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Jeremy Kidwell 2019-02-14 18:08:05 +00:00
parent 328f58e69a
commit c24f041a97
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103
testing_sf_plot_times.R
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@ -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()

66
wilderness_plots.R
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# 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)