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added output via pander for wilderness tables, removed plots (for now)

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Jeremy Kidwell 2019-02-05 19:49:29 +00:00
parent ec21580f31
commit c261595bf1
3 changed files with 83 additions and 72 deletions
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82
mapping_draft.Rmd
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@ -917,102 +917,44 @@ So what did I discover? The results were inconclusive. First, it is important to
```{r wilderness_table} ```{r wilderness_table}
# Calculate number of groups within polygons # Calculate number of groups within polygons
# TODO: run on additional shapefiles # TODO: run on additional shapefiles
# TODO: more efficient code using do.call() function or sapply() as here https://stackoverflow.com/questions/3642535/creating-an-r-dataframe-row-by-row
# Sample code for use below # Sample code for use below
# sum(apply(st_within(pow_pointX_sf, st_buffer(sssi, dist = 50), sparse=FALSE), 1, any)) # sum(apply(st_within(pow_pointX_sf, st_buffer(sssi, dist = 50), sparse=FALSE), 1, any))
# sum(apply(st_within(pow_pointX_sf, sssi, sparse=FALSE), 1, any)) # sum(apply(st_within(pow_pointX_sf, sssi, sparse=FALSE), 1, any))
titles <- c("Within SSSIs", "...50m", "...500m")
ecs_wilderness_row <- c(sum(apply(st_within(ecs_sf, sssi, sparse=FALSE), 1, any)), sum(apply(st_within(ecs_sf, st_buffer(sssi, dist = 50), sparse=FALSE), 1, any)), sum(apply(st_within(ecs_sf, st_buffer(sssi, dist = 500), sparse=FALSE), 1, any))) ecs_wilderness_row <- c(sum(apply(st_within(ecs_sf, sssi, sparse=FALSE), 1, any)), sum(apply(st_within(ecs_sf, st_buffer(sssi, dist = 50), sparse=FALSE), 1, any)), sum(apply(st_within(ecs_sf, st_buffer(sssi, dist = 500), sparse=FALSE), 1, any)))
ecs_wilderness_row ecs_wilderness_row <- rbind(titles, ecs_wilderness_row)
pow_wilderness_row <- c(sum(apply(st_within(pow_pointX_sf, sssi, sparse=FALSE), 1, any)), sum(apply(st_within(pow_pointX_sf, st_buffer(sssi, dist = 50), sparse=FALSE), 1, any)), sum(apply(st_within(pow_pointX_sf, st_buffer(sssi, dist = 500), sparse=FALSE), 1, any))) pow_wilderness_row <- c(sum(apply(st_within(pow_pointX_sf, sssi, sparse=FALSE), 1, any)), sum(apply(st_within(pow_pointX_sf, st_buffer(sssi, dist = 50), sparse=FALSE), 1, any)), sum(apply(st_within(pow_pointX_sf, st_buffer(sssi, dist = 500), sparse=FALSE), 1, any)))
pow_wilderness_row sssi_counts <- rbind(ecs_wilderness_row, pow_wilderness_row)
dtas_wilderness_row <- c(sum(apply(st_within(dtas_sf, sssi, sparse=FALSE), 1, any)), sum(apply(st_within(dtas_sf, st_buffer(sssi, dist = 50), sparse=FALSE), 1, any)), sum(apply(st_within(dtas_sf, st_buffer(sssi, dist = 500), sparse=FALSE), 1, any))) dtas_wilderness_row <- c(sum(apply(st_within(dtas_sf, sssi, sparse=FALSE), 1, any)), sum(apply(st_within(dtas_sf, st_buffer(sssi, dist = 50), sparse=FALSE), 1, any)), sum(apply(st_within(dtas_sf, st_buffer(sssi, dist = 500), sparse=FALSE), 1, any)))
dtas_wilderness_row sssi_counts <- rbind(sssi_counts, dtas_wilderness_row)
transition_wilderness_row <- c(sum(apply(st_within(transition_sf, sssi, sparse=FALSE), 1, any)), sum(apply(st_within(transition_sf, st_buffer(sssi, dist = 50), sparse=FALSE), 1, any)), sum(apply(st_within(transition_sf, st_buffer(sssi, dist = 500), sparse=FALSE), 1, any))) transition_wilderness_row <- c(sum(apply(st_within(transition_sf, sssi, sparse=FALSE), 1, any)), sum(apply(st_within(transition_sf, st_buffer(sssi, dist = 50), sparse=FALSE), 1, any)), sum(apply(st_within(transition_sf, st_buffer(sssi, dist = 500), sparse=FALSE), 1, any)))
transition_wilderness_row sssi_counts <- rbind(sssi_counts, transition_wilderness_row)
permaculture_wilderness_row <- c(sum(apply(st_within(permaculture_sf, sssi, sparse=FALSE), 1, any)), sum(apply(st_within(permaculture_sf, st_buffer(sssi, dist = 50), sparse=FALSE), 1, any)), sum(apply(st_within(permaculture_sf, st_buffer(sssi, dist = 500), sparse=FALSE), 1, any))) permaculture_wilderness_row <- c(sum(apply(st_within(permaculture_sf, sssi, sparse=FALSE), 1, any)), sum(apply(st_within(permaculture_sf, st_buffer(sssi, dist = 50), sparse=FALSE), 1, any)), sum(apply(st_within(permaculture_sf, st_buffer(sssi, dist = 500), sparse=FALSE), 1, any)))
permaculture_wilderness_row sssi_counts <- rbind(sssi_counts, permaculture_wilderness_row)
# Output mmd tables using pander
panderOptions("digits", 2)
pander(sssi_counts)
``` ```
```{r wilderness_plots} ```{r wilderness_plots}
# 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)
``` ```

5
testing_sf_plot_times.R
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@ -15,9 +15,12 @@ if (file.exists("data/National_Forest_Inventory_Woodland_Scotland_2017.shp") ==
forest_inventory <- st_read("data/National_Forest_Inventory_Woodland_Scotland_2017.shp") forest_inventory <- st_read("data/National_Forest_Inventory_Woodland_Scotland_2017.shp")
forest_inventory_sp <- readOGR("./data", "National_Forest_Inventory_Woodland_Scotland_2017") forest_inventory_sp <- readOGR("./data", "National_Forest_Inventory_Woodland_Scotland_2017")
system.time(
ggplot() + ggplot() +
geom_sf(data = forest_inventory) geom_sf(data = forest_inventory)
)
system.time(
ggplot() + ggplot() +
geom_polygon(data = forest_inventory_sp) geom_polygon(data = forest_inventory_sp)
)

66
wilderness_plots.R Normal file
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@ -0,0 +1,66 @@
# 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)