diff --git a/articles/retiring_rgdal_geos_1.html b/articles/retiring_rgdal_geos_1.html index 5e316f6..598cb0e 100644 --- a/articles/retiring_rgdal_geos_1.html +++ b/articles/retiring_rgdal_geos_1.html @@ -298,7 +298,7 @@

Possible difficultiesLoading data and packageslibrary(sf) 
## Linking to GEOS 3.10.2, GDAL 3.4.1, PROJ 8.2.1; sf_use_s2() is TRUE
-nc <- as(read_sf(system.file("gpkg/nc.gpkg", package="sf")), "Spatial")
+nc <- as(st_read(system.file("gpkg/nc.gpkg", package="sf")), "Spatial") +
## Reading layer `nc.gpkg' from data source 
+##   `/home/runner/work/_temp/Library/sf/gpkg/nc.gpkg' using driver `GPKG'
+## Simple feature collection with 100 features and 14 fields
+## Geometry type: MULTIPOLYGON
+## Dimension:     XY
+## Bounding box:  xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965
+## Geodetic CRS:  NAD27

Using base plot

The basic plot command on a Spatial object gives just the geometry, without axes:

-
+
 plot(meuse)

 

 
axes can be added when axes=TRUE is given; plot elements
 can be added incrementally:

-
+
 plot(meuse, pch = 1, cex = sqrt(meuse$zinc)/12, axes = TRUE)
 v = c(100,200,400,800,1600)
 legend("topleft", legend = v, pch = 1, pt.cex = sqrt(v)/12)
 plot(meuse.riv, add = TRUE, col = grey(.9, alpha = .5))

 

 
For local projection systems, such as in this case

-
+
 proj4string(meuse)

 
## [1] "+proj=sterea +lat_0=52.1561605555556 +lon_0=5.38763888888889 +k=0.9999079 +x_0=155000 +y_0=463000 +ellps=bessel +units=m +no_defs"

 
the aspect ratio is set to 1, to make sure that one unit north equals
@@ -148,17 +155,17 @@ 
Using base plot
-
+
 crs.longlat = CRS("+init=epsg:4326")

 
## Warning in CPL_crs_from_input(x): GDAL Message 1: +init=epsg:XXXX syntax is
 ## deprecated. It might return a CRS with a non-EPSG compliant axis order.

-
+
 meuse.longlat = spTransform(meuse, crs.longlat)
 plot(meuse.longlat, axes = TRUE)

 

 
which looks different from the plot where one degree north (latitude)
 equals one degree east (longitude):

-
+
 par(mar = rep(0,4))
 plot(meuse.longlat, asp = 1)

 

@@ -171,7 +178,7 @@ 
Graticules
+
 par(mar = c(0, 0, 1, 0))
 library(methods) # as
 plot(as(meuse, "Spatial"), expandBB = c(.05, 0, 0, 0))
@@ -180,7 +187,7 @@ 
Graticulestext(labels(gridlines(meuse)), col = grey(.7))
 title("default gridlines with Meuse projected data")

 

-
+
 par(mar = c(0, 0, 1, 0))
 grd <- gridlines(meuse.longlat)
 grd_x <- spTransform(grd, CRS(proj4string(meuse)))
@@ -190,12 +197,12 @@ 
Graticulestext(labels(grd_x, crs.longlat), col = grey(.7))

 
## Warning in labels.SpatialLines(grd_x, crs.longlat): this labels method is meant
 ## to operate on SpatialLines created with sp::gridlines

-
+
 title("longitude latitude gridlines and labels")

 

 
These lines look pretty straight, because it concerns a small area.
 For

-
+
 # demonstrate axis labels with angle, both sides:
 
 maps2sp = function(xlim, ylim, l.out = 100, clip = TRUE) {
@@ -206,7 +213,7 @@ 
Graticulespar(mar = c(0, 0, 1, 0))
 m = maps2sp(c(-100,-20), c(10,55))

 
## Loading required package: maps

-
+
 sp = SpatialPoints(rbind(c(-101,9), c(-101,55), c(-19,9), c(-19,55)), CRS("+init=epsg:4326"))
 laea = CRS("+proj=laea +lat_0=30 +lon_0=-40")
 m.laea = spTransform(m, laea)
@@ -219,14 +226,14 @@ 
Graticulestext(labels(gl.laea, crs.longlat))

 
## Warning in labels.SpatialLines(gl.laea, crs.longlat): this labels method is
 ## meant to operate on SpatialLines created with sp::gridlines

-
+
 text(labels(gl.laea, crs.longlat, side = 3:4), col = 'red')

 
## Warning in labels.SpatialLines(gl.laea, crs.longlat, side = 3:4): this labels
 ## method is meant to operate on SpatialLines created with sp::gridlines

-
+
 title("curved text label demo")

 

-
+
 # polar:
 par(mar = c(0, 0, 1, 0))
 pts=SpatialPoints(rbind(c(-180,-70),c(0,-70),c(180,-89),c(180,-70)), CRS("+init=epsg:4326"))
@@ -238,18 +245,18 @@ 
Graticulesl = labels(gl.polar, crs.longlat, side = 3)

 
## Warning in labels.SpatialLines(gl.polar, crs.longlat, side = 3): this labels
 ## method is meant to operate on SpatialLines created with sp::gridlines

-
+
 l$pos = NULL # pos is too simple, use adj:
 text(l, adj = c(0.5, -0.5), cex = .8) 
 l = labels(gl.polar, crs.longlat, side = 4)

 
## Warning in labels.SpatialLines(gl.polar, crs.longlat, side = 4): this labels
 ## method is meant to operate on SpatialLines created with sp::gridlines

-
+
 l$srt = 0 # otherwise they end up upside-down
 text(l, cex = .8)
 title("grid line labels on polar projection, epsg 3031")

 

-
+
 par(mar = c(0, 0, 1, 0))
 m = maps2sp(xlim = c(-180,180), ylim = c(-90,-70), clip = FALSE)
 gl = gridlines(m, easts = seq(-180,180,20))
@@ -261,14 +268,14 @@ 
Graticulesl = labels(gl.polar, crs.longlat, side = 3)

 
## Warning in labels.SpatialLines(gl.polar, crs.longlat, side = 3): this labels
 ## method is meant to operate on SpatialLines created with sp::gridlines

-
+
 # pos is too simple here, use adj:
 l$pos = NULL 
 text(l, adj = c(0.5, -0.3), cex = .8)
 l = labels(gl.polar, crs.longlat, side = 2)

 
## Warning in labels.SpatialLines(gl.polar, crs.longlat, side = 2): this labels
 ## method is meant to operate on SpatialLines created with sp::gridlines

-
+
 l$srt = 0 # otherwise they are upside-down
 text(l, cex = .8)
 title("grid line labels on polar projection, epsg 3031")

@@ -279,19 +286,19 @@ 
Other spatial objects in base plot
 
The following plot shows polygons with county name as labels at their
 center point:

-
+
 par(mar = c(0, 0, 1, 0))
 plot(nc)
 invisible(text(coordinates(nc), labels=as.character(nc$NAME), cex=0.4))

 

 
This plot of a SpatialPolygonsDataFrame uses grey
 shades:

-
+
 names(nc)

 
##  [1] "AREA"      "PERIMETER" "CNTY_"     "CNTY_ID"   "NAME"      "FIPS"     
 ##  [7] "FIPSNO"    "CRESS_ID"  "BIR74"     "SID74"     "NWBIR74"   "BIR79"    
 ## [13] "SID79"     "NWBIR79"

-
+
 rrt <- nc$SID74/nc$BIR74
 brks <- quantile(rrt, seq(0,1,1/7))
 cols <- grey((length(brks):2)/length(brks))
@@ -301,7 +308,7 @@ 
Other spatial objects in base plot

 
The following plot shows a SpatialPolygonsDataFrame,
 using line densities

-
+
 rrt <- nc$SID74/nc$BIR74
 brks <- quantile(rrt, seq(0,1,1/7))
 cols <- grey((length(brks):2)/length(brks))
@@ -310,14 +317,14 @@ 
Other spatial objects in base plotplot(nc, density=dens[findInterval(rrt, brks, all.inside=TRUE)])

 

 
Plot/image of a grid file, using base plot methods:

-
+
 image(meuse.grid)

 

-
+
 plot(meuse.grid["dist"])
 points(meuse, col = 'green')

 

-
+
 plot(meuse.grid["dist"], zlim = c(0,1))
 plot(geometry(meuse.grid), add = TRUE, col = grey(.8))

 

@@ -330,7 +337,7 @@ 
using lattice plot (spplot)
 
The following plot colours points with a legend in the plotting area
 and adds scales:

-
+
 spplot(meuse, "zinc", do.log = TRUE,
     key.space=list(x = 0.1, y = 0.95, corner = c(0, 1)),
     scales=list(draw = TRUE))

@@ -338,14 +345,14 @@ 
using lattice plot (spplot)The following plot has coloured points plot with legend in plotting
 area and scales; it has a non-default number of cuts with user-supplied
 legend entries:

-
+
 spplot(meuse, "zinc", do.log = TRUE,
     key.space=list(x=0.2,y=0.9,corner=c(0,1)),
     scales=list(draw = TRUE), cuts = 3,
     legendEntries = c("low", "intermediate", "high"))

 

 
The following plot adds a scale bar and north arrow:

-
+
 scale = list("SpatialPolygonsRescale", layout.scale.bar(), 
     offset = c(178600,332490), scale = 500, fill=c("transparent","black"))
 text1 = list("sp.text", c(178600,332590), "0")
@@ -358,7 +365,7 @@ 
using lattice plot (spplot)    main = "Zinc (top soil)")

 

 
The following plot has north arrow and text outside panels

-
+
 rv = list("sp.polygons", meuse.riv, fill = "lightblue")
 scale = list("SpatialPolygonsRescale", layout.scale.bar(), 
     offset = c(180500,329800), scale = 500, fill=c("transparent","black"), which = 1)
@@ -374,7 +381,7 @@ 
using lattice plot (spplot)

 
The same plot; north arrow now inside panel, with custom panel
 function instead of sp.layout

-
+
 spplot(meuse, "zinc", panel = function(x, y, ...) {
         sp.polygons(meuse.riv, fill = "lightblue")
         SpatialPolygonsRescale(layout.scale.bar(), offset = c(179900,329600), 
@@ -393,7 +400,7 @@ 
using lattice plot (spplot)which argument in a layout component (if
 which=4 was set as list component of sp.layout, the river
 would as well be drawn only in that (last) panel)

-
+
 rv = list("sp.polygons", meuse.riv, fill = "lightblue")
 scale = list("SpatialPolygonsRescale", layout.scale.bar(), 
     offset = c(180500,329800), scale = 500, fill=c("transparent","black"), which = 4)
@@ -410,7 +417,7 @@ 
using lattice plot (spplot)

 
Comparing four kriging varieties in a multi-panel plot with shared
 scale:

-
+
 rv = list("sp.polygons", meuse.riv, fill = "blue", alpha = 0.1)
 pts = list("sp.points", meuse, pch = 3, col = "grey", alpha = .5)
 text1 = list("sp.text", c(180500,329900), "0", cex = .5, which = 4)
@@ -448,19 +455,19 @@ 
using lattice plot (spplot)

 
Reuse these results; universal kriging standard errors; grid plot
 with point locations and polygon (river):

-
+
 rv = list("sp.polygons", meuse.riv, fill = "blue", alpha = 0.1)
 pts = list("sp.points", meuse, pch = 3, col = "grey", alpha = .7)
 spplot(zn.uk, "var1.pred",
     sp.layout = list(rv, scale, text1, text2, pts),
     main = "log(zinc); universal kriging using sqrt(dist to Meuse)")

 

-
+
 zn.uk[["se"]] = sqrt(zn.uk[["var1.var"]])
 spplot(zn.uk, "se", sp.layout = list(rv, pts),
     main = "log(zinc); universal kriging standard errors")

 

-
+
 arrow = list("SpatialPolygonsRescale", layout.north.arrow(),
     offset = c(-76,34), scale = 0.5, which = 2)
 spplot(nc, c("SID74", "SID79"), names.attr = c("1974","1979"),
@@ -468,7 +475,7 @@ 
using lattice plot (spplot)    main = "SIDS (sudden infant death syndrome) in North Carolina",
     sp.layout = list(arrow), as.table = TRUE)

 

-
+
 arrow = list("SpatialPolygonsRescale", layout.north.arrow(), 
     offset = c(-76,34), scale = 0.5, which = 2)
 #scale = list("SpatialPolygonsRescale", layout.scale.bar(), 
@@ -483,7 +490,7 @@ 
using lattice plot (spplot)    sp.layout = arrow, as.table = TRUE)

 

 
Bubble plots for cadmium and zinc:

-
+
 b1 = bubble(meuse, "cadmium", maxsize = 1.5, main = "cadmium concentrations (ppm)",
     key.entries = 2^(-1:4))
 b2 = bubble(meuse, "zinc", maxsize = 1.5, main = "zinc concentrations (ppm)",
@@ -492,7 +499,7 @@ 
using lattice plot (spplot)print(b2, split = c(2,1,2,1), more = FALSE)

 

 
Factor variables using spplot:

-
+
 # create two dummy factor variables, with equal labels:
 set.seed(31)
 nc$f = factor(sample(1:5, 100,replace = TRUE),labels=letters[1:5])
@@ -514,18 +521,18 @@ 
Interactive maps: leaflet, mapviewR packages leaflet and mapview provide interactive, browser-based
 maps building upon the leaflet javascript library. Example with points,
 grid and polygons follow:

-
+
 library(mapview)
 mapview(meuse, zcol = c("zinc", "lead"), legend = TRUE)

 

-
+
 mapview(meuse.grid, zcol = c("soil", "dist"), legend = TRUE)

 

-
+
 mapview(nc, zcol = c("SID74", "SID79"), alpha.regions = 1.0, legend = TRUE)

 

 
Mapview also allows grids of view that are synced

-
+
 m1 <- mapview(meuse, zcol = "soil", burst = TRUE, legend = TRUE)
 m2 <- mapview(meuse, zcol = "lead", legend = TRUE)
 m3 <- mapview(meuse, zcol = "landuse", map.types = "Esri.WorldImagery", legend = TRUE)
@@ -537,7 +544,7 @@ 
Interactive maps: leaflet, mapview
 
SessionInfo
 

-
+
 
## R version 4.4.0 (2024-04-24)
 ## Platform: x86_64-pc-linux-gnu
@@ -567,27 +574,25 @@ 
SessionInfo##  [1] xfun_0.43               bslib_0.7.0             raster_3.6-26          
 ##  [4] htmlwidgets_1.6.4       lattice_0.22-6          leaflet.providers_2.0.0
 ##  [7] vctrs_0.6.5             tools_4.4.0             crosstalk_1.2.1        
-## [10] stats4_4.4.0            tibble_3.2.1            proxy_0.4-27           
-## [13] spacetime_1.3-1         fansi_1.0.6             highr_0.10             
-## [16] xts_0.13.2              pkgconfig_2.0.3         KernSmooth_2.23-22     
-## [19] satellite_1.0.5         desc_1.4.3              uuid_1.2-0             
-## [22] leaflet_2.2.2           lifecycle_1.0.4         farver_2.1.1           
-## [25] compiler_4.4.0          FNN_1.1.4               textshaping_0.3.7      
-## [28] munsell_0.5.1           terra_1.7-71            codetools_0.2-20       
-## [31] htmltools_0.5.8.1       class_7.3-22            sass_0.4.9             
-## [34] yaml_2.3.8              pillar_1.9.0            pkgdown_2.0.9          
-## [37] jquerylib_0.1.4         classInt_0.4-10         cachem_1.0.8           
-## [40] brew_1.0-10             digest_0.6.35           purrr_1.0.2            
-## [43] fastmap_1.1.1           grid_4.4.0              colorspace_2.1-0       
-## [46] cli_3.6.2               magrittr_2.0.3          base64enc_0.1-3        
-## [49] utf8_1.2.4              leafem_0.2.3            e1071_1.7-14           
-## [52] scales_1.3.0            rmarkdown_2.26          ragg_1.3.0             
-## [55] zoo_1.8-12              png_0.1-8               memoise_2.0.1          
-## [58] evaluate_0.23           knitr_1.46              rlang_1.1.3            
-## [61] leafpop_0.1.0           Rcpp_1.0.12             glue_1.7.0             
-## [64] DBI_1.2.2               svglite_2.1.3           jsonlite_1.8.8         
-## [67] R6_2.5.1                systemfonts_1.0.6       fs_1.6.4               
-## [70] intervals_0.15.4        units_0.8-5

+## [10] stats4_4.4.0            proxy_0.4-27            spacetime_1.3-1        
+## [13] highr_0.10              xts_0.13.2              KernSmooth_2.23-22     
+## [16] satellite_1.0.5         desc_1.4.3              leaflet_2.2.2          
+## [19] uuid_1.2-0              lifecycle_1.0.4         farver_2.1.1           
+## [22] compiler_4.4.0          FNN_1.1.4               textshaping_0.3.7      
+## [25] munsell_0.5.1           terra_1.7-71            codetools_0.2-20       
+## [28] htmltools_0.5.8.1       class_7.3-22            sass_0.4.9             
+## [31] yaml_2.3.8              pkgdown_2.0.9           jquerylib_0.1.4        
+## [34] classInt_0.4-10         cachem_1.0.8            brew_1.0-10            
+## [37] digest_0.6.35           purrr_1.0.2             fastmap_1.1.1          
+## [40] grid_4.4.0              colorspace_2.1-0        cli_3.6.2              
+## [43] magrittr_2.0.3          base64enc_0.1-3         leafem_0.2.3           
+## [46] e1071_1.7-14            scales_1.3.0            rmarkdown_2.26         
+## [49] ragg_1.3.0              zoo_1.8-12              png_0.1-8              
+## [52] memoise_2.0.1           evaluate_0.23           knitr_1.46             
+## [55] rlang_1.1.3             Rcpp_1.0.12             leafpop_0.1.0          
+## [58] glue_1.7.0              DBI_1.2.2               svglite_2.1.3          
+## [61] jsonlite_1.8.8          R6_2.5.1                systemfonts_1.0.6      
+## [64] fs_1.6.4                intervals_0.15.4        units_0.8-5

 

 

   

diff --git a/pkgdown.yml b/pkgdown.yml
index 89e44d0..44626e0 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -5,5 +5,5 @@ articles:
   CRS_warnings: CRS_warnings.html
   retiring_rgdal_geos_1: retiring_rgdal_geos_1.html
   sp_gallery: sp_gallery.html
-last_built: 2024-05-06T18:42Z
+last_built: 2024-05-06T19:03Z