library(jsonlite)

# import most recent epicurve reports and epicurve_ZKH of June 26 (last reported Reff_ZKH on June 12)
filename_epicurve <- paste0("./___UITZONDERINGSGROND_6___epicurve_reports_", analysis_date, ".rds")
if(file.exists(filename_epicurve)) {
  epicurve_Osiris <- readRDS(file = filename_epicurve)
} else { 
  stop(paste("Osiris epicurve file for", analysis_date, "not found. Run EstimationRt first"))
}


# not necessary since temporal split 2022-09-01
# epicurve_ZKH <- readRDS(file = paste0("./___UITZONDERINGSGROND_6___epicurve_", as.Date("2020-06-26"), ".rds"))
# 
# # transition from ZKH to reports on June 12
# epicurve <- bind_rows("ziekenhuis" = epicurve_ZKH %>% rename(date = dates) %>% filter(date <= as.Date("2020-06-12")),
#                       "meldingen" = epicurve_Osiris %>% filter(date > as.Date("2020-06-12")),
#                       .id = "source")

# json file for dashboard
reproduction.json <- epicurve_Osiris %>% 
  # select(date, caseRlower, caseR, caseRupper, source) %>% 
  select(date, caseRlower, caseR, caseRupper) %>% 
  # filter(date >= as.Date("2020-02-17")) %>%
  filter(date >= as.Date("2021-10-04")) %>% # temporal split: only report from 2021 W40 onwards
  mutate(caseR = ifelse(date > last(date) - 13, NA, caseR),
         caseR = ifelse(!is.na(caseR), format(round(caseR, digits = 2), nsmall = 2), NA),
         caseRlower = format(round(caseRlower, digits = 2), nsmall = 2),
         caseRupper = format(round(caseRupper, digits = 2), nsmall = 2),
         source = "testpos",
         # source = ifelse(source == "ziekenhuis", "hosp", "testpos"),
         # per 2022-02-08 berekening op testdatum ipv meldingsdatum -> version 2
         # per 2022-09-02 temporal split -> version 4
         version = 4) %>%
  rename(Date = date,
         Rt_low = caseRlower,
         Rt_avg = caseR,
         Rt_up = caseRupper,
         population = source) %>%
  toJSON 

write(x = reproduction.json, file = "./___UITZONDERINGSGROND_6___COVID-19_reproductiegetal.json")
write(x = reproduction.json, file = paste0("./___UITZONDERINGSGROND_6___COVID-19_reproductiegetal_", analysis_date, ".json"))

rm(filename_epicurve)
rm(epicurve)
rm(epicurve_ZKH)
rm(reproduction.json)