--- title: "README" author: "Bob Rudis" date: August 9, 2015 output: md_document: variant: markdown_github --- ```{r, echo=FALSE} knitr::opts_chunk$set( collapse = TRUE, warning = FALSE, message = FALSE, comment = "#>", fig.path = "README_files/README-", fig.retina = 2 ) ``` **NOTE** If there's a particular data set from http://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](http://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 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 weekly influenza surveillance report from the CDC The following data sets are included: - `hhs_regions` HHS Region Table (a data frame with 59 rows and 4 variables) ### News - Version 0.4.0.999 released : another fix for the CDC API (for region parameter); added data file for 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} devtools::install_github("hrbrmstr/cdcfluview") ``` ```{r echo=FALSE, message=FALSE, warning=FALSE, error=FALSE} options(width=120) ``` ### Usage ```{r} suppressPackageStartupMessages(library(cdcfluview)) suppressPackageStartupMessages(library(ggplot2)) suppressPackageStartupMessages(library(dplyr)) suppressPackageStartupMessages(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=2014) glimpse(state_flu) gg <- ggplot(flu, aes(x=WEEK, y=X..WEIGHTED.ILI, group=REGION)) gg <- gg + geom_line() gg <- gg + facet_wrap(~REGION, ncol=2) gg <- gg + theme_bw() ``` ```{r echo=FALSE, fig.height=10, fig.width=6} gg ``` ```{r 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=X..WEIGHTED.ILI, group=season), color="#969696", size=1, alpa=0.25) gg <- gg + geom_point(data=curr_year, aes(x=season_week, y=X..WEIGHTED.ILI, group=season), color="red", size=1.25, alpha=1) gg <- gg + geom_line(data=curr_year, aes(x=season_week, y=X..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 echo=FALSE, fig.height=10, fig.width=6, warning=FALSE, error=FALSE, message=FALSE} gg ``` ```{r} gg_s <- state_flu %>% filter(WEEKEND=="Jan-03-2015") %>% 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)") ``` ```{r echo=FALSE, fig.height=5, fig.width=7} gg_s ``` ### Test Results ```{r} suppressPackageStartupMessages(library(cdcfluview)) suppressPackageStartupMessages(library(testthat)) date() test_dir("tests/") ```