[![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…eventually. Older functions have been deprecated with warnings and will be removed at some point. 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: - `age_group_distribution`: Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories - `cdc_basemap`: Retrieve CDC U.S. Basemaps - `geographic_spread`: State and Territorial Epidemiologists Reports of Geographic Spread of Influenza - `get_weekly_flu_report`: Retrieves (high-level) weekly (XML) influenza surveillance report from the CDC - `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 metadata 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 MMWR ID Utilities: - `mmwrid_map`: MMWR ID to Calendar Mappings - `mmwr_week`: Convert a Date to an MMWR day+week+year - `mmwr_weekday`: Convert a Date to an MMWR weekday - `mmwr_week_to_date`: Convert an MMWR year+week or year+week+day to a Date object Deprecated functions: - `get_flu_data`: Retrieves state, regional or national influenza statistics from the CDC (deprecated) - `get_hosp_data`: Retrieves influenza hospitalization statistics from the CDC (deprecated) - `get_mortality_surveillance_data`: Mortality Surveillance Data from the National Center for Health Statistics (deprecated) - `get_state_data`: Retrieves state/territory-level influenza statistics from the CDC (deprecated) 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) - `mmwrid_map`: MMWR ID to Calendar Mappings (it is exported & available, no need to use `data()`) ## Installation ``` r devtools::install_github("hrbrmstr/cdcfluview") ``` ## Usage ``` r library(cdcfluview) library(hrbrthemes) library(tidyverse) # current verison packageVersion("cdcfluview") ``` ## [1] '0.7.0' ### Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories ``` r glimpse(age_group_distribution(years=2015)) ``` ## Observations: 1,872 ## Variables: 16 ## $ sea_label "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "... ## $ 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, 0-4 yr, 0-4 yr, ... ## $ vir_label A (Subtyping not Performed), A (Subtyping not Performed), A (Subtyping not Performed), A... ## $ count 0, 1, 0, 1, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 2, 3, 2, 2, 3, 3, 3, 0, 0, 2, 0, 1, 1, 0,... ## $ mmwrid 2806, 2807, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2817, 2818, 2819, 2820,... ## $ seasonid 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 5... ## $ publishyearweekid 2914, 2914, 2914, 2914, 2914, 2914, 2914, 2914, 2914, 2914, 2914, 2914, 2914, 2914, 2914,... ## $ sea_description "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16",... ## $ sea_startweek 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806,... ## $ sea_endweek 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857,... ## $ 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,... ## $ wk_start 2015-10-04, 2015-10-11, 2015-10-18, 2015-10-25, 2015-11-01, 2015-11-08, 2015-11-15, 2015... ## $ wk_end 2015-10-10, 2015-10-17, 2015-10-24, 2015-10-31, 2015-11-07, 2015-11-14, 2015-11-21, 2015... ## $ year_wk_num 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... ### Retrieve CDC U.S. Coverage Map ``` r plot(cdc_basemap("national")) ``` ![](README.gfm-ascii_identifiers_files/figure-gfm/unnamed-chunk-5-1.png) ``` r plot(cdc_basemap("hhs")) ``` ![](README.gfm-ascii_identifiers_files/figure-gfm/unnamed-chunk-5-2.png) ``` r plot(cdc_basemap("census")) ``` ![](README.gfm-ascii_identifiers_files/figure-gfm/unnamed-chunk-5-3.png) ``` r plot(cdc_basemap("states")) ``` ![](README.gfm-ascii_identifiers_files/figure-gfm/unnamed-chunk-5-4.png) ``` r plot(cdc_basemap("spread")) ``` ![](README.gfm-ascii_identifiers_files/figure-gfm/unnamed-chunk-5-5.png) ``` r plot(cdc_basemap("surv")) ``` ![](README.gfm-ascii_identifiers_files/figure-gfm/unnamed-chunk-5-6.png) ### State and Territorial Epidemiologists Reports of Geographic Spread of Influenza ``` r glimpse(geographic_spread()) ``` ## Observations: 25,848 ## 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(fs_nat <- hospitalizations("flusurv")) ``` ## Observations: 1,476 ## Variables: 14 ## $ 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",... ## $ year 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009,... ## $ season 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4... ## $ wk_start 2009-08-30, 2009-09-06, 2009-09-13, 2009-09-20, 2009-09-27, 2009-10-04, 2009-10-11, 2009... ## $ wk_end 2009-09-05, 2009-09-12, 2009-09-19, 2009-09-26, 2009-10-03, 2009-10-10, 2009-10-17, 2009... ## $ year_wk_num 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 1, 2, 3, 4, 5, 6,... ## $ rate 0.5, 2.5, 4.6, 6.7, 10.9, 18.1, 28.3, 39.1, 47.3, 53.3, 57.5, 60.1, 61.6, 62.9, 64.1, 65.... ## $ weeklyrate 0.5, 2.0, 2.0, 2.1, 4.3, 7.2, 10.2, 10.8, 8.2, 6.0, 4.2, 2.6, 1.5, 1.3, 1.3, 1.0, 1.2, 1.... ## $ age 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,... ## $ 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, 0-4 yr, 0-4 yr, ... ## $ sea_label "2009-10", "2009-10", "2009-10", "2009-10", "2009-10", "2009-10", "2009-10", "2009-10", "... ## $ sea_description "Season 2009-10", "Season 2009-10", "Season 2009-10", "Season 2009-10", "Season 2009-10",... ## $ mmwrid 2488, 2489, 2490, 2491, 2492, 2493, 2494, 2495, 2496, 2497, 2498, 2499, 2500, 2501, 2502,... ``` r ggplot(fs_nat, aes(wk_end, rate)) + geom_line(aes(color=age_label, group=age_label)) + facet_wrap(~sea_description, scales="free_x") + scale_color_ipsum(name=NULL) + labs(x=NULL, y="Rates per 100,000 population", title="FluSurv-NET :: Entire Network :: All Seasons :: Cumulative Rate") + theme_ipsum_rc() ``` ![](README.gfm-ascii_identifiers_files/figure-gfm/unnamed-chunk-7-1.png) ``` r glimpse(hospitalizations("eip", years=2015)) ``` ## Observations: 180 ## Variables: 14 ## $ 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",... ## $ year 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2016, 2016,... ## $ season 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 5... ## $ wk_start 2015-10-04, 2015-10-11, 2015-10-18, 2015-10-25, 2015-11-01, 2015-11-08, 2015-11-15, 2015... ## $ wk_end 2015-10-10, 2015-10-17, 2015-10-24, 2015-10-31, 2015-11-07, 2015-11-14, 2015-11-21, 2015... ## $ year_wk_num 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 0.1, 0.3, 0.4, 0.5, 0.8, 0.8, 1.1, 1.4, 1.6, 1.7, 1.8, 2.1, 2.4, 2.9, 3.2, 3.5, 4.2, 5.3,... ## $ weeklyrate 0.1, 0.3, 0.1, 0.1, 0.3, 0.0, 0.3, 0.3, 0.2, 0.1, 0.1, 0.3, 0.3, 0.5, 0.3, 0.3, 0.6, 1.2,... ## $ age 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,... ## $ 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, 0-4 yr, 0-4 yr, ... ## $ sea_label "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "... ## $ sea_description "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16",... ## $ mmwrid 2806, 2807, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2817, 2818, 2819, 2820,... ``` r glimpse(hospitalizations("eip", "Colorado", years=2015)) ``` ## Observations: 180 ## Variables: 14 ## $ surveillance_area "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP"... ## $ region "Colorado", "Colorado", "Colorado", "Colorado", "Colorado", "Colorado", "Colorado", "Colo... ## $ year 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2016, 2016,... ## $ season 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 5... ## $ wk_start 2015-10-04, 2015-10-11, 2015-10-18, 2015-10-25, 2015-11-01, 2015-11-08, 2015-11-15, 2015... ## $ wk_end 2015-10-10, 2015-10-17, 2015-10-24, 2015-10-31, 2015-11-07, 2015-11-14, 2015-11-21, 2015... ## $ year_wk_num 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, 0.6, 0.6, 0.6, 0.6, 1.2, 1.7, 1.7, 1.7, 1.7, 1.7, 2.9, 3.5, 3.5, 3.5, 4.1, 6.4,... ## $ weeklyrate 0.0, 0.0, 0.6, 0.0, 0.0, 0.0, 0.6, 0.6, 0.0, 0.0, 0.0, 0.0, 1.2, 0.6, 0.0, 0.0, 0.6, 2.3,... ## $ age 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,... ## $ 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, 0-4 yr, 0-4 yr, ... ## $ sea_label "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "... ## $ sea_description "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16",... ## $ mmwrid 2806, 2807, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2817, 2818, 2819, 2820,... ``` r glimpse(hospitalizations("ihsp", years=2015)) ``` ## Observations: 180 ## Variables: 14 ## $ surveillance_area "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "... ## $ region "Entire Network", "Entire Network", "Entire Network", "Entire Network", "Entire Network",... ## $ year 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2016, 2016,... ## $ season 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 5... ## $ wk_start 2015-10-04, 2015-10-11, 2015-10-18, 2015-10-25, 2015-11-01, 2015-11-08, 2015-11-15, 2015... ## $ wk_end 2015-10-10, 2015-10-17, 2015-10-24, 2015-10-31, 2015-11-07, 2015-11-14, 2015-11-21, 2015... ## $ year_wk_num 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, 0.4, 0.4, 0.4, 1.1, 1.1, 1.1, 1.1, 1.5, 1.8, 2.2, 2.2, 2.5, 2.5, 2.5, 2.9, 4.0,... ## $ weeklyrate 0.0, 0.0, 0.4, 0.0, 0.0, 0.7, 0.0, 0.0, 0.0, 0.4, 0.4, 0.4, 0.0, 0.4, 0.0, 0.0, 0.4, 1.1,... ## $ age 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,... ## $ 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, 0-4 yr, 0-4 yr, ... ## $ sea_label "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "... ## $ sea_description "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16",... ## $ mmwrid 2806, 2807, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2817, 2818, 2819, 2820,... ``` r glimpse(hospitalizations("ihsp", "Oklahoma", years=2015)) ``` ## Observations: 180 ## Variables: 14 ## $ surveillance_area "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "... ## $ region "Oklahoma", "Oklahoma", "Oklahoma", "Oklahoma", "Oklahoma", "Oklahoma", "Oklahoma", "Okla... ## $ year 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2011, 2011,... ## $ season 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5... ## $ wk_start 2010-10-03, 2010-10-10, 2010-10-17, 2010-10-24, 2010-10-31, 2010-11-07, 2010-11-14, 2010... ## $ wk_end 2010-10-09, 2010-10-16, 2010-10-23, 2010-10-30, 2010-11-06, 2010-11-13, 2010-11-20, 2010... ## $ year_wk_num 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, 1.3, 1.3, 1.3, 1.3, 1.3, 1.3, 1.3, 2.6, 2.6, 6.6, 15.9, 18.5, 35.7, 54.2, 83.3,... ## $ weeklyrate 0.0, 0.0, 1.3, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.3, 0.0, 4.0, 9.3, 2.6, 17.2, 18.5, 29.1, 2... ## $ age 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,... ## $ 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, 0-4 yr, 0-4 yr, ... ## $ 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",... ## $ mmwrid 2545, 2546, 2547, 2548, 2549, 2550, 2551, 2552, 2553, 2554, 2555, 2556, 2557, 2558, 2559,... ### Retrieve ILINet Surveillance Data ``` r walk(c("national", "hhs", "census", "state"), ~{ ili_df <- ilinet(region = .x) print(glimpse(ili_df)) ggplot(ili_df, aes(week_start, unweighted_ili, group=region, color=region)) + geom_line() + viridis::scale_color_viridis(discrete=TRUE) + labs(x=NULL, y="Unweighted ILI", title=ili_df$region_type[1]) + theme_ipsum_rc(grid="XY") + theme(legend.position = "none") -> gg print(gg) }) ``` ## Observations: 1,049 ## Variables: 16 ## $ region_type "National", "National", "National", "National", "National", "National", "National", "Natio... ## $ region "National", "National", "National", "National", "National", "National", "National", "Natio... ## $ year 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1998, ... ## $ week 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,... ## $ weighted_ili 1.101480, 1.200070, 1.378760, 1.199200, 1.656180, 1.413260, 1.986800, 2.447490, 1.739010, ... ## $ unweighted_ili 1.216860, 1.280640, 1.239060, 1.144730, 1.261120, 1.282750, 1.445790, 1.647960, 1.675170, ... ## $ age_0_4 179, 199, 228, 188, 217, 178, 294, 288, 268, 299, 346, 348, 510, 579, 639, 690, 856, 824, ... ## $ age_25_49 NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... ## $ age_25_64 157, 151, 153, 193, 162, 148, 240, 293, 206, 282, 268, 235, 404, 584, 759, 654, 679, 817, ... ## $ age_5_24 205, 242, 266, 236, 280, 281, 328, 456, 343, 415, 388, 362, 492, 576, 810, 1121, 1440, 160... ## $ age_50_64 NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... ## $ age_65 29, 23, 34, 36, 41, 48, 70, 63, 69, 102, 81, 59, 113, 207, 207, 148, 151, 196, 233, 146, 1... ## $ ilitotal 570, 615, 681, 653, 700, 655, 932, 1100, 886, 1098, 1083, 1004, 1519, 1946, 2415, 2613, 31... ## $ num_of_providers 192, 191, 219, 213, 213, 195, 248, 256, 252, 253, 242, 190, 251, 250, 254, 255, 245, 245, ... ## $ total_patients 46842, 48023, 54961, 57044, 55506, 51062, 64463, 66749, 52890, 67887, 61314, 47719, 48429,... ## $ week_start 1997-10-06, 1997-10-13, 1997-10-20, 1997-10-27, 1997-11-03, 1997-11-10, 1997-11-17, 1997-... ## # A tibble: 1,049 x 16 ## 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 National 1997 40 1.10148 1.21686 179 NA 157 205 NA 29 ## 2 National National 1997 41 1.20007 1.28064 199 NA 151 242 NA 23 ## 3 National National 1997 42 1.37876 1.23906 228 NA 153 266 NA 34 ## 4 National National 1997 43 1.19920 1.14473 188 NA 193 236 NA 36 ## 5 National National 1997 44 1.65618 1.26112 217 NA 162 280 NA 41 ## 6 National National 1997 45 1.41326 1.28275 178 NA 148 281 NA 48 ## 7 National National 1997 46 1.98680 1.44579 294 NA 240 328 NA 70 ## 8 National National 1997 47 2.44749 1.64796 288 NA 293 456 NA 63 ## 9 National National 1997 48 1.73901 1.67517 268 NA 206 343 NA 69 ## 10 National National 1997 49 1.93919 1.61739 299 NA 282 415 NA 102 ## # ... with 1,039 more rows, and 4 more variables: ilitotal , num_of_providers , total_patients , ## # week_start ![](README.gfm-ascii_identifiers_files/figure-gfm/unnamed-chunk-8-1.png) ## Observations: 10,490 ## Variables: 16 ## $ region_type "HHS Regions", "HHS Regions", "HHS Regions", "HHS Regions", "HHS Regions", "HHS Regions", ... ## $ region Region 1, Region 2, Region 3, Region 4, Region 5, Region 6, Region 7, Region 8, Region 9,... ## $ year 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, ... ## $ week 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 42, 42, 42... ## $ weighted_ili 0.498535, 0.374963, 1.354280, 0.400338, 1.229260, 1.018980, 0.871791, 0.516017, 1.807610, ... ## $ unweighted_ili 0.623848, 0.384615, 1.341720, 0.450010, 0.901266, 0.747384, 1.152860, 0.422654, 2.258780, ... ## $ age_0_4 15, 0, 6, 12, 31, 2, 0, 2, 80, 31, 14, 0, 4, 21, 36, 2, 0, 0, 103, 19, 35, 0, 3, 19, 66, 2... ## $ age_25_49 NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... ## $ age_25_64 7, 3, 7, 23, 24, 1, 4, 0, 76, 12, 14, 2, 19, 7, 23, 2, 0, 1, 76, 7, 15, 0, 17, 15, 29, 2, ... ## $ age_5_24 22, 0, 15, 11, 30, 2, 18, 3, 74, 30, 29, 0, 16, 14, 41, 2, 13, 8, 84, 35, 35, 0, 24, 18, 7... ## $ age_50_64 NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... ## $ age_65 0, 0, 4, 0, 4, 0, 5, 0, 13, 3, 0, 0, 3, 2, 4, 0, 2, 0, 11, 1, 0, 1, 2, 2, 16, 0, 2, 0, 9, ... ## $ ilitotal 44, 3, 32, 46, 89, 5, 27, 5, 243, 76, 57, 2, 42, 44, 104, 6, 15, 9, 274, 62, 85, 1, 46, 54... ## $ num_of_providers 32, 7, 16, 29, 49, 4, 14, 5, 23, 13, 29, 7, 17, 31, 48, 4, 14, 6, 23, 12, 40, 7, 15, 33, 6... ## $ total_patients 7053, 780, 2385, 10222, 9875, 669, 2342, 1183, 10758, 1575, 6987, 872, 2740, 11310, 9618, ... ## $ week_start 1997-10-06, 1997-10-06, 1997-10-06, 1997-10-06, 1997-10-06, 1997-10-06, 1997-10-06, 1997-... ## # A tibble: 10,490 x 16 ## 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 10,480 more rows, and 4 more variables: ilitotal , num_of_providers , total_patients , ## # week_start ![](README.gfm-ascii_identifiers_files/figure-gfm/unnamed-chunk-8-2.png) ## Observations: 9,441 ## Variables: 16 ## $ region_type "Census Regions", "Census Regions", "Census Regions", "Census Regions", "Census Regions", ... ## $ region "New England", "Mid-Atlantic", "East North Central", "West North Central", "South Atlantic... ## $ year 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, ... ## $ week 40, 40, 40, 40, 40, 40, 40, 40, 40, 41, 41, 41, 41, 41, 41, 41, 41, 41, 42, 42, 42, 42, 42... ## $ weighted_ili 0.4985350, 0.8441440, 0.7924860, 1.7640500, 0.5026620, 0.0542283, 1.0189800, 2.2587800, 2.... ## $ unweighted_ili 0.6238480, 1.3213800, 0.8187380, 1.2793900, 0.7233800, 0.0688705, 0.7473840, 2.2763300, 3.... ## $ age_0_4 15, 4, 28, 3, 14, 0, 2, 87, 26, 14, 4, 36, 0, 21, 0, 2, 93, 29, 35, 3, 65, 1, 19, 0, 2, 84... ## $ age_25_49 NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... ## $ age_25_64 7, 8, 20, 8, 22, 3, 1, 71, 17, 14, 13, 23, 1, 14, 1, 2, 72, 11, 15, 11, 27, 5, 21, 0, 2, 5... ## $ age_5_24 22, 12, 28, 20, 14, 0, 2, 71, 36, 29, 8, 39, 18, 22, 0, 2, 80, 44, 35, 16, 74, 9, 24, 2, 2... ## $ age_50_64 NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... ## $ age_65 0, 4, 3, 6, 0, 0, 0, 15, 1, 0, 2, 2, 4, 3, 0, 0, 10, 2, 0, 3, 12, 6, 2, 0, 0, 9, 2, 0, 1, ... ## $ ilitotal 44, 28, 79, 37, 50, 3, 5, 244, 80, 57, 27, 100, 23, 60, 1, 6, 255, 86, 85, 33, 178, 21, 66... ## $ num_of_providers 32, 13, 47, 17, 30, 9, 4, 16, 24, 29, 13, 46, 17, 32, 10, 4, 17, 23, 40, 12, 62, 16, 33, 1... ## $ total_patients 7053, 2119, 9649, 2892, 6912, 4356, 669, 10719, 2473, 6987, 2384, 9427, 2823, 7591, 4947, ... ## $ week_start 1997-10-06, 1997-10-06, 1997-10-06, 1997-10-06, 1997-10-06, 1997-10-06, 1997-10-06, 1997-... ## # A tibble: 9,441 x 16 ## 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 NA 7 22 ## 2 Census Regions Mid-Atlantic 1997 40 0.8441440 1.3213800 4 NA 8 12 ## 3 Census Regions East North Central 1997 40 0.7924860 0.8187380 28 NA 20 28 ## 4 Census Regions West North Central 1997 40 1.7640500 1.2793900 3 NA 8 20 ## 5 Census Regions South Atlantic 1997 40 0.5026620 0.7233800 14 NA 22 14 ## 6 Census Regions East South Central 1997 40 0.0542283 0.0688705 0 NA 3 0 ## 7 Census Regions West South Central 1997 40 1.0189800 0.7473840 2 NA 1 2 ## 8 Census Regions Mountain 1997 40 2.2587800 2.2763300 87 NA 71 71 ## 9 Census Regions Pacific 1997 40 2.0488300 3.2349400 26 NA 17 36 ## 10 Census Regions New England 1997 41 0.6426690 0.8158010 14 NA 14 29 ## # ... with 9,431 more rows, and 6 more variables: age_50_64 , age_65 , ilitotal , ## # num_of_providers , total_patients , week_start ![](README.gfm-ascii_identifiers_files/figure-gfm/unnamed-chunk-8-3.png) ## Observations: 19,772 ## Variables: 16 ## $ region_type "States", "States", "States", "States", "States", "States", "States", "States", "States", ... ## $ region "Alabama", "Alaska", "Arizona", "Arkansas", "California", "Colorado", "Connecticut", "Dela... ## $ year 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, ... ## $ week 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40... ## $ weighted_ili NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... ## $ unweighted_ili 2.1347700, 0.8751460, 0.6747210, 0.6960560, 1.9541200, 0.6606840, 0.0783085, 0.1001250, 2.... ## $ age_0_4 NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... ## $ age_25_49 NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... ## $ age_25_64 NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... ## $ age_5_24 NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... ## $ age_50_64 NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... ## $ age_65 NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... ## $ ilitotal 249, 15, 172, 18, 632, 134, 3, 4, 73, NA, 647, 20, 19, 505, 65, 10, 39, 19, NA, 22, 117, 1... ## $ num_of_providers 35, 7, 49, 15, 112, 14, 12, 13, 4, NA, 62, 18, 12, 74, 44, 6, 40, 14, NA, 30, 17, 56, 47, ... ## $ total_patients 11664, 1714, 25492, 2586, 32342, 20282, 3831, 3995, 2599, NA, 40314, 1943, 4579, 39390, 12... ## $ week_start 2010-10-04, 2010-10-04, 2010-10-04, 2010-10-04, 2010-10-04, 2010-10-04, 2010-10-04, 2010-... ## # A tibble: 19,772 x 16 ## 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 NA 2.1347700 NA NA NA NA ## 2 States Alaska 2010 40 NA 0.8751460 NA NA NA NA ## 3 States Arizona 2010 40 NA 0.6747210 NA NA NA NA ## 4 States Arkansas 2010 40 NA 0.6960560 NA NA NA NA ## 5 States California 2010 40 NA 1.9541200 NA NA NA NA ## 6 States Colorado 2010 40 NA 0.6606840 NA NA NA NA ## 7 States Connecticut 2010 40 NA 0.0783085 NA NA NA NA ## 8 States Delaware 2010 40 NA 0.1001250 NA NA NA NA ## 9 States District of Columbia 2010 40 NA 2.8087700 NA NA NA NA ## 10 States Florida 2010 40 NA NA NA NA NA NA ## # ... with 19,762 more rows, and 6 more variables: age_50_64 , age_65 , ilitotal , ## # num_of_providers , total_patients , week_start ![](README.gfm-ascii_identifiers_files/figure-gfm/unnamed-chunk-8-4.png) ### Retrieve weekly state-level ILI indicators per-state for a given season ``` r ili_weekly_activity_indicators(2017) ``` ## # A tibble: 270 x 8 ## statename url ## * ## 1 Virgin Islands http://doh.vi.gov/ ## 2 Virgin Islands http://doh.vi.gov/ ## 3 Virgin Islands http://doh.vi.gov/ ## 4 Puerto Rico http://www.salud.gov.pr/Estadisticas-Registros-y-Publicaciones/Pages/Influenza.aspx ## 5 Virgin Islands http://doh.vi.gov/ ## 6 Puerto Rico http://www.salud.gov.pr/Estadisticas-Registros-y-Publicaciones/Pages/Influenza.aspx ## 7 Virgin Islands http://doh.vi.gov/ ## 8 Indiana http://www.in.gov/isdh/22104.htm ## 9 Iowa http://idph.iowa.gov/influenza/surveillance ## 10 Kansas http://www.kdheks.gov/flu/surveillance.htm ## # ... with 260 more rows, and 6 more variables: website , activity_level , activity_level_label , ## # weekend , season , weeknumber ``` r xdf <- map_df(2008:2017, ili_weekly_activity_indicators) count(xdf, weekend, activity_level_label) %>% complete(weekend, activity_level_label) %>% ggplot(aes(weekend, activity_level_label, fill=n)) + geom_tile(color="#c2c2c2", size=0.1) + scale_x_date(expand=c(0,0)) + viridis::scale_fill_viridis(name="# States", na.value="White") + labs(x=NULL, y=NULL, title="Weekly ILI Indicators (all states)") + coord_fixed(100/1) + theme_ipsum_rc(grid="") + theme(legend.position="bottom") ``` ![](README.gfm-ascii_identifiers_files/figure-gfm/unnamed-chunk-9-1.png) ### Pneumonia and Influenza Mortality Surveillance ``` r (nat_pi <- pi_mortality("national")) ``` ## # A tibble: 420 x 19 ## seasonid baseline threshold percent_pni percent_complete number_influenza number_pneumonia all_deaths total_pni ## ## 1 57 0.058 0.061 0.056 0.858 12 2276 40834 2288 ## 2 57 0.058 0.062 0.056 0.764 14 2025 36328 2039 ## 3 57 0.059 0.063 0.058 0.678 17 1844 32279 1861 ## 4 56 0.059 0.063 0.059 1.000 18 3022 51404 3040 ## 5 56 0.060 0.063 0.061 1.000 11 3193 52130 3204 ## 6 56 0.061 0.064 0.062 1.000 7 3178 51443 3185 ## 7 56 0.062 0.065 0.061 1.000 17 3129 51865 3146 ## 8 56 0.063 0.066 0.060 1.000 16 3099 51753 3115 ## 9 56 0.064 0.067 0.061 1.000 19 3208 52541 3227 ## 10 56 0.065 0.068 0.060 1.000 7 3192 53460 3199 ## # ... with 410 more rows, and 10 more variables: weeknumber , geo_description , age_label , ## # wk_start , wk_end , year_wk_num , mmwrid , coverage_area , region_name , ## # callout ``` r select(nat_pi, wk_end, percent_pni, baseline, threshold) %>% gather(measure, value, -wk_end) %>% ggplot(aes(wk_end, value)) + geom_line(aes(group=measure, color=measure)) + scale_y_percent() + scale_color_ipsum(name = NULL, labels=c("Baseline", "Percent P&I", "Threshold")) + labs(x=NULL, y="% of all deaths due to P&I", title="Percentage of all deaths due to pneumonia and influenza, National Summary") + theme_ipsum_rc(grid="XY") + theme(legend.position="bottom") ``` ![](README.gfm-ascii_identifiers_files/figure-gfm/unnamed-chunk-10-1.png) ``` r (st_pi <- pi_mortality("state", years=2015)) ``` ## # A tibble: 2,704 x 19 ## seasonid baseline threshold percent_pni percent_complete number_influenza number_pneumonia all_deaths total_pni ## ## 1 55 NA NA 0.047 1.000 0 46 979 46 ## 2 55 NA NA 0.038 0.963 0 34 889 34 ## 3 55 NA NA 0.053 1.000 0 52 977 52 ## 4 55 NA NA 0.070 1.000 0 68 968 68 ## 5 55 NA NA 0.053 0.981 0 48 906 48 ## 6 55 NA NA 0.058 1.000 0 56 968 56 ## 7 55 NA NA 0.051 1.000 0 53 1041 53 ## 8 55 NA NA 0.062 1.000 1 63 1031 64 ## 9 55 NA NA 0.056 1.000 0 55 976 55 ## 10 55 NA NA 0.054 1.000 0 56 1045 56 ## # ... with 2,694 more rows, and 10 more variables: weeknumber , geo_description , age_label , ## # wk_start , wk_end , year_wk_num , mmwrid , coverage_area , region_name , ## # callout ``` r (reg_pi <- pi_mortality("region", years=2015)) ``` ## # A tibble: 520 x 19 ## seasonid baseline threshold percent_pni percent_complete number_influenza number_pneumonia all_deaths total_pni ## ## 1 55 0.065 0.073 0.071 1 0 178 2520 178 ## 2 55 0.066 0.073 0.063 1 0 159 2505 159 ## 3 55 0.067 0.074 0.058 1 1 141 2452 142 ## 4 55 0.068 0.075 0.071 1 0 171 2422 171 ## 5 55 0.069 0.076 0.066 1 2 166 2554 168 ## 6 55 0.070 0.077 0.067 1 1 160 2404 161 ## 7 55 0.071 0.079 0.079 1 0 195 2478 195 ## 8 55 0.073 0.080 0.072 1 1 176 2463 177 ## 9 55 0.074 0.081 0.067 1 3 154 2347 157 ## 10 55 0.075 0.082 0.062 1 0 151 2437 151 ## # ... with 510 more rows, and 10 more variables: weeknumber , geo_description , age_label , ## # wk_start , wk_end , year_wk_num , mmwrid , coverage_area , region_name , ## # callout ### Retrieve metadata about U.S. State CDC Provider Data ``` 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 glimpse(xdat <- who_nrevss("national")) ``` ## List of 3 ## $ combined_prior_to_2015_16:Classes 'tbl_df', 'tbl' and 'data.frame': 940 obs. of 14 variables: ## ..$ region_type : chr [1:940] "National" "National" "National" "National" ... ## ..$ region : chr [1:940] "National" "National" "National" "National" ... ## ..$ year : int [1:940] 1997 1997 1997 1997 1997 1997 1997 1997 1997 1997 ... ## ..$ week : int [1:940] 40 41 42 43 44 45 46 47 48 49 ... ## ..$ total_specimens : int [1:940] 1291 1513 1552 1669 1897 2106 2204 2533 2242 2607 ... ## ..$ percent_positive : num [1:940] 0 0.727 1.095 0.419 0.527 ... ## ..$ a_2009_h1n1 : int [1:940] 0 0 0 0 0 0 0 0 0 0 ... ## ..$ a_h1 : int [1:940] 0 0 0 0 0 0 0 0 0 0 ... ## ..$ a_h3 : int [1:940] 0 0 3 0 9 0 3 5 14 11 ... ## ..$ a_subtyping_not_performed: int [1:940] 0 11 13 7 1 6 4 17 22 28 ... ## ..$ a_unable_to_subtype : int [1:940] 0 0 0 0 0 0 0 0 0 0 ... ## ..$ b : int [1:940] 0 0 1 0 0 0 1 1 1 1 ... ## ..$ h3n2v : int [1:940] 0 0 0 0 0 0 0 0 0 0 ... ## ..$ wk_date : Date[1:940], format: "1997-09-28" "1997-10-05" "1997-10-12" "1997-10-19" ... ## $ public_health_labs :Classes 'tbl_df', 'tbl' and 'data.frame': 109 obs. of 13 variables: ## ..$ region_type : chr [1:109] "National" "National" "National" "National" ... ## ..$ region : chr [1:109] "National" "National" "National" "National" ... ## ..$ year : int [1:109] 2015 2015 2015 2015 2015 2015 2015 2015 2015 2015 ... ## ..$ week : int [1:109] 40 41 42 43 44 45 46 47 48 49 ... ## ..$ total_specimens : int [1:109] 1139 1152 1198 1244 1465 1393 1458 1157 1550 1518 ... ## ..$ a_2009_h1n1 : int [1:109] 4 5 10 9 4 11 17 17 27 38 ... ## ..$ a_h3 : int [1:109] 65 41 50 31 23 34 42 24 36 37 ... ## ..$ a_subtyping_not_performed: int [1:109] 2 2 1 4 4 1 1 0 3 3 ... ## ..$ b : int [1:109] 10 7 8 9 9 10 4 4 9 11 ... ## ..$ bvic : int [1:109] 0 3 3 1 1 4 0 3 3 2 ... ## ..$ byam : int [1:109] 1 0 2 4 4 2 4 9 12 11 ... ## ..$ h3n2v : int [1:109] 0 0 0 0 0 0 0 0 0 0 ... ## ..$ wk_date : Date[1:109], format: "2015-10-04" "2015-10-11" "2015-10-18" "2015-10-25" ... ## $ clinical_labs :Classes 'tbl_df', 'tbl' and 'data.frame': 109 obs. of 11 variables: ## ..$ region_type : chr [1:109] "National" "National" "National" "National" ... ## ..$ region : chr [1:109] "National" "National" "National" "National" ... ## ..$ year : int [1:109] 2015 2015 2015 2015 2015 2015 2015 2015 2015 2015 ... ## ..$ week : int [1:109] 40 41 42 43 44 45 46 47 48 49 ... ## ..$ total_specimens : int [1:109] 12029 13111 13441 13537 14687 15048 15250 15234 16201 16673 ... ## ..$ total_a : int [1:109] 84 116 97 98 97 122 84 119 145 140 ... ## ..$ total_b : int [1:109] 43 54 52 52 68 86 98 92 81 106 ... ## ..$ percent_positive: num [1:109] 1.06 1.3 1.11 1.11 1.12 ... ## ..$ percent_a : num [1:109] 0.698 0.885 0.722 0.724 0.66 ... ## ..$ percent_b : num [1:109] 0.357 0.412 0.387 0.384 0.463 ... ## ..$ wk_date : Date[1:109], format: "2015-10-04" "2015-10-11" "2015-10-18" "2015-10-25" ... ``` r mutate(xdat$combined_prior_to_2015_16, percent_positive = percent_positive / 100) %>% ggplot(aes(wk_date, percent_positive)) + geom_line() + scale_y_percent(name="% Positive") + labs(x=NULL, title="WHO/NREVSS Surveillance Data (National)") + theme_ipsum_rc(grid="XY") ``` ![](README.gfm-ascii_identifiers_files/figure-gfm/unnamed-chunk-12-1.png) ``` r who_nrevss("hhs", years=2016) ``` ## $public_health_labs ## # A tibble: 520 x 13 ## region_type region year week total_specimens a_2009_h1n1 a_h3 a_subtyping_not_performed b bvic byam ## ## 1 HHS Regions Region 1 2016 31 0 6 0 0 0 0 ## 2 HHS Regions Region 2 2016 31 0 6 0 0 2 0 ## 3 HHS Regions Region 3 2016 112 2 2 0 0 0 0 ## 4 HHS Regions Region 4 2016 112 1 11 0 1 2 0 ## 5 HHS Regions Region 5 2016 204 0 7 0 0 0 1 ## 6 HHS Regions Region 6 2016 39 1 1 0 0 0 0 ## 7 HHS Regions Region 7 2016 24 0 2 0 0 1 0 ## 8 HHS Regions Region 8 2016 46 2 8 0 0 0 0 ## 9 HHS Regions Region 9 2016 186 3 27 0 0 0 3 ## 10 HHS Regions Region 10 2016 113 0 17 0 0 0 0 ## # ... with 510 more rows, and 2 more variables: h3n2v , wk_date ## ## $clinical_labs ## # A tibble: 520 x 11 ## region_type region year week total_specimens total_a total_b percent_positive percent_a percent_b wk_date ## ## 1 HHS Regions Region 1 2016 40 654 5 1 0.917431 0.764526 0.1529050 2016-10-02 ## 2 HHS Regions Region 2 2016 40 1307 10 3 0.994644 0.765111 0.2295330 2016-10-02 ## 3 HHS Regions Region 3 2016 40 941 1 4 0.531350 0.106270 0.4250800 2016-10-02 ## 4 HHS Regions Region 4 2016 40 2758 46 62 3.915880 1.667880 2.2480100 2016-10-02 ## 5 HHS Regions Region 5 2016 40 2386 8 5 0.544845 0.335289 0.2095560 2016-10-02 ## 6 HHS Regions Region 6 2016 40 1914 22 13 1.828630 1.149430 0.6792060 2016-10-02 ## 7 HHS Regions Region 7 2016 40 723 0 0 0.000000 0.000000 0.0000000 2016-10-02 ## 8 HHS Regions Region 8 2016 40 913 8 0 0.876232 0.876232 0.0000000 2016-10-02 ## 9 HHS Regions Region 9 2016 40 1123 7 1 0.712378 0.623330 0.0890472 2016-10-02 ## 10 HHS Regions Region 10 2016 40 590 14 0 2.372880 2.372880 0.0000000 2016-10-02 ## # ... with 510 more rows ``` r who_nrevss("census", years=2016) ``` ## $public_health_labs ## # A tibble: 468 x 13 ## region_type region year week total_specimens a_2009_h1n1 a_h3 a_subtyping_not_performed b ## ## 1 Census Regions New England 2016 31 0 6 0 0 ## 2 Census Regions Mid-Atlantic 2016 50 0 8 0 0 ## 3 Census Regions East North Central 2016 139 0 4 0 0 ## 4 Census Regions West North Central 2016 103 0 6 0 0 ## 5 Census Regions South Atlantic 2016 181 3 11 0 1 ## 6 Census Regions East South Central 2016 24 0 0 0 0 ## 7 Census Regions West South Central 2016 27 0 1 0 0 ## 8 Census Regions Mountain 2016 54 3 10 0 0 ## 9 Census Regions Pacific 2016 289 3 41 0 0 ## 10 Census Regions New England 2016 14 0 2 0 0 ## # ... with 458 more rows, and 4 more variables: bvic , byam , h3n2v , wk_date ## ## $clinical_labs ## # A tibble: 468 x 11 ## region_type region year week total_specimens total_a total_b percent_positive percent_a percent_b ## ## 1 Census Regions New England 2016 40 654 5 1 0.917431 0.764526 0.1529050 ## 2 Census Regions Mid-Atlantic 2016 40 1579 10 4 0.886637 0.633312 0.2533250 ## 3 Census Regions East North Central 2016 40 2176 6 5 0.505515 0.275735 0.2297790 ## 4 Census Regions West North Central 2016 40 1104 3 0 0.271739 0.271739 0.0000000 ## 5 Census Regions South Atlantic 2016 40 2610 43 62 4.022990 1.647510 2.3754800 ## 6 Census Regions East South Central 2016 40 817 4 3 0.856793 0.489596 0.3671970 ## 7 Census Regions West South Central 2016 40 1738 21 13 1.956270 1.208290 0.7479860 ## 8 Census Regions Mountain 2016 40 1067 8 0 0.749766 0.749766 0.0000000 ## 9 Census Regions Pacific 2016 40 1564 21 1 1.406650 1.342710 0.0639386 ## 10 Census Regions New England 2016 41 810 5 1 0.740741 0.617284 0.1234570 ## # ... with 458 more rows, and 1 more variables: wk_date ``` r who_nrevss("state", years=2016) ``` ## $public_health_labs ## # A tibble: 54 x 12 ## region_type region season_description total_specimens a_2009_h1n1 a_h3 a_subtyping_not_performed ## ## 1 States Alabama Season 2016-17 549 3 222 0 ## 2 States Alaska Season 2016-17 5226 14 905 3 ## 3 States Arizona Season 2016-17 2974 63 1630 0 ## 4 States Arkansas Season 2016-17 121 0 51 0 ## 5 States California Season 2016-17 14033 184 4694 120 ## 6 States Colorado Season 2016-17 715 3 267 2 ## 7 States Connecticut Season 2016-17 1347 19 968 0 ## 8 States Delaware Season 2016-17 3090 5 659 4 ## 9 States District of Columbia Season 2016-17 69 1 32 0 ## 10 States Florida Season 2016-17 ## # ... with 44 more rows, and 5 more variables: b , bvic , byam , h3n2v , wk_date ## ## $clinical_labs ## # A tibble: 2,808 x 11 ## region_type region year week total_specimens total_a total_b percent_positive percent_a percent_b ## ## 1 States Alabama 2016 40 379 4 0 1.06 1.06 0 ## 2 States Alaska 2016 40 ## 3 States Arizona 2016 40 133 0 0 0 0 0 ## 4 States Arkansas 2016 40 47 0 0 0 0 0 ## 5 States California 2016 40 799 3 0 0.38 0.38 0 ## 6 States Colorado 2016 40 260 0 0 0 0 0 ## 7 States Connecticut 2016 40 199 3 0 1.51 1.51 0 ## 8 States Delaware 2016 40 40 0 0 0 0 0 ## 9 States District of Columbia 2016 40 ## 10 States Florida 2016 40 ## # ... with 2,798 more rows, and 1 more variables: wk_date ## Code of Conduct Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). 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