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Fig_01_stripes_099_cutoff.R
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Fig_01_stripes_099_cutoff.R
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# Muylaert et al.
# Figure Supplements
# Stripes for characterizing hotspot gradients across space
rm(list = ls())
library(here)
setwd(here())
source('00_packages.R')
setwd('results')
dfgplot <- read.csv('gstar_099.csv' )
colnames(dfgplot)
# similar layers presented in supplements
cor.test(dfgplot$bovliv, dfgplot$cattle_gilbert)
# Plot melt panels
su <- dfgplot %>% dplyr::select(c('x','y', starts_with("col99")))
head(su)
colnames(su) <- sub('col99_', '', colnames(su))
tofocus <- colnames(su %>% dplyr::select(!c(
'trans',
'pollution',
'motor_travel_time_weiss' )) )
sumelt <- melt(su[,tofocus], id=c("x", "y"))
#-------------------------------------------------------------------
# Wildlife
sumelt$valuef <- factor(sumelt$value, levels = c("royalblue3" ,"khaki" , "violetred4"))
valuesfac <- c("royalblue3", "khaki", "violetred4")
labelsfac <- c("Coldspot", "Intermediate", "Hotspot")
pw <- sumelt %>% filter(variable == 'mmb' | variable == 'hosts' ) %>%
ggplot(aes( y=y, x=x, fill = valuef))+
geom_tile()+
facet_wrap(case_when(variable == "hosts" ~ "Bat hosts",
variable == "mmb" ~ "Wild mammals") ~ . , ncol=3)+
scale_fill_manual(values =valuesfac,
labels = labelsfac) + theme_bw() +
theme(legend.title=element_blank(), legend.position = 'bottom',
strip.text = element_text(size = 14)) + labs(x='Longitude', y="Latitude",
title = "Wildlife indicators")
pw
# Potential domestic secondary hosts
unique(sumelt$value)
pdom <- sumelt %>%
filter(variable == 'pig' | variable == 'cattle' ) %>%
ggplot(aes(y=y, x=x, fill = valuef))+
geom_tile()+
facet_wrap(case_when(variable == "pig" ~ "Pig",
variable == "cattle" ~ "Cattle") ~ . , ncol=3)+
scale_fill_manual(values =c("royalblue3", "khaki","violetred4") ,
labels = c( "Coldspot","Intermediate", "Hotspot")) + theme_bw() +
theme(legend.title=element_blank(), legend.position = 'bottom',
strip.text = element_text(size = 14)) + labs(x='Longitude', y="Latitude",
title = "Potential domestic secondary hosts")
pdom
pdomallbovidae <- sumelt %>% filter(variable == 'bovliv' | variable == 'cattle' ) %>%
ggplot(aes(y=y, x=x, fill = valuef))+
geom_tile()+
facet_wrap(case_when(variable == "cattle" ~ "Cattle",
variable == "bovliv" ~ "All domestic bovidae") ~ . , ncol=3)+
scale_fill_manual(values =c("royalblue3", "khaki","violetred4") ,
labels = c( "Coldspot","Intermediate", "Hotspot")) + theme_bw() +
theme(legend.title=element_blank(), legend.position = 'bottom',
strip.text = element_text(size = 14)) + labs(x='Longitude', y="Latitude",
title = "Potential domestic secondary hosts")
pdomallbovidae
# landscape change
#'trans', 'pollution'
want_landscape <- c('builtup', 'energy', 'agriharv',
'forest_integrity_grantham',
'hewson_forest_transition_potential' )
# Factor reorder ---------------------------------------------
myorder <- c('hosts', 'mmb', 'mammals', want_landscape,
'pig',
'cattle',
"bovliv" ,
'pop_2020_worldpop')
sumelt$variable <- factor(sumelt$variable,
levels = myorder)
# --- All
allpp <- sumelt %>%
filter(variable %in% c('hosts', 'mmb', want_landscape, 'pig', 'cattle',
'pop_2020_worldpop') )%>%
mutate(unilabs = fct_recode(variable,
'Bat hosts' = 'hosts',
'Pig' = 'pig',
'Cattle' = 'cattle',
'Wild mammals'= 'mmb',
"Human population" = 'pop_2020_worldpop' ,
"Built up area" = "builtup",
"Energy and mining" = 'energy',
'Agriculture and harvest' = 'agriharv',
'Forest integrity' = 'forest_integrity_grantham',
'Deforestation potential' ='hewson_forest_transition_potential' )) %>%
mutate(unilabs = fct_relevel(unilabs,
'Bat hosts',
'Cattle' ,
'Pig',
'Wild mammals',
"Human population" ,
'Agriculture and harvest',
"Built up area",
"Energy and mining",
'Forest integrity',
'Deforestation potential' )) %>%
ggplot(aes( y=y, x=x, fill = value))+
geom_tile()+
facet_wrap(~unilabs, nrow=2)+
scale_fill_manual(values =c("khaki","royalblue3", "violetred4") ,
labels = c("Neutral", "Coldspot", "Hotspot")) + theme_bw() +
theme(legend.title = element_blank(),
legend.position = 'none', strip.background = element_rect(fill = "whitesmoke"),
strip.text = element_text(size = 14)) +
labs(x='Longitude', y="Latitude", title="A")
allpp
#-----
setwd(here())
setwd('results')
write.table(file='table_pct_099_cutoff.txt', row.names = FALSE,
round(table(sumelt$variable, sumelt$value)/ nrow(dfgplot)*100, digits=2) )
# Proportions per indicator
#--- R1 plot cattle-only
plotpcts <- sumelt %>% filter(variable %in% c('hosts', 'mmb',
want_landscape,
'pig', 'cattle',
'pop_2020_worldpop') ) %>%
mutate(unilabsr1 = fct_recode(variable,
'Forest integrity' = 'forest_integrity_grantham',
'Deforestation potential' ='hewson_forest_transition_potential',
"Human population" = 'pop_2020_worldpop',
'Agriculture and harvest' = 'agriharv',
"Built up area" = "builtup",
"Energy and mining" = 'energy',
'Bat hosts' = 'hosts',
'Wild mammals'= 'mmb',
'Pig' = 'pig',
'Cattle' = 'cattle' )) %>%
mutate(unilabsr1 = fct_relevel(unilabsr1,
'Deforestation potential',
'Forest integrity',
"Energy and mining",
"Built up area",
'Agriculture and harvest',
"Human population" ,
'Wild mammals',
'Pig',
'Cattle' ,
'Bat hosts')) %>%
mutate(scenario = fct_recode(variable,
"All scenarios" = 'pop_2020_worldpop',
"All scenarios" = "builtup",
"All scenarios" = 'energy',
'All scenarios' = 'agriharv',
'All scenarios' = 'forest_integrity_grantham',
'All scenarios' = 'hewson_forest_transition_potential',
'Scenario 1' = 'hosts',
'Scenario 2 & 4' = 'pig',
'Scenario 2 & 4' = 'cattle' ,
'Scenario 3 & 4' = 'mmb' )) %>%
mutate(scenario = fct_relevel(scenario,
'Scenario 1',
'Scenario 2 & 4',
'Scenario 3 & 4',
"All scenarios" )) %>%
ggplot(aes(unilabsr1 )) +
#facet_grid(~scenario) +
geom_bar(aes(fill= valuef), alpha=0.8, position="fill") +
scale_fill_manual(values =valuesfac,
labels = labelsfac)+
theme_minimal(base_size = 15) + geom_rug() +
theme( legend.title = element_blank(),
legend.position = "right",
axis.text.y=element_blank(),
axis.text.x=element_text(size=15,angle=0, vjust=0.3),
#axis.text.y=element_text(size=15)
) + coord_flip() +
labs( x = "", y = "Area (%)",title="")
plotpcts
#--------- Creating scenario dotmatrix
A <- matrix( rev(c(
rep(1, 4),
1, 0, 1, 0,
1, 0, 1, 0,
1, 1, 0, 0,
rep(1, 4),
rep(1, 4),
rep(1, 4),
rep(1, 4),
rep(1, 4),
rep(1, 4) )), byrow=T, nrow=10, ncol=4)
colnames(A) <- c('1', '2', '3', '4')
rownames(A) <- rev(c(
'Bat hosts',
'Cattle' ,
'Pig',
'Wild mammals',
"Human population" ,
'Agriculture and harvest',
"Built up area",
"Energy and mining",
'Forest integrity',
'Deforestation potential'))
print(A)
library(reshape2)
longData<-melt(A)
longData<-longData[longData$value!=0,]
# steelblue4
#stroke = 10 shape = 21, , stroke = 10
scenariodots <- ggplot(longData, aes(x = Var2, y = Var1)) +
geom_point(shape = 19, colour = "grey30", fill = "white", size=10) +
labs(x="Scenario", y="", title="B") +
theme_minimal(base_size = 15) + geom_rug() +
theme(axis.text.x=element_text(size=15,angle=0, vjust=0.3),
axis.text.y=element_text(size=15) )
scenariodots
#----------
# Exporting
ggsave('Figure_01_099_cutoff.png',
plot = grid.arrange(allpp, grid.arrange(scenariodots, plotpcts, ncol = 2), nrow = 2), #last_plot()
dpi = 400,
width = 14, #12
height = 12, #11
limitsize = TRUE)
#------------ Bovidae Livestock
allppb <- sumelt %>%
filter(variable %in% c('hosts', 'mmb', want_landscape, 'pig', 'bovliv',
'pop_2020_worldpop') )%>%
mutate(unilabs = fct_recode(variable,
'Bat hosts' = 'hosts',
'Wild mammals'= 'mmb',
'Pig' = 'pig',
'Bovidae livestock' = 'bovliv',
"Human population" = 'pop_2020_worldpop' ,
"Built up area" = "builtup",
"Energy and mining" = 'energy',
'Agriculture and harvest' = 'agriharv',
'Forest integrity' = 'forest_integrity_grantham',
'Deforestation potential' ='hewson_forest_transition_potential' )) %>%
mutate(unilabs = fct_relevel(unilabs,
'Bat hosts',
'Bovidae livestock' ,
'Pig',
'Wild mammals',
"Human population" ,
'Agriculture and harvest',
"Built up area",
"Energy and mining",
'Forest integrity',
'Deforestation potential' )) %>%
ggplot(aes( y=y, x=x, fill = valuef))+
geom_tile()+
facet_wrap(~unilabs, nrow=2)+
scale_fill_manual(values =valuesfac ,
labels = labelsfac) + theme_bw() +
theme(legend.title = element_blank(),
strip.background = element_rect(fill = "whitesmoke"),
legend.position = 'none',
strip.text = element_text(size = 14)) +
labs(x='Longitude', y="Latitude")
allppb
#----
setwd(here())
setwd('results')
write.table(file='table_pct_bovliv_099_cutoff.txt', row.names = FALSE,
round(table(sumelt$variable, sumelt$value)/ nrow(dfgplot)*100, digits=2) )
# Percentages per indicator - bovidae livestock
plotpctsb <- sumelt %>% filter(variable %in% c('hosts', 'mmb',
want_landscape,
'pig', 'bovliv',
'pop_2020_worldpop') ) %>%
mutate(unilabs = fct_recode(variable,
'Bat hosts' = 'hosts',
'Wild mammals'= 'mmb',
'Pig' = 'pig',
'Bovidae livestock' = 'bovliv',
"Built up area" = "builtup",
"Energy and mining" = 'energy',
'Agriculture and harvest' = 'agriharv',
'Forest integrity' = 'forest_integrity_grantham',
'Deforestation potential' ='hewson_forest_transition_potential',
"Human population" = 'pop_2020_worldpop' )) %>%
mutate(unilabs = fct_relevel(unilabs,
'Deforestation potential',
'Forest integrity',
"Energy and mining",
"Built up area",
'Agriculture and harvest',
"Human population" ,
'Wild mammals',
'Pig',
'Bovidae livestock' ,
'Bat hosts')) %>%
mutate(scenario = fct_recode(variable,
"All scenarios" = 'pop_2020_worldpop',
"All scenarios" = "builtup",
"All scenarios" = 'energy',
'All scenarios' = 'agriharv',
'All scenarios' = 'forest_integrity_grantham',
'All scenarios' = 'hewson_forest_transition_potential',
'Scenario 1' = 'hosts',
'Scenario 2 & 4' = 'pig',
'Scenario 2 & 4' = 'bovliv' ,
'Scenario 3 & 4' = 'mmb' )) %>%
mutate(scenario = fct_relevel(scenario,
'Scenario 1',
'Scenario 2 & 4',
'Scenario 3 & 4',
"All scenarios" )) %>%
ggplot(aes(unilabs )) +
#facet_grid(~scenario) +
geom_bar(aes(fill= valuef), alpha=0.8, position="fill") +
scale_fill_manual(values =valuesfac,
labels = labelsfac)+
theme_minimal(base_size = 15) + geom_rug() +
theme( legend.title = element_blank(),
legend.position = "right",
axis.text.y=element_blank(),
axis.text.x=element_text(size=15,angle=0, vjust=0.3),
#axis.text.y=element_text(size=15)
) + coord_flip() +
labs( x = "", y = "Area (%)",title="")
plotpctsb
# Exporting bovliv -------------------------
ggsave('Figure_01_bovliv_099_cutoff.png',
plot = grid.arrange(allppb, grid.arrange(scenariodots, plotpctsb, ncol = 2), nrow = 2), #last_plot()
dpi = 400,
width = 14, #12
height = 12, #11
limitsize = TRUE)
#------------------------------------------------------------------
# Individual values - Supplements
sumelt$tile <- rep(1:nrow(su))
# Convergence of hotspots
# Hotspot convergence
# Few areas
su$tile <- 1:nrow(su)
allhot <- dplyr::filter(su,
grepl('violetred4', su$`hosts` ) &
grepl('violetred4', su$`mmb` ) &
grepl('violetred4', su$`pig`) &
grepl('violetred4', su$`cattle` ) &
grepl('violetred4', su$`builtup` ) &
grepl('violetred4', su$`energy` ) &
grepl('violetred4', su$`agriharv` ) &
grepl('violetred4', su$`forest_integrity_grantham` ) &
grepl('violetred4', su$`hewson_forest_transition_potential` )
)
allhot
allhot_mammals <- dplyr::filter(su,
grepl('violetred4', su$`hosts` ) &
grepl('violetred4', su$`mmb` ) &
grepl('violetred4', su$`pig`) &
grepl('violetred4', su$`cattle` ) )
allhot_mammals
allhot_mammals_all <- dplyr::filter(su,
grepl('violetred4', su$`hosts` ) &
grepl('violetred4', su$`mammals` ) &
grepl('violetred4', su$`pig`) &
grepl('violetred4', su$`cattle` ) )
# ------------------------------------
# Overlapp - all potential host layers
allhot_mmb <- dplyr::filter(su,
grepl('violetred4', su$`hosts` ) &
grepl('violetred4', su$`mmb` ) &
grepl('violetred4', su$`pig`) &
grepl('violetred4', su$`cattle` ) )
allhot_mammalsb <- dplyr::filter(su,
grepl('violetred4', su$`hosts` ) &
grepl('violetred4', su$`mmb` ) &
grepl('violetred4', su$`pig`) &
grepl('violetred4', su$`bovliv` ) )
nrow(distinct(allhot_mammalsb[, c('x','y')]))
nrow(distinct(allhot_mammals_all[, c('x','y')]))
nrow(distinct(allhot_mmb[, c('x','y')]))
write.csv(file = 'hotspot_overlap_mammals_099_cutoff.csv', allhot_mmb, row.names = FALSE)
write.csv(file = 'hotspot_overlap_mammals_bovidae_099_cutoff.csv', allhot_mammalsb, row.names = FALSE)
#--------------------------------------------------------