dashboard_funnel_condition.Rmd

---
title: "dashboard_condition_funnel"
author: "Richard Wilson"
output: html_document
---

### Funnel 

```{r  funnel condition}

library(FunnelPlotR)  #funnel plots

by_condition_funnel <- data_shmi %>%
  group_by(one_word) %>%
  summarise(Excess_deaths = round(sum(DIED) - sum(RISK, na.rm=TRUE), 0),
            Observed = sum(DIED),
            Expected = round(sum(RISK, na.rm=TRUE), 0),
            Observed = sum(DIED),
            balance_deaths = round(sum(RISK, na.rm=TRUE) + (sum(DIED) - sum(RISK, na.rm=TRUE)), 0)) %>%
  mutate(
#create series for survivors where excess deaths are <0
    survivors = ifelse(Excess_deaths < 0, Excess_deaths, NA),
#create series for excess mortality exc survivors
    excess_mortality = ifelse(Excess_deaths > 0, Excess_deaths, NA)) %>%
#to simplify chart presentation only show conditions with more than 5 deaths
  filter(Observed >= 1)

#create funnel for conditions using FunnelPlotR
#call FunnelPlotR to create funnel chart data

funnel_plot_data <- funnel_plot(numerator = by_condition_funnel$Observed,
                                        denominator = by_condition_funnel$Expected,
                                        group = by_condition_funnel$one_word,  title = "SHMI",
                                        Poisson_limits = FALSE, OD_adjust = TRUE, sr_method = "SHMI",
                                        label_outliers = FALSE)

funnel_plot_data_condition <- funnel_plot_data$aggregated_data

limits <- limits(funnel_plot_data)

#tidy up column names into user friendly labels
limits <- limits %>%
  rename(limit_x = "number.seq") %>%
  select(limit_x, ul95, ll95, ll998, ul998) %>%
  filter(limit_x >= 1) %>%
  arrange(ll95)

funnel_plot_data_condition <- funnel_plot_data_condition %>%
  rename(SHMI = "rr") %>%
#create column to describe the 3 groups of points for the chart
  mutate(
#set up outlier points - this time there are two limits used 95 and 99.8% limits
    linegroups = case_when(
      SHMI > UCL99 ~"Higher than expected 99.8% limits",
      SHMI > UCL95 ~ "Higher than expected 95% limits",
      SHMI < LCL99 ~ "Lower than expected 99.8% limits",
      SHMI < LCL95 ~ "Lower than expected 95% limits",
      TRUE ~ "As expected"),
#round SHMI to just 3 points
        SHMI = round(SHMI, 3),
#add column for excess deaths and for absolute version for sizing markers
        `Excess deaths` = numerator - denominator,
        abs_excess = abs(`Excess deaths`),
#add shmi index line
         index = 1) %>%
  #tidy up user friendly labels
rename(`Expected deaths` = "denominator") %>%
rename(`Observed` = "numerator") %>%
rename(`Lower limit` = "OD95LCL") %>%
rename(`Upper limit` = "OD95UCL") %>%
rename(Condition = "group")

ylimMin <- min(funnel_plot_data_condition$SHMI, na.rm = TRUE)

funnel_plot_data_condition <- funnel_plot_data_condition %>%
  filter(`Expected deaths` >= 1) %>%
   mutate(tooltip = paste0(Condition, ": ", SHMI))

funnel_plot_condition <- ggplot() +
  geom_line(funnel_plot_data_condition, mapping = aes(x = `Expected deaths`, y = index), linetype = 2, colour = "black") +
  geom_point_interactive(funnel_plot_data_condition, mapping = aes(x = `Expected deaths`, y = SHMI, colour = linegroups, size = abs_excess, tooltip = tooltip)) +
  geom_line(limits, mapping = aes(limit_x, ul95), colour = "grey") +
  geom_line(limits, mapping = aes(x = limit_x, y = ll95), colour = "grey") +
  geom_line(limits, mapping = aes(x = limit_x, y = ul998), colour = "grey") +
  geom_line(limits, mapping = aes(x = limit_x, y = ll998), colour = "grey") +
    scale_size("Excess deaths") +
  scale_colour_manual_interactive(values = funnel.conditions.colors) +
  labs(x = "Expected deaths", y = "SHMI", size = "Excess Deaths", shape = "Excess deaths")+
 theme_i7() +
  theme(
                   plot.title =  element_text(size = rel(2)),
                   axis.line.x =  element_blank(),
                   axis.text.x =  element_text(size = rel(1)),
                   axis.text.y =  element_text(size = rel(1)),
                   axis.title.x =  element_text(size = rel(1.5)),
                   axis.title.y =  element_text(size = rel(1.5)),
                   legend.key = element_rect(fill = "white"),
                   legend.position = "right",
                   legend.text =  element_text(size = rel(1))
                   )

```

```{r Condition funnel_chart, results = "asis", include = TRUE, fig.width = 12}

girafe(ggobj = funnel_plot_condition,
       width_svg = 12, height_svg = 4,
                       options = list(
                       opts_sizing(rescale = FALSE),
                         opts_tooltip(css = tooltip_css,use_fill = TRUE)
    ))
```