## create long flu baseline dataset
## Nicholas Reich
## October 2016
library(tidyr)
library(dplyr)
dat <- read.csv("https://raw.githubusercontent.com/cdcepi/FluSight-forecasts/master/wILI_Baseline.csv")
dat <- as_data_frame(dat) %>%
gather(key=year, value=baseline, -X) %>%
transmute(region = as.character(X),
season = substr(year, start=2, stop=10), ## removes X at beginning of season name
baseline=baseline)
dat$season <- gsub("\\.", "/", dat$season) ## replaces . with / in season string
## fill in baselines for seasons before 2007/2008 with means
mean_region_baseline <- dat %>%
group_by(region) %>%
summarize(baseline = round(mean(baseline), 1))
mean_region_baseline <- mean_region_baseline[c(1:2, 4:11, 3), ]
regions <- c("National", paste0("Region", 1:10))
for(first_season_year in 2006:1997) {
dat <- bind_rows(
data.frame(
region = regions,
season = paste0(first_season_year, "/", first_season_year + 1),
baseline = mean_region_baseline$baseline
),
dat
)
}
flu_onset_baselines <- as.data.frame(dat)
write.csv(dat, "data-raw/flu_onset_baselines.csv", quote = FALSE, row.names = FALSE)
save(flu_onset_baselines, file = "data/flu_onset_baselines.rdata")
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