[![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) [![Coverage Status](https://img.shields.io/codecov/c/github/hrbrmstr/cdcfluview/master.svg)](https://codecov.io/github/hrbrmstr/cdcfluview?branch=master) I M P O R T A N T ================= The CDC migrated to a new non-Flash portal and back-end APIs changed. This is a complete reimagining of the package and — as such — all your code is going to break. Please use GitHub issues to identify previous API functionality you would like ported over. There’s a [release candidate for 0.5.2](https://github.com/hrbrmstr/cdcfluview/releases/tag/v0.5.2) which uses the old API but it likely to break in the near future given the changes to the hidden API. You can do what with `devtools::install_github("hrbrmstr/cdcfluview", ref="58c172b")`. All folks providing feedback, code or suggestions will be added to the DESCRIPTION file. Please include how you would prefer to be cited in any issues you file. If there’s a particular data set from 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). :mask: cdcfluview ================= Retrieve U.S. Flu Season Data from the CDC FluView Portal Description ----------- The U.S. Centers for Disease Control (CDC) maintains a portal for accessing state, regional and national influenza statistics as well as Mortality Surveillance Data. The 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. What’s Inside The Tin --------------------- The following functions are implemented: - `agd_ipt`: Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories - `cdc_coverage_map`: Retrieve CDC U.S. Coverage Map - `geographic_spread`: State and Territorial Epidemiologists Reports of Geographic Spread of Influenza - `hospitalizations`: Laboratory-Confirmed Influenza Hospitalizations - `ilinet`: Retrieve ILINet Surveillance Data - `ili_weekly_activity_indicators`: Retrieve weekly state-level ILI indicators per-state for a given season - `pi_mortality`: Pneumonia and Influenza Mortality Surveillance - `state_data_providers`: Retrieve metadat about U.S. State CDC Provider Data - `surveillance_areas`: Retrieve a list of valid sub-regions for each surveillance area. - `who_nrevss`: Retrieve WHO/NREVSS Surveillance Data 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) Installation ------------ ``` r devtools::install_github("hrbrmstr/cdcfluview") ``` Usage ----- ``` r library(cdcfluview) library(tidyverse) # current verison packageVersion("cdcfluview") ``` ## [1] '0.7.0' ### Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories ``` r glimpse(agd_ipt()) ``` ## Observations: 36,144 ## Variables: 13 ## $ sea_label "1997-98", "1997-98", "1997-98", "1997-98", "1997-98", "1997-98", "1997-98", "1997-98", "... ## $ age_label "0-4 yr", "0-4 yr", "0-4 yr", "0-4 yr", "0-4 yr", "0-4 yr", "0-4 yr", "0-4 yr", "0-4 yr",... ## $ vir_label "A (Subtyping not Performed)", "A (Subtyping not Performed)", "A (Subtyping not Performed... ## $ count 0, 1, 0, 0, 0, 0, 0, 3, 0, 6, 0, 1, 1, 2, 11, 8, 18, 26, 22, 19, 2, 5, 2, 1, 4, 0, 0, 0, ... ## $ mmwrid 1866, 1867, 1868, 1869, 1870, 1871, 1872, 1873, 1874, 1875, 1876, 1877, 1878, 1879, 1880,... ## $ seasonid 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 3... ## $ publishyearweekid 2913, 2913, 2913, 2913, 2913, 2913, 2913, 2913, 2913, 2913, 2913, 2913, 2913, 2913, 2913,... ## $ sea_description "Season 1997-98", "Season 1997-98", "Season 1997-98", "Season 1997-98", "Season 1997-98",... ## $ sea_startweek 1866, 1866, 1866, 1866, 1866, 1866, 1866, 1866, 1866, 1866, 1866, 1866, 1866, 1866, 1866,... ## $ sea_endweek 1918, 1918, 1918, 1918, 1918, 1918, 1918, 1918, 1918, 1918, 1918, 1918, 1918, 1918, 1918,... ## $ vir_description "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk",... ## $ vir_startmmwrid 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397,... ## $ vir_endmmwrid 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131,... ### Retrieve CDC U.S. Coverage Map ``` r plot(cdc_coverage_map()) ``` ![](README_files/figure-markdown_github-ascii_identifiers/unnamed-chunk-5-1.png) ### State and Territorial Epidemiologists Reports of Geographic Spread of Influenza ``` r glimpse(geographic_spread()) ``` ## Observations: 25,795 ## Variables: 7 ## $ statename "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "... ## $ url "http://adph.org/influenza/", "http://adph.org/influenza/", "http://adph.org/influenza/",... ## $ website "Influenza Surveillance", "Influenza Surveillance", "Influenza Surveillance", "Influenza ... ## $ activity_estimate "No Activity", "No Activity", "No Activity", "Local Activity", "Sporadic", "Sporadic", "S... ## $ weekend 2003-10-04, 2003-10-11, 2003-10-18, 2003-10-25, 2003-11-01, 2003-11-08, 2003-11-15, 2003... ## $ season "2003-04", "2003-04", "2003-04", "2003-04", "2003-04", "2003-04", "2003-04", "2003-04", "... ## $ weeknumber "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "1", ... ### Laboratory-Confirmed Influenza Hospitalizations ``` r surveillance_areas() ``` ## surveillance_area region ## 1 flusurv Entire Network ## 2 eip California ## 3 eip Colorado ## 4 eip Connecticut ## 5 eip Entire Network ## 6 eip Georgia ## 7 eip Maryland ## 8 eip Minnesota ## 9 eip New Mexico ## 10 eip New York - Albany ## 11 eip New York - Rochester ## 12 eip Oregon ## 13 eip Tennessee ## 14 ihsp Entire Network ## 15 ihsp Idaho ## 16 ihsp Iowa ## 17 ihsp Michigan ## 18 ihsp Ohio ## 19 ihsp Oklahoma ## 20 ihsp Rhode Island ## 21 ihsp South Dakota ## 22 ihsp Utah ``` r glimpse(hospitalizations("flusurv")) ``` ## Observations: 1,476 ## Variables: 20 ## $ mmwrid 2545, 2546, 2547, 2548, 2549, 2550, 2551, 2552, 2553, 2554, 2555, 2556, 2557, 2558, 2559,... ## $ weeknumber 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12... ## $ rate 0.0, 0.0, 0.0, 0.1, 0.1, 0.2, 0.3, 0.3, 0.4, 0.6, 0.8, 1.3, 1.7, 2.2, 2.8, 3.6, 4.4, 5.4,... ## $ weeklyrate 0.0, 0.0, 0.0, 0.0, 0.1, 0.0, 0.1, 0.1, 0.1, 0.2, 0.2, 0.4, 0.4, 0.5, 0.5, 0.8, 0.8, 1.0,... ## $ age 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,... ## $ season 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5... ## $ weekend "2010-10-09", "2010-10-16", "2010-10-23", "2010-10-30", "2010-11-06", "2010-11-13", "2010... ## $ weekstart "2010-10-03", "2010-10-10", "2010-10-17", "2010-10-24", "2010-10-31", "2010-11-07", "2010... ## $ year 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2011, 2011,... ## $ yearweek 201040, 201041, 201042, 201043, 201044, 201045, 201046, 201047, 201048, 201049, 201050, 2... ## $ seasonid 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5... ## $ weekendlabel "Oct 09, 2010", "Oct 16, 2010", "Oct 23, 2010", "Oct 30, 2010", "Nov 06, 2010", "Nov 13, ... ## $ weekendlabel2 "Oct-09-2010", "Oct-16-2010", "Oct-23-2010", "Oct-30-2010", "Nov-06-2010", "Nov-13-2010",... ## $ age_label "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-4... ## $ sea_label "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "... ## $ sea_description "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11",... ## $ sea_startweek 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545,... ## $ sea_endweek 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596,... ## $ surveillance_area "FluSurv-NET", "FluSurv-NET", "FluSurv-NET", "FluSurv-NET", "FluSurv-NET", "FluSurv-NET",... ## $ region "Entire Network", "Entire Network", "Entire Network", "Entire Network", "Entire Network",... ``` r glimpse(hospitalizations("eip")) ``` ## Observations: 2,385 ## Variables: 20 ## $ mmwrid 2545, 2546, 2547, 2548, 2549, 2550, 2551, 2552, 2553, 2554, 2555, 2556, 2557, 2558, 2559,... ## $ weeknumber 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12... ## $ rate 0.0, 0.0, 0.0, 0.1, 0.1, 0.1, 0.2, 0.3, 0.4, 0.5, 0.8, 1.1, 1.4, 1.9, 2.3, 2.8, 3.6, 4.5,... ## $ weeklyrate 0.0, 0.0, 0.0, 0.0, 0.1, 0.0, 0.1, 0.1, 0.1, 0.1, 0.2, 0.4, 0.3, 0.4, 0.4, 0.5, 0.8, 1.0,... ## $ age 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,... ## $ season 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5... ## $ weekend "2010-10-09", "2010-10-16", "2010-10-23", "2010-10-30", "2010-11-06", "2010-11-13", "2010... ## $ weekstart "2010-10-03", "2010-10-10", "2010-10-17", "2010-10-24", "2010-10-31", "2010-11-07", "2010... ## $ year 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2011, 2011,... ## $ yearweek 201040, 201041, 201042, 201043, 201044, 201045, 201046, 201047, 201048, 201049, 201050, 2... ## $ seasonid 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5... ## $ weekendlabel "Oct 09, 2010", "Oct 16, 2010", "Oct 23, 2010", "Oct 30, 2010", "Nov 06, 2010", "Nov 13, ... ## $ weekendlabel2 "Oct-09-2010", "Oct-16-2010", "Oct-23-2010", "Oct-30-2010", "Nov-06-2010", "Nov-13-2010",... ## $ age_label "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-4... ## $ sea_label "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "... ## $ sea_description "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11",... ## $ sea_startweek 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545,... ## $ sea_endweek 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596,... ## $ surveillance_area "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP"... ## $ region "Entire Network", "Entire Network", "Entire Network", "Entire Network", "Entire Network",... ``` r glimpse(hospitalizations("eip", "Colorado")) ``` ## Observations: 2,385 ## Variables: 20 ## $ mmwrid 2545, 2546, 2547, 2548, 2549, 2550, 2551, 2552, 2553, 2554, 2555, 2556, 2557, 2558, 2559,... ## $ weeknumber 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12... ## $ rate 0.0, 0.1, 0.1, 0.1, 0.3, 0.3, 0.4, 0.4, 0.5, 0.6, 0.8, 1.3, 1.8, 2.1, 2.6, 3.4, 4.2, 5.6,... ## $ weeklyrate 0.0, 0.1, 0.0, 0.0, 0.2, 0.0, 0.1, 0.1, 0.1, 0.1, 0.2, 0.5, 0.4, 0.4, 0.4, 0.9, 0.8, 1.4,... ## $ age 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,... ## $ season 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5... ## $ weekend "2010-10-09", "2010-10-16", "2010-10-23", "2010-10-30", "2010-11-06", "2010-11-13", "2010... ## $ weekstart "2010-10-03", "2010-10-10", "2010-10-17", "2010-10-24", "2010-10-31", "2010-11-07", "2010... ## $ year 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2011, 2011,... ## $ yearweek 201040, 201041, 201042, 201043, 201044, 201045, 201046, 201047, 201048, 201049, 201050, 2... ## $ seasonid 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5... ## $ weekendlabel "Oct 09, 2010", "Oct 16, 2010", "Oct 23, 2010", "Oct 30, 2010", "Nov 06, 2010", "Nov 13, ... ## $ weekendlabel2 "Oct-09-2010", "Oct-16-2010", "Oct-23-2010", "Oct-30-2010", "Nov-06-2010", "Nov-13-2010",... ## $ age_label "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-4... ## $ sea_label "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "... ## $ sea_description "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11",... ## $ sea_startweek 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545,... ## $ sea_endweek 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596,... ## $ surveillance_area "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP"... ## $ region "Colorado", "Colorado", "Colorado", "Colorado", "Colorado", "Colorado", "Colorado", "Colo... ``` r glimpse(hospitalizations("ihsp")) ``` ## Observations: 1,476 ## Variables: 20 ## $ mmwrid 2545, 2546, 2547, 2548, 2549, 2550, 2551, 2552, 2553, 2554, 2555, 2556, 2557, 2558, 2559,... ## $ weeknumber 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12... ## $ rate 0.0, 0.0, 0.1, 0.2, 0.2, 0.3, 0.3, 0.4, 0.6, 0.9, 1.1, 1.9, 2.8, 3.9, 4.9, 6.8, 7.6, 9.0,... ## $ weeklyrate 0.0, 0.0, 0.0, 0.1, 0.0, 0.0, 0.0, 0.1, 0.2, 0.4, 0.2, 0.8, 0.9, 1.1, 1.0, 2.0, 0.8, 1.4,... ## $ age 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,... ## $ season 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5... ## $ weekend "2010-10-09", "2010-10-16", "2010-10-23", "2010-10-30", "2010-11-06", "2010-11-13", "2010... ## $ weekstart "2010-10-03", "2010-10-10", "2010-10-17", "2010-10-24", "2010-10-31", "2010-11-07", "2010... ## $ year 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2011, 2011,... ## $ yearweek 201040, 201041, 201042, 201043, 201044, 201045, 201046, 201047, 201048, 201049, 201050, 2... ## $ seasonid 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5... ## $ weekendlabel "Oct 09, 2010", "Oct 16, 2010", "Oct 23, 2010", "Oct 30, 2010", "Nov 06, 2010", "Nov 13, ... ## $ weekendlabel2 "Oct-09-2010", "Oct-16-2010", "Oct-23-2010", "Oct-30-2010", "Nov-06-2010", "Nov-13-2010",... ## $ age_label "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-4... ## $ sea_label "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "... ## $ sea_description "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11",... ## $ sea_startweek 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545,... ## $ sea_endweek 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596,... ## $ surveillance_area "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "... ## $ region "Entire Network", "Entire Network", "Entire Network", "Entire Network", "Entire Network",... ``` r glimpse(hospitalizations("ihsp", "Oklahoma")) ``` ## Observations: 390 ## Variables: 20 ## $ mmwrid 2545, 2546, 2547, 2548, 2549, 2550, 2551, 2552, 2553, 2554, 2555, 2556, 2557, 2558, 2559,... ## $ weeknumber 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12... ## $ rate 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.2, 0.2, 0.4, 0.7, 0.7, 1.3, 2.2, 2.5, 3.4, 4.5, 5.8, 7.6,... ## $ weeklyrate 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.2, 0.0, 0.2, 0.2, 0.0, 0.7, 0.9, 0.2, 0.9, 1.1, 1.3, 1.8,... ## $ age 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,... ## $ season 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5... ## $ weekend "2010-10-09", "2010-10-16", "2010-10-23", "2010-10-30", "2010-11-06", "2010-11-13", "2010... ## $ weekstart "2010-10-03", "2010-10-10", "2010-10-17", "2010-10-24", "2010-10-31", "2010-11-07", "2010... ## $ year 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2011, 2011,... ## $ yearweek 201040, 201041, 201042, 201043, 201044, 201045, 201046, 201047, 201048, 201049, 201050, 2... ## $ seasonid 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5... ## $ weekendlabel "Oct 09, 2010", "Oct 16, 2010", "Oct 23, 2010", "Oct 30, 2010", "Nov 06, 2010", "Nov 13, ... ## $ weekendlabel2 "Oct-09-2010", "Oct-16-2010", "Oct-23-2010", "Oct-30-2010", "Nov-06-2010", "Nov-13-2010",... ## $ age_label "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-4... ## $ sea_label "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "... ## $ sea_description "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11",... ## $ sea_startweek 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545,... ## $ sea_endweek 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596,... ## $ surveillance_area "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "... ## $ region "Oklahoma", "Oklahoma", "Oklahoma", "Oklahoma", "Oklahoma", "Oklahoma", "Oklahoma", "Okla... ### Retrieve ILINet Surveillance Data ``` r ilinet("national") ``` ## # A tibble: 1,048 x 15 ## region_type region year week weighted_ili unweighted_ili age_0_4 age_25_49 age_25_64 age_5_24 age_50_64 age_65 ## ## 1 National 1997 40 1.10148 1.21686 179 157 205 29 ## 2 National 1997 41 1.20007 1.28064 199 151 242 23 ## 3 National 1997 42 1.37876 1.23906 228 153 266 34 ## 4 National 1997 43 1.19920 1.14473 188 193 236 36 ## 5 National 1997 44 1.65618 1.26112 217 162 280 41 ## 6 National 1997 45 1.41326 1.28275 178 148 281 48 ## 7 National 1997 46 1.98680 1.44579 294 240 328 70 ## 8 National 1997 47 2.44749 1.64796 288 293 456 63 ## 9 National 1997 48 1.73901 1.67517 268 206 343 69 ## 10 National 1997 49 1.93919 1.61739 299 282 415 102 ## # ... with 1,038 more rows, and 3 more variables: ilitotal , num_of_providers , total_patients ``` r ilinet("hhs") ``` ## # A tibble: 10,480 x 15 ## region_type region year week weighted_ili unweighted_ili age_0_4 age_25_49 age_25_64 age_5_24 age_50_64 age_65 ## ## 1 HHS Regions Region 1 1997 40 0.498535 0.623848 15 NA 7 22 NA 0 ## 2 HHS Regions Region 2 1997 40 0.374963 0.384615 0 NA 3 0 NA 0 ## 3 HHS Regions Region 3 1997 40 1.354280 1.341720 6 NA 7 15 NA 4 ## 4 HHS Regions Region 4 1997 40 0.400338 0.450010 12 NA 23 11 NA 0 ## 5 HHS Regions Region 5 1997 40 1.229260 0.901266 31 NA 24 30 NA 4 ## 6 HHS Regions Region 6 1997 40 1.018980 0.747384 2 NA 1 2 NA 0 ## 7 HHS Regions Region 7 1997 40 0.871791 1.152860 0 NA 4 18 NA 5 ## 8 HHS Regions Region 8 1997 40 0.516017 0.422654 2 NA 0 3 NA 0 ## 9 HHS Regions Region 9 1997 40 1.807610 2.258780 80 NA 76 74 NA 13 ## 10 HHS Regions Region 10 1997 40 4.743520 4.825400 31 NA 12 30 NA 3 ## # ... with 10,470 more rows, and 3 more variables: ilitotal , num_of_providers , total_patients ``` r ilinet("census") ``` ## # A tibble: 9,432 x 15 ## region_type region year week weighted_ili unweighted_ili age_0_4 age_25_49 age_25_64 age_5_24 ## ## 1 Census Regions New England 1997 40 0.4985350 0.6238480 15 7 22 ## 2 Census Regions Mid-Atlantic 1997 40 0.8441440 1.3213800 4 8 12 ## 3 Census Regions East North Central 1997 40 0.7924860 0.8187380 28 20 28 ## 4 Census Regions West North Central 1997 40 1.7640500 1.2793900 3 8 20 ## 5 Census Regions South Atlantic 1997 40 0.5026620 0.7233800 14 22 14 ## 6 Census Regions East South Central 1997 40 0.0542283 0.0688705 0 3 0 ## 7 Census Regions West South Central 1997 40 1.0189800 0.7473840 2 1 2 ## 8 Census Regions Mountain 1997 40 2.2587800 2.2763300 87 71 71 ## 9 Census Regions Pacific 1997 40 2.0488300 3.2349400 26 17 36 ## 10 Census Regions New England 1997 41 0.6426690 0.8158010 14 14 29 ## # ... with 9,422 more rows, and 5 more variables: age_50_64 , age_65 , ilitotal , ## # num_of_providers , total_patients ``` r ilinet("state") ``` ## # A tibble: 19,718 x 15 ## region_type region year week weighted_ili unweighted_ili age_0_4 age_25_49 age_25_64 age_5_24 ## ## 1 States Alabama 2010 40 2.13477 ## 2 States Alaska 2010 40 0.875146 ## 3 States Arizona 2010 40 0.674721 ## 4 States Arkansas 2010 40 0.696056 ## 5 States California 2010 40 1.95412 ## 6 States Colorado 2010 40 0.660684 ## 7 States Connecticut 2010 40 0.0783085 ## 8 States Delaware 2010 40 0.100125 ## 9 States District of Columbia 2010 40 2.80877 ## 10 States Florida 2010 40 ## # ... with 19,708 more rows, and 5 more variables: age_50_64 , age_65 , ilitotal , ## # num_of_providers , total_patients ### Retrieve weekly state-level ILI indicators per-state for a given season ``` r ili_weekly_activity_indicators(2017) ``` ## # A tibble: 216 x 9 ## statename ili_activity_label ili_activity_group statefips stateabbr weekend weeknumber year seasonid ## ## 1 Alabama Level 2 Minimal 01 AL 2017-10-07 40 2017 57 ## 2 Alabama Level 2 Minimal 01 AL 2017-10-14 41 2017 57 ## 3 Alabama Level 2 Minimal 01 AL 2017-10-21 42 2017 57 ## 4 Alabama Level 3 Minimal 01 AL 2017-10-28 43 2017 57 ## 5 Alaska Level 1 Minimal 02 AK 2017-10-07 40 2017 57 ## 6 Alaska Level 2 Minimal 02 AK 2017-10-14 41 2017 57 ## 7 Alaska Level 4 Low 02 AK 2017-10-21 42 2017 57 ## 8 Alaska Level 3 Minimal 02 AK 2017-10-28 43 2017 57 ## 9 Arizona Level 2 Minimal 04 AZ 2017-10-07 40 2017 57 ## 10 Arizona Level 3 Minimal 04 AZ 2017-10-14 41 2017 57 ## # ... with 206 more rows ``` r ili_weekly_activity_indicators(2015) ``` ## # A tibble: 2,807 x 9 ## statename ili_activity_label ili_activity_group statefips stateabbr weekend weeknumber year seasonid ## ## 1 Alabama Level 1 Minimal 01 AL 2015-10-10 40 2015 55 ## 2 Alabama Level 1 Minimal 01 AL 2015-10-17 41 2015 55 ## 3 Alabama Level 1 Minimal 01 AL 2015-10-24 42 2015 55 ## 4 Alabama Level 1 Minimal 01 AL 2015-10-31 43 2015 55 ## 5 Alabama Level 1 Minimal 01 AL 2015-11-07 44 2015 55 ## 6 Alabama Level 1 Minimal 01 AL 2015-11-14 45 2015 55 ## 7 Alabama Level 1 Minimal 01 AL 2015-11-21 46 2015 55 ## 8 Alabama Level 3 Minimal 01 AL 2015-11-28 47 2015 55 ## 9 Alabama Level 1 Minimal 01 AL 2015-12-05 48 2015 55 ## 10 Alabama Level 1 Minimal 01 AL 2015-12-12 49 2015 55 ## # ... with 2,797 more rows ### Pneumonia and Influenza Mortality Surveillance ``` r pi_mortality("national") ``` ## # A tibble: 419 x 19 ## seasonid baseline threshold percent_pni percent_complete number_influenza number_pneumonia all_deaths total_pni ## ## 1 57 5.8 6.1 0.054 0.763 10 1962 36283 1972 ## 2 57 5.8 6.2 0.056 0.675 10 1795 32107 1805 ## 3 56 5.9 6.3 0.059 1.000 18 3022 51404 3040 ## 4 56 6.0 6.3 0.061 1.000 11 3193 52130 3204 ## 5 56 6.1 6.4 0.062 1.000 7 3178 51443 3185 ## 6 56 6.2 6.5 0.061 1.000 17 3129 51865 3146 ## 7 56 6.3 6.6 0.060 1.000 16 3099 51753 3115 ## 8 56 6.4 6.7 0.061 1.000 19 3208 52541 3227 ## 9 56 6.5 6.8 0.060 1.000 7 3192 53460 3199 ## 10 56 6.6 6.9 0.062 1.000 22 3257 53163 3279 ## # ... with 409 more rows, and 10 more variables: weeknumber , geo_description , age_label , ## # weekend , weekstart , year , yearweek , coverage_area , region_name , callout ``` r pi_mortality("state") ``` ## # A tibble: 21,788 x 19 ## seasonid baseline threshold percent_pni percent_complete number_influenza number_pneumonia all_deaths total_pni ## ## 1 57 NA NA 0.065 0.836 0 50 772 50 ## 2 57 NA NA 0.064 0.767 0 45 708 45 ## 3 57 NA NA 0.063 0.666 1 2 48 3 ## 4 57 NA NA 0.105 0.527 0 4 38 4 ## 5 57 NA NA 0.053 0.412 0 20 374 20 ## 6 57 NA NA 0.059 0.393 0 21 356 21 ## 7 57 NA NA 0.060 0.751 0 25 420 25 ## 8 57 NA NA 0.050 0.604 0 17 338 17 ## 9 57 NA NA 0.065 0.774 1 228 3510 229 ## 10 57 NA NA 0.059 0.758 2 201 3438 203 ## # ... with 21,778 more rows, and 10 more variables: weeknumber , geo_description , age_label , ## # weekend , weekstart , year , yearweek , coverage_area , region_name , callout ``` r pi_mortality("region") ``` ## # A tibble: 4,190 x 19 ## seasonid baseline threshold percent_pni percent_complete number_influenza number_pneumonia all_deaths total_pni ## ## 1 57 6.0 6.7 0.051 0.735 0 85 1683 85 ## 2 57 6.1 6.8 0.060 0.701 0 96 1605 96 ## 3 57 6.0 6.5 0.061 0.608 1 154 2524 155 ## 4 57 6.0 6.6 0.063 0.602 1 157 2497 158 ## 5 57 5.3 5.8 0.045 0.511 1 115 2575 116 ## 6 57 5.4 5.9 0.045 0.440 1 98 2215 99 ## 7 57 5.6 6.0 0.051 0.744 3 394 7753 397 ## 8 57 5.7 6.1 0.052 0.651 1 354 6778 355 ## 9 57 5.5 5.9 0.052 0.914 1 403 7701 404 ## 10 57 5.6 6.0 0.054 0.799 4 358 6733 362 ## # ... with 4,180 more rows, and 10 more variables: weeknumber , geo_description , age_label , ## # weekend , weekstart , year , yearweek , coverage_area , region_name , callout ### Retrieve metadat about U.S. State CDC Provider Data ### Retrieve a list of valid sub-regions for each surveillance area. ``` r state_data_providers() ``` ## # A tibble: 59 x 5 ## statename statehealthdeptname ## * ## 1 Alabama Alabama Department of Public Health ## 2 Alaska State of Alaska Health and Social Services ## 3 Arizona Arizona Department of Health Services ## 4 Arkansas Arkansas Department of Health ## 5 California California Department of Public Health ## 6 Colorado Colorado Department of Public Health and Environment ## 7 Connecticut Connecticut Department of Public Health ## 8 Delaware Delaware Health and Social Services ## 9 District of Columbia District of Columbia Department of Health ## 10 Florida Florida Department of Health ## # ... with 49 more rows, and 3 more variables: url , statewebsitename , statefluphonenum ### Retrieve WHO/NREVSS Surveillance Data ``` r who_nrevss("national") ``` ## $combined_prior_to_2015_16 ## # A tibble: 940 x 13 ## region_type region year week total_specimens percent_positive a_2009_h1n1 a_h1 a_h3 a_subtyping_not_performed ## ## 1 National 1997 40 1291 0.000000 0 0 0 0 ## 2 National 1997 41 1513 0.727032 0 0 0 11 ## 3 National 1997 42 1552 1.095360 0 0 3 13 ## 4 National 1997 43 1669 0.419413 0 0 0 7 ## 5 National 1997 44 1897 0.527148 0 0 9 1 ## 6 National 1997 45 2106 0.284900 0 0 0 6 ## 7 National 1997 46 2204 0.362976 0 0 3 4 ## 8 National 1997 47 2533 0.908014 0 0 5 17 ## 9 National 1997 48 2242 1.650310 0 0 14 22 ## 10 National 1997 49 2607 1.534330 0 0 11 28 ## # ... with 930 more rows, and 3 more variables: a_unable_to_subtype , b , h3n2v ## ## $public_health_labs ## # A tibble: 108 x 12 ## region_type region year week total_specimens a_2009_h1n1 a_h3 a_subtyping_not_performed b bvic byam h3n2v ## ## 1 National 2015 40 1139 4 65 2 10 0 1 0 ## 2 National 2015 41 1152 5 41 2 7 3 0 0 ## 3 National 2015 42 1198 10 50 1 8 3 2 0 ## 4 National 2015 43 1244 9 31 4 9 1 4 0 ## 5 National 2015 44 1465 4 23 4 9 1 4 0 ## 6 National 2015 45 1393 11 34 1 10 4 2 0 ## 7 National 2015 46 1458 17 42 1 4 0 4 0 ## 8 National 2015 47 1157 17 24 0 4 3 9 0 ## 9 National 2015 48 1550 27 36 3 9 3 12 0 ## 10 National 2015 49 1518 38 37 3 11 2 11 0 ## # ... with 98 more rows ## ## $clinical_labs ## # A tibble: 108 x 10 ## region_type region year week total_specimens total_a total_b percent_positive percent_a percent_b ## ## 1 National 2015 40 12029 84 43 1.05578 0.698312 0.357469 ## 2 National 2015 41 13111 116 54 1.29662 0.884753 0.411868 ## 3 National 2015 42 13441 97 52 1.10855 0.721672 0.386876 ## 4 National 2015 43 13537 98 52 1.10807 0.723942 0.384132 ## 5 National 2015 44 14687 97 68 1.12344 0.660448 0.462994 ## 6 National 2015 45 15048 122 86 1.38224 0.810739 0.571505 ## 7 National 2015 46 15250 84 98 1.19344 0.550820 0.642623 ## 8 National 2015 47 15234 119 92 1.38506 0.781147 0.603912 ## 9 National 2015 48 16201 145 81 1.39498 0.895006 0.499969 ## 10 National 2015 49 16673 140 106 1.47544 0.839681 0.635758 ## # ... with 98 more rows ``` r who_nrevss("hhs") ``` ## $combined_prior_to_2015_16 ## # A tibble: 9,400 x 13 ## region_type region year week total_specimens percent_positive a_2009_h1n1 a_h1 a_h3 a_subtyping_not_performed ## ## 1 HHS Regions Region 1 1997 40 51 0 0 0 0 0 ## 2 HHS Regions Region 2 1997 40 152 0 0 0 0 0 ## 3 HHS Regions Region 3 1997 40 143 0 0 0 0 0 ## 4 HHS Regions Region 4 1997 40 98 0 0 0 0 0 ## 5 HHS Regions Region 5 1997 40 147 0 0 0 0 0 ## 6 HHS Regions Region 6 1997 40 343 0 0 0 0 0 ## 7 HHS Regions Region 7 1997 40 133 0 0 0 0 0 ## 8 HHS Regions Region 8 1997 40 78 0 0 0 0 0 ## 9 HHS Regions Region 9 1997 40 98 0 0 0 0 0 ## 10 HHS Regions Region 10 1997 40 48 0 0 0 0 0 ## # ... with 9,390 more rows, and 3 more variables: a_unable_to_subtype , b , h3n2v ## ## $public_health_labs ## # A tibble: 1,080 x 12 ## region_type region year week total_specimens a_2009_h1n1 a_h3 a_subtyping_not_performed b bvic byam ## ## 1 HHS Regions Region 1 2015 XX 39 0 5 0 0 0 0 ## 2 HHS Regions Region 2 2015 XX 56 1 4 0 1 0 0 ## 3 HHS Regions Region 3 2015 XX 132 1 3 0 0 0 0 ## 4 HHS Regions Region 4 2015 XX 83 0 5 0 1 0 0 ## 5 HHS Regions Region 5 2015 XX 218 2 7 0 0 0 1 ## 6 HHS Regions Region 6 2015 XX 97 0 2 0 0 0 0 ## 7 HHS Regions Region 7 2015 XX 36 0 2 0 0 0 0 ## 8 HHS Regions Region 8 2015 XX 71 0 2 0 0 0 0 ## 9 HHS Regions Region 9 2015 XX 273 0 22 2 8 0 0 ## 10 HHS Regions Region 10 2015 XX 134 0 13 0 0 0 0 ## # ... with 1,070 more rows, and 1 more variables: h3n2v ## ## $clinical_labs ## # A tibble: 1,080 x 10 ## region_type region year week total_specimens total_a total_b percent_positive percent_a percent_b ## ## 1 HHS Regions Region 1 2015 40 693 2 3 0.721501 0.288600 0.432900 ## 2 HHS Regions Region 2 2015 40 1220 5 0 0.409836 0.409836 0.000000 ## 3 HHS Regions Region 3 2015 40 896 0 1 0.111607 0.000000 0.111607 ## 4 HHS Regions Region 4 2015 40 2486 24 16 1.609010 0.965406 0.643604 ## 5 HHS Regions Region 5 2015 40 2138 14 3 0.795136 0.654818 0.140318 ## 6 HHS Regions Region 6 2015 40 1774 8 16 1.352870 0.450958 0.901917 ## 7 HHS Regions Region 7 2015 40 621 2 1 0.483092 0.322061 0.161031 ## 8 HHS Regions Region 8 2015 40 824 1 1 0.242718 0.121359 0.121359 ## 9 HHS Regions Region 9 2015 40 980 25 2 2.755100 2.551020 0.204082 ## 10 HHS Regions Region 10 2015 40 397 3 0 0.755668 0.755668 0.000000 ## # ... with 1,070 more rows ``` r who_nrevss("census") ``` ## $combined_prior_to_2015_16 ## # A tibble: 8,460 x 13 ## region_type region year week total_specimens percent_positive a_2009_h1n1 a_h1 a_h3 ## ## 1 Census Regions New England 1997 40 51 0 0 0 0 ## 2 Census Regions Mid-Atlantic 1997 40 155 0 0 0 0 ## 3 Census Regions East North Central 1997 40 127 0 0 0 0 ## 4 Census Regions West North Central 1997 40 183 0 0 0 0 ## 5 Census Regions South Atlantic 1997 40 204 0 0 0 0 ## 6 Census Regions East South Central 1997 40 34 0 0 0 0 ## 7 Census Regions West South Central 1997 40 339 0 0 0 0 ## 8 Census Regions Mountain 1997 40 85 0 0 0 0 ## 9 Census Regions Pacific 1997 40 113 0 0 0 0 ## 10 Census Regions New England 1997 41 54 0 0 0 0 ## # ... with 8,450 more rows, and 4 more variables: a_subtyping_not_performed , a_unable_to_subtype , b , ## # h3n2v ## ## $public_health_labs ## # A tibble: 972 x 12 ## region_type region year week total_specimens a_2009_h1n1 a_h3 a_subtyping_not_performed b ## ## 1 Census Regions New England 2015 XX 39 0 5 0 0 ## 2 Census Regions Mid-Atlantic 2015 XX 63 1 5 0 1 ## 3 Census Regions East North Central 2015 XX 91 2 5 0 0 ## 4 Census Regions West North Central 2015 XX 169 0 4 0 0 ## 5 Census Regions South Atlantic 2015 XX 187 1 7 0 0 ## 6 Census Regions East South Central 2015 XX 21 0 0 0 1 ## 7 Census Regions West South Central 2015 XX 72 0 2 0 0 ## 8 Census Regions Mountain 2015 XX 111 0 6 0 0 ## 9 Census Regions Pacific 2015 XX 386 0 31 2 8 ## 10 Census Regions New England 2015 XX 39 2 3 0 0 ## # ... with 962 more rows, and 3 more variables: bvic , byam , h3n2v ## ## $clinical_labs ## # A tibble: 972 x 10 ## region_type region year week total_specimens total_a total_b percent_positive percent_a percent_b ## ## 1 Census Regions New England 2015 40 693 2 3 0.721501 0.288600 0.4329000 ## 2 Census Regions Mid-Atlantic 2015 40 1584 5 1 0.378788 0.315657 0.0631313 ## 3 Census Regions East North Central 2015 40 1918 13 3 0.834202 0.677789 0.1564130 ## 4 Census Regions West North Central 2015 40 978 3 1 0.408998 0.306748 0.1022490 ## 5 Census Regions South Atlantic 2015 40 2403 20 12 1.331670 0.832293 0.4993760 ## 6 Census Regions East South Central 2015 40 615 4 4 1.300810 0.650407 0.6504070 ## 7 Census Regions West South Central 2015 40 1592 8 16 1.507540 0.502513 1.0050300 ## 8 Census Regions Mountain 2015 40 943 1 1 0.212089 0.106045 0.1060450 ## 9 Census Regions Pacific 2015 40 1303 28 2 2.302380 2.148890 0.1534920 ## 10 Census Regions New England 2015 41 752 11 4 1.994680 1.462770 0.5319150 ## # ... with 962 more rows ``` r who_nrevss("state") ``` ## $combined_prior_to_2015_16 ## # A tibble: 14,094 x 13 ## region_type region year week total_specimens percent_positive a_2009_h1n1 a_h1 a_h3 ## ## 1 States Alabama 2010 40 54 0 0 0 0 ## 2 States Alaska 2010 40 40 0 0 0 0 ## 3 States Arizona 2010 40 40 2.5 0 0 1 ## 4 States Arkansas 2010 40 15 0 0 0 0 ## 5 States California 2010 40 183 3.28 2 0 3 ## 6 States Colorado 2010 40 126 0.79 0 0 1 ## 7 States Connecticut 2010 40 54 0 0 0 0 ## 8 States Delaware 2010 40 75 4 0 0 3 ## 9 States District of Columbia 2010 40 14 0 0 0 0 ## 10 States Florida 2010 40 ## # ... with 14,084 more rows, and 4 more variables: a_subtyping_not_performed , a_unable_to_subtype , b , ## # h3n2v ## ## $public_health_labs ## # A tibble: 162 x 11 ## region_type region season_description total_specimens a_2009_h1n1 a_h3 a_subtyping_not_performed ## ## 1 States Alabama Season 2015-16 256 59 16 1 ## 2 States Alaska Season 2015-16 4691 607 98 0 ## 3 States Arizona Season 2015-16 2110 762 580 0 ## 4 States Arkansas Season 2015-16 128 20 8 0 ## 5 States California Season 2015-16 12241 1394 825 28 ## 6 States Colorado Season 2015-16 1625 912 243 3 ## 7 States Connecticut Season 2015-16 1581 662 52 0 ## 8 States Delaware Season 2015-16 2754 414 20 12 ## 9 States District of Columbia Season 2015-16 172 68 3 0 ## 10 States Florida Season 2015-16 ## # ... with 152 more rows, and 4 more variables: b , bvic , byam , h3n2v ## ## $clinical_labs ## # A tibble: 5,832 x 10 ## region_type region year week total_specimens total_a total_b percent_positive percent_a percent_b ## ## 1 States Alabama 2015 40 167 2 3 2.99 1.2 1.8 ## 2 States Alaska 2015 40 ## 3 States Arizona 2015 40 55 0 0 0 0 0 ## 4 States Arkansas 2015 40 26 0 1 3.85 0 3.85 ## 5 States California 2015 40 679 2 0 0.29 0.29 0 ## 6 States Colorado 2015 40 255 0 1 0.39 0 0.39 ## 7 States Connecticut 2015 40 304 1 0 0.33 0.33 0 ## 8 States Delaware 2015 40 22 0 0 0 0 0 ## 9 States District of Columbia 2015 40 ## 10 States Florida 2015 40 ## # ... with 5,822 more rows Code of Conduct --------------- Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). 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