INVERT_SDM_GRAPHS.R
In HMB3/nenswniche: Rapidly estimate species ranges and intersect with other layers
## ENVIRONMENT SETTINGS =============================================================
# \
#
# Load the packages ::
#
#
# \
#
# To install, run :
## Set env
rm(list = ls())
options(java.parameters = "-Xmx64000m")
Sys.setenv(JAVA_HOME='C:\\Program Files\\Java\\jre1.8.0_321')
## Function to load or install packages
ipak <- function(pkg){
new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]
if (length(new.pkg))
install.packages(new.pkg, dependencies = TRUE, repos = "https://cran.csiro.au/")
sapply(pkg, require, character.only = TRUE)
}
## Load packages
#devtools::install_github("HMB3/nenswniche")
library(nenswniche)
library(cowplot)
data('sdmgen_packages')
ipak(sdmgen_packages)
## The functions expect these folders,
inv_rs_dir <- './output/invert_maxent_pbi_ala_site/'
inv_back_dir <- './output/invert_maxent_pbi_ala_site/back_sel_models/'
inv_results_dir <- './output/invert_maxent_pbi_ala_site/results/'
inv_fire_dir <- './output/invert_maxent_pbi_ala_site/Habitat_suitability/FESM_SDM_intersect/'
## 5). INDIVIDUAL TAXA GRAPHS =============================================================
## Species % burnt scatter plots ----
INVERT.FESM.TABLE.TAXA.RANGE <- INVERT.FESM.TABLE %>%
left_join(., dplyr::select(invert_LUT,
Taxa,
Aus_records,
AOO,
EOO,
KOP_count), by = c('Taxa')) %>%
dplyr::select(Percent_burnt, Habitat_km2, Habitat_burnt_km2, AOO, EOO, Aus_records, KOP_count)
INVERT.FESM.TABLE.FAM.RANGE <- INVERT.FESM.TABLE.FAM %>%
left_join(., dplyr::select(invert_LUT,
Taxa,
Aus_records,
AOO,
EOO,
KOP_count), by = c('Taxa')) %>%
dplyr::select(Percent_burnt, Habitat_km2, Habitat_burnt_km2, AOO, EOO, Aus_records, KOP_count)
INVERT.FESM.TABLE.GEN.RANGE <- INVERT.FESM.TABLE.GEN %>%
left_join(., dplyr::select(invert_LUT,
Taxa,
Aus_records,
AOO,
EOO,
KOP_count), by = c('Taxa')) %>%
dplyr::select(Percent_burnt, Habitat_km2, Habitat_burnt_km2, AOO, EOO, Aus_records, KOP_count)
INVERT.FESM.TABLE.SPP.RANGE <- INVERT.FESM.TABLE.SPP %>%
left_join(., dplyr::select(invert_LUT,
Taxa,
Aus_records,
AOO,
EOO,
KOP_count), by = c('Taxa')) %>%
dplyr::select(Percent_burnt, Habitat_km2, Habitat_burnt_km2, AOO, EOO, Aus_records, KOP_count)
INVERT.FESM.TABLE.SPP.LOG <-
INVERT.FESM.TABLE.SPP.RANGE %>% mutate(log_AOO = log(AOO),
log_EOO = log(EOO),
log_Habit = log(Habitat_km2),
log_Burnt = log(Habitat_burnt_km2),
log_Records = log(Aus_records)) %>%
dplyr::select(-AOO, -EOO, -Habitat_km2, -Habitat_burnt_km2, -Aus_records) %>%
dplyr::select(Percent_burnt, log_Habit, log_Burnt, log_AOO, log_EOO, log_Records)
## Could create a standard graph here :: pairs.panel
png(paste0(inv_fire_dir, 'fesm_inv_taxa_scatter_plots.png'),
12, 8, units = 'in', res = 500)
psych::pairs.panels(INVERT.FESM.TABLE.TAXA.RANGE,
method = "pearson", # correlation method
hist.col = "#00AFBB",
density = TRUE, # show density plots
ellipses = FALSE,
cex = 1.2,
cex.labels = 1.2,
lwd = 2,
col = "blue")
dev.off()
gc()
png(paste0(inv_fire_dir, 'fesm_inv_species_scatter_plots.png'),
12, 8, units = 'in', res = 500)
psych::pairs.panels(INVERT.FESM.TABLE.SPP.LOG,
method = "pearson", # correlation method
hist.col = "#00AFBB",
density = TRUE, # show density plots
ellipses = FALSE,
cex = 1.2,
cex.labels = 0.9,
lwd = 2,
col = "blue")
dev.off()
gc()
## Species % burnt graphs ----
# for(taxa in INVERT.FESM.TABLE$Taxa) {
#
# ## taxa = INVERT.FESM.TABLE$Taxa[1]
# bar_df <- INVERT.FESM.TABLE %>% filter(Taxa == taxa) %>%
# mutate(Percent_unburnt = 100 - Percent_burnt)
#
# plot <- ggplot(bar_df, aes(fill=Percent_burnt, y=Percent_burnt, x=Taxa)) +
# geom_bar(position="stack", stat="identity")
#
# print(plot)
#
# }
## Graphs for each species ----
## Graphs of the % burnt and un-burnt
# for(taxa in INVERT.FESM.TABLE$Taxa) {
#
# ## taxa = INVERT.FESM.TABLE$Taxa[1]
# bar_df <- INVERT.FESM.TABLE %>% filter(Taxa == taxa) %>%
# mutate(Percent_unburnt = 100 - Percent_burnt)
#
# plot <- ggplot(bar_df, aes(fill=Percent_burnt, y=Percent_burnt, x=Taxa)) +
# geom_bar(position="stack", stat="identity")
#
# print(plot)
#
# }
## Set variables
tsize = 30
capt_size = 20
xsize = 10
ysize = 30
ycol = 'black'
lab_size = 8
mar = 1.5
ymin = 0
axis_multiplier = 0.2
ylab = '\nPercent (%)\n'
xlab = ''
spp_run <- nrow(INVERT.MAXENT.SPP.RESULTS)
## Graphs of the % burnt in each Vegetation type
for(taxa in unique(INVERT.FESM.VEG.TABLE$Taxa)) {
## Update the table
# taxa <- unique(INVERT.FESM.VEG.TABLE$Taxa)[10]
message('writing sdm fire vegetation for ', taxa)
save_name <- gsub(' ', '_', taxa)
bar_df <- INVERT.FESM.VEG.TABLE %>% filter(Taxa == taxa) %>%
mutate(Habitat_Veg_burnt_perc = round(Habitat_Veg_burnt_perc, 2))
bar_df$Vegetation <- factor(bar_df$Vegetation,
levels = bar_df$Vegetation[order(bar_df$Habitat_Veg_burnt_perc,
decreasing = TRUE)])
overall_burnt <- INVERT.FESM.TABLE %>% filter(Taxa == taxa) %>%
.$Percent_burn %>% round(., 2)
area_burnt <- INVERT.FESM.TABLE %>% filter(Taxa == taxa) %>%
.$Habitat_burnt_km2 %>% round(., 0)
##
ymax = max(bar_df$Habitat_Veg_burnt_perc) +
max(bar_df$Habitat_Veg_burnt_perc * axis_multiplier)
sdm_fire_veg_plot <- ggplot(bar_df,
aes(x = Vegetation,
y = Habitat_Veg_burnt_perc,
fill = Vegetation)) +
geom_bar(stat = "identity", position = "dodge") +
coord_flip() +
scale_fill_manual(values = c('Extremely tall open forest' = 'forestgreen',
'Low open forest' = 'lightgoldenrod1',
'Medium Open forest' = "yellowgreen",
'Very tall open forest' = "palegreen3",
'Tall open forest' = "mediumspringgreen",
'Tall closed forest' = "limegreen",
'very tall closed forest' = "mediumseagreen"), na.value = "grey") +
geom_text(aes(label = Habitat_Veg_burnt_perc, hjust = + 0.5),
hjust = -0.5,
position = position_dodge(width = 1),
inherit.aes = TRUE,
size = lab_size) +
theme_classic(base_size = 16) +
ylab('Percentage (%) Burnt') +
ggtitle(taxa) +
xlab('') +
labs(caption = paste0(overall_burnt, ' % Burnt overall (',
area_burnt, ' km2)')) +
ylim(c(ymin, ymax)) +
theme(plot.margin = unit(c(mar, mar, mar, mar), "cm"),
plot.title = element_text(vjust = 5, size = tsize, face = "bold"),
axis.text.x = element_text(size = xsize),
axis.title.x = element_text(size = xsize, face = "bold"),
legend.position = 'none',
axis.title.y = element_text(size = ysize, face = "bold"),
axis.text.y = element_text(size = ysize, color = "black"),
plot.subtitle = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"),
plot.caption = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"))
png(paste0(inv_fire_dir, save_name, '_sdm_veg_intersect_fire_barplots.png'),
12, 6, units = 'in', res = 500)
plot(sdm_fire_veg_plot)
dev.off()
gc()
}
## Graphs of the % burnt in each Burn category
for(taxa in unique(INVERT.FESM.CLASS.TABLE$Taxa)) {
## Update the table
# taxa <- unique(INVERT.FESM.CLASS.TABLE$Taxa)[10]
message('writing sdm fire classes for ', taxa)
save_name <- gsub(' ', '_', taxa)
bar_df <- INVERT.FESM.CLASS.TABLE %>% filter(Taxa == taxa)
bar_df$Burn_Category <- factor(bar_df$Burn_Category,
levels = bar_df$Burn_Category[order(bar_df$Burn_Category_burnt_perc,
decreasing = TRUE)])
area_burnt <- INVERT.FESM.CLASS.TABLE %>% filter(Taxa == taxa) %>%
.$ Burn_Category_burnt_area %>% sum()
## Update the
ymax = max(bar_df$Burn_Category_burnt_perc) +
max(bar_df$Burn_Category_burnt_perc * axis_multiplier)
sdm_fire_class_plot <- ggplot(bar_df,
aes(x = Burn_Category,
y = Burn_Category_burnt_perc,
fill = Burn_Category)) +
geom_bar(stat = "identity", position = "dodge") +
coord_flip() +
scale_fill_manual(values = c('Low severity' = "#FEEDDE",
'Moderate-low severity' = "#FDBE85",
'Moderate-high severity' = "#FD8D3C",
'High severity' = "#D94701"), na.value = "grey") +
geom_text(aes(label = Burn_Category_burnt_perc, hjust = + 0.5),
hjust = -0.5,
position = position_dodge(width = 1),
inherit.aes = TRUE,
size = lab_size) +
theme_classic(base_size = 16) +
ylab('Percentage (%) Burnt') +
ggtitle(taxa) +
xlab('') +
labs(caption = paste0(area_burnt, ' km2 Burnt across classes ')) +
ylim(c(ymin, ymax)) +
theme(plot.margin = unit(c(mar, mar, mar, mar), "cm"),
plot.title = element_text(vjust = 5, size = tsize, face = "bold.italic"),
axis.text.x = element_text(size = xsize),
axis.title.x = element_text(size = xsize, face = "bold"),
legend.position = 'none',
axis.title.y = element_text(size = ysize, face = "bold"),
axis.text.y = element_text(size = ysize, color = "black"),
plot.subtitle = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"),
plot.caption = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"))
png(paste0(inv_fire_dir, save_name, '_sdm_fire_classes_barplots.png'),
12, 6, units = 'in', res = 500)
plot(sdm_fire_class_plot)
dev.off()
gc()
}
## 6). ALL TAXA GRAPHS =============================================================
##
INVERT.GEN.FESM.VEG.GROUP <- INVERT.FESM.VEG.TABLE.SPP %>%
## group by Vegetation
group_by(Vegetation) %>%
summarise(Average_burnt_area = mean(Habitat_Veg_burnt_area),
Average_burnt_percent = mean(Habitat_Veg_burnt_perc),
Average_burnt_area = round(Average_burnt_area, 2),
Average_burnt_percent = round(Average_burnt_percent, 2)) %>%
arrange(-Average_burnt_percent)
## Factor
INVERT.GEN.FESM.VEG.GROUP$Vegetation <-
factor(INVERT.GEN.FESM.VEG.GROUP$Vegetation,
levels = INVERT.GEN.FESM.VEG.GROUP$Vegetation
[order(INVERT.GEN.FESM.VEG.GROUP$Average_burnt_percent,
decreasing = TRUE)])
## Vegetation burnt across all species ----
ymax = max(INVERT.GEN.FESM.VEG.GROUP$Average_burnt_percent) +
max(INVERT.GEN.FESM.VEG.GROUP$Average_burnt_percent * axis_multiplier)
all_sdm_fire_veg_plot <- ggplot(INVERT.GEN.FESM.VEG.GROUP,
aes(x = Vegetation,
y = Average_burnt_percent,
fill = Vegetation)) +
geom_bar(stat = "identity", position = "dodge") +
coord_flip() +
scale_fill_manual(values = c('Extremely tall open forest' = 'forestgreen',
'Low open forest' = 'lightgoldenrod1',
'Medium Open forest' = "yellowgreen",
'Very tall open forest' = "palegreen3",
'Tall open forest' = "mediumspringgreen",
'Tall closed forest' = "limegreen",
'very tall closed forest' = "mediumseagreen"), na.value = "grey") +
geom_text(aes(label = Average_burnt_percent, hjust = + 0.5),
hjust = -0.5,
position = position_dodge(width = 1),
inherit.aes = TRUE,
size = lab_size) +
theme_classic(base_size = 16) +
ylab('Percentage (%) Habitat Burnt') +
ggtitle('') +
xlab('') +
# labs(caption = caption) +
ylim(c(ymin, ymax)) +
theme(plot.margin = unit(c(mar, mar, mar, mar), "cm"),
plot.title = element_text(vjust = 5, size = tsize, face = "bold"),
axis.text.x = element_text(size = xsize),
axis.title.x = element_text(size = xsize, face = "bold"),
legend.position = 'none',
axis.title.y = element_text(size = ysize, face = "bold"),
axis.text.y = element_text(size = ysize, color = "black"),
plot.subtitle = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"),
plot.caption = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"))
png(paste0(inv_fire_dir, 'all_sdm_fire_veg_plot.png'),
12, 8, units = 'in', res = 500)
plot(all_sdm_fire_veg_plot)
dev.off()
##
INVERT.GEN.FESM.CLASS.GROUP <- INVERT.FESM.CLASS.TABLE.SPP %>%
## group by Vegetation
group_by(Burn_Category) %>%
summarise(Average_burnt_area = mean(Burn_Category_burnt_area),
Average_burnt_percent = mean(Burn_Category_burnt_perc),
Average_burnt_area = round(Average_burnt_area, 2),
Average_burnt_percent = round(Average_burnt_percent, 2)) %>%
arrange(-Average_burnt_percent)
INVERT.GEN.FESM.CLASS.GROUP$Burn_Category <-
factor(INVERT.GEN.FESM.CLASS.GROUP$Burn_Category,
levels = INVERT.GEN.FESM.CLASS.GROUP$Burn_Category
[order(INVERT.GEN.FESM.CLASS.GROUP$Average_burnt_percent,
decreasing = TRUE)])
## Classes burnt across all species ----
ymax = max(INVERT.GEN.FESM.CLASS.GROUP$Average_burnt_percent) +
max(INVERT.GEN.FESM.CLASS.GROUP$Average_burnt_percent * axis_multiplier)
all_sdm_fire_class_plot <- ggplot(INVERT.GEN.FESM.CLASS.GROUP,
aes(x = Burn_Category,
y = Average_burnt_percent,
fill = Burn_Category)) +
geom_bar(stat = "identity", position = "dodge") +
coord_flip() +
scale_fill_manual(values = c('Low severity' = "#FEEDDE",
'Moderate-low severity' = "#FDBE85",
'Moderate-high severity' = "#FD8D3C",
'High severity' = "#D94701"), na.value = "grey") +
geom_text(aes(label = Average_burnt_percent, hjust = + 0.5),
hjust = -0.5,
position = position_dodge(width = 1),
inherit.aes = TRUE,
size = lab_size) +
theme_classic(base_size = 16) +
ylab('Percentage (%) Habitat Burnt') +
ggtitle('') +
xlab('') +
# labs(caption = caption) +
ylim(c(ymin, ymax)) +
theme(plot.margin = unit(c(mar, mar, mar, mar), "cm"),
plot.title = element_text(vjust = 5, size = tsize, face = "bold"),
axis.text.x = element_text(size = xsize),
axis.title.x = element_text(size = xsize, face = "bold"),
legend.position = 'none',
axis.title.y = element_text(size = ysize, face = "bold"),
axis.text.y = element_text(size = ysize, color = "black"),
plot.subtitle = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"),
plot.caption = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"))
png(paste0(inv_fire_dir, 'all_sdm_fire_class_plot.png'),
12, 8, units = 'in', res = 500)
plot(all_sdm_fire_class_plot)
dev.off()
gc()
## Invert Types burnt across all species ---
INVERT.GEN.FESM.TYPE.GROUP <- INVERT.FESM.TABLE.SPP %>%
## group by TYPE
group_by(Type) %>%
summarise(Average_burnt_area = mean(Habitat_burnt_km2),
Average_burnt_percent = mean(Percent_burnt),
Average_burnt_area = round(Average_burnt_area, 2),
Average_burnt_percent = round(Average_burnt_percent, 2)) %>%
arrange(-Average_burnt_percent)
## Factor
INVERT.GEN.FESM.TYPE.GROUP$Type <-
factor(INVERT.GEN.FESM.TYPE.GROUP$Type,
levels = INVERT.GEN.FESM.TYPE.GROUP$Type
[order(INVERT.GEN.FESM.TYPE.GROUP$Average_burnt_percent,
decreasing = TRUE)])
##
ymax = max(INVERT.GEN.FESM.TYPE.GROUP$Average_burnt_percent) +
max(INVERT.GEN.FESM.TYPE.GROUP$Average_burnt_percent * axis_multiplier)
all_sdm_fire_type_plot <- ggplot(INVERT.GEN.FESM.TYPE.GROUP,
aes(x = Type,
y = Average_burnt_percent,
fill = Type)) +
geom_bar(stat = "identity", position = "dodge") +
coord_flip() +
scale_fill_manual(values = c('Spiders' = 'forestgreen',
'Beetles' = 'lightgoldenrod1',
'Snails' = "yellowgreen",
'Bugs' = "palegreen3")) +
geom_text(aes(label = Average_burnt_percent, hjust = + 0.5),
hjust = -0.5,
position = position_dodge(width = 1),
inherit.aes = TRUE,
size = lab_size) +
theme_classic(base_size = 16) +
ylab('Percentage (%) Habitat Burnt') +
ggtitle('All Invert Taxa') +
xlab('') +
ylim(c(ymin, ymax)) +
theme(plot.margin = unit(c(mar, mar, mar, mar), "cm"),
plot.title = element_text(vjust = 5, size = tsize, face = "bold"),
axis.text.x = element_text(size = xsize),
axis.title.x = element_text(size = xsize, face = "bold"),
legend.position = 'none',
axis.title.y = element_text(size = ysize, face = "bold"),
axis.text.y = element_text(size = ysize, color = "black"),
plot.subtitle = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"),
plot.caption = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"))
png(paste0(inv_fire_dir, 'all_sdm_fire_type_plot.png'),
12, 8, units = 'in', res = 500)
plot(all_sdm_fire_type_plot)
dev.off()
##
INVERT.GEN.FESM.VEG.TYPE.GROUP <- INVERT.FESM.VEG.TABLE.SPP %>%
## group by Vegetation
group_by(Vegetation, Type) %>%
summarise(Average_burnt_area = mean(Habitat_Veg_burnt_area),
Average_burnt_percent = mean(Habitat_Veg_burnt_perc),
Average_burnt_area = round(Average_burnt_area, 2),
Average_burnt_percent = round(Average_burnt_percent, 2)) %>%
arrange(-Average_burnt_percent)
## Create Factors
INVERT.GEN.FESM.VEG.TYPE.GROUP$Type <-
factor(INVERT.GEN.FESM.VEG.TYPE.GROUP$Type,
levels = unique(INVERT.GEN.FESM.VEG.TYPE.GROUP$Type)
[order(INVERT.GEN.FESM.VEG.TYPE.GROUP$Average_burnt_percent,
decreasing = TRUE)])
INVERT.GEN.FESM.VEG.TYPE.GROUP$Vegetation <-
factor(INVERT.GEN.FESM.VEG.TYPE.GROUP$Vegetation,
levels = unique(INVERT.GEN.FESM.VEG.TYPE.GROUP$Vegetation)
[order(INVERT.GEN.FESM.VEG.TYPE.GROUP$Average_burnt_percent,
decreasing = TRUE)])
## Veg/Types burnt across all species ----
xvar = 'Average_burnt_percent'
yvar = 'Vegetation'
title = '' #'Habitat burnt by Vegetation'
caption = paste0(spp_run, ' Invert Species Analysed')
col_palette = "Pastel2"
tsize = 30
strip_size = 20
capt_size = 20
xsize = 10
ysize = 15
lab_angle = 45
ycol = 'black'
lab_size = 4
mar = 1.5
ymin = 0
axis_multiplier = 0.2
ylab = ''
xlab = 'Percentage (%) habitat burnt'
facet_var = 'Type'
col_var = 'Vegetation'
wrap_scale = "fixed"
##
all_sdm_fire_veg_type <- ggplot(INVERT.GEN.FESM.VEG.TYPE.GROUP,
aes(x = !!sym(xvar),
y = !!sym(yvar),
fill = !!sym(yvar))) +
geom_bar(stat = "identity", position = "dodge") +
coord_flip() +
geom_text(aes(label = Average_burnt_percent, hjust = + 1.2),
hjust = 0.7,
vjust = 0.8,
position = position_dodge(width = 1),
inherit.aes = TRUE,
size = lab_size) +
scale_fill_manual(values = c('Extremely tall open forest' = 'forestgreen',
'Low open forest' = 'lightgoldenrod1',
'Medium Open forest' = "yellowgreen",
'Very tall open forest' = "palegreen3",
'Tall open forest' = "mediumspringgreen",
'Tall closed forest' = "limegreen",
'very tall closed forest' = "mediumseagreen"), na.value = "grey") +
theme_classic(base_size = 16) +
ylab(ylab) +
# ggtitle(title) +
xlab(xlab) +
labs(caption = caption) +
theme(plot.margin = unit(c(mar, mar, mar, mar), "cm"),
plot.title = element_text(vjust = 5, size = tsize, face = "bold"),
strip.text = element_text(size = strip_size, face = 'bold'),
axis.text.x = element_blank(),
axis.title.x = element_text(size = xsize, face = "bold"),
legend.position = 'bottom',
legend.title = element_blank(),
axis.title.y = element_text(size = ysize, face = "bold"),
axis.text.y = element_text(size = ysize, color = ycol),
plot.subtitle = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"),
plot.caption = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black")) +
facet_wrap(as.formula(paste("~", facet_var)), scales = wrap_scale)
png(paste0(inv_fire_dir, 'all_habitat_veg_type_barplot.png'),
12, 8, units = 'in', res = 500)
plot(all_sdm_fire_veg_type)
dev.off()
## Classes/Types burnt across all species ----
xvar = 'Average_burnt_percent'
yvar = 'Burn_Category'
title = '' #'Habitat burnt by Class'
caption = paste0(spp_run, ' Invert Species Analysed')
ylab = ''
xlab = 'Percentage (%) of burnt'
col_var = 'Burn_Category'
##
INVERT.GEN.FESM.CLASS.TYPE.GROUP <- INVERT.FESM.CLASS.TABLE.SPP %>%
## group by Vegetation
group_by(Burn_Category, Type) %>%
summarise(Average_burnt_area = mean(Burn_Category_burnt_area),
Average_burnt_percent = mean(Burn_Category_burnt_perc),
Average_burnt_area = round(Average_burnt_area, 2),
Average_burnt_percent = round(Average_burnt_percent, 2)) %>%
arrange(-Average_burnt_percent)
## Create Factors
INVERT.GEN.FESM.CLASS.TYPE.GROUP$Type <-
factor(INVERT.GEN.FESM.CLASS.TYPE.GROUP$Type,
levels = unique(INVERT.GEN.FESM.CLASS.TYPE.GROUP$Type)
[order(INVERT.GEN.FESM.CLASS.TYPE.GROUP$Average_burnt_percent,
decreasing = TRUE)])
INVERT.GEN.FESM.CLASS.TYPE.GROUP$Burn_Category <-
factor(INVERT.GEN.FESM.CLASS.TYPE.GROUP$Burn_Category,
levels = unique(INVERT.GEN.FESM.CLASS.TYPE.GROUP$Burn_Category)
[order(INVERT.GEN.FESM.CLASS.TYPE.GROUP$Average_burnt_percent,
decreasing = TRUE)])
## Can't set the maximum
all_sdm_fire_class_type <- ggplot(INVERT.GEN.FESM.CLASS.TYPE.GROUP,
aes(x = !!sym(xvar),
y = !!sym(yvar),
fill = !!sym(yvar))) +
geom_bar(stat = "identity", position = "dodge") +
coord_flip() +
geom_text(aes(label = Average_burnt_percent, hjust = + 1.2),
hjust = 0.7,
vjust = 0.8,
position = position_dodge(width = 1),
inherit.aes = TRUE,
size = lab_size) +
scale_fill_manual(values = c('Low severity' = "#FEEDDE",
'Moderate-low severity' = "#FDBE85",
'Moderate-high severity' = "#FD8D3C",
'High severity' = "#D94701"), na.value = "grey") +
theme_classic(base_size = 16) +
ylab(ylab) +
# ggtitle(title) +
xlab(xlab) +
labs(caption = caption) +
theme(plot.margin = unit(c(mar, mar, mar, mar), "cm"),
plot.title = element_text(vjust = 5, size = tsize, face = "bold"),
strip.text = element_text(size = strip_size, face = 'bold'),
axis.text.x = element_blank(),
axis.title.x = element_text(size = xsize, face = "bold"),
legend.position = 'bottom',
legend.title = element_blank(),
axis.title.y = element_text(size = ysize, face = "bold"),
axis.text.y = element_text(size = ysize, color = ycol),
plot.subtitle = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"),
plot.caption = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black")) +
facet_wrap(as.formula(paste("~", facet_var)), scales = wrap_scale)
png(paste0(inv_fire_dir, 'all_habitat_fesm_class_type_barplot.png'),
12, 8, units = 'in', res = 500)
plot(all_sdm_fire_class_type)
dev.off()
## Arrange all plots into one graph
grid_plot <- plot_grid(all_sdm_fire_veg_plot,
all_sdm_fire_class_plot,
all_sdm_fire_veg_type,
all_sdm_fire_class_type,
nrow = 2,
label_size = 3,
align = 'hv')
png(paste0(inv_fire_dir, 'sdm_invert_combined_barplots.png'),
20, 16, units = 'in', res = 600)
plot(grid_plot)
dev.off()
## END =============================================================
HMB3/nenswniche documentation built on Jan. 31, 2023, 11:46 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
## ENVIRONMENT SETTINGS =============================================================
# \
#
# Load the packages ::
#
#
# \
#
# To install, run :
## Set env
rm(list = ls())
options(java.parameters = "-Xmx64000m")
Sys.setenv(JAVA_HOME='C:\\Program Files\\Java\\jre1.8.0_321')
## Function to load or install packages
ipak <- function(pkg){
new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]
if (length(new.pkg))
install.packages(new.pkg, dependencies = TRUE, repos = "https://cran.csiro.au/")
sapply(pkg, require, character.only = TRUE)
}
## Load packages
#devtools::install_github("HMB3/nenswniche")
library(nenswniche)
library(cowplot)
data('sdmgen_packages')
ipak(sdmgen_packages)
## The functions expect these folders,
inv_rs_dir <- './output/invert_maxent_pbi_ala_site/'
inv_back_dir <- './output/invert_maxent_pbi_ala_site/back_sel_models/'
inv_results_dir <- './output/invert_maxent_pbi_ala_site/results/'
inv_fire_dir <- './output/invert_maxent_pbi_ala_site/Habitat_suitability/FESM_SDM_intersect/'
## 5). INDIVIDUAL TAXA GRAPHS =============================================================
## Species % burnt scatter plots ----
INVERT.FESM.TABLE.TAXA.RANGE <- INVERT.FESM.TABLE %>%
left_join(., dplyr::select(invert_LUT,
Taxa,
Aus_records,
AOO,
EOO,
KOP_count), by = c('Taxa')) %>%
dplyr::select(Percent_burnt, Habitat_km2, Habitat_burnt_km2, AOO, EOO, Aus_records, KOP_count)
INVERT.FESM.TABLE.FAM.RANGE <- INVERT.FESM.TABLE.FAM %>%
left_join(., dplyr::select(invert_LUT,
Taxa,
Aus_records,
AOO,
EOO,
KOP_count), by = c('Taxa')) %>%
dplyr::select(Percent_burnt, Habitat_km2, Habitat_burnt_km2, AOO, EOO, Aus_records, KOP_count)
INVERT.FESM.TABLE.GEN.RANGE <- INVERT.FESM.TABLE.GEN %>%
left_join(., dplyr::select(invert_LUT,
Taxa,
Aus_records,
AOO,
EOO,
KOP_count), by = c('Taxa')) %>%
dplyr::select(Percent_burnt, Habitat_km2, Habitat_burnt_km2, AOO, EOO, Aus_records, KOP_count)
INVERT.FESM.TABLE.SPP.RANGE <- INVERT.FESM.TABLE.SPP %>%
left_join(., dplyr::select(invert_LUT,
Taxa,
Aus_records,
AOO,
EOO,
KOP_count), by = c('Taxa')) %>%
dplyr::select(Percent_burnt, Habitat_km2, Habitat_burnt_km2, AOO, EOO, Aus_records, KOP_count)
INVERT.FESM.TABLE.SPP.LOG <-
INVERT.FESM.TABLE.SPP.RANGE %>% mutate(log_AOO = log(AOO),
log_EOO = log(EOO),
log_Habit = log(Habitat_km2),
log_Burnt = log(Habitat_burnt_km2),
log_Records = log(Aus_records)) %>%
dplyr::select(-AOO, -EOO, -Habitat_km2, -Habitat_burnt_km2, -Aus_records) %>%
dplyr::select(Percent_burnt, log_Habit, log_Burnt, log_AOO, log_EOO, log_Records)
## Could create a standard graph here :: pairs.panel
png(paste0(inv_fire_dir, 'fesm_inv_taxa_scatter_plots.png'),
12, 8, units = 'in', res = 500)
psych::pairs.panels(INVERT.FESM.TABLE.TAXA.RANGE,
method = "pearson", # correlation method
hist.col = "#00AFBB",
density = TRUE, # show density plots
ellipses = FALSE,
cex = 1.2,
cex.labels = 1.2,
lwd = 2,
col = "blue")
dev.off()
gc()
png(paste0(inv_fire_dir, 'fesm_inv_species_scatter_plots.png'),
12, 8, units = 'in', res = 500)
psych::pairs.panels(INVERT.FESM.TABLE.SPP.LOG,
method = "pearson", # correlation method
hist.col = "#00AFBB",
density = TRUE, # show density plots
ellipses = FALSE,
cex = 1.2,
cex.labels = 0.9,
lwd = 2,
col = "blue")
dev.off()
gc()
## Species % burnt graphs ----
# for(taxa in INVERT.FESM.TABLE$Taxa) {
#
# ## taxa = INVERT.FESM.TABLE$Taxa[1]
# bar_df <- INVERT.FESM.TABLE %>% filter(Taxa == taxa) %>%
# mutate(Percent_unburnt = 100 - Percent_burnt)
#
# plot <- ggplot(bar_df, aes(fill=Percent_burnt, y=Percent_burnt, x=Taxa)) +
# geom_bar(position="stack", stat="identity")
#
# print(plot)
#
# }
## Graphs for each species ----
## Graphs of the % burnt and un-burnt
# for(taxa in INVERT.FESM.TABLE$Taxa) {
#
# ## taxa = INVERT.FESM.TABLE$Taxa[1]
# bar_df <- INVERT.FESM.TABLE %>% filter(Taxa == taxa) %>%
# mutate(Percent_unburnt = 100 - Percent_burnt)
#
# plot <- ggplot(bar_df, aes(fill=Percent_burnt, y=Percent_burnt, x=Taxa)) +
# geom_bar(position="stack", stat="identity")
#
# print(plot)
#
# }
## Set variables
tsize = 30
capt_size = 20
xsize = 10
ysize = 30
ycol = 'black'
lab_size = 8
mar = 1.5
ymin = 0
axis_multiplier = 0.2
ylab = '\nPercent (%)\n'
xlab = ''
spp_run <- nrow(INVERT.MAXENT.SPP.RESULTS)
## Graphs of the % burnt in each Vegetation type
for(taxa in unique(INVERT.FESM.VEG.TABLE$Taxa)) {
## Update the table
# taxa <- unique(INVERT.FESM.VEG.TABLE$Taxa)[10]
message('writing sdm fire vegetation for ', taxa)
save_name <- gsub(' ', '_', taxa)
bar_df <- INVERT.FESM.VEG.TABLE %>% filter(Taxa == taxa) %>%
mutate(Habitat_Veg_burnt_perc = round(Habitat_Veg_burnt_perc, 2))
bar_df$Vegetation <- factor(bar_df$Vegetation,
levels = bar_df$Vegetation[order(bar_df$Habitat_Veg_burnt_perc,
decreasing = TRUE)])
overall_burnt <- INVERT.FESM.TABLE %>% filter(Taxa == taxa) %>%
.$Percent_burn %>% round(., 2)
area_burnt <- INVERT.FESM.TABLE %>% filter(Taxa == taxa) %>%
.$Habitat_burnt_km2 %>% round(., 0)
##
ymax = max(bar_df$Habitat_Veg_burnt_perc) +
max(bar_df$Habitat_Veg_burnt_perc * axis_multiplier)
sdm_fire_veg_plot <- ggplot(bar_df,
aes(x = Vegetation,
y = Habitat_Veg_burnt_perc,
fill = Vegetation)) +
geom_bar(stat = "identity", position = "dodge") +
coord_flip() +
scale_fill_manual(values = c('Extremely tall open forest' = 'forestgreen',
'Low open forest' = 'lightgoldenrod1',
'Medium Open forest' = "yellowgreen",
'Very tall open forest' = "palegreen3",
'Tall open forest' = "mediumspringgreen",
'Tall closed forest' = "limegreen",
'very tall closed forest' = "mediumseagreen"), na.value = "grey") +
geom_text(aes(label = Habitat_Veg_burnt_perc, hjust = + 0.5),
hjust = -0.5,
position = position_dodge(width = 1),
inherit.aes = TRUE,
size = lab_size) +
theme_classic(base_size = 16) +
ylab('Percentage (%) Burnt') +
ggtitle(taxa) +
xlab('') +
labs(caption = paste0(overall_burnt, ' % Burnt overall (',
area_burnt, ' km2)')) +
ylim(c(ymin, ymax)) +
theme(plot.margin = unit(c(mar, mar, mar, mar), "cm"),
plot.title = element_text(vjust = 5, size = tsize, face = "bold"),
axis.text.x = element_text(size = xsize),
axis.title.x = element_text(size = xsize, face = "bold"),
legend.position = 'none',
axis.title.y = element_text(size = ysize, face = "bold"),
axis.text.y = element_text(size = ysize, color = "black"),
plot.subtitle = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"),
plot.caption = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"))
png(paste0(inv_fire_dir, save_name, '_sdm_veg_intersect_fire_barplots.png'),
12, 6, units = 'in', res = 500)
plot(sdm_fire_veg_plot)
dev.off()
gc()
}
## Graphs of the % burnt in each Burn category
for(taxa in unique(INVERT.FESM.CLASS.TABLE$Taxa)) {
## Update the table
# taxa <- unique(INVERT.FESM.CLASS.TABLE$Taxa)[10]
message('writing sdm fire classes for ', taxa)
save_name <- gsub(' ', '_', taxa)
bar_df <- INVERT.FESM.CLASS.TABLE %>% filter(Taxa == taxa)
bar_df$Burn_Category <- factor(bar_df$Burn_Category,
levels = bar_df$Burn_Category[order(bar_df$Burn_Category_burnt_perc,
decreasing = TRUE)])
area_burnt <- INVERT.FESM.CLASS.TABLE %>% filter(Taxa == taxa) %>%
.$ Burn_Category_burnt_area %>% sum()
## Update the
ymax = max(bar_df$Burn_Category_burnt_perc) +
max(bar_df$Burn_Category_burnt_perc * axis_multiplier)
sdm_fire_class_plot <- ggplot(bar_df,
aes(x = Burn_Category,
y = Burn_Category_burnt_perc,
fill = Burn_Category)) +
geom_bar(stat = "identity", position = "dodge") +
coord_flip() +
scale_fill_manual(values = c('Low severity' = "#FEEDDE",
'Moderate-low severity' = "#FDBE85",
'Moderate-high severity' = "#FD8D3C",
'High severity' = "#D94701"), na.value = "grey") +
geom_text(aes(label = Burn_Category_burnt_perc, hjust = + 0.5),
hjust = -0.5,
position = position_dodge(width = 1),
inherit.aes = TRUE,
size = lab_size) +
theme_classic(base_size = 16) +
ylab('Percentage (%) Burnt') +
ggtitle(taxa) +
xlab('') +
labs(caption = paste0(area_burnt, ' km2 Burnt across classes ')) +
ylim(c(ymin, ymax)) +
theme(plot.margin = unit(c(mar, mar, mar, mar), "cm"),
plot.title = element_text(vjust = 5, size = tsize, face = "bold.italic"),
axis.text.x = element_text(size = xsize),
axis.title.x = element_text(size = xsize, face = "bold"),
legend.position = 'none',
axis.title.y = element_text(size = ysize, face = "bold"),
axis.text.y = element_text(size = ysize, color = "black"),
plot.subtitle = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"),
plot.caption = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"))
png(paste0(inv_fire_dir, save_name, '_sdm_fire_classes_barplots.png'),
12, 6, units = 'in', res = 500)
plot(sdm_fire_class_plot)
dev.off()
gc()
}
## 6). ALL TAXA GRAPHS =============================================================
##
INVERT.GEN.FESM.VEG.GROUP <- INVERT.FESM.VEG.TABLE.SPP %>%
## group by Vegetation
group_by(Vegetation) %>%
summarise(Average_burnt_area = mean(Habitat_Veg_burnt_area),
Average_burnt_percent = mean(Habitat_Veg_burnt_perc),
Average_burnt_area = round(Average_burnt_area, 2),
Average_burnt_percent = round(Average_burnt_percent, 2)) %>%
arrange(-Average_burnt_percent)
## Factor
INVERT.GEN.FESM.VEG.GROUP$Vegetation <-
factor(INVERT.GEN.FESM.VEG.GROUP$Vegetation,
levels = INVERT.GEN.FESM.VEG.GROUP$Vegetation
[order(INVERT.GEN.FESM.VEG.GROUP$Average_burnt_percent,
decreasing = TRUE)])
## Vegetation burnt across all species ----
ymax = max(INVERT.GEN.FESM.VEG.GROUP$Average_burnt_percent) +
max(INVERT.GEN.FESM.VEG.GROUP$Average_burnt_percent * axis_multiplier)
all_sdm_fire_veg_plot <- ggplot(INVERT.GEN.FESM.VEG.GROUP,
aes(x = Vegetation,
y = Average_burnt_percent,
fill = Vegetation)) +
geom_bar(stat = "identity", position = "dodge") +
coord_flip() +
scale_fill_manual(values = c('Extremely tall open forest' = 'forestgreen',
'Low open forest' = 'lightgoldenrod1',
'Medium Open forest' = "yellowgreen",
'Very tall open forest' = "palegreen3",
'Tall open forest' = "mediumspringgreen",
'Tall closed forest' = "limegreen",
'very tall closed forest' = "mediumseagreen"), na.value = "grey") +
geom_text(aes(label = Average_burnt_percent, hjust = + 0.5),
hjust = -0.5,
position = position_dodge(width = 1),
inherit.aes = TRUE,
size = lab_size) +
theme_classic(base_size = 16) +
ylab('Percentage (%) Habitat Burnt') +
ggtitle('') +
xlab('') +
# labs(caption = caption) +
ylim(c(ymin, ymax)) +
theme(plot.margin = unit(c(mar, mar, mar, mar), "cm"),
plot.title = element_text(vjust = 5, size = tsize, face = "bold"),
axis.text.x = element_text(size = xsize),
axis.title.x = element_text(size = xsize, face = "bold"),
legend.position = 'none',
axis.title.y = element_text(size = ysize, face = "bold"),
axis.text.y = element_text(size = ysize, color = "black"),
plot.subtitle = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"),
plot.caption = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"))
png(paste0(inv_fire_dir, 'all_sdm_fire_veg_plot.png'),
12, 8, units = 'in', res = 500)
plot(all_sdm_fire_veg_plot)
dev.off()
##
INVERT.GEN.FESM.CLASS.GROUP <- INVERT.FESM.CLASS.TABLE.SPP %>%
## group by Vegetation
group_by(Burn_Category) %>%
summarise(Average_burnt_area = mean(Burn_Category_burnt_area),
Average_burnt_percent = mean(Burn_Category_burnt_perc),
Average_burnt_area = round(Average_burnt_area, 2),
Average_burnt_percent = round(Average_burnt_percent, 2)) %>%
arrange(-Average_burnt_percent)
INVERT.GEN.FESM.CLASS.GROUP$Burn_Category <-
factor(INVERT.GEN.FESM.CLASS.GROUP$Burn_Category,
levels = INVERT.GEN.FESM.CLASS.GROUP$Burn_Category
[order(INVERT.GEN.FESM.CLASS.GROUP$Average_burnt_percent,
decreasing = TRUE)])
## Classes burnt across all species ----
ymax = max(INVERT.GEN.FESM.CLASS.GROUP$Average_burnt_percent) +
max(INVERT.GEN.FESM.CLASS.GROUP$Average_burnt_percent * axis_multiplier)
all_sdm_fire_class_plot <- ggplot(INVERT.GEN.FESM.CLASS.GROUP,
aes(x = Burn_Category,
y = Average_burnt_percent,
fill = Burn_Category)) +
geom_bar(stat = "identity", position = "dodge") +
coord_flip() +
scale_fill_manual(values = c('Low severity' = "#FEEDDE",
'Moderate-low severity' = "#FDBE85",
'Moderate-high severity' = "#FD8D3C",
'High severity' = "#D94701"), na.value = "grey") +
geom_text(aes(label = Average_burnt_percent, hjust = + 0.5),
hjust = -0.5,
position = position_dodge(width = 1),
inherit.aes = TRUE,
size = lab_size) +
theme_classic(base_size = 16) +
ylab('Percentage (%) Habitat Burnt') +
ggtitle('') +
xlab('') +
# labs(caption = caption) +
ylim(c(ymin, ymax)) +
theme(plot.margin = unit(c(mar, mar, mar, mar), "cm"),
plot.title = element_text(vjust = 5, size = tsize, face = "bold"),
axis.text.x = element_text(size = xsize),
axis.title.x = element_text(size = xsize, face = "bold"),
legend.position = 'none',
axis.title.y = element_text(size = ysize, face = "bold"),
axis.text.y = element_text(size = ysize, color = "black"),
plot.subtitle = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"),
plot.caption = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"))
png(paste0(inv_fire_dir, 'all_sdm_fire_class_plot.png'),
12, 8, units = 'in', res = 500)
plot(all_sdm_fire_class_plot)
dev.off()
gc()
## Invert Types burnt across all species ---
INVERT.GEN.FESM.TYPE.GROUP <- INVERT.FESM.TABLE.SPP %>%
## group by TYPE
group_by(Type) %>%
summarise(Average_burnt_area = mean(Habitat_burnt_km2),
Average_burnt_percent = mean(Percent_burnt),
Average_burnt_area = round(Average_burnt_area, 2),
Average_burnt_percent = round(Average_burnt_percent, 2)) %>%
arrange(-Average_burnt_percent)
## Factor
INVERT.GEN.FESM.TYPE.GROUP$Type <-
factor(INVERT.GEN.FESM.TYPE.GROUP$Type,
levels = INVERT.GEN.FESM.TYPE.GROUP$Type
[order(INVERT.GEN.FESM.TYPE.GROUP$Average_burnt_percent,
decreasing = TRUE)])
##
ymax = max(INVERT.GEN.FESM.TYPE.GROUP$Average_burnt_percent) +
max(INVERT.GEN.FESM.TYPE.GROUP$Average_burnt_percent * axis_multiplier)
all_sdm_fire_type_plot <- ggplot(INVERT.GEN.FESM.TYPE.GROUP,
aes(x = Type,
y = Average_burnt_percent,
fill = Type)) +
geom_bar(stat = "identity", position = "dodge") +
coord_flip() +
scale_fill_manual(values = c('Spiders' = 'forestgreen',
'Beetles' = 'lightgoldenrod1',
'Snails' = "yellowgreen",
'Bugs' = "palegreen3")) +
geom_text(aes(label = Average_burnt_percent, hjust = + 0.5),
hjust = -0.5,
position = position_dodge(width = 1),
inherit.aes = TRUE,
size = lab_size) +
theme_classic(base_size = 16) +
ylab('Percentage (%) Habitat Burnt') +
ggtitle('All Invert Taxa') +
xlab('') +
ylim(c(ymin, ymax)) +
theme(plot.margin = unit(c(mar, mar, mar, mar), "cm"),
plot.title = element_text(vjust = 5, size = tsize, face = "bold"),
axis.text.x = element_text(size = xsize),
axis.title.x = element_text(size = xsize, face = "bold"),
legend.position = 'none',
axis.title.y = element_text(size = ysize, face = "bold"),
axis.text.y = element_text(size = ysize, color = "black"),
plot.subtitle = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"),
plot.caption = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"))
png(paste0(inv_fire_dir, 'all_sdm_fire_type_plot.png'),
12, 8, units = 'in', res = 500)
plot(all_sdm_fire_type_plot)
dev.off()
##
INVERT.GEN.FESM.VEG.TYPE.GROUP <- INVERT.FESM.VEG.TABLE.SPP %>%
## group by Vegetation
group_by(Vegetation, Type) %>%
summarise(Average_burnt_area = mean(Habitat_Veg_burnt_area),
Average_burnt_percent = mean(Habitat_Veg_burnt_perc),
Average_burnt_area = round(Average_burnt_area, 2),
Average_burnt_percent = round(Average_burnt_percent, 2)) %>%
arrange(-Average_burnt_percent)
## Create Factors
INVERT.GEN.FESM.VEG.TYPE.GROUP$Type <-
factor(INVERT.GEN.FESM.VEG.TYPE.GROUP$Type,
levels = unique(INVERT.GEN.FESM.VEG.TYPE.GROUP$Type)
[order(INVERT.GEN.FESM.VEG.TYPE.GROUP$Average_burnt_percent,
decreasing = TRUE)])
INVERT.GEN.FESM.VEG.TYPE.GROUP$Vegetation <-
factor(INVERT.GEN.FESM.VEG.TYPE.GROUP$Vegetation,
levels = unique(INVERT.GEN.FESM.VEG.TYPE.GROUP$Vegetation)
[order(INVERT.GEN.FESM.VEG.TYPE.GROUP$Average_burnt_percent,
decreasing = TRUE)])
## Veg/Types burnt across all species ----
xvar = 'Average_burnt_percent'
yvar = 'Vegetation'
title = '' #'Habitat burnt by Vegetation'
caption = paste0(spp_run, ' Invert Species Analysed')
col_palette = "Pastel2"
tsize = 30
strip_size = 20
capt_size = 20
xsize = 10
ysize = 15
lab_angle = 45
ycol = 'black'
lab_size = 4
mar = 1.5
ymin = 0
axis_multiplier = 0.2
ylab = ''
xlab = 'Percentage (%) habitat burnt'
facet_var = 'Type'
col_var = 'Vegetation'
wrap_scale = "fixed"
##
all_sdm_fire_veg_type <- ggplot(INVERT.GEN.FESM.VEG.TYPE.GROUP,
aes(x = !!sym(xvar),
y = !!sym(yvar),
fill = !!sym(yvar))) +
geom_bar(stat = "identity", position = "dodge") +
coord_flip() +
geom_text(aes(label = Average_burnt_percent, hjust = + 1.2),
hjust = 0.7,
vjust = 0.8,
position = position_dodge(width = 1),
inherit.aes = TRUE,
size = lab_size) +
scale_fill_manual(values = c('Extremely tall open forest' = 'forestgreen',
'Low open forest' = 'lightgoldenrod1',
'Medium Open forest' = "yellowgreen",
'Very tall open forest' = "palegreen3",
'Tall open forest' = "mediumspringgreen",
'Tall closed forest' = "limegreen",
'very tall closed forest' = "mediumseagreen"), na.value = "grey") +
theme_classic(base_size = 16) +
ylab(ylab) +
# ggtitle(title) +
xlab(xlab) +
labs(caption = caption) +
theme(plot.margin = unit(c(mar, mar, mar, mar), "cm"),
plot.title = element_text(vjust = 5, size = tsize, face = "bold"),
strip.text = element_text(size = strip_size, face = 'bold'),
axis.text.x = element_blank(),
axis.title.x = element_text(size = xsize, face = "bold"),
legend.position = 'bottom',
legend.title = element_blank(),
axis.title.y = element_text(size = ysize, face = "bold"),
axis.text.y = element_text(size = ysize, color = ycol),
plot.subtitle = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"),
plot.caption = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black")) +
facet_wrap(as.formula(paste("~", facet_var)), scales = wrap_scale)
png(paste0(inv_fire_dir, 'all_habitat_veg_type_barplot.png'),
12, 8, units = 'in', res = 500)
plot(all_sdm_fire_veg_type)
dev.off()
## Classes/Types burnt across all species ----
xvar = 'Average_burnt_percent'
yvar = 'Burn_Category'
title = '' #'Habitat burnt by Class'
caption = paste0(spp_run, ' Invert Species Analysed')
ylab = ''
xlab = 'Percentage (%) of burnt'
col_var = 'Burn_Category'
##
INVERT.GEN.FESM.CLASS.TYPE.GROUP <- INVERT.FESM.CLASS.TABLE.SPP %>%
## group by Vegetation
group_by(Burn_Category, Type) %>%
summarise(Average_burnt_area = mean(Burn_Category_burnt_area),
Average_burnt_percent = mean(Burn_Category_burnt_perc),
Average_burnt_area = round(Average_burnt_area, 2),
Average_burnt_percent = round(Average_burnt_percent, 2)) %>%
arrange(-Average_burnt_percent)
## Create Factors
INVERT.GEN.FESM.CLASS.TYPE.GROUP$Type <-
factor(INVERT.GEN.FESM.CLASS.TYPE.GROUP$Type,
levels = unique(INVERT.GEN.FESM.CLASS.TYPE.GROUP$Type)
[order(INVERT.GEN.FESM.CLASS.TYPE.GROUP$Average_burnt_percent,
decreasing = TRUE)])
INVERT.GEN.FESM.CLASS.TYPE.GROUP$Burn_Category <-
factor(INVERT.GEN.FESM.CLASS.TYPE.GROUP$Burn_Category,
levels = unique(INVERT.GEN.FESM.CLASS.TYPE.GROUP$Burn_Category)
[order(INVERT.GEN.FESM.CLASS.TYPE.GROUP$Average_burnt_percent,
decreasing = TRUE)])
## Can't set the maximum
all_sdm_fire_class_type <- ggplot(INVERT.GEN.FESM.CLASS.TYPE.GROUP,
aes(x = !!sym(xvar),
y = !!sym(yvar),
fill = !!sym(yvar))) +
geom_bar(stat = "identity", position = "dodge") +
coord_flip() +
geom_text(aes(label = Average_burnt_percent, hjust = + 1.2),
hjust = 0.7,
vjust = 0.8,
position = position_dodge(width = 1),
inherit.aes = TRUE,
size = lab_size) +
scale_fill_manual(values = c('Low severity' = "#FEEDDE",
'Moderate-low severity' = "#FDBE85",
'Moderate-high severity' = "#FD8D3C",
'High severity' = "#D94701"), na.value = "grey") +
theme_classic(base_size = 16) +
ylab(ylab) +
# ggtitle(title) +
xlab(xlab) +
labs(caption = caption) +
theme(plot.margin = unit(c(mar, mar, mar, mar), "cm"),
plot.title = element_text(vjust = 5, size = tsize, face = "bold"),
strip.text = element_text(size = strip_size, face = 'bold'),
axis.text.x = element_blank(),
axis.title.x = element_text(size = xsize, face = "bold"),
legend.position = 'bottom',
legend.title = element_blank(),
axis.title.y = element_text(size = ysize, face = "bold"),
axis.text.y = element_text(size = ysize, color = ycol),
plot.subtitle = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black"),
plot.caption = element_text(size = capt_size, hjust = 0.5, face = "italic", color="black")) +
facet_wrap(as.formula(paste("~", facet_var)), scales = wrap_scale)
png(paste0(inv_fire_dir, 'all_habitat_fesm_class_type_barplot.png'),
12, 8, units = 'in', res = 500)
plot(all_sdm_fire_class_type)
dev.off()
## Arrange all plots into one graph
grid_plot <- plot_grid(all_sdm_fire_veg_plot,
all_sdm_fire_class_plot,
all_sdm_fire_veg_type,
all_sdm_fire_class_type,
nrow = 2,
label_size = 3,
align = 'hv')
png(paste0(inv_fire_dir, 'sdm_invert_combined_barplots.png'),
20, 16, units = 'in', res = 600)
plot(grid_plot)
dev.off()
## END =============================================================
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.