##############################################
# Plot functions Rt figure
# 2020-05-28 
# ___UITZONDERINGSGROND_2___ -> ___UITZONDERINGSGROND_2___
##############################################

library(tidyverse)
library(lubridate)
library(cowplot)

epicurve <- readRDS("/___UITZONDERINGSGROND_6___epicurve_2020-05-28.rds")

plot_totcurve_Osiris <- function(epicurve, IC = FALSE) {
  
  perc_reportedSO <- round(100*sum(epicurve$incidenceTOT)/sum(epicurve$incidence_mean))
  perc_estimatedSO <- 100 - perc_reportedSO
  
  p <- ggplot(data = epicurve,
              mapping = aes(x = dates)) + 
    geom_bar(data = . %>% mutate(adm_incidenceEXTRA = adm_incidenceEXPECTED - adm_incidenceTOT) %>%
               pivot_longer(cols = c(adm_incidenceABROAD, adm_incidenceNL, adm_incidenceEXTRA), names_to = "incidenceType", values_to = "incidence") %>%
               mutate(incidenceType = factor(incidenceType) %>% fct_relevel("adm_incidenceEXTRA", "adm_incidenceNL", "adm_incidenceABROAD")),
             mapping = aes(y = incidence, fill = incidenceType),
             stat = "identity") +
    geom_ribbon(mapping = aes(ymin = incidence_lower, ymax = incidence_upper),
                fill = adjustcolor("#d52b1e", alpha = 0.5)) +
    geom_line(mapping = aes(y = incidence_mean, col = cut(incidence_lower, breaks = c(-1, 1000, 2000)))) +
    scale_fill_manual(
      values = c("grey", "#01689b", "#ffb612"),
      labels = c("verwacht op basis van\nrapportagevertraging", paste0("opnamedatum ", if(IC) "IC" else "ziekenhuis", ", geïnfecteerd\nin Nederland"), paste0("opnamedatum ", if(IC) "IC" else "ziekenhuis", ", geïnfecteerd\nbuiten Nederland"))) +
    scale_color_manual(
      values = c("#d52b1e", 1),
      labels = c(paste0("eerste ziektedag\n (", perc_reportedSO, "% gerapporteerd, ", perc_estimatedSO, "% geschat)"), "")) +
    scale_x_date(
      limits = c(as.Date("2020-02-14"), last(epicurve$dates)+1),
      expand = expansion(add = -0.5),
      breaks = "4 days",
      minor_breaks = "1 day",
      date_labels = "%e %b") +
    labs(x = NULL,
         y = "aantal per dag",
         subtitle = paste("gebaseerd op", if(IC) "IC" else "ziekenhuis", "opnames uit OSIRIS data", last(epicurve$dates))) +
    theme_minimal() +
    theme(legend.position = c(1, 1),
          legend.justification = c(1, 1),
          legend.title = element_blank(),   
          axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5),
          panel.grid.minor = element_blank()) +
    guides(fill = guide_legend(order = 1),
           color = guide_legend(order = 2))
  
  return(p)
}

plot_Reff_Osiris <- function(epicurve, caseReff = TRUE, IC = TRUE) {
  p <- 
    ggplot(data = epicurve,
           mapping = aes(x = dates, 
                         y = if(caseReff) caseR else instR, 
                         ymin = if(caseReff) caseRlower else instRlower, 
                         ymax = if(caseReff) caseRupper else instRupper)) + 
    geom_ribbon(fill = "#c6b8cf", col = NA) +
    geom_line(col = "#42145f") +
    geom_line(y = 1, lty = 2) +
    coord_cartesian(
      ylim = c(0,4)) +
    scale_x_date(
      limits = c(as.Date("2020-02-14"), last(epicurve$dates)+1),
      expand = expansion(add = -0.5),
      breaks = "4 days",
      minor_breaks = "1 day",
      date_labels = "%e %b") +
    labs(x = NULL,
         y = if(caseReff) "effectieve R" else "instantane R",
         subtitle = paste("gebaseerd op", if(IC) "IC" else "ziekenhuis", "opnames uit OSIRIS data", last(epicurve$dates))) +
    theme_minimal() +
    theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5),
          panel.grid.minor = element_blank())
  
  return(p)
}

plot_grid(plot_totcurve_Osiris(epicurve = epicurve, IC = FALSE),
          plot_Reff_Osiris(epicurve %>% mutate(caseR = ifelse(dates > report_date - 14, NA, caseR)), caseR = TRUE, IC = FALSE) + labs(subtitle = NULL),
          ncol = 1,
          align = "hv")