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NRSDeaths_GraphsCheck.R
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NRSDeaths_GraphsCheck.R
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setwd(GraphsDirectory)
ScaleDeathLinetypes <- c("All" = "solid",
"Baseline" = "dashed")
ScaleDeathPointTypes <- c("All" = 1,
"Baseline" = 2)
LineLabels <- c("All" = "All causes deaths (2021)",
"Baseline" = "Expected deaths (based on 2015-2019 deaths)")
VlinesYears <- data.frame(Date = c(as.Date("2015-01-01"),
as.Date("2016-01-01"),
as.Date("2017-01-01"),
as.Date("2018-01-01"),
as.Date("2019-01-01")),
Year = c(2015,2016,2017,2018,2019)
)
YearLabelPositions2015_2019 <- c(as.Date("2015-03-06"),
as.Date("2016-03-06"),
as.Date("2017-03-06"),
as.Date("2018-03-06"),
as.Date("2019-03-06"))
###################################
#
#
# Weekly deaths by age (All) (Scotland) - faceted
#
#
###################################
GraphFileName = " NRS Weekly Deaths by Age (2015-2019) - faceted.png"
NRSWeeklyDeaths_2015_2019_Graph = ggplot(data = DeathsWeekly_pivot_aggregate_2015_2019,
mapping = aes(x=Date,
y=Deaths,
group=Age)
)+
theme_minimal()+
theme(panel.background = element_rect(fill = 'white', color = 'white'),
plot.background = element_rect(fill = 'white', color = 'white'),
legend.position="bottom",
legend.justification = "centre",
strip.background = element_blank(),
strip.placement = "outside",
plot.caption = element_text(hjust = 0)
)+
scale_x_date(name = "Date",
breaks = c(as.Date("2015-01-01"),
as.Date("2016-01-01"),
as.Date("2017-01-01"),
as.Date("2018-01-01"),
as.Date("2019-01-01")),
date_labels = "%Y")+
scale_y_continuous(name = "Weekly Deaths",
limits = c(NA,NA),
labels = label_comma(accuracy = 1))+
ggtitle("NRS Weekly Deaths by Age (2015-2019)",
subtitle = GraphSubtitle)+
labs(caption = GraphCaption)+
geom_line(size = 0.25,
alpha = 1,
linetype = 1,
show.legend = TRUE)+
facet_wrap(vars(Age),
ncol = 4,
scales = "free_y")
#Save graph
ggsave(filename = paste(GraphFileNameRoot,GraphFileName,sep=""),
plot = NRSWeeklyDeaths_2015_2019_Graph,
device="png",
width=500,
height=graphheight,
units="mm",
dpi=300
)
###########################################
###################################
#
#
# Average Weekly deaths by age (All) (Scotland)
#
#
###################################
GraphFileName = " NRS Weekly Deaths by Age (2015-2019, average) - faceted.png"
NRSWeeklyDeaths_Average_Graph = ggplot(data = DeathsWeekly_mean_2015_2019,
mapping = aes(x=Week,
y=Deaths,
group=Age)
)+
theme_minimal()+
theme(panel.background = element_rect(fill = 'white', color = 'white'),
plot.background = element_rect(fill = 'white', color = 'white'),
legend.position="bottom",
legend.justification = "centre",
strip.background = element_blank(),
strip.placement = "outside",
plot.caption = element_text(hjust = 0)
)+
scale_x_continuous(name = "Week number",
breaks = c(0,10,20,30,40,50))+
scale_y_continuous(name = "Weekly Deaths",
limits = c(NA,NA),
labels = label_number(accuracy = NULL))+
ggtitle("NRS Weekly Deaths by Age (2015-2019, average)",
subtitle = GraphSubtitle)+
labs(caption = GraphCaption)+
geom_line(size = 0.5,
alpha = 1,
linetype = 1,
show.legend = TRUE)+
facet_wrap(vars(Age),
ncol = 4,
scales = "free_y")
#Save graph
ggsave(filename = paste(GraphFileNameRoot,GraphFileName,sep=""),
plot = NRSWeeklyDeaths_Average_Graph,
device="png",
width=graphwidth,
height=graphheight,
units="mm",
dpi=300
)
###################################
#
#
# Average Weekly deaths by age (All) (Scotland) [2016-2019 plus 2021]
#
#
###################################
DeathsWeekly_mean_2016_2019_2021_labelled <- cbind.data.frame(DeathsWeekly_mean_2016_2019_2021,rep("2016 to 2019 plus 2021",nrow(DeathsWeekly_mean_2016_2019_2021)))
colnames(DeathsWeekly_mean_2016_2019_2021_labelled) <- c("Week","Age","Deaths","Baseline")
DeathsWeekly_mean_2015_2019_labelled <- cbind.data.frame(DeathsWeekly_mean_2015_2019,rep("2015 to 2019",nrow(DeathsWeekly_mean_2015_2019)))
colnames(DeathsWeekly_mean_2015_2019_labelled) <- c("Week","Age","Deaths","Baseline")
DeathsWeekly_mean_labelled <- rbind.data.frame(DeathsWeekly_mean_2016_2019_2021_labelled,DeathsWeekly_mean_2015_2019_labelled)
BaselineColours = c("2015 to 2019" = "grey50",
"2016 to 2019 plus 2021" = "black")
GraphFileName = " NRS Weekly Deaths by Age (2016-2019 plus 2021, average) - faceted.png"
NRSWeeklyDeaths_Average_Graph_2022 = ggplot(data = DeathsWeekly_mean_labelled,
mapping = aes(x=Week,
y=Deaths,
group=Baseline,
colour = Baseline
)
)+
theme_minimal()+
theme(panel.background = element_rect(fill = 'white', color = 'white'),
plot.background = element_rect(fill = 'white', color = 'white'),
legend.position="bottom",
legend.justification = "centre",
strip.background = element_blank(),
strip.placement = "outside",
plot.caption = element_text(hjust = 0)
)+
scale_x_continuous(name = "Week number",
breaks = c(0,10,20,30,40,50))+
scale_y_continuous(name = "Weekly Deaths",
limits = c(NA,NA),
labels = label_number(accuracy = NULL))+
ggtitle("NRS Weekly Deaths by Age (2016 to 2019 plus 2021, average)",
subtitle = GraphSubtitle)+
labs(caption = GraphCaption)+
geom_line(size = 0.5,
alpha = 1,
linetype = 1,
show.legend = TRUE)+
facet_wrap(vars(Age),
ncol = 4,
scales = "free_y")+
scale_colour_manual(name = "Baseline",
values = BaselineColours)
#Save graph
ggsave(filename = paste(GraphFileNameRoot,GraphFileName,sep=""),
plot = NRSWeeklyDeaths_Average_Graph_2022,
device="png",
width=graphwidth,
height=graphheight,
units="mm",
dpi=300
)
###########################################
# Calculate summary data
###########################################
DeathsTogetherSummary <- DeathsTogether %>%
filter(Date >= as.Date("2021-04-01")) %>%
select(Age,Deaths,Cause) %>%
group_by(Age,Cause) %>%
summarise(deaths = sum(Deaths)) %>%
pivot_wider(names_from = "Cause",
values_from = "deaths") %>%
mutate(Difference = All - Baseline)
DeathsTogetherSummarySum = sum(DeathsTogetherSummary$Difference)
##########################################
###################################
#
#
# ExcessDeaths - faceted
#
#
###################################
GraphFileName = " Excess Deaths in Scotland (2020-2022) - faceted.png"
NRSWeeklyDeaths_Excess_Graph = ggplot(data = filter(DeathsTogether,Cause == "All"),
mapping = aes(x=Date,
y=Excess,
group=Age)
)+
theme_minimal()+
theme(panel.background = element_rect(fill = 'white', color = 'white'),
plot.background = element_rect(fill = 'white', color = 'white'),
legend.position="bottom",
legend.justification = "centre",
strip.background = element_blank(),
strip.placement = "outside",
#panel.grid = element_blank(),
plot.caption = element_text(hjust = 0)
)+
scale_x_date(#limits = c(as.Date("2021-04-01"),NA),
name = "Date",
#date_breaks = "12 months",
breaks = c(as.Date("2020-01-01"),as.Date("2021-01-01"),as.Date("2022-01-01")),
date_labels = "%Y")+
scale_y_continuous(name = "Weekly Deaths",
#limits = c(-25,100),
labels = label_number(accuracy = NULL))+
ggtitle("Excess Deaths in Scotland (2020-2022) using average of 2015 to 2019 deaths as baseline",
subtitle = GraphSubtitle)+
labs(caption = GraphCaption)+
geom_line(size = 0.5,
alpha = 1,
#linetype = 1,
#aes(),
show.legend = TRUE)+
facet_wrap(vars(Age),
ncol = 4,
scales = "free_y")
#Save graph
ggsave(filename = paste(GraphFileNameRoot,GraphFileName,sep=""),
plot = NRSWeeklyDeaths_Excess_Graph,
device="png",
width=graphwidth*2,
height=graphheight,
units="mm",
dpi=300
)
###########################################
###################################
#
#
# ExcessDeaths - faceted (2022 NRS baseline)
#
#
###################################
GraphFileName = " Excess Deaths in Scotland (2020-2022 using updated baseline) - faceted.png"
NRSWeeklyDeaths_Excess_Graph_2022 = ggplot(data = filter(DeathsTogether2022,Cause == "All"),
mapping = aes(x=Date,
y=Excess,
group=Age)
)+
theme_minimal()+
theme(panel.background = element_rect(fill = 'white', color = 'white'),
plot.background = element_rect(fill = 'white', color = 'white'),
legend.position="bottom",
legend.justification = "centre",
strip.background = element_blank(),
strip.placement = "outside",
#panel.grid = element_blank(),
plot.caption = element_text(hjust = 0)
)+
scale_x_date(#limits = c(as.Date("2021-04-01"),NA),
name = "Date",
#date_breaks = "12 months",
breaks = c(as.Date("2020-01-01"),as.Date("2021-01-01"),as.Date("2022-01-01")),
date_labels = "%Y")+
scale_y_continuous(name = "Weekly Deaths",
#limits = c(-25,100),
labels = label_number(accuracy = NULL))+
ggtitle("Excess Deaths in Scotland (2020-2022) using average of 2016 to 2019 plus 2021 deaths as 2022 baseline",
subtitle = GraphSubtitle)+
labs(caption = GraphCaption)+
geom_line(size = 0.5,
alpha = 1,
#linetype = 1,
#aes(),
show.legend = TRUE)+
facet_wrap(vars(Age),
ncol = 4,
scales = "free_y")
#Save graph
ggsave(filename = paste(GraphFileNameRoot,GraphFileName,sep=""),
plot = NRSWeeklyDeaths_Excess_Graph_2022,
device="png",
width=graphwidth*2,
height=graphheight,
units="mm",
dpi=300
)
###########################################
setwd(RootDirectory)