--- output: rmarkdown::github_document --- ```{r, echo=FALSE} knitr::opts_chunk$set( collapse = TRUE, warning = FALSE, message = FALSE, comment = "#>", fig.path = "README_files/README-", fig.retina = 2 ) ``` ### :mask: cdcfluview - Retrieve U.S. Flu Season Data from the CDC FluView Portal [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/cdcfluview)](https://cran.r-project.org/package=cdcfluview) [![Travis-CI Build Status](https://travis-ci.org/hrbrmstr/cdcfluview.svg?branch=master)](https://travis-ci.org/hrbrmstr/cdcfluview) **NOTE** If there's a particular data set from https://www.cdc.gov/flu/weekly/fluviewinteractive.htm that you want and that isn't in the package, please file it as an issue and be as specific as you can (screen shot if possible). ----- The U.S. Centers for Disease Control (CDC) maintains a [portal](https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html) for accessing state, regional and national influenza statistics. The portal's Flash interface makes it difficult and time-consuming to select and retrieve influenza data. This package provides functions to access the data provided by the portal's underlying API. The following functions are implemented: - `get_flu_data`: Retrieves state, regional or national influenza statistics from the CDC - `get_state_data`: Retrieves state/territory-level influenza statistics from the CDC - `get_weekly_flu_report`: Retrieves (high-level) weekly influenza surveillance report from the CDC - `get_mortality_surveillance_data` : (fairly self explanatory but also pretty new to the pkg and uses data from: https://www.cdc.gov/flu/weekly/nchs.htm The following data sets are included: - `hhs_regions` HHS Region Table (a data frame with 59 rows and 4 variables) - `census_regions` Census Region Table (a data frame with 51 rows and 2 variables) ### News - See NEWS - Version 0.4.0 - [CRAN release](http://cran.r-project.org/web/packages/cdcfluview) - Version 0.4.0.999 released : another fix for the CDC API (for region parameter); added data files for HHS/Census region lookups; added weekly high-level flu report retrieval - Version 0.3 released : fix for the CDC API (it changed how year & region params are encoded in the request) - Version 0.2.1 released : bumped up `httr` version # requirement in `DESCRIPTION` (via Issue [1](https://github.com/hrbrmstr/cdcfluview/issues/1)) - Version 0.2 released : added state-level data retrieval - Version 0.1 released ### Installation ```{r eval=FALSE} install.packages("cdcfluview") # **OR** devtools::install_github("hrbrmstr/cdcfluview") ``` ```{r echo=FALSE, message=FALSE, warning=FALSE, error=FALSE} options(width=120) ``` ### Usage ```{r state2015, message=FALSE, warning=FALSE, fig.height=10, fig.width=6} library(cdcfluview) library(ggplot2) library(dplyr) library(statebins) # current verison packageVersion("cdcfluview") flu <- get_flu_data("hhs", sub_region=1:10, "ilinet", years=2014) glimpse(flu) state_flu <- get_state_data(years=2015) glimpse(state_flu) gg <- ggplot(flu, aes(x=WEEK, y=`% WEIGHTED ILI`, group=REGION)) gg <- gg + geom_line() gg <- gg + facet_wrap(~REGION, ncol=2) gg <- gg + theme_bw() gg ``` ```{r mortality, message=FALSE, warning=FALSE, fig.height=6, fig.width=10} msd <- get_mortality_surveillance_data() mutate(msd$by_state, ym=as.Date(sprintf("%04d-%02d-1", Year, Week), "%Y-%U-%u")) %>% select(state, wk=ym, death_pct=`Percent of Deaths Due to Pneumonia and Influenza`) %>% mutate(death_pct=death_pct/100) -> df gg <- ggplot() + geom_smooth(data=df, aes(wk, death_pct, group=state), se=FALSE, color="#2b2b2b", size=0.25) gb <- ggplot_build(gg) gb$data[[1]] %>% arrange(desc(x)) %>% group_by(group) %>% slice(1) %>% ungroup() %>% arrange(desc(y)) %>% head(1) -> top top_state <- sort(unique(msd$by_state$state))[top$group] gg <- gg + geom_text(data=top, aes(as.Date(x, origin="1970-01-01"), y, label=top_state), hjust=1, family="Arial Narrow", size=3, nudge_x=-5, nudge_y=-0.001) gg <- gg + scale_x_date(expand=c(0,0)) gg <- gg + scale_y_continuous(label=scales::percent) gg <- gg + labs(x=NULL, y=NULL, title="Percent of In-State Deaths Due to Pneumonia and Pnfluenza (2010-Present)") gg <- gg + theme_bw(base_family="Arial Narrow") gg <- gg + theme(axis.text.x=element_text(margin=margin(0,0,0,0))) gg <- gg + theme(axis.text.y=element_text(margin=margin(0,0,0,0))) gg <- gg + theme(axis.ticks=element_blank()) gg <- gg + theme(plot.title=element_text(face="bold", size=16)) gg ``` ```{r region, eval=FALSE, include=FALSE, warning=FALSE, error=FALSE, message=FALSE} dat <- get_flu_data(region="hhs", sub_region=1:10, data_source="ilinet", years=2000:2014) dat %>% mutate(REGION=factor(REGION, levels=unique(REGION), labels=c("Boston", "New York", "Philadelphia", "Atlanta", "Chicago", "Dallas", "Kansas City", "Denver", "San Francisco", "Seattle"), ordered=TRUE)) %>% mutate(season_week=ifelse(WEEK>=40, WEEK-40, WEEK), season=ifelse(WEEK<40, sprintf("%d-%d", YEAR-1, YEAR), sprintf("%d-%d", YEAR, YEAR+1))) -> dat prev_years <- dat %>% filter(season != "2014-2015") curr_year <- dat %>% filter(season == "2014-2015") curr_week <- tail(dat, 1)$season_week gg <- ggplot() gg <- gg + geom_point(data=prev_years, aes(x=season_week, y=`% WEIGHTED ILI`, group=season), color="#969696", size=1, alpha=0.25) gg <- gg + geom_point(data=curr_year, aes(x=season_week, y=`% WEIGHTED ILI`, group=season), color="red", size=1.25, alpha=1) gg <- gg + geom_line(data=curr_year, aes(x=season_week, y=`% WEIGHTED ILI`, group=season), size=1.25, color="#d7301f") gg <- gg + geom_vline(xintercept=curr_week, color="#d7301f", size=0.5, linetype="dashed", alpha=0.5) gg <- gg + facet_wrap(~REGION, ncol=3) gg <- gg + labs(x=NULL, y="Weighted ILI Index", title="ILINet - 1999-2015 year weighted flu index history by CDC region\nWeek Ending Jan 3, 2015 (Red == 2014-2015 season)\n") gg <- gg + theme_bw() gg <- gg + theme(panel.grid=element_blank()) gg <- gg + theme(strip.background=element_blank()) gg <- gg + theme(axis.ticks.x=element_blank()) gg <- gg + theme(axis.text.x=element_blank()) ``` ```{r bins, message=FALSE, fig.height=5, fig.width=7} gg_s <- state_flu %>% filter(weekend=="Jan-02-2016") %>% select(state=statename, value=activity_level) %>% filter(!(state %in% c("Puerto Rico", "New York City"))) %>% # need to add PR to statebins mutate(value=as.numeric(gsub("Level ", "", value))) %>% statebins(brewer_pal="RdPu", breaks=4, labels=c("Minimal", "Low", "Moderate", "High"), legend_position="bottom", legend_title="ILI Activity Level") + ggtitle("CDC State FluView (2015-01-03)") gg_s ``` ### Test Results ```{r message=FALSE} library(cdcfluview) library(testthat) date() test_dir("tests/") ```