Merge branch 'middle-ridge' into 'master'

Middle ridge See merge request WEEL_grp/study-area-figures!9
wildlifeevoeco · May 22, 2020 · c8158bc · c8158bc
2 parents 544ccc1 + e4255e4
commit c8158bc
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diff --git a/R/00-palette.R b/R/00-palette.R
@@ -1,4 +1,4 @@
-### Palette - Study area figure ====
+# === Palette - Study area figures ----------------------------------------
 # Alec Robitaille
 
 # Water
@@ -24,7 +24,7 @@ forestcol <- '#A4BC9C'
 gridcol <- '#323232'
 
 
-# Road hiearchy
+# Road hierarchy
 levels <- c('motorway', 'trunk', 'primary', 'secondary', 'tertiary',
 						'unclassified', 'residential', 'motorway_link', 'trunk_link',
 						'primary_link', 'secondary_link', 'tertiary_link',

diff --git a/R/01-fogo-island-prep.R b/R/01-fogo-island-prep.R
@@ -1,13 +1,15 @@
-### Fogo island prep ====
+# === Fogo Island Prep ----------------------------------------------------
 # Alec L. Robitaille
 
 
-### Packages ----
+# Packages ----------------------------------------------------------------
 libs <- c('sf',
 					'osmdata')
 lapply(libs, require, character.only = TRUE)
 
-### Download OSM data ----
+
+
+# Download OSM data -------------------------------------------------------
 # Set up bounding box - order: xmin, ymin, xmax, ymax
 bb <- c(xmin = -54.3533,
 				ymin = 49.5194,
@@ -65,6 +67,7 @@ cutisles <- st_difference(islands, waterpols)
 
 
 
+
 ### Reproject ----
 # Projections
 utm <- st_crs('+proj=utm +zone=21 ellps=WGS84')

diff --git a/R/02-fogo-island-figure.R b/R/02-fogo-island-figure.R
@@ -1,8 +1,8 @@
-### Fogo Study Area Figure ====
+# === Fogo Island Prep ----------------------------------------------------
 # Alec L. Robitaille
 
 
-### Packages ----
+# Packages ----------------------------------------------------------------
 libs <- c(
 	'data.table',
 	'ggplot2',
@@ -11,15 +11,16 @@ libs <- c(
 lapply(libs, require, character.only = TRUE)
 
 
-### Data ----
+# Data --------------------------------------------------------------------
 fogo <- st_read('output/fogo-island-polygons.gpkg')
 roads <- st_read('output/fogo-roads.gpkg')
 
+
 # CRS
 utm <- st_crs('+proj=utm +zone=21 ellps=WGS84')
 
 
-### Theme ----
+# Theme -------------------------------------------------------------------
 # Colors
 source('R/00-palette.R')
 
@@ -36,7 +37,8 @@ themeMap <- theme(panel.border = element_rect(size = 1, fill = NA),
 									axis.text = element_text(size = 11, color = 'black'),
 									axis.title = element_blank())
 
-### Plot ----
+
+# Plot --------------------------------------------------------------------
 # Base fogo
 (gfogo <- ggplot() +
  	geom_sf(fill = islandcol, size = 0.3, color = coastcol, data = fogo) +
@@ -46,7 +48,8 @@ themeMap <- theme(panel.border = element_rect(size = 1, fill = NA),
  	themeMap)
 
 
-### Output ----
+
+# Output ------------------------------------------------------------------
 ggsave(
 	'graphics/02-fogo-island.png',
 	gfogo,

diff --git a/R/03-newfoundland-prep.R b/R/03-newfoundland-prep.R
@@ -1,12 +1,15 @@
-### Newfoundland prep ====
+# === Newfoundland Prep ---------------------------------------------------
 # Alec L. Robitaille
 
 
-### Packages ----
+
+# Packages ----------------------------------------------------------------
 libs <- c('sf', 'osmdata')
 lapply(libs, require, character.only = TRUE)
 
-### Download OSM data ----
+
+
+# Download OSM data -------------------------------------------------------
 # Download osm coastlines in bbox
 # NOTE: This steps takes a few moments
 zz <- opq(getbb('Newfoundland')) %>%
@@ -23,13 +26,15 @@ castpolys <- st_cast(st_polygonize(st_union(lns)))
 nl <- st_as_sf(castpolys)
 
 
-### Reproject islands ----
+
+# Reproject islands -------------------------------------------------------
 # Projections
 utm <- st_crs('+proj=utm +zone=21 ellps=WGS84')
 
 # Project to UTM
 utmNL <- st_transform(nl, utm)
 
 
-### Output ----
+
+# Output ------------------------------------------------------------------
 st_write(utmNL, 'output/newfoundland-polygons.gpkg')
diff --git a/R/04-newfoundland-figure.R b/R/04-newfoundland-figure.R
@@ -1,8 +1,9 @@
-### Newfoundland Study Area Figure ====
+# === Newfoundland - Figure -----------------------------------------------
 # Alec L. Robitaille
 
 
-### Packages ----
+
+# Packages ----------------------------------------------------------------
 libs <- c(
 	'data.table',
 	'ggplot2',
@@ -11,14 +12,14 @@ libs <- c(
 lapply(libs, require, character.only = TRUE)
 
 
-### Data ----
+# Data --------------------------------------------------------------------
 nl <- st_read('output/newfoundland-polygons.gpkg')
 
 # CRS
 utm <- st_crs('+proj=utm +zone=21 ellps=WGS84')
 
 
-### Theme ----
+# Theme -------------------------------------------------------------------
 # Colors
 source('R/00-palette.R')
 
@@ -29,15 +30,17 @@ themeMap <- theme(panel.border = element_rect(size = 1, fill = NA),
 									axis.text = element_text(size = 11, color = 'black'),
 									axis.title = element_blank())
 
-### Plot ----
+
+# Plot --------------------------------------------------------------------
 # NOTE: this figure only has the main island's coastline (eg missing Fogo)
 # Base NL
 (gnl <- ggplot(nl) +
  	geom_sf(fill = islandcol, color = coastcol, size = 0.3) +
  	themeMap)
 
 
-### Output ----
+
+# Output ------------------------------------------------------------------
 ggsave(
 	'graphics/04-newfoundland.png',
 	gnl,

diff --git a/R/05-fogo-inset-newfoundland-figure.R b/R/05-fogo-inset-newfoundland-figure.R
@@ -1,8 +1,9 @@
-### Fogo Inset in NL Study Area Figure ====
+# === Fogo Inset in NL Study Area Figure ----------------------------------
 # Alec L. Robitaille
 
 
-### Packages ----
+
+# Packages ----------------------------------------------------------------
 libs <- c(
 	'data.table',
 	'ggplot2',
@@ -12,7 +13,8 @@ libs <- c(
 lapply(libs, require, character.only = TRUE)
 
 
-### Data ----
+
+# Data --------------------------------------------------------------------
 fogo <- st_read('output/fogo-island-polygons.gpkg')
 roads <- st_read('output/fogo-roads.gpkg')
 
@@ -38,10 +40,11 @@ utmBB <- data.table(dtbb[, project(cbind(x, y), utm$proj4string)])
 
 
 
-### Theme ----
+# Theme -------------------------------------------------------------------
 # Colors
 source('R/00-palette.R')
 
+
 roadcols <- data.table(highway = c("primary", "secondary", "residential",
 																	 "service", "unclassified", "footway"))
 roadcols[, cols := gray.colors(.N, start = 0.1, end = 0.4)]
@@ -55,7 +58,8 @@ themeMap <- theme(panel.border = element_rect(size = 1, fill = NA),
 									axis.text = element_text(size = 11, color = 'black'),
 									axis.title = element_blank())
 
-### Plot ----
+
+# Plot --------------------------------------------------------------------
 # Base Fogo
 gfogo <- ggplot(fogo) +
 	geom_sf(fill = islandcol, size = 0.3, color = coastcol) +
@@ -99,7 +103,8 @@ gnl <- ggplot(nl) +
 )
 
 
-### Output ----
+
+# Output  -----------------------------------------------------------------
 ggsave(
 	'graphics/05-fogo-inset-nl.png',
 	g,
@@ -110,7 +115,8 @@ ggsave(
 
 
 
-### Alternative options ----
+
+# Alternative options -----------------------------------------------------
 # Fogo with NL coastline visible
 # (gnl <- ggplot(nl) +
 #  	geom_sf(fill = islandcol) +

diff --git a/R/06-terra-nova-prep.R b/R/06-terra-nova-prep.R
@@ -1,13 +1,15 @@
-### Terra Nova prep ====
+# === Terra Nova - Prep ---------------------------------------------------
 # Alec L. Robitaille, Isabella Richmond
 
 
-### Packages ----
+
+# Packages ----------------------------------------------------------------
 libs <- c('curl', 'zip', 'sf', 'osmdata')
 lapply(libs, require, character.only = TRUE)
 
 
-### Download Terra Nova data ----
+
+# Download TN data --------------------------------------------------------
 ## Polygon from Open Canada
 # https://open.canada.ca/data/en/dataset/e1f0c975-f40c-4313-9be2-beb951e35f4e
 curl_download('http://ftp.maps.canada.ca/pub/pc_pc/National-parks_Parc-national/national_parks_boundaries/national_parks_boundaries.shp.zip', 'input/national-parks.zip')
@@ -49,8 +51,9 @@ waterways <- opq(bb) %>%
 streamsPol <- st_cast(st_polygonize(st_union(waterways$osm_lines)))
 streamsLns <- waterways$osm_lines
 
-### Reproject ----
-# Projection
+
+
+# Reprojection ------------------------------------------------------------
 utm <- st_crs('+proj=utm +zone=21 ellps=WGS84')
 
 # Project to UTM
@@ -60,7 +63,10 @@ utmWater <- st_transform(waterpols, utm)
 utmStreamsLns <- st_transform(streamsLns, utm)
 utmStreamsPol <- st_transform(streamsPol, utm)
 
-### Output ----
+
+
+
+# Output ------------------------------------------------------------------
 st_write(utmTN, 'output/terra-nova-polygons.gpkg')
 st_write(utmRoads, 'output/terra-nova-roads.gpkg')
 st_write(utmWater, 'output/terra-nova-water.gpkg')

diff --git a/R/07-terra-nova-figure.R b/R/07-terra-nova-figure.R
@@ -1,8 +1,8 @@
-### Terra Nova Study Area Figure ====
+# === Terra Nova - Figure -------------------------------------------------
 # Alec L. Robitaille, Isabella Richmond
 
 
-### Packages ----
+# Packages ----------------------------------------------------------------
 libs <- c(
 	'data.table',
 	'ggplot2',
@@ -11,7 +11,8 @@ libs <- c(
 lapply(libs, require, character.only = TRUE)
 
 
-### Data ----
+
+# Data --------------------------------------------------------------------
 tn <- st_read('output/terra-nova-polygons.gpkg')
 roads <- st_read('output/terra-nova-roads.gpkg')
 
@@ -29,7 +30,8 @@ selroads <- c('trunk', 'primary')
 highway <- roads[roads$highway %in% selroads,]
 
 
-### Theme ----
+
+# Theme -------------------------------------------------------------------
 # Colors
 source('R/00-palette.R')
 
@@ -49,7 +51,8 @@ themeMap <- theme(panel.border = element_rect(size = 1, fill = NA),
 bb <- st_bbox(tn) - rep(c(1e3, -1e3), each = 2)
 
 
-### Plot ----
+
+# Plot --------------------------------------------------------------------
 # Crop NL
 nlcrop <- st_crop(nl, bb + rep(c(-5e4, 5e4), each = 2))
 
@@ -69,7 +72,7 @@ nlcrop <- st_crop(nl, bb + rep(c(-5e4, 5e4), each = 2))
  	themeMap)
 
 
-### Output ----
+# Output ------------------------------------------------------------------
 ggsave(
 	'graphics/07-terra-nova.png',
 	gtn,

diff --git a/R/08-terra-nova-buns-figure.R b/R/08-terra-nova-buns-figure.R
@@ -1,8 +1,8 @@
-### Terra Nova Buns Grid Study Area Figure ====
+# === Terra Nova Buns Grid - Figure ---------------------------------------
 # Alec L. Robitaille, Isabella Richmond
 
 
-### Packages ----
+# Packages ----------------------------------------------------------------
 libs <- c(
 	'data.table',
 	'ggplot2',
@@ -12,7 +12,8 @@ libs <- c(
 lapply(libs, require, character.only = TRUE)
 
 
-### Data ----
+
+# Data --------------------------------------------------------------------
 grids <- data.table(
 	SiteName = c("Bloomfield",
 							 "Dunphy's Pond", "TNNP North", "Unicorn"),
@@ -51,7 +52,8 @@ selroads <- c('trunk', 'primary')
 highway <- roads[roads$highway %in% selroads,]
 
 
-### Theme ----
+
+# Theme -------------------------------------------------------------------
 # Colors
 source('R/00-palette.R')
 
@@ -72,7 +74,8 @@ bb <- st_bbox(tn) + rep(c(-5e3, 5e3), each = 2)
 bbadjust <- bb #+ c(-1e3, 0, 0, 0)
 
 
-### Plot ----
+
+# Plot --------------------------------------------------------------------
 # Crop NL
 nlcrop <- st_crop(nl, bbadjust + rep(c(-5e4, 5e4), each = 2))
 
@@ -134,7 +137,8 @@ annotateBB <- st_bbox(st_transform(annotateSf, utm))
 
 
 
-### Output ----
+
+# Output ------------------------------------------------------------------
 ggsave(
 	'graphics/08-terra-nova-buns.png',
 	g,