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06_dwormstacked.R
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06_dwormstacked.R
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#ZD and deworming overlap
#load csv of priority countries
country_regions <- read.csv("country_selection.csv")
country_regions <- country_regions %>%
dplyr::select(.id, region, CountryName) %>%
dplyr::filter(.id!="")
# combine list
combined <- bind_rows(ir)
combined <- merge(combined, country_regions, by="CountryName")
combined <- combined %>%
filter(youngest_1259m == 1) %>%
select(CountryName, youngest_1259m, zd, vas6,dwormed, region, v005)
#analytical weights
counts <- combined %>%
group_by(CountryName) %>%
summarise(
zd0_dwormed1 = sum((zd == 0 & dwormed == 1) * v005) / sum(v005) * 100,
zd0_dwormed0 = sum((zd == 0 & dwormed == 0) * v005) / sum(v005) * 100,
zd1_dwormed1 = sum((zd == 1 & dwormed == 1) * v005) / sum(v005) * 100,
zd1_dwormed0 = sum((zd == 1 & dwormed == 0) * v005) / sum(v005) * 100
)
# Add combined length column and sort by it
counts <- counts %>%
mutate(combined_length = zd1_dwormed0 + zd1_dwormed1) %>%
arrange(combined_length)
# Reshape the data from wide to long format
counts_long <- counts %>%
select(-combined_length) %>%
gather(key = "Scenario", value = "Percentage", -CountryName)
# Reorder CountryName factor levels based on sorted combined_length values
counts_long$CountryName <- factor(counts_long$CountryName, levels = counts$CountryName)
# Reorder the fill colors for consistent stacking
counts_long$Scenario <- factor(counts_long$Scenario, levels = c("zd0_dwormed1", "zd0_dwormed0", "zd1_dwormed1", "zd1_dwormed0"))
# Define custom colors for each scenario
custom_colors <- c("zd0_dwormed1" = "grey", "zd0_dwormed0" = "skyblue", "zd1_dwormed1" = "pink", "zd1_dwormed0" = "red")
# Plot the data
ggplot(counts_long, aes(x = CountryName, y = Percentage, fill = Scenario)) +
geom_bar(stat = "identity", position = "stack", width = 0.8) +
labs(x = "Country", y = "Percentage (%)") +
ggtitle("Zero Dose and Deworming Scenarios by Country (age=12-59m)") +
scale_fill_manual(values = custom_colors) +
theme_minimal() +
theme(
axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1),
axis.line = element_line(colour = "black"),
plot.title = element_text(hjust = 0.5),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()
)
write.csv(counts_long, file="ZD_dewormed_stacked_longformat.csv")
##region grouping
counts <- combined %>%
group_by(CountryName, region) %>%
summarise(
zd0_dwormed1 = sum((zd == 0 & dwormed == 1) * v005) / sum(v005) * 100,
zd0_dwormed0 = sum((zd == 0 & dwormed == 0) * v005) / sum(v005) * 100,
zd1_dwormed1 = sum((zd == 1 & dwormed == 1) * v005) / sum(v005) * 100,
zd1_dwormed0 = sum((zd == 1 & dwormed == 0) * v005) / sum(v005) * 100
)
# Add combined length column and sort within each region by it
counts <- counts %>%
mutate(combined_length = zd1_dwormed0 + zd1_dwormed1) %>%
arrange(region, combined_length)
# Reshape the data from wide to long format
counts_long <- counts %>%
select(-combined_length) %>%
gather(key = "Scenario", value = "Percentage", -CountryName, -region)
# Reorder CountryName factor levels based on sorted combined_length values within each region
counts_long$CountryName <- factor(counts_long$CountryName, levels = counts$CountryName)
# Reorder the fill colors for consistent stacking
counts_long$Scenario <- factor(counts_long$Scenario, levels = c("zd0_dwormed1", "zd0_dwormed0", "zd1_dwormed1", "zd1_dwormed0"))
# Define custom colors for each scenario
custom_colors <- c("zd0_dwormed1" = "grey", "zd0_dwormed0" = "skyblue", "zd1_dwormed1" = "pink", "zd1_dwormed0" = "red")
# Plot the data
ggplot(counts_long, aes(x = CountryName, y = Percentage, fill = Scenario)) +
geom_bar(stat = "identity", position = "stack", width = 0.8) +
labs(x = "Country", y = "Percentage (%)") +
ggtitle("Zero Dose and Deworming Scenarios by Country (age=12-23m)") +
scale_fill_manual(values = custom_colors) +
theme_minimal() +
theme(
axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1),
axis.line = element_line(colour = "black"),
plot.title = element_text(hjust = 0.5),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()
) +
facet_wrap(~ region, scales = "free_x", nrow = 1) +
theme(legend.position = "bottom")