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{orig → migrated}/cm_mod.R RENAMED
@@ -105,7 +105,8 @@
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  ### code chunk number 25: cm.Rnw:528-533
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  ###################################################
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  m <- matrix(c(0,0,1,1), ncol=2, dimnames=list(NULL, c("min", "max")))
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- crs <- CRS(projargs=as.character(NA))
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+ library(sf)
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+ crs <- as(st_crs(as.character(NA)), "CRS")
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  crs
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  S <- Spatial(bbox=m, proj4string=crs)
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  S
@@ -115,7 +116,8 @@
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  ### code chunk number 27: cm.Rnw:555-558
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  ###################################################
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  bb <- matrix(c(350, 85, 370, 95), ncol=2, dimnames=list(NULL, c("min", "max")))
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- res <- try(Spatial(bb, proj4string=CRS("+proj=longlat +ellps=WGS84")))
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+ res <- try(Spatial(bb, proj4string=as(sf::st_crs("+proj=longlat +ellps=WGS84"),
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+ "CRS")))
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  ###################################################
@@ -136,7 +138,7 @@
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  ###################################################
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  ### code chunk number 33: cm.Rnw:671-674
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  ###################################################
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- llCRS <- CRS("+proj=longlat +ellps=WGS84")
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+ llCRS <- as(st_crs("+proj=longlat +ellps=WGS84"), "CRS")
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  CRAN_sp <- SpatialPoints(CRAN_mat, proj4string=llCRS)
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  summary(CRAN_sp)
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@@ -151,7 +153,7 @@
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  ### code chunk number 35: cm.Rnw:720-724
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  ###################################################
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  proj4string(CRAN_sp)
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- proj4string(CRAN_sp) <- CRS(as.character(NA))
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+ proj4string(CRAN_sp) <- as(st_crs(as.character(NA)), "CRS")
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  proj4string(CRAN_sp)
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  proj4string(CRAN_sp) <- llCRS
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@@ -269,21 +271,21 @@
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  turtle_df1$lon <- ifelse(turtle_df1$lon < 0, turtle_df1$lon+360, turtle_df1$lon)
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  turtle_sp <- turtle_df1[order(turtle_df1$timestamp),]
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  coordinates(turtle_sp) <- c("lon", "lat")
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- proj4string(turtle_sp) <- CRS("+proj=longlat +ellps=WGS84")
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+ proj4string(turtle_sp) <- as(st_crs("+proj=longlat +ellps=WGS84"), "CRS")
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  ###################################################
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  ### code chunk number 55: cm.Rnw:1031-1034
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  ###################################################
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- library(maptools)
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- gshhs.c.b <- system.file("share/gshhs_c.b", package="maptools")
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- pac <- Rgshhs(gshhs.c.b, level=1, xlim=c(130,250), ylim=c(15,60), verbose=FALSE)
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+ library(maps)
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+ pac <- map("world", fill=TRUE, plot=FALSE, wrap=c(0,360))
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+ pac <- as(st_as_sf(pac), "Spatial")
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  ###################################################
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  ### code chunk number 56: cm.Rnw:1039-1051
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  ###################################################
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- plot(pac$SP, axes=TRUE, col="khaki2", xaxs="i", yaxs="i")
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+ plot(pac, axes=TRUE, xlim=c(130,250), ylim=c(15,60), col="khaki2", xaxs="i", yaxs="i")
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  plot(turtle_sp, add=TRUE)
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  m_rle <- rle(months(turtle_sp$timestamp))
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  clen <- cumsum(m_rle$lengths[-length(m_rle$lengths)])-1
@@ -308,10 +310,9 @@
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  ### code chunk number 59: cm.Rnw:1140-1146
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  ###################################################
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  library(maps)
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- japan <- map("world", "japan", plot=FALSE)
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- p4s <- CRS("+proj=longlat +ellps=WGS84")
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- library(maptools)
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- SLjapan <- map2SpatialLines(japan, proj4string=p4s)
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+ japan <- map("world", "japan", fill=FALSE, plot=FALSE)
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+ p4s <- st_crs("+proj=longlat +ellps=WGS84")
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+ SLjapan <- as(st_geometry(st_as_sf(japan, fill=FALSE, crs=p4s)), "Spatial")
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  str(SLjapan, max.level=2)
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@@ -325,16 +326,22 @@
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  ###################################################
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  ### code chunk number 61: cm.Rnw:1189-1191
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  ###################################################
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- volcano_sl <- ContourLines2SLDF(contourLines(volcano))
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+ data(volcano)
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+ x = contourLines(volcano)
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+ xx = lapply(x, function(x) cbind(x$x, x$y))
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+ xxx = split(xx, sapply(x, "[[", "level"))
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+ x2a = st_sfc(lapply(xxx, st_multilinestring))
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+ x2 = st_as_sf(x2a, level=names(xxx))
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+ volcano_sl <- as(x2, "Spatial")
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+ #volcano_sl <- ContourLines2SLDF(contourLines(volcano))
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  t(slot(volcano_sl, "data"))
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  ###################################################
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  ### code chunk number 63: cm.Rnw:1217-1220
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  ###################################################
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- llCRS <- CRS("+proj=longlat +ellps=WGS84")
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- auck_shore <- MapGen2SL("auckland_mapgen.dat", llCRS)
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- summary(auck_shore)
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+ # MapGen format defunct https://www.ngdc.noaa.gov/mgg/shorelines/shorelines.html
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+ auck_shore <- as(st_geometry(st_read("auck_shore.gpkg")), "Spatial")
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  ###################################################
@@ -351,7 +358,7 @@
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  Polygons(list(Polygon(slot(slot(x, "Lines")[[1]], "coords"))),
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  ID=slot(x, "ID"))
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  }),
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- proj4string=CRS("+proj=longlat +ellps=WGS84"))
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+ proj4string=as(st_crs("+proj=longlat +ellps=WGS84"), "CRS"))
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  ###################################################
@@ -403,7 +410,7 @@
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  Polygons(list(Polygon(slot(slot(x, "Lines")[[1]], "coords"))),
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  ID=slot(x, "ID"))
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  }),
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- proj4string=CRS("+proj=longlat +ellps=WGS84"))
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+ proj4string=as(st_crs("+proj=longlat +ellps=WGS84"), "CRS"))
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  summary(islands_sp)
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  slot(islands_sp, "plotOrder")
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  order(sapply(slot(islands_sp, "polygons"),
@@ -415,10 +422,10 @@
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  ###################################################
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  library(maps)
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  state.map <- map("state", plot=FALSE, fill=TRUE)
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- IDs <- sapply(strsplit(state.map$names, ":"), function(x) x[1])
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- library(maptools)
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- state.sp <- map2SpatialPolygons(state.map, IDs=IDs,
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- proj4string=CRS("+proj=longlat +ellps=WGS84"))
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+ state_sf <- st_as_sf(state.map, fill=TRUE, group=TRUE,
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+ crs=st_crs("+proj=longlat +ellps=WGS84"))
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+ state.sp <- as(st_geometry(state_sf), "Spatial")
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+ row.names(state.sp) <- state_sf$ID
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  ###################################################
@@ -477,23 +484,27 @@
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  ###################################################
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  ### code chunk number 82: cm.Rnw:1643-1644
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  ###################################################
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- library(rgeos)
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+ #library(rgeos)
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  ###################################################
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  ### code chunk number 83: cm.Rnw:1646-1648
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  ###################################################
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- manitoulin_sp <- createSPComment(manitoulin_sp)
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+ comment(slot(manitoulin_sp, "polygons")[[1]]) <- rep("0", 19)
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+ comment(manitoulin_sp) <- "TRUE"
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+ manitoulin_sf <- st_make_valid(st_geometry(st_as_sf(manitoulin_sp)))
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+ manitoulin_sp <- as(manitoulin_sf, "Spatial")
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  sapply(slot(manitoulin_sp, "polygons"), comment)
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+ # eastern edge lake assigned here to exterior, minor differences
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  ###################################################
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  ### code chunk number 84: cm.Rnw:1674-1687
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  ###################################################
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- plot(manitoulin_sp, pbg="lightsteelblue2", col="khaki2", usePolypath=FALSE)
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+ plot(manitoulin_sp, bg="lightsteelblue2", col="khaki2", usePolypath=TRUE, xaxs="i", yaxs="i")
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  text(t(sapply(slot(slot(manitoulin_sp, "polygons")[[1]], "Polygons"), function(x) slot(x, "labpt")))[-c(1,2),], label=high$polydata$level[-c(1,2)], col="black", font=2)
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  cmt <- unlist(strsplit(sapply(slot(manitoulin_sp, "polygons"), comment), " "))
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- plot(manitoulin_sp, pbg="lightsteelblue2", col="khaki2", usePolypath=FALSE)
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+ plot(manitoulin_sp, bg="lightsteelblue2", col="khaki2", usePolypath=TRUE, xaxs="i", yaxs="i")
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  text(t(sapply(slot(slot(manitoulin_sp, "polygons")[[1]], "Polygons"), function(x) slot(x, "labpt")))[-c(1,2),], label=cmt[-c(1,2)], col="black", font=2)
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@@ -524,7 +535,7 @@
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  ###################################################
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  ### code chunk number 89: cm.Rnw:1772-1775
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  ###################################################
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- p4s <- CRS(proj4string(manitoulin_sp))
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+ p4s <- slot(manitoulin_sp, "proj4string")
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  manitoulin_SG <- SpatialGrid(manitoulin_grd, proj4string=p4s)
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  summary(manitoulin_SG)
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@@ -609,57 +620,56 @@
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  ###################################################
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  ### code chunk number 100: cm.Rnw:1983-1984
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  ###################################################
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- library(raster)
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+ library(stars)
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  ###################################################
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  ### code chunk number 101: cm.Rnw:1986-1987
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  ###################################################
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- r <- raster("70042108.tif")
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+ r <- read_stars("70042108.tif", proxy = TRUE)
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  ###################################################
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  ### code chunk number 103: cm.Rnw:1992-1998
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  ###################################################
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  class(r)
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- inMemory(r)
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  object.size(r)
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- cellStats(r, max)
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- cellStats(r, min)
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- inMemory(r)
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+ max(as.vector(st_as_stars(r)[[1]]), na.rm = TRUE)
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+ min(as.vector(st_as_stars(r)[[1]]), na.rm = TRUE)
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+ inherits(r, "stars_proxy") # out-of-memory?
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+ object.size(r)
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+ object.size(st_as_stars(r))
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  ###################################################
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  ### code chunk number 104: cm.Rnw:2012-2024
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  ###################################################
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- out <- raster(r)
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- bs <- blockSize(out)
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- out <- writeStart(out, filename=tempfile(), overwrite=TRUE)
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- for (i in 1:bs$n) {
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- v <- getValues(r, row=bs$row[i], nrows=bs$nrows[i])
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- v[v <= 0] <- NA
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- writeValues(out, v, bs$row[i])
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- }
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- out <- writeStop(out)
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- cellStats(out, min)
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- cellStats(out, max)
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- inMemory(out)
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+ out = r
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+ out[ r <= 0 ] = NA
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+ dout <- st_as_stars(out)
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+ max(as.vector(dout[[1]]), na.rm = TRUE)
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+ min(as.vector(dout[[1]]), na.rm = TRUE)
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  ###################################################
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  ### code chunk number 106: cm.Rnw:2044-2052
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  ###################################################
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- plot(out, col=terrain.colors(100))
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- plot(auck_gshhs, add=TRUE)
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+ r1 <- as(dout, "Spatial")
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+ image(r1, col = terrain.colors(100))
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+ plot(auck_gshhs, add = TRUE)
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  ###################################################
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  ### code chunk number 107: cm.Rnw:2069-2073
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  ###################################################
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- r1 <- as(out, "SpatialGridDataFrame")
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  summary(r1)
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- r2 <- as(r1, "RasterLayer")
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+ r2 <- as(dout, "SpatRaster")
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  summary(r2)
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+ (sI <- sessionInfo()) # check: no sp?
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+
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+ "rgdal" %in% c(names(sI$otherPkgs), names(sI$loadedOnly))
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+ "rgeos" %in% c(names(sI$otherPkgs), names(sI$loadedOnly))
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+ "maptools" %in% c(names(sI$otherPkgs), names(sI$loadedOnly))
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