From c24f041a97246e20555e04315876ccac648537f9 Mon Sep 17 00:00:00 2001 From: Jeremy Kidwell Date: Thu, 14 Feb 2019 18:08:05 +0000 Subject: [PATCH] removed wip --- testing_sf_plot_times.R | 103 ---------------------------------------- wilderness_plots.R | 66 ------------------------- 2 files changed, 169 deletions(-) delete mode 100644 testing_sf_plot_times.R delete mode 100644 wilderness_plots.R diff --git a/testing_sf_plot_times.R b/testing_sf_plot_times.R deleted file mode 100644 index 804bdb5..0000000 --- a/testing_sf_plot_times.R +++ /dev/null @@ -1,103 +0,0 @@ -require(RCurl) # used for fetching reproducible datasets -require(sf) # new simplefeature data class, supercedes sp in many ways -# using GEOS 3.6.1, GDAL 2.1.3, PROJ 4.9.3 -require(sp) # needed for proj4string, deprecated by sf() -require(rgdal) # version version: 1.3-6 -require(rgeos) # used for buffering below -require(devtools) -require(ggplot2) - -# setwd("~/Downloads/test") -# load data - -transition_wgs <- read.csv(text=getURL("https://zenodo.org/record/165519/files/SCCAN_1.4.csv")) -coordinates(transition_wgs) <- c("X", "Y") -proj4string(transition_wgs) <- CRS(wgs84) -transition_sp <- spTransform(transition_wgs, bng) -transition_sf <- st_as_sf(transition, coords = c("X", "Y"), crs=27700) - -# Download data as ESRI Shapefile from page at: https://gateway.snh.gov.uk/natural-spaces/dataset.jsp?dsid=SSSI - -unzip("SSSI_SCOTLAND_ESRI.zip") - -# # Download data as ESRI Shapefile from page at: http://data-forestry.opendata.arcgis.com/datasets/3cb1abc185a247a48b9d53e4c4a8be87_0 - -unzip("National_Forest_Inventory_Woodland_Scotland_2017.zip") - -sssi_sf <- st_read("./data/SSSI_SCOTLAND.shp") -sssi_sp <- readOGR("./data", "SSSI_SCOTLAND") - -forest_inventory_sf <- st_read("./data/National_Forest_Inventory_Woodland_Scotland_2017.shp") -forest_inventory_sp <- readOGR("./data", "National_Forest_Inventory_Woodland_Scotland_2017") - -# Test validity of geometry - -rgeos::gIsValid(sssi_sp) -valid <- st_is_valid(sssi_sf) - valid[valid == FALSE] - -# Alternative approach from stackexchange using simplified geometry - - sssi_sp2 <- rgeos::gSimplify(sssi_sp, tol=3) - par(mfrow=c(1,2)) - plot(sssi_sp[1,]) - plot(sssi_sp2[1,]) - - system.time( - sssi_b1000 <- rgeos::gBuffer(sssi_sp2, width = 20, quadsegs = 30) - ) - - sssi_sf2 <- sf::st_simplify(sssi_sf) - system.time( - sssi_b1000 <- sf::st_buffer(sssi_sf2, dist = 20) - ) - -# Render ggplot2 plot on simplified geometry - -ggplot(sssi_sf2) + geom_sf(aes(fill = PA_CODE)) -plot(sssi_sf2) - -# Plot - -pdf(file = "sssi_polygons.pdf", width=5, height=6, res=300, units="in") -plot(st_geometry(sssi_simple), col='#aaaaaa', border=0) -dev.off() - - -# First test out plots using spatialfeatures and spdf with core R - -system.time( -plot(sssi_sf2) - ) - -system.time( - plot() - ) - -system.time( -plot(sssi_sp) - ) - -# First test out plots using spatialfeatures and spdf with ggplot2 - -system.time( - ggplot() + - geom_sf(data = sssi_sf) -) - -system.time( - ggplot() + - geom_polygon(data = sssi_sp) -) -# Now try to run a count within a buffer: - -st_crs(sssi_sf) <- 27700 -st_crs(transition_sf) <- 27700 - -# CRS uses meters for units, so buffer here should be a modest 50m: - -count_data_sf <- sum(apply(st_within(points_sf, st_buffer(sssi, dist = 50), sparse=FALSE), 1, any)) - -# count_data_sf <- sum(apply(gWithin(points_sf, gBuffer(sssi,width=50) - -sessioninfo::session_info() \ No newline at end of file diff --git a/wilderness_plots.R b/wilderness_plots.R deleted file mode 100644 index 6900966..0000000 --- a/wilderness_plots.R +++ /dev/null @@ -1,66 +0,0 @@ -# Plot SSSI polygons with ECS points (using sp, for now) - -ggplot() + - geom_polygon(aes(x = long, y = lat, group = group), - data = sssi_sp, - colour = 'black', - alpha = .7, - size = .005) + - geom_point(aes(X, Y, fill = NULL, group = NULL), size = 1, data=ecs_df, - colour = "black", - fill = "white", - size = .15, - stroke = .002, - alpha = .6, - show.legend = TRUE) + - labs(x = NULL, y = NULL, fill = "Groups", - title = "Figure 11", - subtitle="Sites of Special Scientific Interest with points marked", - caption = paste("Jeremy H. Kidwell :: jeremykidwell.info", - "Data: UK Data Service (OGL) & Jeremy H. Kidwell", - "You may redistribute this graphic under the terms of the CC-by-SA 4.0 license.", - sep = "\n")) - -# # ggplot using sf seems to be severely broken for now. Commenting out and reverting to sp -# if (utils::packageVersion("ggplot2") > "2.2.1") -# ggplot() + geom_sf(data = sssi) + -# geom_point(aes(X, Y, fill = NULL, group = NULL), size = 1, data=ecs_df, -# colour = "black", -# fill = "white", -# size = .3, -# stroke = .1, -# show.legend = FALSE) + -# labs(x = NULL, -# title = "Figure 11", -# subtitle="Sites of Special Scientific Interest with points marked", -# caption = paste("Jeremy H. Kidwell :: jeremykidwell.info", -# "Data: UK Data Service (OGL) & Jeremy H. Kidwell", -# "You may redistribute this graphic under the terms of the CC-by-SA 4.0 license.", -# sep = "\n")) - -# Plot Forest Inventory - -ggplot() + - geom_polygon(aes(x = long, y = lat, group = group), - data = forest_inventory_sp, - colour = 'black', - alpha = .7, - size = .005) + - geom_point(aes(X, Y, fill = NULL, group = NULL), size = 1, data=ecs_df, - colour = "black", - fill = "white", - size = .15, - stroke = .002, - alpha = .6, - show.legend = TRUE) + - labs(x = NULL, y = NULL, fill = "Groups", - title = "Figure 11", - subtitle="Sites of Special Scientific Interest with points marked", - caption = paste("Jeremy H. Kidwell :: jeremykidwell.info", - "Data: UK Data Service (OGL) & Jeremy H. Kidwell", - "You may redistribute this graphic under the terms of the CC-by-SA 4.0 license.", - sep = "\n")) - -# # ggplot using sf seems to be severely broken for now. Commenting out and reverting to sp -# ggplot() + -# geom_sf(data = forest_inventory) \ No newline at end of file