|
|
|
@ -71,8 +71,6 @@ Deprecated functions: |
|
|
|
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) |
|
|
|
|
|
|
|
@ -102,7 +100,7 @@ library(tidyverse) |
|
|
|
packageVersion("cdcfluview") |
|
|
|
``` |
|
|
|
|
|
|
|
## [1] '0.7.0' |
|
|
|
## [1] '0.8.0' |
|
|
|
|
|
|
|
### Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories |
|
|
|
|
|
|
|
@ -113,12 +111,12 @@ glimpse(age_group_distribution(years=2015)) |
|
|
|
## Observations: 1,872 |
|
|
|
## Variables: 16 |
|
|
|
## $ sea_label <chr> "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "... |
|
|
|
## $ age_label <fctr> 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 <fctr> A (Subtyping not Performed), A (Subtyping not Performed), A (Subtyping not Performed), A... |
|
|
|
## $ age_label <fct> 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, 0... |
|
|
|
## $ vir_label <fct> A (Subtyping not Performed), A (Subtyping not Performed), A (Subtyping not Performed), A ... |
|
|
|
## $ count <int> 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 <int> 2806, 2807, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2817, 2818, 2819, 2820,... |
|
|
|
## $ seasonid <int> 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 5... |
|
|
|
## $ publishyearweekid <int> 2914, 2914, 2914, 2914, 2914, 2914, 2914, 2914, 2914, 2914, 2914, 2914, 2914, 2914, 2914,... |
|
|
|
## $ publishyearweekid <int> 2956, 2956, 2956, 2956, 2956, 2956, 2956, 2956, 2956, 2956, 2956, 2956, 2956, 2956, 2956,... |
|
|
|
## $ sea_description <chr> "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16",... |
|
|
|
## $ sea_startweek <int> 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806,... |
|
|
|
## $ sea_endweek <int> 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857,... |
|
|
|
@ -135,37 +133,37 @@ glimpse(age_group_distribution(years=2015)) |
|
|
|
plot(cdc_basemap("national")) |
|
|
|
``` |
|
|
|
|
|
|
|
<!-- --> |
|
|
|
<img src="README_files/figure-gfm/cdc-basemaps-1.png" width="672" /> |
|
|
|
|
|
|
|
``` r |
|
|
|
plot(cdc_basemap("hhs")) |
|
|
|
``` |
|
|
|
|
|
|
|
<!-- --> |
|
|
|
<img src="README_files/figure-gfm/cdc-basemaps-2.png" width="672" /> |
|
|
|
|
|
|
|
``` r |
|
|
|
plot(cdc_basemap("census")) |
|
|
|
``` |
|
|
|
|
|
|
|
<!-- --> |
|
|
|
<img src="README_files/figure-gfm/cdc-basemaps-3.png" width="672" /> |
|
|
|
|
|
|
|
``` r |
|
|
|
plot(cdc_basemap("states")) |
|
|
|
``` |
|
|
|
|
|
|
|
<!-- --> |
|
|
|
<img src="README_files/figure-gfm/cdc-basemaps-4.png" width="672" /> |
|
|
|
|
|
|
|
``` r |
|
|
|
plot(cdc_basemap("spread")) |
|
|
|
``` |
|
|
|
|
|
|
|
<!-- --> |
|
|
|
<img src="README_files/figure-gfm/cdc-basemaps-5.png" width="672" /> |
|
|
|
|
|
|
|
``` r |
|
|
|
plot(cdc_basemap("surv")) |
|
|
|
``` |
|
|
|
|
|
|
|
<!-- --> |
|
|
|
<img src="README_files/figure-gfm/cdc-basemaps-6.png" width="672" /> |
|
|
|
|
|
|
|
### State and Territorial Epidemiologists Reports of Geographic Spread of Influenza |
|
|
|
|
|
|
|
@ -173,7 +171,7 @@ plot(cdc_basemap("surv")) |
|
|
|
glimpse(geographic_spread()) |
|
|
|
``` |
|
|
|
|
|
|
|
## Observations: 25,848 |
|
|
|
## Observations: 27,351 |
|
|
|
## Variables: 7 |
|
|
|
## $ statename <chr> "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "... |
|
|
|
## $ url <chr> "http://adph.org/influenza/", "http://adph.org/influenza/", "http://adph.org/influenza/",... |
|
|
|
@ -217,7 +215,7 @@ surveillance_areas() |
|
|
|
glimpse(fs_nat <- hospitalizations("flusurv")) |
|
|
|
``` |
|
|
|
|
|
|
|
## Observations: 1,476 |
|
|
|
## Observations: 1,656 |
|
|
|
## Variables: 14 |
|
|
|
## $ surveillance_area <chr> "FluSurv-NET", "FluSurv-NET", "FluSurv-NET", "FluSurv-NET", "FluSurv-NET", "FluSurv-NET",... |
|
|
|
## $ region <chr> "Entire Network", "Entire Network", "Entire Network", "Entire Network", "Entire Network",... |
|
|
|
@ -229,7 +227,7 @@ glimpse(fs_nat <- hospitalizations("flusurv")) |
|
|
|
## $ rate <dbl> 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 <dbl> 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 <int> 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 <fctr> 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, ... |
|
|
|
## $ age_label <fct> 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, 0... |
|
|
|
## $ sea_label <chr> "2009-10", "2009-10", "2009-10", "2009-10", "2009-10", "2009-10", "2009-10", "2009-10", "... |
|
|
|
## $ sea_description <chr> "Season 2009-10", "Season 2009-10", "Season 2009-10", "Season 2009-10", "Season 2009-10",... |
|
|
|
## $ mmwrid <int> 2488, 2489, 2490, 2491, 2492, 2493, 2494, 2495, 2496, 2497, 2498, 2499, 2500, 2501, 2502,... |
|
|
|
@ -244,7 +242,7 @@ ggplot(fs_nat, aes(wk_end, rate)) + |
|
|
|
theme_ipsum_rc() |
|
|
|
``` |
|
|
|
|
|
|
|
<!-- --> |
|
|
|
<img src="README_files/figure-gfm/surveillance-areas-1.png" width="960" /> |
|
|
|
|
|
|
|
``` r |
|
|
|
glimpse(hospitalizations("eip", years=2015)) |
|
|
|
@ -262,7 +260,7 @@ glimpse(hospitalizations("eip", years=2015)) |
|
|
|
## $ rate <dbl> 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 <dbl> 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 <int> 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 <fctr> 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, ... |
|
|
|
## $ age_label <fct> 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, 0... |
|
|
|
## $ sea_label <chr> "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "... |
|
|
|
## $ sea_description <chr> "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16",... |
|
|
|
## $ mmwrid <int> 2806, 2807, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2817, 2818, 2819, 2820,... |
|
|
|
@ -280,10 +278,10 @@ glimpse(hospitalizations("eip", "Colorado", years=2015)) |
|
|
|
## $ wk_start <date> 2015-10-04, 2015-10-11, 2015-10-18, 2015-10-25, 2015-11-01, 2015-11-08, 2015-11-15, 2015... |
|
|
|
## $ wk_end <date> 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 <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, 0.6, 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,... |
|
|
|
## $ rate <dbl> 0.0, 0.0, 0.6, 0.6, 0.6, 0.6, 1.2, 1.8, 1.8, 1.8, 1.8, 1.8, 2.9, 3.5, 3.5, 3.5, 4.1, 6.4,... |
|
|
|
## $ weeklyrate <dbl> 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 <int> 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 <fctr> 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, ... |
|
|
|
## $ age_label <fct> 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, 0... |
|
|
|
## $ sea_label <chr> "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "... |
|
|
|
## $ sea_description <chr> "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16",... |
|
|
|
## $ mmwrid <int> 2806, 2807, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2817, 2818, 2819, 2820,... |
|
|
|
@ -304,7 +302,7 @@ glimpse(hospitalizations("ihsp", years=2015)) |
|
|
|
## $ rate <dbl> 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 <dbl> 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 <int> 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 <fctr> 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, ... |
|
|
|
## $ age_label <fct> 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, 0... |
|
|
|
## $ sea_label <chr> "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "... |
|
|
|
## $ sea_description <chr> "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16",... |
|
|
|
## $ mmwrid <int> 2806, 2807, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2817, 2818, 2819, 2820,... |
|
|
|
@ -322,10 +320,10 @@ glimpse(hospitalizations("ihsp", "Oklahoma", years=2015)) |
|
|
|
## $ wk_start <date> 2010-10-03, 2010-10-10, 2010-10-17, 2010-10-24, 2010-10-31, 2010-11-07, 2010-11-14, 2010... |
|
|
|
## $ wk_end <date> 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 <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, 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,... |
|
|
|
## $ rate <dbl> 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, 83.4,... |
|
|
|
## $ weeklyrate <dbl> 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 <int> 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 <fctr> 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, ... |
|
|
|
## $ age_label <fct> 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, 0... |
|
|
|
## $ 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",... |
|
|
|
## $ mmwrid <int> 2545, 2546, 2547, 2548, 2549, 2550, 2551, 2552, 2553, 2554, 2555, 2556, 2557, 2558, 2559,... |
|
|
|
@ -351,7 +349,7 @@ walk(c("national", "hhs", "census", "state"), ~{ |
|
|
|
}) |
|
|
|
``` |
|
|
|
|
|
|
|
## Observations: 1,049 |
|
|
|
## Observations: 1,093 |
|
|
|
## Variables: 16 |
|
|
|
## $ region_type <chr> "National", "National", "National", "National", "National", "National", "National", "Natio... |
|
|
|
## $ region <chr> "National", "National", "National", "National", "National", "National", "National", "Natio... |
|
|
|
@ -369,28 +367,28 @@ walk(c("national", "hhs", "census", "state"), ~{ |
|
|
|
## $ num_of_providers <dbl> 192, 191, 219, 213, 213, 195, 248, 256, 252, 253, 242, 190, 251, 250, 254, 255, 245, 245, ... |
|
|
|
## $ total_patients <dbl> 46842, 48023, 54961, 57044, 55506, 51062, 64463, 66749, 52890, 67887, 61314, 47719, 48429,... |
|
|
|
## $ week_start <date> 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 |
|
|
|
## <chr> <chr> <int> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> |
|
|
|
## 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 <dbl>, num_of_providers <dbl>, total_patients <dbl>, |
|
|
|
## # A tibble: 1,093 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 |
|
|
|
## <chr> <chr> <int> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> |
|
|
|
## 1 National National 1997 40 1.10 1.22 179 NA 157 205 NA 29 |
|
|
|
## 2 National National 1997 41 1.20 1.28 199 NA 151 242 NA 23 |
|
|
|
## 3 National National 1997 42 1.38 1.24 228 NA 153 266 NA 34 |
|
|
|
## 4 National National 1997 43 1.20 1.14 188 NA 193 236 NA 36 |
|
|
|
## 5 National National 1997 44 1.66 1.26 217 NA 162 280 NA 41 |
|
|
|
## 6 National National 1997 45 1.41 1.28 178 NA 148 281 NA 48 |
|
|
|
## 7 National National 1997 46 1.99 1.45 294 NA 240 328 NA 70 |
|
|
|
## 8 National National 1997 47 2.45 1.65 288 NA 293 456 NA 63 |
|
|
|
## 9 National National 1997 48 1.74 1.68 268 NA 206 343 NA 69 |
|
|
|
## 10 National National 1997 49 1.94 1.62 299 NA 282 415 NA 102 |
|
|
|
## # ... with 1,083 more rows, and 4 more variables: ilitotal <dbl>, num_of_providers <dbl>, total_patients <dbl>, |
|
|
|
## # week_start <date> |
|
|
|
|
|
|
|
<!-- --> |
|
|
|
<img src="README_files/figure-gfm/ili-df-1.png" width="672" /> |
|
|
|
|
|
|
|
## Observations: 10,490 |
|
|
|
## Observations: 10,930 |
|
|
|
## Variables: 16 |
|
|
|
## $ region_type <chr> "HHS Regions", "HHS Regions", "HHS Regions", "HHS Regions", "HHS Regions", "HHS Regions", ... |
|
|
|
## $ region <fctr> Region 1, Region 2, Region 3, Region 4, Region 5, Region 6, Region 7, Region 8, Region 9,... |
|
|
|
## $ region <fct> Region 1, Region 2, Region 3, Region 4, Region 5, Region 6, Region 7, Region 8, Region 9, ... |
|
|
|
## $ year <int> 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, ... |
|
|
|
## $ week <int> 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 <dbl> 0.498535, 0.374963, 1.354280, 0.400338, 1.229260, 1.018980, 0.871791, 0.516017, 1.807610, ... |
|
|
|
@ -405,25 +403,25 @@ walk(c("national", "hhs", "census", "state"), ~{ |
|
|
|
## $ num_of_providers <dbl> 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 <dbl> 7053, 780, 2385, 10222, 9875, 669, 2342, 1183, 10758, 1575, 6987, 872, 2740, 11310, 9618, ... |
|
|
|
## $ week_start <date> 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 |
|
|
|
## <chr> <fctr> <int> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> |
|
|
|
## 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 <dbl>, num_of_providers <dbl>, total_patients <dbl>, |
|
|
|
## # A tibble: 10,930 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 |
|
|
|
## <chr> <fct> <int> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> |
|
|
|
## 1 HHS Regions Region 1 1997 40 0.499 0.624 15 NA 7 22 NA 0 |
|
|
|
## 2 HHS Regions Region 2 1997 40 0.375 0.385 0 NA 3 0 NA 0 |
|
|
|
## 3 HHS Regions Region 3 1997 40 1.35 1.34 6 NA 7 15 NA 4 |
|
|
|
## 4 HHS Regions Region 4 1997 40 0.400 0.450 12 NA 23 11 NA 0 |
|
|
|
## 5 HHS Regions Region 5 1997 40 1.23 0.901 31 NA 24 30 NA 4 |
|
|
|
## 6 HHS Regions Region 6 1997 40 1.02 0.747 2 NA 1 2 NA 0 |
|
|
|
## 7 HHS Regions Region 7 1997 40 0.872 1.15 0 NA 4 18 NA 5 |
|
|
|
## 8 HHS Regions Region 8 1997 40 0.516 0.423 2 NA 0 3 NA 0 |
|
|
|
## 9 HHS Regions Region 9 1997 40 1.81 2.26 80 NA 76 74 NA 13 |
|
|
|
## 10 HHS Regions Region 10 1997 40 4.74 4.83 31 NA 12 30 NA 3 |
|
|
|
## # ... with 10,920 more rows, and 4 more variables: ilitotal <dbl>, num_of_providers <dbl>, total_patients <dbl>, |
|
|
|
## # week_start <date> |
|
|
|
|
|
|
|
<!-- --> |
|
|
|
<img src="README_files/figure-gfm/ili-df-2.png" width="672" /> |
|
|
|
|
|
|
|
## Observations: 9,441 |
|
|
|
## Observations: 9,837 |
|
|
|
## Variables: 16 |
|
|
|
## $ region_type <chr> "Census Regions", "Census Regions", "Census Regions", "Census Regions", "Census Regions", ... |
|
|
|
## $ region <chr> "New England", "Mid-Atlantic", "East North Central", "West North Central", "South Atlantic... |
|
|
|
@ -441,25 +439,25 @@ walk(c("national", "hhs", "census", "state"), ~{ |
|
|
|
## $ num_of_providers <dbl> 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 <dbl> 7053, 2119, 9649, 2892, 6912, 4356, 669, 10719, 2473, 6987, 2384, 9427, 2823, 7591, 4947, ... |
|
|
|
## $ week_start <date> 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 |
|
|
|
## <chr> <chr> <int> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> |
|
|
|
## 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 <dbl>, age_65 <dbl>, ilitotal <dbl>, |
|
|
|
## # num_of_providers <dbl>, total_patients <dbl>, week_start <date> |
|
|
|
|
|
|
|
<!-- --> |
|
|
|
|
|
|
|
## Observations: 19,772 |
|
|
|
## # A tibble: 9,837 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 |
|
|
|
## <chr> <chr> <int> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> |
|
|
|
## 1 Census Regi… New Engl… 1997 40 0.499 0.624 15 NA 7 22 NA 0 |
|
|
|
## 2 Census Regi… Mid-Atla… 1997 40 0.844 1.32 4 NA 8 12 NA 4 |
|
|
|
## 3 Census Regi… East Nor… 1997 40 0.792 0.819 28 NA 20 28 NA 3 |
|
|
|
## 4 Census Regi… West Nor… 1997 40 1.76 1.28 3 NA 8 20 NA 6 |
|
|
|
## 5 Census Regi… South At… 1997 40 0.503 0.723 14 NA 22 14 NA 0 |
|
|
|
## 6 Census Regi… East Sou… 1997 40 0.0542 0.0689 0 NA 3 0 NA 0 |
|
|
|
## 7 Census Regi… West Sou… 1997 40 1.02 0.747 2 NA 1 2 NA 0 |
|
|
|
## 8 Census Regi… Mountain 1997 40 2.26 2.28 87 NA 71 71 NA 15 |
|
|
|
## 9 Census Regi… Pacific 1997 40 2.05 3.23 26 NA 17 36 NA 1 |
|
|
|
## 10 Census Regi… New Engl… 1997 41 0.643 0.816 14 NA 14 29 NA 0 |
|
|
|
## # ... with 9,827 more rows, and 4 more variables: ilitotal <dbl>, num_of_providers <dbl>, total_patients <dbl>, |
|
|
|
## # week_start <date> |
|
|
|
|
|
|
|
<img src="README_files/figure-gfm/ili-df-3.png" width="672" /> |
|
|
|
|
|
|
|
## Observations: 22,148 |
|
|
|
## Variables: 16 |
|
|
|
## $ region_type <chr> "States", "States", "States", "States", "States", "States", "States", "States", "States", ... |
|
|
|
## $ region <chr> "Alabama", "Alaska", "Arizona", "Arkansas", "California", "Colorado", "Connecticut", "Dela... |
|
|
|
@ -473,27 +471,27 @@ walk(c("national", "hhs", "census", "state"), ~{ |
|
|
|
## $ age_5_24 <dbl> 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 <dbl> 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 <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA... |
|
|
|
## $ ilitotal <dbl> 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 <dbl> 35, 7, 49, 15, 112, 14, 12, 13, 4, NA, 62, 18, 12, 74, 44, 6, 40, 14, NA, 30, 17, 56, 47, ... |
|
|
|
## $ ilitotal <dbl> 249, 15, 172, 18, 632, 134, 3, 4, 73, NA, 647, 20, 19, 505, 65, 10, 39, 19, 391, 22, 117, ... |
|
|
|
## $ num_of_providers <dbl> 35, 7, 49, 15, 112, 14, 12, 13, 4, NA, 62, 18, 12, 74, 44, 6, 40, 14, 41, 30, 17, 56, 47, ... |
|
|
|
## $ total_patients <dbl> 11664, 1714, 25492, 2586, 32342, 20282, 3831, 3995, 2599, NA, 40314, 1943, 4579, 39390, 12... |
|
|
|
## $ week_start <date> 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 |
|
|
|
## <chr> <chr> <int> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> |
|
|
|
## 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 <dbl>, age_65 <dbl>, ilitotal <dbl>, |
|
|
|
## # num_of_providers <dbl>, total_patients <dbl>, week_start <date> |
|
|
|
|
|
|
|
<!-- --> |
|
|
|
## # A tibble: 22,148 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 |
|
|
|
## <chr> <chr> <int> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> |
|
|
|
## 1 States Alabama 2010 40 NA 2.13 NA NA NA NA NA NA |
|
|
|
## 2 States Alaska 2010 40 NA 0.875 NA NA NA NA NA NA |
|
|
|
## 3 States Arizona 2010 40 NA 0.675 NA NA NA NA NA NA |
|
|
|
## 4 States Arkansas 2010 40 NA 0.696 NA NA NA NA NA NA |
|
|
|
## 5 States California 2010 40 NA 1.95 NA NA NA NA NA NA |
|
|
|
## 6 States Colorado 2010 40 NA 0.661 NA NA NA NA NA NA |
|
|
|
## 7 States Connectic… 2010 40 NA 0.0783 NA NA NA NA NA NA |
|
|
|
## 8 States Delaware 2010 40 NA 0.100 NA NA NA NA NA NA |
|
|
|
## 9 States District … 2010 40 NA 2.81 NA NA NA NA NA NA |
|
|
|
## 10 States Florida 2010 40 NA NA NA NA NA NA NA NA |
|
|
|
## # ... with 22,138 more rows, and 4 more variables: ilitotal <dbl>, num_of_providers <dbl>, total_patients <dbl>, |
|
|
|
## # week_start <date> |
|
|
|
|
|
|
|
<img src="README_files/figure-gfm/ili-df-4.png" width="672" /> |
|
|
|
|
|
|
|
### Retrieve weekly state-level ILI indicators per-state for a given season |
|
|
|
|
|
|
|
@ -501,21 +499,20 @@ walk(c("national", "hhs", "census", "state"), ~{ |
|
|
|
ili_weekly_activity_indicators(2017) |
|
|
|
``` |
|
|
|
|
|
|
|
## # A tibble: 270 x 8 |
|
|
|
## statename url |
|
|
|
## * <chr> <chr> |
|
|
|
## 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 <chr>, activity_level <dbl>, activity_level_label <chr>, |
|
|
|
## # weekend <date>, season <chr>, weeknumber <dbl> |
|
|
|
## # A tibble: 1,782 x 8 |
|
|
|
## statename url website activity_level activity_level_label weekend season weeknumber |
|
|
|
## * <chr> <chr> <chr> <dbl> <chr> <date> <chr> <dbl> |
|
|
|
## 1 Virgin Islands http://doh.vi.gov/ Influenza 0 Insufficient Data 2017-10-07 2017-18 40 |
|
|
|
## 2 Virgin Islands http://doh.vi.gov/ Influenza 0 Insufficient Data 2017-10-14 2017-18 41 |
|
|
|
## 3 Virgin Islands http://doh.vi.gov/ Influenza 0 Insufficient Data 2017-10-21 2017-18 42 |
|
|
|
## 4 Virgin Islands http://doh.vi.gov/ Influenza 0 Insufficient Data 2017-10-28 2017-18 43 |
|
|
|
## 5 Virgin Islands http://doh.vi.gov/ Influenza 0 Insufficient Data 2017-11-04 2017-18 44 |
|
|
|
## 6 Virgin Islands http://doh.vi.gov/ Influenza 0 Insufficient Data 2017-11-11 2017-18 45 |
|
|
|
## 7 Virgin Islands http://doh.vi.gov/ Influenza 0 Insufficient Data 2017-12-02 2017-18 48 |
|
|
|
## 8 Virgin Islands http://doh.vi.gov/ Influenza 0 Insufficient Data 2017-12-09 2017-18 49 |
|
|
|
## 9 Virgin Islands http://doh.vi.gov/ Influenza 0 Insufficient Data 2017-12-23 2017-18 51 |
|
|
|
## 10 Virgin Islands http://doh.vi.gov/ Influenza 0 Insufficient Data 2017-12-30 2017-18 52 |
|
|
|
## # ... with 1,772 more rows |
|
|
|
|
|
|
|
``` r |
|
|
|
xdf <- map_df(2008:2017, ili_weekly_activity_indicators) |
|
|
|
@ -532,7 +529,7 @@ count(xdf, weekend, activity_level_label) %>% |
|
|
|
theme(legend.position="bottom") |
|
|
|
``` |
|
|
|
|
|
|
|
<!-- --> |
|
|
|
<img src="README_files/figure-gfm/ili-weekly-activity-1.png" width="960" /> |
|
|
|
|
|
|
|
### Pneumonia and Influenza Mortality Surveillance |
|
|
|
|
|
|
|
@ -540,20 +537,20 @@ count(xdf, weekend, activity_level_label) %>% |
|
|
|
(nat_pi <- pi_mortality("national")) |
|
|
|
``` |
|
|
|
|
|
|
|
## # A tibble: 420 x 19 |
|
|
|
## # A tibble: 464 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 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 <chr>, geo_description <chr>, age_label <chr>, |
|
|
|
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> |
|
|
|
## 1 57 0.057 0.06 0.0580 1 16 3020 52110 3036 |
|
|
|
## 2 57 0.0580 0.061 0.059 1 18 3000 51572 3018 |
|
|
|
## 3 57 0.059 0.062 0.061 1 28 3154 52222 3182 |
|
|
|
## 4 57 0.06 0.063 0.063 1 23 3279 52548 3302 |
|
|
|
## 5 57 0.06 0.063 0.061 1 36 3214 53679 3250 |
|
|
|
## 6 57 0.061 0.064 0.06 1 45 3177 53258 3222 |
|
|
|
## 7 57 0.062 0.065 0.063 1 50 3315 53771 3365 |
|
|
|
## 8 57 0.063 0.066 0.06 1 48 3200 54120 3248 |
|
|
|
## 9 57 0.064 0.067 0.065 1 83 3491 54760 3574 |
|
|
|
## 10 57 0.065 0.068 0.066 1 118 3526 55595 3644 |
|
|
|
## # ... with 454 more rows, and 10 more variables: weeknumber <chr>, geo_description <chr>, age_label <chr>, |
|
|
|
## # wk_start <date>, wk_end <date>, year_wk_num <int>, mmwrid <chr>, coverage_area <chr>, region_name <chr>, |
|
|
|
## # callout <chr> |
|
|
|
|
|
|
|
@ -570,7 +567,7 @@ select(nat_pi, wk_end, percent_pni, baseline, threshold) %>% |
|
|
|
theme(legend.position="bottom") |
|
|
|
``` |
|
|
|
|
|
|
|
<!-- --> |
|
|
|
<img src="README_files/figure-gfm/nat-pi-mortality-1.png" width="672" /> |
|
|
|
|
|
|
|
``` r |
|
|
|
(st_pi <- pi_mortality("state", years=2015)) |
|
|
|
@ -578,17 +575,17 @@ select(nat_pi, wk_end, percent_pni, baseline, threshold) %>% |
|
|
|
|
|
|
|
## # A tibble: 2,704 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 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 |
|
|
|
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> |
|
|
|
## 1 55 NA NA 0.047 1 0 46 979 46 |
|
|
|
## 2 55 NA NA 0.038 0.963 0 34 889 34 |
|
|
|
## 3 55 NA NA 0.053 1 0 52 977 52 |
|
|
|
## 4 55 NA NA 0.07 1 0 68 968 68 |
|
|
|
## 5 55 NA NA 0.053 0.981 0 48 906 48 |
|
|
|
## 6 55 NA NA 0.0580 1 0 56 968 56 |
|
|
|
## 7 55 NA NA 0.051 1 0 53 1041 53 |
|
|
|
## 8 55 NA NA 0.062 1 1 63 1031 64 |
|
|
|
## 9 55 NA NA 0.0560 1 0 55 976 55 |
|
|
|
## 10 55 NA NA 0.054 1 0 56 1045 56 |
|
|
|
## # ... with 2,694 more rows, and 10 more variables: weeknumber <chr>, geo_description <chr>, age_label <chr>, |
|
|
|
## # wk_start <date>, wk_end <date>, year_wk_num <int>, mmwrid <chr>, coverage_area <chr>, region_name <chr>, |
|
|
|
## # callout <chr> |
|
|
|
@ -599,17 +596,17 @@ select(nat_pi, wk_end, percent_pni, baseline, threshold) %>% |
|
|
|
|
|
|
|
## # A tibble: 520 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 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 |
|
|
|
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> |
|
|
|
## 1 55 0.066 0.073 0.071 1 0 178 2520 178 |
|
|
|
## 2 55 0.067 0.074 0.063 1 0 159 2505 159 |
|
|
|
## 3 55 0.067 0.075 0.0580 1 1 141 2452 142 |
|
|
|
## 4 55 0.068 0.076 0.071 1 0 171 2422 171 |
|
|
|
## 5 55 0.07 0.077 0.066 1 2 166 2554 168 |
|
|
|
## 6 55 0.071 0.078 0.067 1 1 160 2404 161 |
|
|
|
## 7 55 0.072 0.079 0.079 1 0 195 2478 195 |
|
|
|
## 8 55 0.073 0.081 0.072 1 1 176 2463 177 |
|
|
|
## 9 55 0.074 0.0820 0.067 1 3 154 2347 157 |
|
|
|
## 10 55 0.076 0.083 0.062 1 0 151 2437 151 |
|
|
|
## # ... with 510 more rows, and 10 more variables: weeknumber <chr>, geo_description <chr>, age_label <chr>, |
|
|
|
## # wk_start <date>, wk_end <date>, year_wk_num <int>, mmwrid <chr>, coverage_area <chr>, region_name <chr>, |
|
|
|
## # callout <chr> |
|
|
|
@ -621,19 +618,19 @@ 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> |
|
|
|
## statename statehealthdeptname url statewebsitename statefluphonenum |
|
|
|
## * <chr> <chr> <chr> <chr> <chr> |
|
|
|
## 1 Alabama Alabama Department of Public Health http://… Influenza Surve… 334-206-5300 |
|
|
|
## 2 Alaska State of Alaska Health and Social Services "http:/… Influenza Surve… 907-269-8000 |
|
|
|
## 3 Arizona Arizona Department of Health Services http://… Influenza & RSV… 602-542-1025 |
|
|
|
## 4 Arkansas Arkansas Department of Health http://… Communicable Di… 501-661-2000 |
|
|
|
## 5 California California Department of Public Health https:/… Influenza (Flu) 916-558-1784 |
|
|
|
## 6 Colorado Colorado Department of Public Health and Environment https:/… Influenza Surve… 303-692-2000 |
|
|
|
## 7 Connecticut Connecticut Department of Public Health http://… Flu Statistics 860-509-8000 |
|
|
|
## 8 Delaware Delaware Health and Social Services http://… Weekly Influenz… 302-744-4700 |
|
|
|
## 9 District of Columbia District of Columbia Department of Health http://… Influenza Infor… 202-442-5955 |
|
|
|
## 10 Florida Florida Department of Health "http:/… Weekly Influenz… 850-245-4300 |
|
|
|
## # ... with 49 more rows |
|
|
|
|
|
|
|
### Retrieve WHO/NREVSS Surveillance Data |
|
|
|
|
|
|
|
@ -657,32 +654,32 @@ glimpse(xdat <- who_nrevss("national")) |
|
|
|
## ..$ 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" ... |
|
|
|
## $ public_health_labs :Classes 'tbl_df', 'tbl' and 'data.frame': 153 obs. of 13 variables: |
|
|
|
## ..$ region_type : chr [1:153] "National" "National" "National" "National" ... |
|
|
|
## ..$ region : chr [1:153] "National" "National" "National" "National" ... |
|
|
|
## ..$ year : int [1:153] 2015 2015 2015 2015 2015 2015 2015 2015 2015 2015 ... |
|
|
|
## ..$ week : int [1:153] 40 41 42 43 44 45 46 47 48 49 ... |
|
|
|
## ..$ total_specimens : int [1:153] 1139 1152 1198 1244 1465 1393 1458 1157 1550 1518 ... |
|
|
|
## ..$ a_2009_h1n1 : int [1:153] 4 5 10 9 4 11 17 17 27 38 ... |
|
|
|
## ..$ a_h3 : int [1:153] 65 41 50 31 23 34 42 24 36 37 ... |
|
|
|
## ..$ a_subtyping_not_performed: int [1:153] 2 2 1 4 4 1 1 0 3 3 ... |
|
|
|
## ..$ b : int [1:153] 10 7 8 9 9 10 4 4 9 11 ... |
|
|
|
## ..$ bvic : int [1:153] 0 3 3 1 1 4 0 3 3 2 ... |
|
|
|
## ..$ byam : int [1:153] 1 0 2 4 4 2 4 9 12 11 ... |
|
|
|
## ..$ h3n2v : int [1:153] 0 0 0 0 0 0 0 0 0 0 ... |
|
|
|
## ..$ wk_date : Date[1:153], format: "2015-10-04" "2015-10-11" "2015-10-18" "2015-10-25" ... |
|
|
|
## $ clinical_labs :Classes 'tbl_df', 'tbl' and 'data.frame': 153 obs. of 11 variables: |
|
|
|
## ..$ region_type : chr [1:153] "National" "National" "National" "National" ... |
|
|
|
## ..$ region : chr [1:153] "National" "National" "National" "National" ... |
|
|
|
## ..$ year : int [1:153] 2015 2015 2015 2015 2015 2015 2015 2015 2015 2015 ... |
|
|
|
## ..$ week : int [1:153] 40 41 42 43 44 45 46 47 48 49 ... |
|
|
|
## ..$ total_specimens : int [1:153] 12029 13111 13441 13537 14687 15048 15250 15234 16201 16673 ... |
|
|
|
## ..$ total_a : int [1:153] 84 116 97 98 97 122 84 119 145 140 ... |
|
|
|
## ..$ total_b : int [1:153] 43 54 52 52 68 86 98 92 81 106 ... |
|
|
|
## ..$ percent_positive: num [1:153] 1.06 1.3 1.11 1.11 1.12 ... |
|
|
|
## ..$ percent_a : num [1:153] 0.698 0.885 0.722 0.724 0.66 ... |
|
|
|
## ..$ percent_b : num [1:153] 0.357 0.412 0.387 0.384 0.463 ... |
|
|
|
## ..$ wk_date : Date[1:153], format: "2015-10-04" "2015-10-11" "2015-10-18" "2015-10-25" ... |
|
|
|
|
|
|
|
``` r |
|
|
|
mutate(xdat$combined_prior_to_2015_16, |
|
|
|
@ -694,7 +691,7 @@ mutate(xdat$combined_prior_to_2015_16, |
|
|
|
theme_ipsum_rc(grid="XY") |
|
|
|
``` |
|
|
|
|
|
|
|
<!-- --> |
|
|
|
<img src="README_files/figure-gfm/who-vrevss-1.png" width="672" /> |
|
|
|
|
|
|
|
``` r |
|
|
|
who_nrevss("hhs", years=2016) |
|
|
|
@ -702,34 +699,34 @@ 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 |
|
|
|
## <chr> <chr> <int> <chr> <int> <int> <int> <int> <int> <int> <int> |
|
|
|
## 1 HHS Regions Region 1 2016 <NA> 31 0 6 0 0 0 0 |
|
|
|
## 2 HHS Regions Region 2 2016 <NA> 31 0 6 0 0 2 0 |
|
|
|
## 3 HHS Regions Region 3 2016 <NA> 112 2 2 0 0 0 0 |
|
|
|
## 4 HHS Regions Region 4 2016 <NA> 112 1 11 0 1 2 0 |
|
|
|
## 5 HHS Regions Region 5 2016 <NA> 204 0 7 0 0 0 1 |
|
|
|
## 6 HHS Regions Region 6 2016 <NA> 39 1 1 0 0 0 0 |
|
|
|
## 7 HHS Regions Region 7 2016 <NA> 24 0 2 0 0 1 0 |
|
|
|
## 8 HHS Regions Region 8 2016 <NA> 46 2 8 0 0 0 0 |
|
|
|
## 9 HHS Regions Region 9 2016 <NA> 186 3 27 0 0 0 3 |
|
|
|
## 10 HHS Regions Region 10 2016 <NA> 113 0 17 0 0 0 0 |
|
|
|
## # ... with 510 more rows, and 2 more variables: h3n2v <int>, wk_date <date> |
|
|
|
## region_type region year week total_specimens a_2009_h1n1 a_h3 a_subtyping_not… b bvic byam h3n2v wk_date |
|
|
|
## <chr> <chr> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <date> |
|
|
|
## 1 HHS Regions Regio… 2016 40 31 0 6 0 0 0 0 0 2016-10-02 |
|
|
|
## 2 HHS Regions Regio… 2016 40 31 0 6 0 0 2 0 0 2016-10-02 |
|
|
|
## 3 HHS Regions Regio… 2016 40 112 2 2 0 0 0 0 0 2016-10-02 |
|
|
|
## 4 HHS Regions Regio… 2016 40 112 1 11 0 1 2 0 0 2016-10-02 |
|
|
|
## 5 HHS Regions Regio… 2016 40 204 0 7 0 0 0 1 0 2016-10-02 |
|
|
|
## 6 HHS Regions Regio… 2016 40 39 1 1 0 0 0 0 0 2016-10-02 |
|
|
|
## 7 HHS Regions Regio… 2016 40 24 0 2 0 0 1 0 0 2016-10-02 |
|
|
|
## 8 HHS Regions Regio… 2016 40 46 2 8 0 0 0 0 0 2016-10-02 |
|
|
|
## 9 HHS Regions Regio… 2016 40 186 3 27 0 0 0 3 0 2016-10-02 |
|
|
|
## 10 HHS Regions Regio… 2016 40 113 0 17 0 0 0 0 0 2016-10-02 |
|
|
|
## # ... with 510 more rows |
|
|
|
## |
|
|
|
## $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 |
|
|
|
## <chr> <chr> <int> <int> <int> <int> <int> <dbl> <dbl> <dbl> <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 |
|
|
|
## region_type region year week total_specimens total_a total_b percent_positive percent_a percent_b wk_date |
|
|
|
## <chr> <chr> <int> <int> <int> <int> <int> <dbl> <dbl> <dbl> <date> |
|
|
|
## 1 HHS Regions Region 1 2016 40 654 5 1 0.917 0.765 0.153 2016-10-02 |
|
|
|
## 2 HHS Regions Region 2 2016 40 1307 10 3 0.995 0.765 0.230 2016-10-02 |
|
|
|
## 3 HHS Regions Region 3 2016 40 941 1 4 0.531 0.106 0.425 2016-10-02 |
|
|
|
## 4 HHS Regions Region 4 2016 40 2960 46 63 3.68 1.55 2.13 2016-10-02 |
|
|
|
## 5 HHS Regions Region 5 2016 40 2386 8 5 0.545 0.335 0.210 2016-10-02 |
|
|
|
## 6 HHS Regions Region 6 2016 40 1914 22 13 1.83 1.15 0.679 2016-10-02 |
|
|
|
## 7 HHS Regions Region 7 2016 40 723 0 0 0 0 0 2016-10-02 |
|
|
|
## 8 HHS Regions Region 8 2016 40 913 8 0 0.876 0.876 0 2016-10-02 |
|
|
|
## 9 HHS Regions Region 9 2016 40 992 6 1 0.706 0.605 0.101 2016-10-02 |
|
|
|
## 10 HHS Regions Region 10 2016 40 590 14 0 2.37 2.37 0 2016-10-02 |
|
|
|
## # ... with 510 more rows |
|
|
|
|
|
|
|
``` r |
|
|
|
@ -738,35 +735,35 @@ 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 |
|
|
|
## <chr> <chr> <int> <chr> <int> <int> <int> <int> <int> |
|
|
|
## 1 Census Regions New England 2016 <NA> 31 0 6 0 0 |
|
|
|
## 2 Census Regions Mid-Atlantic 2016 <NA> 50 0 8 0 0 |
|
|
|
## 3 Census Regions East North Central 2016 <NA> 139 0 4 0 0 |
|
|
|
## 4 Census Regions West North Central 2016 <NA> 103 0 6 0 0 |
|
|
|
## 5 Census Regions South Atlantic 2016 <NA> 181 3 11 0 1 |
|
|
|
## 6 Census Regions East South Central 2016 <NA> 24 0 0 0 0 |
|
|
|
## 7 Census Regions West South Central 2016 <NA> 27 0 1 0 0 |
|
|
|
## 8 Census Regions Mountain 2016 <NA> 54 3 10 0 0 |
|
|
|
## 9 Census Regions Pacific 2016 <NA> 289 3 41 0 0 |
|
|
|
## 10 Census Regions New England 2016 <NA> 14 0 2 0 0 |
|
|
|
## # ... with 458 more rows, and 4 more variables: bvic <int>, byam <int>, h3n2v <int>, wk_date <date> |
|
|
|
## region_type region year week total_specimens a_2009_h1n1 a_h3 a_subtyping_not… b bvic byam h3n2v wk_date |
|
|
|
## <chr> <chr> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <date> |
|
|
|
## 1 Census Reg… New E… 2016 40 31 0 6 0 0 0 0 0 2016-10-02 |
|
|
|
## 2 Census Reg… Mid-A… 2016 40 50 0 8 0 0 2 0 0 2016-10-02 |
|
|
|
## 3 Census Reg… East … 2016 40 139 0 4 0 0 0 1 0 2016-10-02 |
|
|
|
## 4 Census Reg… West … 2016 40 103 0 6 0 0 1 0 0 2016-10-02 |
|
|
|
## 5 Census Reg… South… 2016 40 181 3 11 0 1 2 0 0 2016-10-02 |
|
|
|
## 6 Census Reg… East … 2016 40 24 0 0 0 0 0 0 0 2016-10-02 |
|
|
|
## 7 Census Reg… West … 2016 40 27 0 1 0 0 0 0 0 2016-10-02 |
|
|
|
## 8 Census Reg… Mount… 2016 40 54 3 10 0 0 0 1 0 2016-10-02 |
|
|
|
## 9 Census Reg… Pacif… 2016 40 289 3 41 0 0 0 2 0 2016-10-02 |
|
|
|
## 10 Census Reg… New E… 2016 41 14 0 2 0 0 0 0 0 2016-10-09 |
|
|
|
## # ... with 458 more rows |
|
|
|
## |
|
|
|
## $clinical_labs |
|
|
|
## # A tibble: 468 x 11 |
|
|
|
## 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 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 <date> |
|
|
|
## region_type region year week total_specimens total_a total_b percent_positive percent_a percent_b wk_date |
|
|
|
## <chr> <chr> <int> <int> <int> <int> <int> <dbl> <dbl> <dbl> <date> |
|
|
|
## 1 Census Regions New Engl… 2016 40 654 5 1 0.917 0.765 0.153 2016-10-02 |
|
|
|
## 2 Census Regions Mid-Atla… 2016 40 1579 10 4 0.887 0.633 0.253 2016-10-02 |
|
|
|
## 3 Census Regions East Nor… 2016 40 2176 6 5 0.506 0.276 0.230 2016-10-02 |
|
|
|
## 4 Census Regions West Nor… 2016 40 1104 3 0 0.272 0.272 0 2016-10-02 |
|
|
|
## 5 Census Regions South At… 2016 40 2785 43 62 3.77 1.54 2.23 2016-10-02 |
|
|
|
## 6 Census Regions East Sou… 2016 40 844 4 4 0.948 0.474 0.474 2016-10-02 |
|
|
|
## 7 Census Regions West Sou… 2016 40 1738 21 13 1.96 1.21 0.748 2016-10-02 |
|
|
|
## 8 Census Regions Mountain 2016 40 1067 8 0 0.750 0.750 0 2016-10-02 |
|
|
|
## 9 Census Regions Pacific 2016 40 1433 20 1 1.47 1.40 0.0698 2016-10-02 |
|
|
|
## 10 Census Regions New Engl… 2016 41 810 5 1 0.741 0.617 0.123 2016-10-09 |
|
|
|
## # ... with 458 more rows |
|
|
|
|
|
|
|
``` r |
|
|
|
who_nrevss("state", years=2016) |
|
|
|
@ -774,35 +771,35 @@ 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 |
|
|
|
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> |
|
|
|
## 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 <NA> <NA> <NA> <NA> |
|
|
|
## # ... with 44 more rows, and 5 more variables: b <chr>, bvic <chr>, byam <chr>, h3n2v <chr>, wk_date <date> |
|
|
|
## region_type region season_descript… total_specimens a_2009_h1n1 a_h3 a_subtyping_not_p… b bvic byam h3n2v |
|
|
|
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> |
|
|
|
## 1 States Alabama Season 2016-17 570 3 227 1 2 15 14 0 |
|
|
|
## 2 States Alaska Season 2016-17 5222 14 905 3 252 2 11 0 |
|
|
|
## 3 States Arizona Season 2016-17 2975 63 1630 0 5 227 578 0 |
|
|
|
## 4 States Arkansas Season 2016-17 121 0 51 0 0 4 0 0 |
|
|
|
## 5 States California Season 2016-17 14074 184 4696 120 116 28 152 0 |
|
|
|
## 6 States Colorado Season 2016-17 714 3 267 2 4 31 219 0 |
|
|
|
## 7 States Connectic… Season 2016-17 1348 19 968 0 0 62 263 0 |
|
|
|
## 8 States Delaware Season 2016-17 3090 5 659 4 11 27 127 1 |
|
|
|
## 9 States District … Season 2016-17 73 1 34 0 3 0 4 0 |
|
|
|
## 10 States Florida Season 2016-17 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> |
|
|
|
## # ... with 44 more rows, and 1 more variable: wk_date <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 |
|
|
|
## <chr> <chr> <int> <int> <chr> <chr> <chr> <chr> <chr> <chr> |
|
|
|
## 1 States Alabama 2016 40 379 4 0 1.06 1.06 0 |
|
|
|
## 2 States Alaska 2016 40 <NA> <NA> <NA> <NA> <NA> <NA> |
|
|
|
## 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 <NA> <NA> <NA> <NA> <NA> <NA> |
|
|
|
## 10 States Florida 2016 40 <NA> <NA> <NA> <NA> <NA> <NA> |
|
|
|
## # ... with 2,798 more rows, and 1 more variables: wk_date <date> |
|
|
|
## region_type region year week total_specimens total_a total_b percent_positive percent_a percent_b wk_date |
|
|
|
## <chr> <chr> <int> <int> <chr> <chr> <chr> <chr> <chr> <chr> <date> |
|
|
|
## 1 States Alabama 2016 40 406 4 1 1.23 0.99 0.25 2016-10-02 |
|
|
|
## 2 States Alaska 2016 40 <NA> <NA> <NA> <NA> <NA> <NA> 2016-10-02 |
|
|
|
## 3 States Arizona 2016 40 133 0 0 0 0 0 2016-10-02 |
|
|
|
## 4 States Arkansas 2016 40 47 0 0 0 0 0 2016-10-02 |
|
|
|
## 5 States California 2016 40 668 2 0 0.3 0.3 0 2016-10-02 |
|
|
|
## 6 States Colorado 2016 40 260 0 0 0 0 0 2016-10-02 |
|
|
|
## 7 States Connecticut 2016 40 199 3 0 1.51 1.51 0 2016-10-02 |
|
|
|
## 8 States Delaware 2016 40 40 0 0 0 0 0 2016-10-02 |
|
|
|
## 9 States District of… 2016 40 <NA> <NA> <NA> <NA> <NA> <NA> 2016-10-02 |
|
|
|
## 10 States Florida 2016 40 <NA> <NA> <NA> <NA> <NA> <NA> 2016-10-02 |
|
|
|
## # ... with 2,798 more rows |
|
|
|
|
|
|
|
## Code of Conduct |
|
|
|
|
|
|
|
|
