covid-model

An initial repo to test spatio-temporal modeling of covid-19.

Example Data

There are now 4 files under data/

Newer expanded data

• 2020-03-30-covid19-nyt.csv: a csv of the latest pull of the NYT county level data with some additional formating. Most states should be fine, but a couple of notes.

  • New York reports New York City with a geoid = NA instead of the 5 boroughs. Here are the county fips if you want to do anything with them nyc_county_fips <- c("36061", "36047", "36081", "36005", "36085")
  • Unknown county data is reported for almost all states.
  • Kansas City, Missouri data is reported seperately from the counties it is apart of. I wrote some code to distribute its counts into the counties using multinomial based on county population. I didn’t include it here. Will clean it up and add later if wanted

• us-acs.RData: data.frame including sf geometries for the whole US. Contains example variables from ACS (now including median age) as well as county membership of MSAs

older washingston data

• washington-acs.RData: data.frame including sf geometries. Contains example variables from ACS as well as county membership of MSAs
• washington-covid19.csv: csv of daily county level covid19 cases and deaths.

Both of these files can be recreated with the scripts in data-raw/

Daily Mobility data

I didn’t pull it into this but you might be interested in using Descartes Labs Mobility Data

mobility_df <- readr::read_csv("https://github.com/descarteslabs/DL-COVID-19/raw/master/DL-us-mobility-daterow.csv")
#> Parsed with column specification:
#> cols(
#>   date = col_date(format = ""),
#>   country_code = col_character(),
#>   admin_level = col_double(),
#>   admin1 = col_character(),
#>   admin2 = col_character(),
#>   fips = col_character(),
#>   samples = col_double(),
#>   m50 = col_double(),
#>   m50_index = col_double()
#> )

knitr::kable(head(mobility_df))

date	country_code	admin_level	admin1	admin2	fips	samples	m50	m50_index
2020-03-01	US	1	Alabama	NA	01	133826	8.331	79
2020-03-02	US	1	Alabama	NA	01	143632	10.398	98
2020-03-03	US	1	Alabama	NA	01	146009	10.538	100
2020-03-04	US	1	Alabama	NA	01	149352	10.144	96
2020-03-05	US	1	Alabama	NA	01	144109	10.982	104
2020-03-06	US	1	Alabama	NA	01	141491	13.024	123