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removed wip
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Jeremy Kidwell
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328f58e69a
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c24f041a97
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require(RCurl) # used for fetching reproducible datasets
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require(sf) # new simplefeature data class, supercedes sp in many ways
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# using GEOS 3.6.1, GDAL 2.1.3, PROJ 4.9.3
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require(sp) # needed for proj4string, deprecated by sf()
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require(rgdal) # version version: 1.3-6
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require(rgeos) # used for buffering below
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require(devtools)
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require(ggplot2)
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# setwd("~/Downloads/test")
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# load data
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transition_wgs <- read.csv(text=getURL("https://zenodo.org/record/165519/files/SCCAN_1.4.csv"))
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coordinates(transition_wgs) <- c("X", "Y")
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proj4string(transition_wgs) <- CRS(wgs84)
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transition_sp <- spTransform(transition_wgs, bng)
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transition_sf <- st_as_sf(transition, coords = c("X", "Y"), crs=27700)
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# Download data as ESRI Shapefile from page at: https://gateway.snh.gov.uk/natural-spaces/dataset.jsp?dsid=SSSI
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unzip("SSSI_SCOTLAND_ESRI.zip")
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# # Download data as ESRI Shapefile from page at: http://data-forestry.opendata.arcgis.com/datasets/3cb1abc185a247a48b9d53e4c4a8be87_0
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unzip("National_Forest_Inventory_Woodland_Scotland_2017.zip")
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sssi_sf <- st_read("./data/SSSI_SCOTLAND.shp")
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sssi_sp <- readOGR("./data", "SSSI_SCOTLAND")
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forest_inventory_sf <- st_read("./data/National_Forest_Inventory_Woodland_Scotland_2017.shp")
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forest_inventory_sp <- readOGR("./data", "National_Forest_Inventory_Woodland_Scotland_2017")
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# Test validity of geometry
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rgeos::gIsValid(sssi_sp)
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valid <- st_is_valid(sssi_sf)
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valid[valid == FALSE]
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# Alternative approach from stackexchange using simplified geometry
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sssi_sp2 <- rgeos::gSimplify(sssi_sp, tol=3)
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par(mfrow=c(1,2))
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plot(sssi_sp[1,])
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plot(sssi_sp2[1,])
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system.time(
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sssi_b1000 <- rgeos::gBuffer(sssi_sp2, width = 20, quadsegs = 30)
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)
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sssi_sf2 <- sf::st_simplify(sssi_sf)
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system.time(
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sssi_b1000 <- sf::st_buffer(sssi_sf2, dist = 20)
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)
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# Render ggplot2 plot on simplified geometry
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ggplot(sssi_sf2) + geom_sf(aes(fill = PA_CODE))
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plot(sssi_sf2)
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# Plot
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pdf(file = "sssi_polygons.pdf", width=5, height=6, res=300, units="in")
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plot(st_geometry(sssi_simple), col='#aaaaaa', border=0)
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dev.off()
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# First test out plots using spatialfeatures and spdf with core R
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system.time(
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plot(sssi_sf2)
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)
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system.time(
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plot()
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)
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system.time(
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plot(sssi_sp)
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)
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# First test out plots using spatialfeatures and spdf with ggplot2
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system.time(
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ggplot() +
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geom_sf(data = sssi_sf)
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)
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system.time(
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ggplot() +
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geom_polygon(data = sssi_sp)
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)
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# Now try to run a count within a buffer:
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st_crs(sssi_sf) <- 27700
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st_crs(transition_sf) <- 27700
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# CRS uses meters for units, so buffer here should be a modest 50m:
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count_data_sf <- sum(apply(st_within(points_sf, st_buffer(sssi, dist = 50), sparse=FALSE), 1, any))
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# count_data_sf <- sum(apply(gWithin(points_sf, gBuffer(sssi,width=50)
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sessioninfo::session_info()
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# Plot SSSI polygons with ECS points (using sp, for now)
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ggplot() +
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geom_polygon(aes(x = long, y = lat, group = group),
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data = sssi_sp,
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colour = 'black',
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alpha = .7,
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size = .005) +
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geom_point(aes(X, Y, fill = NULL, group = NULL), size = 1, data=ecs_df,
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colour = "black",
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fill = "white",
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size = .15,
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stroke = .002,
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alpha = .6,
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show.legend = TRUE) +
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labs(x = NULL, y = NULL, fill = "Groups",
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title = "Figure 11",
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subtitle="Sites of Special Scientific Interest with points marked",
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caption = paste("Jeremy H. Kidwell :: jeremykidwell.info",
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"Data: UK Data Service (OGL) & Jeremy H. Kidwell",
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"You may redistribute this graphic under the terms of the CC-by-SA 4.0 license.",
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sep = "\n"))
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# # ggplot using sf seems to be severely broken for now. Commenting out and reverting to sp
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# if (utils::packageVersion("ggplot2") > "2.2.1")
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# ggplot() + geom_sf(data = sssi) +
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# geom_point(aes(X, Y, fill = NULL, group = NULL), size = 1, data=ecs_df,
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# colour = "black",
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# fill = "white",
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# size = .3,
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# stroke = .1,
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# show.legend = FALSE) +
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# labs(x = NULL,
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# title = "Figure 11",
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# subtitle="Sites of Special Scientific Interest with points marked",
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# caption = paste("Jeremy H. Kidwell :: jeremykidwell.info",
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# "Data: UK Data Service (OGL) & Jeremy H. Kidwell",
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# "You may redistribute this graphic under the terms of the CC-by-SA 4.0 license.",
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# sep = "\n"))
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# Plot Forest Inventory
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ggplot() +
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geom_polygon(aes(x = long, y = lat, group = group),
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data = forest_inventory_sp,
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colour = 'black',
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alpha = .7,
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size = .005) +
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geom_point(aes(X, Y, fill = NULL, group = NULL), size = 1, data=ecs_df,
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colour = "black",
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fill = "white",
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size = .15,
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stroke = .002,
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alpha = .6,
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show.legend = TRUE) +
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labs(x = NULL, y = NULL, fill = "Groups",
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title = "Figure 11",
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subtitle="Sites of Special Scientific Interest with points marked",
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caption = paste("Jeremy H. Kidwell :: jeremykidwell.info",
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"Data: UK Data Service (OGL) & Jeremy H. Kidwell",
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"You may redistribute this graphic under the terms of the CC-by-SA 4.0 license.",
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sep = "\n"))
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# # ggplot using sf seems to be severely broken for now. Commenting out and reverting to sp
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# ggplot() +
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# geom_sf(data = forest_inventory)
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