deletes temporary url when saving to png (or png and html).
-  * internal function mapview:::nrings now calculates number of polygon rings correctly. #181
+  * internal function `mapview:::nrings` now calculates number of polygon rings correctly. #181
 
 ## mapview 2.5.0
 
@@ -156,12 +156,12 @@ new features:
 
 bugfixes:
 
-  * leaflet::addScalebar would prevent Raster* method from rendering correctly for multiple layers.
+  * `leaflet::addScalebar()` would prevent Raster* method from rendering correctly for multiple layers.
   * cex was not respected when burst = TRUE. #149
-  * popupTable no longer causes a stack overflow with large point data. #154
-  * popupGraph no longer relies on png files on disk but embeds graphs via base64. #156
+  * `popupTable()` no longer causes a stack overflow with large point data. #154
+  * `popupGraph()` no longer relies on png files on disk but embeds graphs via base64. #156
   * in mapshot, remove temporary url files only if remove_url = TRUE. #157
-  * removeMouseCoordinates should work properly now (also exported). #145
+  * `removeMouseCoordinates()` should work properly now (also exported). #145
   * home button for single point now zooms to maximum zoom 18.
 
 miscellaneous:
@@ -227,7 +227,7 @@ new features:
   * we now have mapview method for class 'numeric' which enables interactive plots of a numeric variable.
   * updated slideView to accommodate more than one incident in a flexdashboard #95
   * if supplied data has only one attribute/field column mapview will now colour the plot automatically according to that attribute/field.
-  * new mapview method for class 'bbox' -> mapview(st_bbox(x)) is equivalent to viewExtent(x)
+  * new mapview method for class 'bbox' -> `mapview(st_bbox(x))` is equivalent to `viewExtent(x)`
   * plainview now provides mouse coordinates
 
 enhancements:
@@ -247,22 +247,22 @@ new features:
 
 bugfixes:
 
-  * na.alpha caused list/burst methods to fail.
-  * legend did not work when zcol only had one unique value. This was actually a delibarate choice as for a single map it doesn't really make sense to have a legend for only one color. However, for latticeView/sync this does actually make sense, hence re-enabled.
+  * `na.alpha` caused list/burst methods to fail.
+  * legend did not work when zcol only had one unique value. This was actually a deliberate choice as for a single map it doesn't really make sense to have a legend for only one color. However, for latticeView/sync this does actually make sense, hence re-enabled.
 
 ## mapview 2.1.0
 
 new features:
 
-  * plainview/cubeview now respects/has gained argument na.color.
-  * mapview now supports st_GEOMETRY with truely mixed feature types (e.g. LINESTRING and POLYGON) - fixes #85
-  * addFeatures: one function to add them all. Type agnostic version of leaflet::add* functions for simple features objects.
+  * plainview/cubeview now respects/has gained argument `na.color`.
+  * mapview now supports st_GEOMETRY with truly mixed feature types (e.g. LINESTRING and POLYGON) - fixes #85
+  * `addFeatures()`: one function to add them all. Type agnostic version of leaflet::add* functions for simple features objects.
   * mapview (for vector data only) has gained argument na.alpha to control opacity of missing values.
 
 bugfixes:
 
   * deleted obsolete data.table import.
-  * fixed #79: colnames of popupTables are now converted to utf-8.
+  * fixed #79: colnames of popup Tables are now converted to utf-8.
   * fixed #78: respect explicit setting of 'layer.name' argument.
   * included NEWS file as R-help doesn't render NEWS.md
   * highlight now respects alpha/alpha.regions = 0
@@ -331,7 +331,7 @@ new features:
   * mapshot: to save maps as html page or static image or both.
   * knitr integration (i.e. no need to call the @map slot anymore to render in knitr).
   * cubeView: view raster bricks or stacks hovmoeller style, use keys up & down, left & right, page up & page down to navigate through y, x, z dimensions, respectively.
-  * labels: if zcol is set, mouseover will now show the repesctive values of zcol, if zcol is not set moseover shows feature ID. Only available if suitable leaflet package version is installed.
+  * labels: if zcol is set, mouseover will now show the respective values of zcol, if zcol is not set moseover shows feature ID. Only available if suitable leaflet package version is installed.
   * new popup functions popupTable, popupGraph and popupImage.
   * functions to turn coordinates into spatial lines or spatial polygons.
   * mapview objects now work natively on shiny applications (i.e. renderMapview and mapviewOutput now available).

R/color.R

@@ -6,13 +6,13 @@
 #' specified in at
 #' @param at numeric vector giving the breakpoints for the colors
 #' @param na.color the color for NA values.
-#' @param ... additional arguments passed on to \code{\link{level.colors}}
+#' @param ... additional arguments passed on to \code{\link[lattice]{level.colors}}
 #'
 #' @author
 #' Tim Appelhans
 #'
 #' @seealso
-#' \code{\link{level.colors}}
+#' \code{\link[lattice]{level.colors}}
 #'
 #' @name mapviewColors
 #' @export mapviewColors

R/cubeView.R

@@ -2,8 +2,8 @@
 # #'
 # #' @param x a RasterStack or RasterBrick
 # #' @param at the breakpoints used for the visualisation. See
-# #' \code{\link{levelplot}} for details.
-# #' @param col.regions color (palette).See \code{\link{levelplot}} for details.
+# #' \code{\link[lattice]{levelplot}} for details.
+# #' @param col.regions color (palette).See \code{\link[lattice]{levelplot}} for details.
 # #' @param na.color color for missing values.
 # #' @param legend logical. Whether to plot a legend.
 # #' @param ... currently not used.

R/extent.R

@@ -7,13 +7,13 @@
 #' @param map a leaflet or mapview map the extent should be added to. If NULL
 #' standard background layers are created.
 #' @param popup a \code{list} of HTML strings with the popup contents, usually
-#' created from \code{\link{popupTable}}. See \code{\link{addControl}} for
+#' created from \code{\link[leafpop]{popupTable}}. See \code{\link[leaflet]{addControl}} for
 #' details.
 #' @param layer.name the name of the layer to be shown on the map.
 #' @param alpha.regions opacity of the fills or the raster layer(s).
 #' @param label a character vector of labels to be shown on mouseover. See
-#' \code{\link{addControl}} for details.
-#' @param ... additional arguments passed on to \code{\link{addRectangles}}
+#' \code{\link[leaflet]{addControl}} for details.
+#' @inheritDotParams leaflet::addRectangles
 #'
 #' @author
 #' Tim Appelhans
@@ -27,14 +27,14 @@
 #' leaflet() %>% addProviderTiles("OpenStreetMap") %>% leafem::addExtent(breweries)
 #' leaflet() %>% addProviderTiles("OpenStreetMap") %>% leafem::addExtent(breweries)
 #'
-#' @export viewExtent
 #' @name viewExtent
 #' @aliases viewExtent
 #'
 NULL
 
 ## View Extent ============================================================
 #' @rdname viewExtent
+#' @export
 viewExtent <- function(x,
                        map = NULL,
                        popup = NULL,

R/mapView.R

@@ -29,7 +29,7 @@ if ( !isGeneric('mapView') ) {
 #' @param map an optional existing map to be updated/added to.
 #' @param band for stars layers, the band number to be plotted.
 #' @param pane name of the map pane in which to render features. See
-#' \code{\link{addMapPane}} for details. Currently only supported for vector layers.
+#' \code{\link[leaflet]{addMapPane}} for details. Currently only supported for vector layers.
 #'   Ignored if \code{canvas = TRUE}. The default \code{"auto"} will create different panes
 #'   for points, lines and polygons such that points overlay lines overlay polygons.
 #'   Set to \code{NULL} to get default leaflet behaviour where allfeatures
@@ -44,12 +44,12 @@ if ( !isGeneric('mapView') ) {
 #'   If maxpixels < \code{ncell(x)}, sampleRegular is used before plotting.
 #' @param color color (palette) for points/polygons/lines
 #' @param col.regions color (palette) pixels.
-#'   See \code{\link{levelplot}} for details.
+#'   See \code{\link[lattice]{levelplot}} for details.
 #' @param at the breakpoints used for the visualisation.
-#'   See \code{\link{levelplot}} for details.
+#'   See \code{\link[lattice]{levelplot}} for details.
 #' @param na.color color for missing values
 #' @param use.layer.names should layer names of the Raster* object be used?
-#' @param map.types character spcifications for the base maps.
+#' @param map.types character specifications for the base maps.
 #'   see \url{https://leaflet-extras.github.io/leaflet-providers/preview/}
 #'   for available options.
 #' @param burst whether to show all (TRUE) or only one (FALSE) layer(s).
@@ -75,13 +75,13 @@ if ( !isGeneric('mapView') ) {
 #'   Defaults to TRUE
 #' @param popup either \code{logical}, \code{character vector} or a \code{list}
 #'   of HTML strings with the popup contents, usually created from
-#'   \code{\link[leafpop]{popupTable}}. See \code{\link{addControl}} for details.
+#'   \code{\link[leafpop]{popupTable}}. See \code{\link[leaflet]{addControl}} for details.
 #'   If \code{FALSE} or \code{NULL} no popups will be created, if \code{TRUE}
 #'   a table with all feature attributes/columns will be created.
 #'   If a \code{character vector} of column names, the table will only show the
 #'   respective column entries.
 #' @param label For vector data (sf/sp) a character vector of labels to be
-#'   shown on mouseover. See \code{\link{addControl}} for details. For raster
+#'   shown on mouseover. See \code{\link[leaflet]{addControl}} for details. For raster
 #'   data (Raster*/stars) a logical indicating whether to add image query.
 #' @param native.crs logical whether to reproject to web map coordinate
 #'   reference system (web mercator - epsg:3857) or render using native CRS of
@@ -98,7 +98,7 @@ if ( !isGeneric('mapView') ) {
 #'   layer is of class \code{factor} in which case "ngb" is used.
 #' @param highlight either \code{FALSE}, \code{NULL} or a list of styling
 #'   options for feature highlighting on mouse hover.
-#'   See \code{\link{highlightOptions}} for details.
+#'   See \code{\link[leaflet]{highlightOptions}} for details.
 #' @param maxpoints the maximum number of points making up the geometry.
 #'   In case of lines and polygons this refers to the number of vertices. See
 #'   Details for more information.
@@ -107,21 +107,21 @@ if ( !isGeneric('mapView') ) {
 #' @param query.digits for raster methods only. The amount of digits to be shown
 #'   by raster value query. Ignored if \code{label = FALSE}.
 #' @param query.position for raster methods only. The position of the raster
-#'   value query info box. See \code{position} argument of \code{\link{addLegend}}
+#'   value query info box. See \code{position} argument of \code{\link[leaflet]{addLegend}}
 #'   for possible values. Ignored if \code{label = FALSE}.
 #' @param query.prefix for raster methods only. a character string to be shown
 #'   as prefix for the layerId. Ignored if \code{label = FALSE}.
 #' @param hide either a logical, a vector of layer names or a vector of layer indices.
 #'   See Details for more information on what exactly it does for different raster types.
 #' @param ... additional arguments passed on to respective functions.
-#'   See \code{\link{addRasterImage}}, \code{\link{addCircles}},
-#'   \code{\link{addPolygons}}, \code{\link{addPolylines}} for details.
+#'   See \code{\link[leaflet]{addRasterImage}}, \code{\link[leaflet]{addCircles}},
+#'   \code{\link[leaflet]{addPolygons}}, \code{\link[leaflet]{addPolylines}} for details.
 #'   Furthermore, you can pass hidden arguments to some methods. See Details for
 #'   a list of supported hidden arguments.
 #'
 #' @details
 #' \code{maxpoints} is taken to determine when to switch rendering from svg
-#'   to canvas overlay for perfomance. The threshold calculation is done as follows: \cr
+#'   to canvas overlay for performance. The threshold calculation is done as follows: \cr
 #'   if the number of points (in case of point data) or vertices (in case of
 #'   polygon or line data) > \code{maxpoints} then render using special render
 #'   function. Within this render function we approximate the complexity of
@@ -460,7 +460,7 @@ setMethod('mapView', signature(x = 'SpatRaster'), .stars_method)
 
 
 ## Raster Stack/Brick ===========================================================
-#' @describeIn mapView \code{\link{stack}} / \code{\link{brick}}
+#' @describeIn mapView \code{\link[raster]{stack}} / \code{\link[raster]{brick}}
 
 setMethod('mapView', signature(x = 'RasterStackBrick'),
           function(x,
@@ -531,7 +531,7 @@ setMethod('mapView', signature(x = 'RasterStackBrick'),
 
 
 ## Satellite object =======================================================
-#' @describeIn mapView \code{\link{satellite}}
+#' @describeIn mapView \code{\link[satellite]{satellite}}
 
 setMethod('mapView', signature(x = 'Satellite'),
           function(x,
@@ -840,7 +840,7 @@ setMethod('mapView', signature(x = 'SpatVector'), .sf_method)
 
 
 ## sfc ====================================================================
-#' @describeIn mapView \code{\link{st_sfc}}
+#' @describeIn mapView \code{\link[sf]{st_sfc}}
 
 setMethod('mapView', signature(x = 'sfc'),
           function(x,
@@ -1105,10 +1105,10 @@ setMethod('mapView', signature(x = 'numeric'),
 #' data.frame method.
 #' @param grid whether to plot a (scatter plot) xy-grid to aid interpretation
 #' of the visualisation. Only relevant for the data.frame method.
-#' @param aspect the ratio of x/y axis corrdinates to adjust the plotting
+#' @param aspect the ratio of x/y axis coordinates to adjust the plotting
 #' space to fit the screen. Only relevant for the data.frame method.
 #' @param crs an optional crs specification for the provided data to enable
-#' rendering on a basemap. See argument description in \code{\link{st_sf}}
+#' rendering on a basemap. See argument description in \code{\link[sf]{st_sf}}
 #' for details.
 setMethod('mapView', signature(x = 'data.frame'),
           function(x,
@@ -1151,7 +1151,7 @@ setMethod('mapView', signature(x = 'data.frame'),
 
 
 ## XY =====================================================================
-#' @describeIn mapView \code{\link{st_sfc}}
+#' @describeIn mapView \code{\link[sf]{st_sfc}}
 
 setMethod('mapView', signature(x = 'XY'),
           function(x,
@@ -1219,7 +1219,7 @@ setMethod('mapView', signature(x = 'XY'),
 
 
 ## XYZ ====================================================================
-#' @describeIn mapView \code{\link{st_sfc}}
+#' @describeIn mapView \code{\link[sf]{st_sfc}}
 
 setMethod('mapView', signature(x = 'XYZ'),
           function(x,
@@ -1233,7 +1233,7 @@ setMethod('mapView', signature(x = 'XYZ'),
 
 
 ## XYM ====================================================================
-#' @describeIn mapView \code{\link{st_sfc}}
+#' @describeIn mapView \code{\link[sf]{st_sfc}}
 
 setMethod('mapView', signature(x = 'XYM'),
           function(x,
@@ -1247,7 +1247,7 @@ setMethod('mapView', signature(x = 'XYM'),
 
 
 ## XYZM ===================================================================
-#' @describeIn mapView \code{\link{st_sfc}}
+#' @describeIn mapView \code{\link[sf]{st_sfc}}
 
 setMethod('mapView', signature(x = 'XYZM'),
           function(x,
@@ -1261,7 +1261,7 @@ setMethod('mapView', signature(x = 'XYZM'),
 
 
 ## bbox =======================================================
-#' @describeIn mapView \code{\link{st_bbox}}
+#' @describeIn mapView \code{\link[sf]{st_bbox}}
 
 setMethod('mapView', signature(x = 'bbox'),
           function(x,
@@ -1416,7 +1416,7 @@ setMethod('mapview', signature('ANY'),
 ######## SP ###############################################################
 
 ## SpatialPixelsDataFrame =================================================
-#' @describeIn mapView \code{\link{SpatialPixelsDataFrame}}
+#' @describeIn mapView \code{\link[sp]{SpatialPixelsDataFrame}}
 #'
 setMethod('mapView', signature(x = 'SpatialPixelsDataFrame'),
           function(x,
@@ -1482,7 +1482,7 @@ setMethod('mapView', signature(x = 'SpatialPixelsDataFrame'),
 
 
 ## SpatialGridDataFrame =================================================
-#' @describeIn mapView \code{\link{SpatialGridDataFrame}}
+#' @describeIn mapView \code{\link[sp]{SpatialGridDataFrame}}
 #'
 setMethod('mapView', signature(x = 'SpatialGridDataFrame'),
           function(x,
@@ -1548,7 +1548,7 @@ setMethod('mapView', signature(x = 'SpatialGridDataFrame'),
 
 
 ## SpatialPointsDataFrame =================================================
-#' @describeIn mapView \code{\link{SpatialPointsDataFrame}}
+#' @describeIn mapView \code{\link[sp]{SpatialPointsDataFrame}}
 setMethod('mapView', signature(x = 'SpatialPointsDataFrame'),
           function(x,
                    zcol = NULL,
@@ -1562,7 +1562,7 @@ setMethod('mapView', signature(x = 'SpatialPointsDataFrame'),
 
 
 ## SpatialPoints ==========================================================
-#' @describeIn mapView \code{\link{SpatialPoints}}
+#' @describeIn mapView \code{\link[sp]{SpatialPoints}}
 
 setMethod('mapView', signature(x = 'SpatialPoints'),
           function(x,
@@ -1577,7 +1577,7 @@ setMethod('mapView', signature(x = 'SpatialPoints'),
 
 
 ## SpatialPolygonsDataFrame ===============================================
-#' @describeIn mapView \code{\link{SpatialPolygonsDataFrame}}
+#' @describeIn mapView \code{\link[sp]{SpatialPolygonsDataFrame}}
 
 setMethod('mapView', signature(x = 'SpatialPolygonsDataFrame'),
           function(x,
@@ -1592,7 +1592,7 @@ setMethod('mapView', signature(x = 'SpatialPolygonsDataFrame'),
 
 
 ## SpatialPolygons ========================================================
-#' @describeIn mapView \code{\link{SpatialPolygons}}
+#' @describeIn mapView \code{\link[sp]{SpatialPolygons}}
 
 setMethod('mapView', signature(x = 'SpatialPolygons'),
           function(x,
@@ -1607,7 +1607,7 @@ setMethod('mapView', signature(x = 'SpatialPolygons'),
 
 
 ## SpatialLinesDataFrame =================================================
-#' @describeIn mapView \code{\link{SpatialLinesDataFrame}}
+#' @describeIn mapView \code{\link[sp]{SpatialLinesDataFrame}}
 
 setMethod('mapView', signature(x = 'SpatialLinesDataFrame'),
           function(x,
@@ -1622,7 +1622,7 @@ setMethod('mapView', signature(x = 'SpatialLinesDataFrame'),
 
 
 ## SpatialLines ===========================================================
-#' @describeIn mapView \code{\link{SpatialLines}}
+#' @describeIn mapView \code{\link[sp]{SpatialLines}}
 
 setMethod('mapView', signature(x = 'SpatialLines'),
           function(x,