## download and clean regional US flu data
## October 5 2016 - Nicholas Reich - created
## October 7 2016 - Evan Ray - calculate time using MMWRweek package, fix bug in
## computation of season week
## October 7 2016 - Nicholas Reich - merged US and Regional data into one file.
## November 2 2017 - Nicholas Reich - forked for state-level data
library(plyr)
library(dplyr)
library(tidyr)
library(lubridate)
library(MMWRweek)
library(cdcfluview) ## devtools::install_github("hrbrmstr/cdcfluview")
library(forcats)
flu_data_raw <- get_flu_data(
region = "state",
sub_region = "all",
data_source = "ilinet",
years = 1997:2017
)
## ggplot(flu_data, aes(x=YEAR+WEEK/53, y=`%UNWEIGHTED ILI`)) + geom_line() + facet_wrap(~REGION)
flu_data <- transmute(flu_data_raw,
region.type = `REGION TYPE`,
region = REGION,
year = YEAR,
week = WEEK,
time = as.POSIXct(MMWRweek2Date(YEAR, WEEK)),
unweighted_ili = as.numeric(`%UNWEIGHTED ILI`),
ili_count = ILITOTAL,
patient_count = `TOTAL PATIENTS`,
provider_count = `NUM. OF PROVIDERS`
)
## set rows with denominator zeroes to NAs
flu_data[which(flu_data$patient_count==0),"weighted_ili"] <- NA
## Add time_index column: the number of days since some origin date
## (1970-1-1 in this case). The origin is arbitrary.
flu_data$time_index <- as.integer(date(flu_data$time) - ymd("1970-01-01"))
## Season column: for example, weeks of 2010 up through and including week 30
## get season 2009/2010; weeks after week 30 get season 2010/2011
## Official CDC flu season for the purposes of prediction runs from week 40 of
## one year to week 20 of the next; the season start week we define here is the
## mid-point of the "off-season"
flu_data$season <- ifelse(
flu_data$week <= 30,
paste0(flu_data$year - 1, "/", flu_data$year),
paste0(flu_data$year, "/", flu_data$year + 1)
)
## Season week column: week number within season
## weeks after week 30 get season_week = week - 30
## weeks before week 30 get season_week = week + (number of weeks in previous year) - 30
## This computation relies on the start_date function in package MMWRweek,
## which is not exported from that package's namespace!!!
flu_data$season_week <- ifelse(
flu_data$week <= 30,
flu_data$week + MMWRweek(MMWRweek:::start_date(flu_data$year) - 1)$MMWRweek - 30,
flu_data$week - 30
)
state_flu <- as.data.frame(flu_data)
write.csv(state_flu, file = "data-raw/state_flu_data.csv")
save(state_flu, file = "data/state_flu_data.rdata")
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