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.Rhistory[Conflict]
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dfplot <-
test %>%
pdp::partial(pred.var = paste(x),
grid.resolution = 102,
n.trees = test$n.trees,
prob = TRUE) %>%
autoplot(rug = TRUE, train = sppData)
theme_classic()
print(dfplot)
#dev.off()
})
summary(test, cBars = 10)
sppData <-
rawSpp %>%
# remove collinear covariates
dplyr::select(-X1, -ISO3, -logFishProd, -logIuu,
-logChondLand, logFinUSD, -EPI, -ReefFishers, -logFinUSD) %>%
as.data.frame()
# need to randomize the data ---------------------------
randomIndex <- sample(1:nrow(sppData), nrow(sppData))
sppData <- sppData[randomIndex, ]
# separate the data into training set (80%) and test set (20%) ------------------
n <- nrow(sppData)
ntrain <- round(0.8*n)
trainIndex <- sample(1:n, ntrain)
sppTrain <- sppData[trainIndex, ]
sppTest <- sppData[-trainIndex, ]
test <- gbm(formula = occurrence ~ .,
distribution = 'bernoulli',
data = sppTrain,
n.trees = 5000,
interaction.depth = 10,
shrinkage = 0.001,
bag.fraction = 0.5,
n.minobsinnode = 5,
cv.folds = 10,
n.cores = NULL,
verbose = FALSE)
test
summary(test, cBars = 10)
testpred <- predict(object = test,
newdata = sppTest,
n.trees = 2400)
auc1 <- auc(actual = sppTest$occurrence, predicted = testpred)
print(auc1)
pdpplots <-
lapply(names(sppTrain), function(x) {
#pdf(paste('initGBMout', x, '.pdf', sep = ''))
dfplot <-
test %>%
pdp::partial(pred.var = paste(x),
grid.resolution = 102,
n.trees = test$n.trees,
prob = TRUE) %>%
autoplot(rug = TRUE, train = sppData)
theme_classic()
print(dfplot)
#dev.off()
})
summary(test, cBars = 10)
View(sppTrain)
gbm.roc.area(sppTest$occurrence, testpred)
library(maptools)
library(broom)
library(RColorBrewer)
library(mapviews)
library(mapview)
worldmap <- map_data('world')
worldmap <-
worldmap %>%
filter(region != 'Antarctica')
?fortify
worldmap <-
worldmap %>%
filter(region != 'Antarctica') %>%
broom::tidy()
head(worldmap)
worldmap <-
worldmap %>%
filter(region != 'Antarctica') %>%
broom::tidy(worldmap)
worldmap <-
worldmap %>%
filter(region != 'Antarctica')
glimpse(worldmap)
str(worldmap)
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = 'white', colour = 'blue', size 0.5) +
coord_fixed()
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = 'white', colour = 'blue', size = 0.5) +
coord_fixed()
map_theme <- function(legendSpace = 0.2, legendText = 13) {
theme(plot.background = element_rect(fill = 'transparent', colour = NA),
panel.background = element_rect(fill = '#080818', colour = '#080818'),
axis.text = element_blank(),
axis.ticks = element_blank(),
legend.text = element_text(size = legendText),
legend.title = element_blank(),
legend.spacing.x = unit(legendSpace, 'cm'),
legend.background = element_rect(fill = 'transparent', colour = 'transparent'),
legend.key = element_rect(fill = 'transparent', colour = 'transparent'))
}
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = 'grey80', colour = 'white', size = 0.5) +
coord_fixed() +
map_theme()
theme(plot.background = element_rect(fill = 'transparent', colour = NA),
panel.background = element_rect(fill = '#080818', colour = '#080818'),
panel.grid = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank(),
legend.text = element_text(size = legendText),
legend.title = element_blank(),
legend.spacing.x = unit(legendSpace, 'cm'),
legend.background = element_rect(fill = 'transparent', colour = 'transparent'),
legend.key = element_rect(fill = 'transparent', colour = 'transparent'))
map_theme <- function(legendSpace = 0.2, legendText = 13) {
theme(plot.background = element_rect(fill = 'transparent', colour = NA),
panel.background = element_rect(fill = '#080818', colour = '#080818'),
panel.grid = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank(),
legend.text = element_text(size = legendText),
legend.title = element_blank(),
legend.spacing.x = unit(legendSpace, 'cm'),
legend.background = element_rect(fill = 'transparent', colour = 'transparent'),
legend.key = element_rect(fill = 'transparent', colour = 'transparent'))
}
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = 'grey80', colour = 'white', size = 0.5) +
coord_fixed() +
map_theme()
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = 'grey70', colour = 'white', size = 0.5) +
coord_fixed() +
labs(x = ' ', y = ' ') +
map_theme()
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = 'grey70', colour = '#080818', size = 0.5) +
coord_fixed() +
labs(x = ' ', y = ' ') +
map_theme()
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = 'grey70', colour = '#7BFFCB', size = 0.5) +
coord_fixed() +
labs(x = ' ', y = ' ') +
map_theme()
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = 'white', colour = '#7BFFCB', size = 0.5) +
coord_fixed() +
labs(x = ' ', y = ' ') +
map_theme()
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#7BFFCB', colour = '#080818', size = 0.5) +
coord_fixed() +
labs(x = ' ', y = ' ') +
map_theme()
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#7BFFCB', colour = '#080818', size = 0.5) +
coord_map('rectangular', lat0 = 0, xlim = c(-180, 180), ylim = c(-60, 90)) +
labs(x = ' ', y = ' ') +
map_theme()
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#7BFFCB', colour = '#080818', size = 0.5) +
coord_map('rectangular', lat0 = 0, xlim = c(-170, 180), ylim = c(-60, 90)) +
labs(x = ' ', y = ' ') +
map_theme()
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#7BFFCB', colour = '#080818', size = 0.5) +
coord_map('rectangular', lat0 = 0, xlim = c(-180, 180), ylim = c(-60, 90)) +
labs(x = ' ', y = ' ') +
map_theme()
worldmap$region
test <-
worldmap %>%
as.factor(region)
test <-
worldmap %>%
mutate(region = as.factor(region))
levels(test$region)
condf <-
data.frame(region = c('China', 'Indonesia', 'USA', 'Canada'),
value = c('panda', 'orang', 'orca', 'orca'),
stringsAsFactors = FALSE)
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#7BFFCB', colour = '#080818', size = 0.5) +
geom_map(data = condf, map = worldmap,
aes(fill = value, map_id = region),
colour = 'pink', size = 0.5) +
coord_map('rectangular', lat0 = 0, xlim = c(-180, 180), ylim = c(-60, 90)) +
labs(x = ' ', y = ' ') +
map_theme()
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#7BFFCB', colour = '#080818', size = 0.5) +
geom_map(data = condf, map = worldmap,
aes(fill = value, map_id = region),
colour = '080818', size = 0.5) +
coord_map('rectangular', lat0 = 0, xlim = c(-180, 180), ylim = c(-60, 90)) +
labs(x = ' ', y = ' ') +
map_theme()
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#7BFFCB', colour = '#080818', size = 0.5) +
geom_map(data = condf, map = worldmap,
aes(fill = value, map_id = region),
colour = '#080818', size = 0.5) +
coord_map('rectangular', lat0 = 0, xlim = c(-180, 180), ylim = c(-60, 90)) +
labs(x = ' ', y = ' ') +
map_theme()
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#8DFF92', colour = '#080818', size = 0.5) +
geom_map(data = condf, map = worldmap,
aes(fill = value, map_id = region),
colour = '#080818', size = 0.5) +
coord_map('rectangular', lat0 = 0, xlim = c(-180, 180), ylim = c(-60, 90)) +
labs(x = ' ', y = ' ') +
map_theme()
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#C2FFBB', colour = '#080818', size = 0.5) +
geom_map(data = condf, map = worldmap,
aes(fill = value, map_id = region),
colour = '#080818', size = 0.5) +
coord_map('rectangular', lat0 = 0, xlim = c(-180, 180), ylim = c(-60, 90)) +
labs(x = ' ', y = ' ') +
map_theme()
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#C2FFBB', colour = '#080818', size = 0.5) +
geom_map(data = condf, map = worldmap,
aes(fill = value, map_id = region),
colour = '#080818', size = 0.5) +
scale_fill_discrete(values = c('#f4cae4', '#cbd5e8', '#fdcdac')) +
coord_map('rectangular', lat0 = 0, xlim = c(-180, 180), ylim = c(-60, 90)) +
labs(x = ' ', y = ' ') +
map_theme()
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#C2FFBB', colour = '#080818', size = 0.5) +
geom_map(data = condf, map = worldmap,
aes(fill = value, map_id = region),
colour = '#080818', size = 0.5) +
scale_fill_manual(values = c('#f4cae4', '#cbd5e8', '#fdcdac')) +
coord_map('rectangular', lat0 = 0, xlim = c(-180, 180), ylim = c(-60, 90)) +
labs(x = ' ', y = ' ') +
map_theme()
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#C2FFBB', colour = '#080818', size = 0.5) +
geom_map(data = condf, map = worldmap,
aes(fill = value, map_id = region),
colour = '#080818', size = 0.5) +
scale_fill_manual(values = c('#decbe4', '#fbb4ae', '#fed9a6')) +
coord_map('rectangular', lat0 = 0, xlim = c(-180, 180), ylim = c(-60, 90)) +
labs(x = ' ', y = ' ') +
map_theme()
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#C2FFBB', colour = '#080818', size = 0.5) +
geom_map(data = condf, map = worldmap,
aes(fill = value, map_id = region),
colour = '#080818', size = 0.5) +
scale_fill_manual(values = c('#beaed4', '#fbb4ae', '#fed9a6')) +
coord_map('rectangular', lat0 = 0, xlim = c(-180, 180), ylim = c(-60, 90)) +
labs(x = ' ', y = ' ') +
map_theme()
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#C2FFBB', colour = '#080818', size = 0.5) +
geom_map(data = condf, map = worldmap,
aes(fill = value, map_id = region),
colour = '#080818', size = 0.5) +
scale_fill_manual(values = c('#fed9a6', '#fbb4ae', '#beaed4')) +
coord_map('rectangular', lat0 = 0, xlim = c(-180, 180), ylim = c(-60, 90)) +
labs(x = ' ', y = ' ') +
map_theme()
map_theme <- function(legendSpace = 0.2, legendText = 13) {
theme(plot.background = element_rect(fill = 'transparent', colour = NA),
panel.background = element_rect(fill = '#080818', colour = '#080818'),
panel.grid = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank(),
legend = element_blank())
}
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#C2FFBB', colour = '#080818', size = 0.5) +
geom_map(data = condf, map = worldmap,
aes(fill = value, map_id = region),
colour = '#080818', size = 0.5) +
scale_fill_manual(values = c('#fed9a6', '#fbb4ae', '#beaed4')) +
coord_map('rectangular', lat0 = 0, xlim = c(-180, 180), ylim = c(-60, 90)) +
labs(x = ' ', y = ' ') +
map_theme()
map_theme <- function(legendSpace = 0.2, legendText = 13) {
theme(plot.background = element_rect(fill = 'transparent', colour = NA),
panel.background = element_rect(fill = '#080818', colour = '#080818'),
panel.grid = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank(),
legend.text = element_text(size = legendText),
legend.title = element_blank(),
legend.spacing.x = unit(legendSpace, 'cm'),
legend.background = element_rect(fill = 'transparent', colour = 'transparent'),
legend.key = element_rect(fill = 'transparent', colour = 'transparent'))
}
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#C2FFBB', colour = '#080818', size = 0.5) +
geom_map(data = condf, map = worldmap,
aes(fill = value, map_id = region),
colour = '#080818', size = 0.5, legend = FALSE) +
scale_fill_manual(values = c('#fed9a6', '#fbb4ae', '#beaed4')) +
coord_map('rectangular', lat0 = 0, xlim = c(-180, 180), ylim = c(-60, 90)) +
labs(x = ' ', y = ' ') +
map_theme()
map_theme <- function(legendSpace = 0.2, legendText = 13) {
theme(plot.background = element_rect(fill = 'transparent', colour = NA),
panel.background = element_rect(fill = '#080818', colour = '#080818'),
panel.grid = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank(),
legend.text = element_blank(),
legend.title = element_blank(),
legend.background = element_blank(),
legend.key = element_blank())
}
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#C2FFBB', colour = '#080818', size = 0.5) +
geom_map(data = condf, map = worldmap,
aes(fill = value, map_id = region),
colour = '#080818', size = 0.5) +
scale_fill_manual(values = c('#fed9a6', '#fbb4ae', '#beaed4')) +
coord_map('rectangular', lat0 = 0, xlim = c(-180, 180), ylim = c(-60, 90)) +
labs(x = ' ', y = ' ') +
map_theme()
map_theme <- function(legendSpace = 0.2, legendText = 13) {
theme(plot.background = element_rect(fill = 'transparent', colour = NA),
panel.background = element_rect(fill = '#080818', colour = '#080818'),
panel.grid = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank(),
legend.position = 'none')
}
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#C2FFBB', colour = '#080818', size = 0.5) +
geom_map(data = condf, map = worldmap,
aes(fill = value, map_id = region),
colour = '#080818', size = 0.5) +
scale_fill_manual(values = c('#fed9a6', '#fbb4ae', '#beaed4')) +
coord_map('rectangular', lat0 = 0, xlim = c(-180, 180), ylim = c(-60, 90)) +
labs(x = ' ', y = ' ') +
map_theme()
map_theme <- function(legendSpace = 0.2, legendText = 13) {
theme(plot.background = element_rect(fill = 'transparent', colour = NA),
panel.background = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank(),
legend.text = element_text(size = legendText),
legend.title = element_blank(),
legend.spacing.x = unit(legendSpace, 'cm'),
legend.background = element_rect(fill = 'transparent', colour = 'transparent'),
legend.key = element_rect(fill = 'transparent', colour = 'transparent'))
}
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#C2FFBB', colour = '#080818', size = 0.5) +
geom_map(data = condf, map = worldmap,
aes(fill = value, map_id = region),
colour = '#080818', size = 0.5) +
scale_fill_manual(values = c('#fed9a6', '#fbb4ae', '#beaed4')) +
coord_map('rectangular', lat0 = 0, xlim = c(-180, 180), ylim = c(-60, 90)) +
labs(x = ' ', y = ' ') +
map_theme()
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#C2FFBB', colour = '#080818', size = 0.5) +
geom_map(data = condf, map = worldmap,
aes(fill = value, map_id = region),
colour = '#080818', size = 0.5) +
scale_fill_manual(values = c('#fed9a6', '#fbb4ae', '#beaed4')) +
coord_map('rectangular', lat0 = 0, xlim = c(-180, 180), ylim = c(-60, 90)) +
labs(x = ' ', y = ' ') +
map_theme() +
theme(legend.position = 'none')
map_theme <- function(legendSpace = 0.2, legendText = 13) {
theme(plot.background = element_rect(fill = 'transparent', colour = NA),
panel.background = element_rect(fill = '#080818', colour = '#080818'),
axis.text = element_blank(),
axis.ticks = element_blank(),
legend.text = element_text(size = legendText),
legend.title = element_blank(),
legend.spacing.x = unit(legendSpace, 'cm'),
legend.background = element_rect(fill = 'transparent', colour = 'transparent'),
legend.key = element_rect(fill = 'transparent', colour = 'transparent'))
}
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#C2FFBB', colour = '#080818', size = 0.5) +
geom_map(data = condf, map = worldmap,
aes(fill = value, map_id = region),
colour = '#080818', size = 0.5) +
scale_fill_manual(values = c('#fed9a6', '#fbb4ae', '#beaed4')) +
coord_map('rectangular', lat0 = 0, xlim = c(-180, 180), ylim = c(-60, 90)) +
labs(x = ' ', y = ' ') +
map_theme() +
theme(legend.position = 'none')
theme(plot.background = element_rect(fill = 'transparent', colour = NA),
panel.background = element_rect(fill = '#080818', colour = '#080818'),
panel.grid = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank(),
legend.text = element_text(size = legendText),
legend.title = element_blank(),
legend.spacing.x = unit(legendSpace, 'cm'),
legend.background = element_rect(fill = 'transparent', colour = 'transparent'),
legend.key = element_rect(fill = 'transparent', colour = 'transparent'))
map_theme <- function(legendSpace = 0.2, legendText = 13) {
theme(plot.background = element_rect(fill = 'transparent', colour = NA),
panel.background = element_rect(fill = '#080818', colour = '#080818'),
panel.grid = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank(),
legend.text = element_text(size = legendText),
legend.title = element_blank(),
legend.spacing.x = unit(legendSpace, 'cm'),
legend.background = element_rect(fill = 'transparent', colour = 'transparent'),
legend.key = element_rect(fill = 'transparent', colour = 'transparent'))
}
ggplot() +
geom_map(data = worldmap, map = worldmap,
aes(x = long, y = lat, group = group, map_id = region),
fill = '#C2FFBB', colour = '#080818', size = 0.5) +
geom_map(data = condf, map = worldmap,
aes(fill = value, map_id = region),
colour = '#080818', size = 0.5) +
scale_fill_manual(values = c('#fed9a6', '#fbb4ae', '#beaed4')) +
coord_map('rectangular', lat0 = 0, xlim = c(-180, 180), ylim = c(-60, 90)) +
labs(x = ' ', y = ' ') +
map_theme() +
theme(legend.position = 'none')
SppIso <- read_csv('CompleteSpeciesISO_180924.csv')
head(SppIso)
View(SppIso)
test <- read_csv('CountryCovariates_181109.csv')
View(test)
dunno <- SppIso %>% filter(presence == 'unknown')
head(dunno)
duplicated(dunno$country)
View(dunno)
dunno2 <- dunno %>% distinct(., ISO3, .keep_all = TRUE)
duplicated(dunno$country)
duplicated(dunno2$country)
nrow(dunno2)
know <- SppIso %>% filter(presence != 'unknown')
View(known)
View(know)
all <- SppIso %>% distinct(., ISO3, .keep_all = TRUE)
duplicated(all$ISO3)
nrow(all)
View(90)
View(all)
42/90
detectCores()
install.packages('parallel')