## ----setup, include = FALSE----------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
message = FALSE,
fig.align = "center"
)
## ------------------------------------------------------------------------
library(dplyr)
library(stringr)
library(tidyr)
library(ggplot2)
library(viridis)
library(boulder)
tabs <- get_all_tables(lang = "en")
tabs
## ------------------------------------------------------------------------
tabs %>%
mutate(descr = str_to_lower(Title)) %>%
filter(str_detect(descr, "neoplasm")) %>%
select(Name, Title, Node, Updated) %>%
knitr::kable()
## ------------------------------------------------------------------------
pk30 <- pull_table("PK30", lang = "en")
pk30
## ------------------------------------------------------------------------
pk30 %>%
select(Site) %>%
distinct()
## ------------------------------------------------------------------------
colo <- pk30 %>%
mutate_at("Site", str_to_lower) %>%
filter(str_detect(Site, "colon"))
colo
## ------------------------------------------------------------------------
colo %>%
mutate(Year = as.numeric(Year),
`Age group` = factor(`Age group`, levels = unique(colo$`Age group`)),
Site = gsub("^[.]+([a-z])", "\\U\\1", Site, perl = TRUE)) %>%
ggplot(aes(Year, value, group = `Age group`, color = `Age group`)) +
geom_line() +
facet_wrap(~ Sex) +
scale_color_viridis(discrete = TRUE) +
guides(color = guide_legend(ncol = 2)) +
labs(title = "Incidence of colon (C18) cancer",
y = "Age-specific incidence per 100 000")
## ------------------------------------------------------------------------
tabs %>%
mutate(Node = str_to_lower(Node)) %>%
filter(str_detect(Node, "deaths"))
## ------------------------------------------------------------------------
sd22 <- pull_table("SD22", lang = "en")
sd22
## ------------------------------------------------------------------------
mort <- sd22 %>%
mutate(`Cause of death` = str_to_lower(`Cause of death`)) %>%
filter(str_detect(`Cause of death`, "c18"))
mort
## ------------------------------------------------------------------------
colo_mort <- mort %>%
filter(Year >= 2000,
`Age group` %in% colo$`Age group`,
!is.na(value))
colo_mort
## ------------------------------------------------------------------------
colo_mort %>%
mutate(Year = as.numeric(Year),
`Age group` = factor(`Age group`, levels = unique(colo_mort$`Age group`)),
`Cause of death` = gsub("^[.]+([a-z])", "\\U\\1", `Cause of death`, perl = TRUE)) %>%
ggplot(aes(Year, value, group = `Age group`, color = `Age group`)) +
geom_line() +
facet_wrap(~ Sex) +
scale_color_viridis(discrete = TRUE) +
guides(color = guide_legend(ncol = 2)) +
labs(title = "Colon cancer (C18) mortality",
y = "Deaths per 100 000")
## ------------------------------------------------------------------------
c18 <- inner_join(
colo %>% select(-Site) %>% rename(incidence = value),
colo_mort %>% select(-`Cause of death`) %>% rename(mortality = value)
) %>%
filter(incidence != 0)
c18
## ------------------------------------------------------------------------
c18 %>%
mutate(Year = as.numeric(Year)) %>%
gather(key, value, -c("Year", "Sex", "Age group")) %>%
ggplot(aes(Year, value, color = key)) +
geom_line() +
facet_grid(Sex ~ `Age group`) +
scale_color_viridis(discrete = TRUE, direction = -1) +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, size = 6),
legend.title = element_blank(),
legend.position = "bottom") +
labs(y = "Incidence vs. mortality per 100000")
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