Datasets:

chuxuan
/

REPRO-Bench

#plotting maps
source("set_up_inla.R")

metrics_joined <- metrics_joined %>%
  filter(!is.na(L1_log10_st)) %>%
  rename(L1_log_st = L1_log10_st) %>%
  mutate(L1_copy = L1_log_st) %>%
  filter(!is.na(L2_prop)) %>%
  dplyr::mutate(L2_prop  = scale(L2_prop)[, 1]) %>%
  mutate(L2_copy = L2_prop) %>%
  filter(!is.na(neighboring_languages_st)) %>%
  filter(!is.na(Official)) %>%
  filter(!is.na(Education)) %>%
  filter(!is.na(boundness_st)) %>%
  filter(!is.na(informativity_st)) %>%
  filter(
    Macroarea == "Africa" |
      Macroarea == "Papunesia" |
      Macroarea == "Australia" | Macroarea == "Eurasia"
  ) %>%
  filter(180 > Longitude & Longitude > -24) %>%
  filter(80 > Latitude & Latitude > -45)

#an overview of area and family coverage
tab_areas <- as.data.frame(table(metrics_joined$AUTOTYP_area)) %>%
  arrange(desc(Freq))

tab_families <- as.data.frame(table(metrics_joined$Family_ID)) %>%
  arrange(desc(Freq))


#dropping tips not in Grambank
metrics_joined <-
  metrics_joined[metrics_joined$Language_ID %in% tree$tip.label,]
tree <- keep.tip(tree, metrics_joined$Language_ID)

x <-
  assert_that(all(tree$tip.label %in% metrics_joined$Language_ID), msg = "The data and phylogeny taxa do not match")

lakes <-
  map_data(
    "lakes",
    col = "white",
    border = "gray",
    margin = T,
    ylim = c(-45, 80),
    xlim = c(-30, 180),
    wrap = c(-25, 335)
  )

world <-
  map_data(
    "world",
    wrap = c(-25, 335),
    ylim = c(-45, 80),
    xlim = c(-30, 180),
    margin = T
  )

world <-
  subset(world,!(
    region %in% c(
      "USA",
      "Brazil",
      "Mexico",
      "Colombia",
      "Argentina",
      "Canada",
      "Peru",
      "Venezuela",
      "Chile",
      "Guatemala",
      "Ecuador",
      "Bolivia",
      "Cuba",
      "Honduras",
      "Paraguay",
      "Nicaragua",
      "El Salvador",
      "Costa Rica",
      "Panama",
      "Uruguay",
      "Jamaica",
      "Trinidad and Tobago",
      "Guyana",
      "Suriname",
      "Belize",
      "Barbados",
      "Saint Lucia",
      "Grenada",
      "Saint Vincent and the Grenadines",
      "Antigua and Barbuda",
      "Saint Kitts and Nevis",
      "Greenland"
    )
  ))

#shifting the longlat of the dataframe to match the pacific centered map
combination <- metrics_joined %>%
  mutate(Longitude = if_else(Longitude <= -25, Longitude + 360, Longitude))

#duplicates?

combination %>%
  group_by(Language_ID) %>%
  mutate(dupe = n() > 1) -> combination_dup
dupes <- combination_dup[combination_dup$dupe == "TRUE", ]

#Basemap
basemap <- ggplot(combination) +
  geom_polygon(
    data = world,
    aes(x = long, y = lat, group = group),
    colour = "gray87",
    fill = "gray87",
    size = 0.5
  ) +
  geom_polygon(
    data = lakes,
    aes(x = long, y = lat, group = group),
    colour = "gray87",
    fill = "white",
    size = 0.3
  )  +
  theme(
    panel.grid.major = element_blank(),
    #all of these lines are just removing default things like grid lines, axises etc
    panel.grid.minor = element_blank(),
    axis.title.x = element_blank(),
    axis.title.y = element_blank(),
    axis.line = element_blank(),
    panel.border = element_blank(),
    panel.background = element_rect(fill = "white"),
    axis.text.x = element_blank(),
    axis.text.y = element_blank(),
    axis.ticks = element_blank()
  )  +
  coord_map(
    projection = "vandergrinten",
    ylim = c(-45, 80),
    xlim = c(-30, 180)
  )


#plotting boundness map with cumstom labels

#tswa1253 is almost overlapping in the location with hoaa1235; plotting hoaa1235 for the purposes of the plot
combination_ordered_0 <- combination %>%
  mutate(plotted_last = case_when(Language_ID == "hoaa1235" ~ 1,
                                  Language_ID != "hoaa1235" ~ 0)) %>%
  arrange(plotted_last) %>%
  mutate(
    langs_of_interest = case_when(
      Language_ID == "hoaa1235" |
        Language_ID == "huaa1248" |
        Language_ID == "tswa1255" |
        Language_ID == "tson1249" |
        Language_ID == "sout2807" ~ 1,
      Language_ID != "hoaa1235" &
        Language_ID != "huaa1248" &
        Language_ID != "tswa1255" &
        Language_ID != "tson1249" &
        Language_ID != "sout2807" ~ 0
    )
  ) %>%
  mutate(langs_of_interest = as.factor(langs_of_interest)) %>%
  filter(langs_of_interest == "0")

combination_ordered_1 <- combination %>%
  mutate(plotted_last = case_when(Language_ID == "hoaa1235" ~ 1,
                                  Language_ID != "hoaa1235" ~ 0)) %>%
  arrange(plotted_last) %>%
  mutate(
    langs_of_interest = case_when(
      Language_ID == "hoaa1235" |
        Language_ID == "huaa1248" |
        Language_ID == "tswa1255" |
        Language_ID == "tson1249" |
        Language_ID == "sout2807" ~ 1,
      Language_ID != "hoaa1235" &
        Language_ID != "huaa1248" &
        Language_ID != "tswa1255" &
        Language_ID != "tson1249" &
        Language_ID != "sout2807" ~ 0
    )
  ) %>%
  mutate(langs_of_interest = as.factor(langs_of_interest)) %>%
  filter(langs_of_interest != "0")

b_labelled <-
  basemap + geom_point(
    data = combination_ordered_0,
    aes(
      x = Longitude,
      y = Latitude,
      color = boundness_st,
      fill = boundness_st
    ),
    size = 1,
    pch = 21,
    # stroke=NA,
    position = position_jitter(
      width = 1,
      height = 1,
      seed = 123
    )
  ) +
  geom_point(
    data = combination_ordered_1,
    aes(x = Longitude, y = Latitude, fill = boundness_st),
    pch = 21,
    size = 2.5,
    colour = "black",
    position = position_jitter(
      width = 1,
      height = 1,
      seed = 123
    )
  ) +
  #scale_fill_gradient2(low = muted("blue"), mid = "white", high = muted("red"), midpoint=0) +
  #scale_color_gradient2(low = muted("blue"), mid = "white", high = muted("red"), midpoint=0, guide="none") +
  scale_fill_viridis_c(option = "magma", direction = -1) +
  scale_color_viridis_c(option = "magma",
                        guide = "none",
                        direction = -1) +
  theme(
    text = element_text(size = 20),
    legend.key.size = unit(0.5, units = "cm"),
    legend.position = "right"
  ) +
  guides(fill = guide_colourbar()) +
  labs(fill = "fusion") +
  geom_text_repel(
    aes(x = Longitude, y = Latitude, label = Name),
    #size=5,
    data  = subset(
      combination,
      AUTOTYP_area == "S Africa" &
        Latitude < -23 &
        boundness_st < 0 |
        Language_ID == "sout2807" | Language_ID == "tswa1255"
    ),
    size          = 5,
    box.padding   = 0.7,
    max.overlaps = Inf,
    point.padding = 0.1
  )
b_labelled

ggsave(
  file = "output/map_boundness_labelled.svg",
  plot = b_labelled,
  width = 10,
  height = 9, 
  dpi=300
)

	#plotting maps
	source("set_up_inla.R")

	metrics_joined <- metrics_joined %>%
	filter(!is.na(L1_log10_st)) %>%
	rename(L1_log_st = L1_log10_st) %>%
	mutate(L1_copy = L1_log_st) %>%
	filter(!is.na(L2_prop)) %>%
	dplyr::mutate(L2_prop = scale(L2_prop)[, 1]) %>%
	mutate(L2_copy = L2_prop) %>%
	filter(!is.na(neighboring_languages_st)) %>%
	filter(!is.na(Official)) %>%
	filter(!is.na(Education)) %>%
	filter(!is.na(boundness_st)) %>%
	filter(!is.na(informativity_st)) %>%
	filter(
	Macroarea == "Africa" \|
	Macroarea == "Papunesia" \|
	Macroarea == "Australia" \| Macroarea == "Eurasia"
	) %>%
	filter(180 > Longitude & Longitude > -24) %>%
	filter(80 > Latitude & Latitude > -45)

	#an overview of area and family coverage
	tab_areas <- as.data.frame(table(metrics_joined$AUTOTYP_area)) %>%
	arrange(desc(Freq))

	tab_families <- as.data.frame(table(metrics_joined$Family_ID)) %>%
	arrange(desc(Freq))


	#dropping tips not in Grambank
	metrics_joined <-
	metrics_joined[metrics_joined$Language_ID %in% tree$tip.label,]
	tree <- keep.tip(tree, metrics_joined$Language_ID)

	x <-
	assert_that(all(tree$tip.label %in% metrics_joined$Language_ID), msg = "The data and phylogeny taxa do not match")

	lakes <-
	map_data(
	"lakes",
	col = "white",
	border = "gray",
	margin = T,
	ylim = c(-45, 80),
	xlim = c(-30, 180),
	wrap = c(-25, 335)
	)

	world <-
	map_data(
	"world",
	wrap = c(-25, 335),
	ylim = c(-45, 80),
	xlim = c(-30, 180),
	margin = T
	)

	world <-
	subset(world,!(
	region %in% c(
	"USA",
	"Brazil",
	"Mexico",
	"Colombia",
	"Argentina",
	"Canada",
	"Peru",
	"Venezuela",
	"Chile",
	"Guatemala",
	"Ecuador",
	"Bolivia",
	"Cuba",
	"Honduras",
	"Paraguay",
	"Nicaragua",
	"El Salvador",
	"Costa Rica",
	"Panama",
	"Uruguay",
	"Jamaica",
	"Trinidad and Tobago",
	"Guyana",
	"Suriname",
	"Belize",
	"Barbados",
	"Saint Lucia",
	"Grenada",
	"Saint Vincent and the Grenadines",
	"Antigua and Barbuda",
	"Saint Kitts and Nevis",
	"Greenland"
	)
	))

	#shifting the longlat of the dataframe to match the pacific centered map
	combination <- metrics_joined %>%
	mutate(Longitude = if_else(Longitude <= -25, Longitude + 360, Longitude))

	#duplicates?

	combination %>%
	group_by(Language_ID) %>%
	mutate(dupe = n() > 1) -> combination_dup
	dupes <- combination_dup[combination_dup$dupe == "TRUE", ]

	#Basemap
	basemap <- ggplot(combination) +
	geom_polygon(
	data = world,
	aes(x = long, y = lat, group = group),
	colour = "gray87",
	fill = "gray87",
	size = 0.5
	) +
	geom_polygon(
	data = lakes,
	aes(x = long, y = lat, group = group),
	colour = "gray87",
	fill = "white",
	size = 0.3
	) +
	theme(
	panel.grid.major = element_blank(),
	#all of these lines are just removing default things like grid lines, axises etc
	panel.grid.minor = element_blank(),
	axis.title.x = element_blank(),
	axis.title.y = element_blank(),
	axis.line = element_blank(),
	panel.border = element_blank(),
	panel.background = element_rect(fill = "white"),
	axis.text.x = element_blank(),
	axis.text.y = element_blank(),
	axis.ticks = element_blank()
	) +
	coord_map(
	projection = "vandergrinten",
	ylim = c(-45, 80),
	xlim = c(-30, 180)
	)


	#plotting boundness map with cumstom labels

	#tswa1253 is almost overlapping in the location with hoaa1235; plotting hoaa1235 for the purposes of the plot
	combination_ordered_0 <- combination %>%
	mutate(plotted_last = case_when(Language_ID == "hoaa1235" ~ 1,
	Language_ID != "hoaa1235" ~ 0)) %>%
	arrange(plotted_last) %>%
	mutate(
	langs_of_interest = case_when(
	Language_ID == "hoaa1235" \|
	Language_ID == "huaa1248" \|
	Language_ID == "tswa1255" \|
	Language_ID == "tson1249" \|
	Language_ID == "sout2807" ~ 1,
	Language_ID != "hoaa1235" &
	Language_ID != "huaa1248" &
	Language_ID != "tswa1255" &
	Language_ID != "tson1249" &
	Language_ID != "sout2807" ~ 0
	)
	) %>%
	mutate(langs_of_interest = as.factor(langs_of_interest)) %>%
	filter(langs_of_interest == "0")

	combination_ordered_1 <- combination %>%
	mutate(plotted_last = case_when(Language_ID == "hoaa1235" ~ 1,
	Language_ID != "hoaa1235" ~ 0)) %>%
	arrange(plotted_last) %>%
	mutate(
	langs_of_interest = case_when(
	Language_ID == "hoaa1235" \|
	Language_ID == "huaa1248" \|
	Language_ID == "tswa1255" \|
	Language_ID == "tson1249" \|
	Language_ID == "sout2807" ~ 1,
	Language_ID != "hoaa1235" &
	Language_ID != "huaa1248" &
	Language_ID != "tswa1255" &
	Language_ID != "tson1249" &
	Language_ID != "sout2807" ~ 0
	)
	) %>%
	mutate(langs_of_interest = as.factor(langs_of_interest)) %>%
	filter(langs_of_interest != "0")

	b_labelled <-
	basemap + geom_point(
	data = combination_ordered_0,
	aes(
	x = Longitude,
	y = Latitude,
	color = boundness_st,
	fill = boundness_st
	),
	size = 1,
	pch = 21,
	# stroke=NA,
	position = position_jitter(
	width = 1,
	height = 1,
	seed = 123
	)
	) +
	geom_point(
	data = combination_ordered_1,
	aes(x = Longitude, y = Latitude, fill = boundness_st),
	pch = 21,
	size = 2.5,
	colour = "black",
	position = position_jitter(
	width = 1,
	height = 1,
	seed = 123
	)
	) +
	#scale_fill_gradient2(low = muted("blue"), mid = "white", high = muted("red"), midpoint=0) +
	#scale_color_gradient2(low = muted("blue"), mid = "white", high = muted("red"), midpoint=0, guide="none") +
	scale_fill_viridis_c(option = "magma", direction = -1) +
	scale_color_viridis_c(option = "magma",
	guide = "none",
	direction = -1) +
	theme(
	text = element_text(size = 20),
	legend.key.size = unit(0.5, units = "cm"),
	legend.position = "right"
	) +
	guides(fill = guide_colourbar()) +
	labs(fill = "fusion") +
	geom_text_repel(
	aes(x = Longitude, y = Latitude, label = Name),
	#size=5,
	data = subset(
	combination,
	AUTOTYP_area == "S Africa" &
	Latitude < -23 &
	boundness_st < 0 \|
	Language_ID == "sout2807" \| Language_ID == "tswa1255"
	),
	size = 5,
	box.padding = 0.7,
	max.overlaps = Inf,
	point.padding = 0.1
	)
	b_labelled

	ggsave(
	file = "output/map_boundness_labelled.svg",
	plot = b_labelled,
	width = 10,
	height = 9,
	dpi=300
	)