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[](https://cran.r-project.org/package=cdcfluview)
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[](https://travis-ci.org/hrbrmstr/cdcfluview)
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[](https://codecov.io/github/hrbrmstr/cdcfluview?branch=master)
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I M P O R T A N T
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=================
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The CDC migrated to a new non-Flash portal and back-end APIs changed.
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This is a complete reimagining of the package and — as such — all your
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code is going to break. Please use GitHub issues to identify previous
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API functionality you would like ported over. There’s a [release
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candidate for
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0.5.2](https://github.com/hrbrmstr/cdcfluview/releases/tag/v0.5.2) which
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uses the old API but it likely to break in the near future given the
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changes to the hidden API. You can do what with
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`devtools::install_github("hrbrmstr/cdcfluview", ref="58c172b")`.
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All folks providing feedback, code or suggestions will be added to the
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DESCRIPTION file. Please include how you would prefer to be cited in any
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issues you file.
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If there’s a particular data set from
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<https://www.cdc.gov/flu/weekly/fluviewinteractive.htm> that you want
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and that isn’t in the package, please file it as an issue and be as
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specific as you can (screen shot if possible).
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:mask: cdcfluview
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=================
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Retrieve U.S. Flu Season Data from the CDC FluView Portal
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Description
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-----------
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The U.S. Centers for Disease Control (CDC) maintains a portal
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<http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html> for accessing
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state, regional and national influenza statistics as well as Mortality
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Surveillance Data. The Flash interface makes it difficult and
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time-consuming to select and retrieve influenza data. This package
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provides functions to access the data provided by the portal’s
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underlying API.
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What’s Inside The Tin
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---------------------
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The following functions are implemented:
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- `agd_ipt`: Age Group Distribution of Influenza Positive Tests
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Reported by Public Health Laboratories
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- `cdc_coverage_map`: Retrieve CDC U.S. Coverage Map
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- `geographic_spread`: State and Territorial Epidemiologists Reports
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of Geographic Spread of Influenza
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- `hospitalizations`: Laboratory-Confirmed Influenza Hospitalizations
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- `ilinet`: Retrieve ILINet Surveillance Data
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- `ili_weekly_activity_indicators`: Retrieve weekly state-level ILI
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indicators per-state for a given season
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- `pi_mortality`: Pneumonia and Influenza Mortality Surveillance
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- `state_data_providers`: Retrieve metadata about U.S. State CDC
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Provider Data
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- `surveillance_areas`: Retrieve a list of valid sub-regions for each
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surveillance area.
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- `who_nrevss`: Retrieve WHO/NREVSS Surveillance Data
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The following data sets are included:
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- `hhs_regions` HHS Region Table (a data frame with 59 rows and 4
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variables)
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- `census_regions` Census Region Table (a data frame with 51 rows and
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2 variables)
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Installation
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------------
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``` r
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devtools::install_github("hrbrmstr/cdcfluview")
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```
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Usage
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-----
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``` r
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library(cdcfluview)
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library(tidyverse)
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# current verison
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packageVersion("cdcfluview")
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```
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## [1] '0.7.0'
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### Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories
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``` r
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glimpse(agd_ipt())
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```
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## Observations: 36,144
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## Variables: 13
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## $ sea_label <chr> "1997-98", "1997-98", "1997-98", "1997-98", "1997-98", "1997-98", "1997-98", "1997-98", "...
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## $ age_label <chr> "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",...
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## $ vir_label <chr> "A (Subtyping not Performed)", "A (Subtyping not Performed)", "A (Subtyping not Performed...
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## $ count <int> 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, ...
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## $ mmwrid <int> 1866, 1867, 1868, 1869, 1870, 1871, 1872, 1873, 1874, 1875, 1876, 1877, 1878, 1879, 1880,...
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## $ seasonid <int> 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 3...
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## $ publishyearweekid <int> 2913, 2913, 2913, 2913, 2913, 2913, 2913, 2913, 2913, 2913, 2913, 2913, 2913, 2913, 2913,...
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## $ sea_description <chr> "Season 1997-98", "Season 1997-98", "Season 1997-98", "Season 1997-98", "Season 1997-98",...
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## $ sea_startweek <int> 1866, 1866, 1866, 1866, 1866, 1866, 1866, 1866, 1866, 1866, 1866, 1866, 1866, 1866, 1866,...
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## $ sea_endweek <int> 1918, 1918, 1918, 1918, 1918, 1918, 1918, 1918, 1918, 1918, 1918, 1918, 1918, 1918, 1918,...
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## $ vir_description <chr> "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk",...
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## $ vir_startmmwrid <int> 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397,...
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## $ vir_endmmwrid <int> 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131,...
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### Retrieve CDC U.S. Coverage Map
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``` r
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plot(cdc_coverage_map())
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```
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|
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### State and Territorial Epidemiologists Reports of Geographic Spread of Influenza
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``` r
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glimpse(geographic_spread())
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```
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## Observations: 25,795
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## Variables: 7
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## $ statename <chr> "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "...
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## $ url <chr> "http://adph.org/influenza/", "http://adph.org/influenza/", "http://adph.org/influenza/",...
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## $ website <chr> "Influenza Surveillance", "Influenza Surveillance", "Influenza Surveillance", "Influenza ...
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## $ activity_estimate <chr> "No Activity", "No Activity", "No Activity", "Local Activity", "Sporadic", "Sporadic", "S...
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## $ weekend <date> 2003-10-04, 2003-10-11, 2003-10-18, 2003-10-25, 2003-11-01, 2003-11-08, 2003-11-15, 2003...
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## $ season <chr> "2003-04", "2003-04", "2003-04", "2003-04", "2003-04", "2003-04", "2003-04", "2003-04", "...
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## $ weeknumber <chr> "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "1", ...
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|
|
### Laboratory-Confirmed Influenza Hospitalizations
|
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|
|
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|
|
|
``` r
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|
|
surveillance_areas()
|
|
|
|
|
```
|
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|
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## surveillance_area region
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|
|
## 1 flusurv Entire Network
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|
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## 2 eip California
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## 3 eip Colorado
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## 4 eip Connecticut
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## 5 eip Entire Network
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|
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## 6 eip Georgia
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|
## 7 eip Maryland
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## 8 eip Minnesota
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|
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## 9 eip New Mexico
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## 10 eip New York - Albany
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## 11 eip New York - Rochester
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## 12 eip Oregon
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|
|
## 13 eip Tennessee
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|
## 14 ihsp Entire Network
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|
## 15 ihsp Idaho
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|
|
## 16 ihsp Iowa
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|
|
## 17 ihsp Michigan
|
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|
|
## 18 ihsp Ohio
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|
|
## 19 ihsp Oklahoma
|
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|
|
## 20 ihsp Rhode Island
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|
|
## 21 ihsp South Dakota
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|
|
|
## 22 ihsp Utah
|
|
|
|
|
|
|
|
|
|
``` r
|
|
|
|
|
glimpse(hospitalizations("flusurv"))
|
|
|
|
|
```
|
|
|
|
|
|
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|
|
|
## Observations: 1,476
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|
|
|
## Variables: 20
|
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|
|
## $ mmwrid <int> 2545, 2546, 2547, 2548, 2549, 2550, 2551, 2552, 2553, 2554, 2555, 2556, 2557, 2558, 2559,...
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|
## $ weeknumber <int> 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...
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|
## $ rate <dbl> 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,...
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|
## $ weeklyrate <dbl> 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,...
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|
## $ age <int> 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,...
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## $ season <int> 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5...
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|
|
## $ weekend <chr> "2010-10-09", "2010-10-16", "2010-10-23", "2010-10-30", "2010-11-06", "2010-11-13", "2010...
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|
## $ weekstart <chr> "2010-10-03", "2010-10-10", "2010-10-17", "2010-10-24", "2010-10-31", "2010-11-07", "2010...
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## $ year <int> 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2011, 2011,...
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|
## $ yearweek <int> 201040, 201041, 201042, 201043, 201044, 201045, 201046, 201047, 201048, 201049, 201050, 2...
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|
|
## $ seasonid <int> 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5...
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## $ weekendlabel <chr> "Oct 09, 2010", "Oct 16, 2010", "Oct 23, 2010", "Oct 30, 2010", "Nov 06, 2010", "Nov 13, ...
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## $ weekendlabel2 <chr> "Oct-09-2010", "Oct-16-2010", "Oct-23-2010", "Oct-30-2010", "Nov-06-2010", "Nov-13-2010",...
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## $ age_label <chr> "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-49 yr", "18-4...
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## $ sea_label <chr> "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "...
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## $ sea_description <chr> "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11",...
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## $ sea_startweek <int> 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545,...
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|
## $ sea_endweek <int> 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596,...
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|
|
## $ surveillance_area <chr> "FluSurv-NET", "FluSurv-NET", "FluSurv-NET", "FluSurv-NET", "FluSurv-NET", "FluSurv-NET",...
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## $ region <chr> "Entire Network", "Entire Network", "Entire Network", "Entire Network", "Entire Network",...
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|
|
|
|
|
``` r
|
|
|
|
|
glimpse(hospitalizations("eip"))
|
|
|
|
|
```
|
|
|
|
|
|
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|
|
## Observations: 2,385
|
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|
|
## Variables: 20
|
|
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|
|
## $ mmwrid <int> 2545, 2546, 2547, 2548, 2549, 2550, 2551, 2552, 2553, 2554, 2555, 2556, 2557, 2558, 2559,...
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|
|
## $ weeknumber <int> 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...
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|
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|
## $ rate <dbl> 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,...
|
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|
|
|
## $ weeklyrate <dbl> 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,...
|
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|
|
|
## $ age <int> 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,...
|
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|
|
|
## $ season <int> 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5...
|
|
|
|
|
## $ weekend <chr> "2010-10-09", "2010-10-16", "2010-10-23", "2010-10-30", "2010-11-06", "2010-11-13", "2010...
|
|
|
|
|
## $ weekstart <chr> "2010-10-03", "2010-10-10", "2010-10-17", "2010-10-24", "2010-10-31", "2010-11-07", "2010...
|
|
|
|
|
## $ year <int> 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2011, 2011,...
|
|
|
|
|
## $ yearweek <int> 201040, 201041, 201042, 201043, 201044, 201045, 201046, 201047, 201048, 201049, 201050, 2...
|
|
|
|
|
## $ seasonid <int> 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5...
|
|
|
|
|
## $ weekendlabel <chr> "Oct 09, 2010", "Oct 16, 2010", "Oct 23, 2010", "Oct 30, 2010", "Nov 06, 2010", "Nov 13, ...
|
|
|
|
|
## $ weekendlabel2 <chr> "Oct-09-2010", "Oct-16-2010", "Oct-23-2010", "Oct-30-2010", "Nov-06-2010", "Nov-13-2010",...
|
|
|
|
|
## $ age_label <chr> "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 <chr> "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "...
|
|
|
|
|
## $ sea_description <chr> "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11",...
|
|
|
|
|
## $ sea_startweek <int> 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545,...
|
|
|
|
|
## $ sea_endweek <int> 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596,...
|
|
|
|
|
## $ surveillance_area <chr> "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP"...
|
|
|
|
|
## $ region <chr> "Entire Network", "Entire Network", "Entire Network", "Entire Network", "Entire Network",...
|
|
|
|
|
|
|
|
|
|
``` r
|
|
|
|
|
glimpse(hospitalizations("eip", "Colorado"))
|
|
|
|
|
```
|
|
|
|
|
|
|
|
|
|
## Observations: 2,385
|
|
|
|
|
## Variables: 20
|
|
|
|
|
## $ mmwrid <int> 2545, 2546, 2547, 2548, 2549, 2550, 2551, 2552, 2553, 2554, 2555, 2556, 2557, 2558, 2559,...
|
|
|
|
|
## $ weeknumber <int> 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...
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|
|
## $ rate <dbl> 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 <dbl> 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 <int> 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 <int> 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5...
|
|
|
|
|
## $ weekend <chr> "2010-10-09", "2010-10-16", "2010-10-23", "2010-10-30", "2010-11-06", "2010-11-13", "2010...
|
|
|
|
|
## $ weekstart <chr> "2010-10-03", "2010-10-10", "2010-10-17", "2010-10-24", "2010-10-31", "2010-11-07", "2010...
|
|
|
|
|
## $ year <int> 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2011, 2011,...
|
|
|
|
|
## $ yearweek <int> 201040, 201041, 201042, 201043, 201044, 201045, 201046, 201047, 201048, 201049, 201050, 2...
|
|
|
|
|
## $ seasonid <int> 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5...
|
|
|
|
|
## $ weekendlabel <chr> "Oct 09, 2010", "Oct 16, 2010", "Oct 23, 2010", "Oct 30, 2010", "Nov 06, 2010", "Nov 13, ...
|
|
|
|
|
## $ weekendlabel2 <chr> "Oct-09-2010", "Oct-16-2010", "Oct-23-2010", "Oct-30-2010", "Nov-06-2010", "Nov-13-2010",...
|
|
|
|
|
## $ age_label <chr> "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 <chr> "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "...
|
|
|
|
|
## $ sea_description <chr> "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11",...
|
|
|
|
|
## $ sea_startweek <int> 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545,...
|
|
|
|
|
## $ sea_endweek <int> 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596,...
|
|
|
|
|
## $ surveillance_area <chr> "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP"...
|
|
|
|
|
## $ region <chr> "Colorado", "Colorado", "Colorado", "Colorado", "Colorado", "Colorado", "Colorado", "Colo...
|
|
|
|
|
|
|
|
|
|
``` r
|
|
|
|
|
glimpse(hospitalizations("ihsp"))
|
|
|
|
|
```
|
|
|
|
|
|
|
|
|
|
## Observations: 1,476
|
|
|
|
|
## Variables: 20
|
|
|
|
|
## $ mmwrid <int> 2545, 2546, 2547, 2548, 2549, 2550, 2551, 2552, 2553, 2554, 2555, 2556, 2557, 2558, 2559,...
|
|
|
|
|
## $ weeknumber <int> 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 <dbl> 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 <dbl> 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 <int> 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 <int> 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5...
|
|
|
|
|
## $ weekend <chr> "2010-10-09", "2010-10-16", "2010-10-23", "2010-10-30", "2010-11-06", "2010-11-13", "2010...
|
|
|
|
|
## $ weekstart <chr> "2010-10-03", "2010-10-10", "2010-10-17", "2010-10-24", "2010-10-31", "2010-11-07", "2010...
|
|
|
|
|
## $ year <int> 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2011, 2011,...
|
|
|
|
|
## $ yearweek <int> 201040, 201041, 201042, 201043, 201044, 201045, 201046, 201047, 201048, 201049, 201050, 2...
|
|
|
|
|
## $ seasonid <int> 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5...
|
|
|
|
|
## $ weekendlabel <chr> "Oct 09, 2010", "Oct 16, 2010", "Oct 23, 2010", "Oct 30, 2010", "Nov 06, 2010", "Nov 13, ...
|
|
|
|
|
## $ weekendlabel2 <chr> "Oct-09-2010", "Oct-16-2010", "Oct-23-2010", "Oct-30-2010", "Nov-06-2010", "Nov-13-2010",...
|
|
|
|
|
## $ age_label <chr> "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 <chr> "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "...
|
|
|
|
|
## $ sea_description <chr> "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11",...
|
|
|
|
|
## $ sea_startweek <int> 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545,...
|
|
|
|
|
## $ sea_endweek <int> 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596,...
|
|
|
|
|
## $ surveillance_area <chr> "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "...
|
|
|
|
|
## $ region <chr> "Entire Network", "Entire Network", "Entire Network", "Entire Network", "Entire Network",...
|
|
|
|
|
|
|
|
|
|
``` r
|
|
|
|
|
glimpse(hospitalizations("ihsp", "Oklahoma"))
|
|
|
|
|
```
|
|
|
|
|
|
|
|
|
|
## Observations: 390
|
|
|
|
|
## Variables: 20
|
|
|
|
|
## $ mmwrid <int> 2545, 2546, 2547, 2548, 2549, 2550, 2551, 2552, 2553, 2554, 2555, 2556, 2557, 2558, 2559,...
|
|
|
|
|
## $ weeknumber <int> 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 <dbl> 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 <dbl> 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 <int> 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 <int> 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5...
|
|
|
|
|
## $ weekend <chr> "2010-10-09", "2010-10-16", "2010-10-23", "2010-10-30", "2010-11-06", "2010-11-13", "2010...
|
|
|
|
|
## $ weekstart <chr> "2010-10-03", "2010-10-10", "2010-10-17", "2010-10-24", "2010-10-31", "2010-11-07", "2010...
|
|
|
|
|
## $ year <int> 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2011, 2011,...
|
|
|
|
|
## $ yearweek <int> 201040, 201041, 201042, 201043, 201044, 201045, 201046, 201047, 201048, 201049, 201050, 2...
|
|
|
|
|
## $ seasonid <int> 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5...
|
|
|
|
|
## $ weekendlabel <chr> "Oct 09, 2010", "Oct 16, 2010", "Oct 23, 2010", "Oct 30, 2010", "Nov 06, 2010", "Nov 13, ...
|
|
|
|
|
## $ weekendlabel2 <chr> "Oct-09-2010", "Oct-16-2010", "Oct-23-2010", "Oct-30-2010", "Nov-06-2010", "Nov-13-2010",...
|
|
|
|
|
## $ age_label <chr> "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 <chr> "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "...
|
|
|
|
|
## $ sea_description <chr> "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11",...
|
|
|
|
|
## $ sea_startweek <int> 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545, 2545,...
|
|
|
|
|
## $ sea_endweek <int> 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596, 2596,...
|
|
|
|
|
## $ surveillance_area <chr> "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "...
|
|
|
|
|
## $ region <chr> "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
|
|
|
|
|
## <chr> <chr> <int> <int> <dbl> <dbl> <int> <chr> <chr> <int> <chr> <int>
|
|
|
|
|
## 1 National <NA> 1997 40 1.10148 1.21686 179 <NA> 157 205 <NA> 29
|
|
|
|
|
## 2 National <NA> 1997 41 1.20007 1.28064 199 <NA> 151 242 <NA> 23
|
|
|
|
|
## 3 National <NA> 1997 42 1.37876 1.23906 228 <NA> 153 266 <NA> 34
|
|
|
|
|
## 4 National <NA> 1997 43 1.19920 1.14473 188 <NA> 193 236 <NA> 36
|
|
|
|
|
## 5 National <NA> 1997 44 1.65618 1.26112 217 <NA> 162 280 <NA> 41
|
|
|
|
|
## 6 National <NA> 1997 45 1.41326 1.28275 178 <NA> 148 281 <NA> 48
|
|
|
|
|
## 7 National <NA> 1997 46 1.98680 1.44579 294 <NA> 240 328 <NA> 70
|
|
|
|
|
## 8 National <NA> 1997 47 2.44749 1.64796 288 <NA> 293 456 <NA> 63
|
|
|
|
|
## 9 National <NA> 1997 48 1.73901 1.67517 268 <NA> 206 343 <NA> 69
|
|
|
|
|
## 10 National <NA> 1997 49 1.93919 1.61739 299 <NA> 282 415 <NA> 102
|
|
|
|
|
## # ... with 1,038 more rows, and 3 more variables: ilitotal <int>, num_of_providers <int>, total_patients <int>
|
|
|
|
|
|
|
|
|
|
``` 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
|
|
|
|
|
## <chr> <chr> <int> <int> <dbl> <dbl> <int> <int> <int> <int> <int> <int>
|
|
|
|
|
## 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 <int>, num_of_providers <int>, total_patients <int>
|
|
|
|
|
|
|
|
|
|
``` 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
|
|
|
|
|
## <chr> <chr> <int> <int> <dbl> <dbl> <int> <chr> <chr> <int>
|
|
|
|
|
## 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 9,422 more rows, and 5 more variables: age_50_64 <chr>, age_65 <int>, ilitotal <int>,
|
|
|
|
|
## # num_of_providers <int>, total_patients <int>
|
|
|
|
|
|
|
|
|
|
``` 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
|
|
|
|
|
## <chr> <chr> <int> <int> <chr> <chr> <chr> <chr> <chr> <chr>
|
|
|
|
|
## 1 States Alabama 2010 40 <NA> 2.13477 <NA> <NA> <NA> <NA>
|
|
|
|
|
## 2 States Alaska 2010 40 <NA> 0.875146 <NA> <NA> <NA> <NA>
|
|
|
|
|
## 3 States Arizona 2010 40 <NA> 0.674721 <NA> <NA> <NA> <NA>
|
|
|
|
|
## 4 States Arkansas 2010 40 <NA> 0.696056 <NA> <NA> <NA> <NA>
|
|
|
|
|
## 5 States California 2010 40 <NA> 1.95412 <NA> <NA> <NA> <NA>
|
|
|
|
|
## 6 States Colorado 2010 40 <NA> 0.660684 <NA> <NA> <NA> <NA>
|
|
|
|
|
## 7 States Connecticut 2010 40 <NA> 0.0783085 <NA> <NA> <NA> <NA>
|
|
|
|
|
## 8 States Delaware 2010 40 <NA> 0.100125 <NA> <NA> <NA> <NA>
|
|
|
|
|
## 9 States District of Columbia 2010 40 <NA> 2.80877 <NA> <NA> <NA> <NA>
|
|
|
|
|
## 10 States Florida 2010 40 <NA> <NA> <NA> <NA> <NA> <NA>
|
|
|
|
|
## # ... with 19,708 more rows, and 5 more variables: age_50_64 <chr>, age_65 <chr>, ilitotal <chr>,
|
|
|
|
|
## # num_of_providers <chr>, total_patients <chr>
|
|
|
|
|
|
|
|
|
|
### 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
|
|
|
|
|
## <chr> <fctr> <chr> <chr> <chr> <date> <int> <int> <int>
|
|
|
|
|
## 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
|
|
|
|
|
## <chr> <fctr> <chr> <chr> <chr> <date> <int> <int> <int>
|
|
|
|
|
## 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
|
|
|
|
|
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
|
|
|
|
|
## 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 <chr>, geo_description <chr>, age_label <chr>,
|
|
|
|
|
## # weekend <date>, weekstart <date>, year <int>, yearweek <int>, coverage_area <chr>, region_name <chr>, callout <chr>
|
|
|
|
|
|
|
|
|
|
``` 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
|
|
|
|
|
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
|
|
|
|
|
## 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 <chr>, geo_description <chr>, age_label <chr>,
|
|
|
|
|
## # weekend <date>, weekstart <date>, year <int>, yearweek <int>, coverage_area <chr>, region_name <chr>, callout <chr>
|
|
|
|
|
|
|
|
|
|
``` 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
|
|
|
|
|
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
|
|
|
|
|
## 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 <chr>, geo_description <chr>, age_label <chr>,
|
|
|
|
|
## # weekend <date>, weekstart <date>, year <int>, yearweek <int>, coverage_area <chr>, region_name <chr>, callout <chr>
|
|
|
|
|
|
|
|
|
|
### Retrieve metadata about U.S. State CDC Provider Data
|
|
|
|
|
|
|
|
|
|
``` r
|
|
|
|
|
state_data_providers()
|
|
|
|
|
```
|
|
|
|
|
|
|
|
|
|
## # A tibble: 59 x 5
|
|
|
|
|
## statename statehealthdeptname
|
|
|
|
|
## * <chr> <chr>
|
|
|
|
|
## 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 <chr>, statewebsitename <chr>, statefluphonenum <chr>
|
|
|
|
|
|
|
|
|
|
### 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
|
|
|
|
|
## <chr> <chr> <int> <int> <int> <dbl> <int> <int> <int> <int>
|
|
|
|
|
## 1 National <NA> 1997 40 1291 0.000000 0 0 0 0
|
|
|
|
|
## 2 National <NA> 1997 41 1513 0.727032 0 0 0 11
|
|
|
|
|
## 3 National <NA> 1997 42 1552 1.095360 0 0 3 13
|
|
|
|
|
## 4 National <NA> 1997 43 1669 0.419413 0 0 0 7
|
|
|
|
|
## 5 National <NA> 1997 44 1897 0.527148 0 0 9 1
|
|
|
|
|
## 6 National <NA> 1997 45 2106 0.284900 0 0 0 6
|
|
|
|
|
## 7 National <NA> 1997 46 2204 0.362976 0 0 3 4
|
|
|
|
|
## 8 National <NA> 1997 47 2533 0.908014 0 0 5 17
|
|
|
|
|
## 9 National <NA> 1997 48 2242 1.650310 0 0 14 22
|
|
|
|
|
## 10 National <NA> 1997 49 2607 1.534330 0 0 11 28
|
|
|
|
|
## # ... with 930 more rows, and 3 more variables: a_unable_to_subtype <int>, b <int>, h3n2v <int>
|
|
|
|
|
##
|
|
|
|
|
## $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
|
|
|
|
|
## <chr> <chr> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int>
|
|
|
|
|
## 1 National <NA> 2015 40 1139 4 65 2 10 0 1 0
|
|
|
|
|
## 2 National <NA> 2015 41 1152 5 41 2 7 3 0 0
|
|
|
|
|
## 3 National <NA> 2015 42 1198 10 50 1 8 3 2 0
|
|
|
|
|
## 4 National <NA> 2015 43 1244 9 31 4 9 1 4 0
|
|
|
|
|
## 5 National <NA> 2015 44 1465 4 23 4 9 1 4 0
|
|
|
|
|
## 6 National <NA> 2015 45 1393 11 34 1 10 4 2 0
|
|
|
|
|
## 7 National <NA> 2015 46 1458 17 42 1 4 0 4 0
|
|
|
|
|
## 8 National <NA> 2015 47 1157 17 24 0 4 3 9 0
|
|
|
|
|
## 9 National <NA> 2015 48 1550 27 36 3 9 3 12 0
|
|
|
|
|
## 10 National <NA> 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
|
|
|
|
|
## <chr> <chr> <int> <int> <int> <int> <int> <dbl> <dbl> <dbl>
|
|
|
|
|
## 1 National <NA> 2015 40 12029 84 43 1.05578 0.698312 0.357469
|
|
|
|
|
## 2 National <NA> 2015 41 13111 116 54 1.29662 0.884753 0.411868
|
|
|
|
|
## 3 National <NA> 2015 42 13441 97 52 1.10855 0.721672 0.386876
|
|
|
|
|
## 4 National <NA> 2015 43 13537 98 52 1.10807 0.723942 0.384132
|
|
|
|
|
## 5 National <NA> 2015 44 14687 97 68 1.12344 0.660448 0.462994
|
|
|
|
|
## 6 National <NA> 2015 45 15048 122 86 1.38224 0.810739 0.571505
|
|
|
|
|
## 7 National <NA> 2015 46 15250 84 98 1.19344 0.550820 0.642623
|
|
|
|
|
## 8 National <NA> 2015 47 15234 119 92 1.38506 0.781147 0.603912
|
|
|
|
|
## 9 National <NA> 2015 48 16201 145 81 1.39498 0.895006 0.499969
|
|
|
|
|
## 10 National <NA> 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
|
|
|
|
|
## <chr> <chr> <int> <int> <int> <dbl> <int> <int> <int> <int>
|
|
|
|
|
## 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 <int>, b <int>, h3n2v <int>
|
|
|
|
|
##
|
|
|
|
|
## $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
|
|
|
|
|
## <chr> <chr> <int> <chr> <int> <int> <int> <int> <int> <int> <int>
|
|
|
|
|
## 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 <int>
|
|
|
|
|
##
|
|
|
|
|
## $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
|
|
|
|
|
## <chr> <chr> <int> <int> <int> <int> <int> <dbl> <dbl> <dbl>
|
|
|
|
|
## 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
|
|
|
|
|
## <chr> <chr> <int> <int> <int> <dbl> <int> <int> <int>
|
|
|
|
|
## 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 <int>, a_unable_to_subtype <int>, b <int>,
|
|
|
|
|
## # h3n2v <int>
|
|
|
|
|
##
|
|
|
|
|
## $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
|
|
|
|
|
## <chr> <chr> <int> <chr> <int> <int> <int> <int> <int>
|
|
|
|
|
## 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 <int>, byam <int>, h3n2v <int>
|
|
|
|
|
##
|
|
|
|
|
## $clinical_labs
|
|
|
|
|
## # A tibble: 972 x 10
|
|
|
|
|
## region_type region year week total_specimens total_a total_b percent_positive percent_a percent_b
|
|
|
|
|
## <chr> <chr> <int> <int> <int> <int> <int> <dbl> <dbl> <dbl>
|
|
|
|
|
## 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
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## 7 Census Regions West South Central 2015 40 1592 8 16 1.507540 0.502513 1.0050300
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## 8 Census Regions Mountain 2015 40 943 1 1 0.212089 0.106045 0.1060450
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## 9 Census Regions Pacific 2015 40 1303 28 2 2.302380 2.148890 0.1534920
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## 10 Census Regions New England 2015 41 752 11 4 1.994680 1.462770 0.5319150
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## # ... with 962 more rows
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``` r
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who_nrevss("state")
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```
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## $combined_prior_to_2015_16
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## # A tibble: 14,094 x 13
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## region_type region year week total_specimens percent_positive a_2009_h1n1 a_h1 a_h3
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## <chr> <chr> <int> <int> <chr> <chr> <chr> <chr> <chr>
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## 1 States Alabama 2010 40 54 0 0 0 0
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## 2 States Alaska 2010 40 40 0 0 0 0
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## 3 States Arizona 2010 40 40 2.5 0 0 1
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## 4 States Arkansas 2010 40 15 0 0 0 0
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## 5 States California 2010 40 183 3.28 2 0 3
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## 6 States Colorado 2010 40 126 0.79 0 0 1
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## 7 States Connecticut 2010 40 54 0 0 0 0
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## 8 States Delaware 2010 40 75 4 0 0 3
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## 9 States District of Columbia 2010 40 14 0 0 0 0
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## 10 States Florida 2010 40 <NA> <NA> <NA> <NA> <NA>
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## # ... with 14,084 more rows, and 4 more variables: a_subtyping_not_performed <chr>, a_unable_to_subtype <chr>, b <chr>,
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## # h3n2v <chr>
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##
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## $public_health_labs
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## # A tibble: 162 x 11
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## region_type region season_description total_specimens a_2009_h1n1 a_h3 a_subtyping_not_performed
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## <chr> <chr> <chr> <chr> <chr> <chr> <chr>
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## 1 States Alabama Season 2015-16 256 59 16 1
|
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## 2 States Alaska Season 2015-16 4691 607 98 0
|
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## 3 States Arizona Season 2015-16 2110 762 580 0
|
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## 4 States Arkansas Season 2015-16 128 20 8 0
|
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## 5 States California Season 2015-16 12241 1394 825 28
|
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## 6 States Colorado Season 2015-16 1625 912 243 3
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|
## 7 States Connecticut Season 2015-16 1581 662 52 0
|
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|
## 8 States Delaware Season 2015-16 2754 414 20 12
|
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## 9 States District of Columbia Season 2015-16 172 68 3 0
|
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## 10 States Florida Season 2015-16 <NA> <NA> <NA> <NA>
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|
## # ... with 152 more rows, and 4 more variables: b <chr>, bvic <chr>, byam <chr>, h3n2v <chr>
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|
|
##
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|
## $clinical_labs
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|
## # A tibble: 5,832 x 10
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|
|
## region_type region year week total_specimens total_a total_b percent_positive percent_a percent_b
|
|
|
|
|
## <chr> <chr> <int> <int> <chr> <chr> <chr> <chr> <chr> <chr>
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|
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|
## 1 States Alabama 2015 40 167 2 3 2.99 1.2 1.8
|
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|
## 2 States Alaska 2015 40 <NA> <NA> <NA> <NA> <NA> <NA>
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|
## 3 States Arizona 2015 40 55 0 0 0 0 0
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|
## 4 States Arkansas 2015 40 26 0 1 3.85 0 3.85
|
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|
## 5 States California 2015 40 679 2 0 0.29 0.29 0
|
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|
## 6 States Colorado 2015 40 255 0 1 0.39 0 0.39
|
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|
|
|
## 7 States Connecticut 2015 40 304 1 0 0.33 0.33 0
|
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|
|
## 8 States Delaware 2015 40 22 0 0 0 0 0
|
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|
## 9 States District of Columbia 2015 40 <NA> <NA> <NA> <NA> <NA> <NA>
|
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|
|
## 10 States Florida 2015 40 <NA> <NA> <NA> <NA> <NA> <NA>
|
|
|
|
|
## # ... with 5,822 more rows
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|
Code of Conduct
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|
|
---------------
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Please note that this project is released with a [Contributor Code of
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|
|
Conduct](CONDUCT.md). By participating in this project you agree to
|
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|
|
abide by its terms.
|
