## This code is based on inst/data-processing/create-clean-flu-data.R
library(plyr)
library(dplyr)
library(tidyr)
library(lubridate)
library(MMWRweek)
library(cdcfluview)
library(KoTflu20162017)
library(forecast)
library(kcde)
library(copula)
library(FluSight)
source("R/utils.R") # temporary
source("inst/estimation/kde/kde-utils.R")
source("inst/estimation/trunc-kde/trunc-kde-utils.R")
source("inst/estimation/trunc-kde/make-one-trunc-kde-prediction-file.R")
source("inst/estimation/kde/kde-prediction-utils.R")
kde_fits_save_path <- "inst/estimation/kde/current-fits"
n_sims <- 10000
data <- download_and_preprocess_flu_data()
data$rounded_weighted_ili <- round(data$weighted_ili, digits = 1)
submissions_save_path <- file.path("inst/submissions/submissions-KoT-dev",
paste0(tail(data$year, 1),
"-",
tail(data$week, 1)))
make_one_trunc_kde_prediction_file(
fits_path = kde_fits_save_path,
results_path = submissions_save_path,
season = tail(data$season, 1),
season_week = tail(data$season_week, 1),
n_sim = n_sims,
dat = data,
first_analysis_time_season_week = 10
)
res_file <- paste0(
submissions_save_path,
"/EW",
tail(data$week, 1),
"-KOTtrunckde-",
Sys.Date(),
".csv")
(FluSight::verify_entry_file(res_file))
### Plots for sanity
make_predictions_plots(
preds_save_file = res_file,
plots_save_file = paste0(
submissions_save_path,
"/",
"KOTtrunckde-plots.pdf"),
data = data
)
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