R/param_estimates_published.R
param_estimates_published.RdPublished estimates of epidemiological characteristics from both peer-reviewed and non-peer-reviewed resources, encoded by community members and approved by authors. For complete information on each estimate, see the actual dataset items.
param_estimates_published()a data.frame
Other data-import:
acaps_government_measures_data(),
acaps_secondary_impact_data(),
apple_mobility_data(),
beoutbreakprepared_data(),
cci_us_vaccine_data(),
cdc_aggregated_projections(),
cdc_excess_deaths(),
cdc_social_vulnerability_index(),
coronadatascraper_data(),
coronanet_government_response_data(),
cov_glue_lineage_data(),
cov_glue_newick_data(),
cov_glue_snp_lineage(),
covidtracker_data(),
descartes_mobility_data(),
ecdc_data(),
econ_tracker_consumer_spending,
econ_tracker_employment,
econ_tracker_unemp_data,
economist_excess_deaths(),
financial_times_excess_deaths(),
google_mobility_data(),
government_policy_timeline(),
jhu_data(),
jhu_us_data(),
kff_icu_beds(),
nytimes_county_data(),
oecd_unemployment_data(),
owid_data(),
test_and_trace_data(),
us_county_geo_details(),
us_county_health_rankings(),
us_healthcare_capacity(),
us_hospital_details(),
us_state_distancing_policy(),
usa_facts_data(),
who_cases()
library(dplyr)
params = param_estimates_published()
colnames(params)
#> [1] "id" "peer_review" "peer_review_location"
#> [4] "name" "abbreviation" "units"
#> [7] "country" "location_name" "location_type"
#> [10] "start_date" "end_date" "value_type"
#> [13] "value" "uncertainty_type" "lower_bound"
#> [16] "upper_bound" "population" "age_range"
#> [19] "method_description" "data_description" "data_URL"
#> [22] "date_publication" "title_publication" "type_publication"
#> [25] "authors" "publication_URL" "entry_date"
#> [28] "entry_person" "entry_email"
head(params)
#> # A tibble: 6 × 29
#> id peer_review peer_review_location name abbreviation units country
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 covid1 NA NA cumulative… NA pers… China
#> 2 covid2 NA MedRxiv cumulative… NA pers… China
#> 3 covid3 NA NA date of em… NA NA China
#> 4 covid4 positive Eurosurveillance basic repr… R0 Nb China
#> 5 covid5 NA BioRxiv basic repr… R0 Nb China
#> 6 covid6 NA NA basic repr… R0 Nb China
#> # … with 22 more variables: location_name <chr>, location_type <chr>,
#> # start_date <date>, end_date <date>, value_type <chr>, value <chr>,
#> # uncertainty_type <chr>, lower_bound <chr>, upper_bound <chr>,
#> # population <chr>, age_range <chr>, method_description <chr>,
#> # data_description <chr>, data_URL <chr>, date_publication <date>,
#> # title_publication <chr>, type_publication <chr>, authors <chr>,
#> # publication_URL <chr>, entry_date <date>, entry_person <chr>, …
dplyr::glimpse(params)
#> Rows: 845
#> Columns: 29
#> $ id <chr> "covid1", "covid2", "covid3", "covid4", "covid5",…
#> $ peer_review <chr> NA, NA, NA, "positive", NA, NA, "positive", NA, N…
#> $ peer_review_location <chr> NA, "MedRxiv", NA, "Eurosurveillance", "BioRxiv",…
#> $ name <chr> "cumulative case count", "cumulative case count",…
#> $ abbreviation <chr> NA, NA, NA, "R0", "R0", "R0", "R0", "R0", "k", NA…
#> $ units <chr> "persons", "persons", NA, "Nb", "Nb", "Nb", "Nb",…
#> $ country <chr> "China", "China", "China", "China", "China", "Chi…
#> $ location_name <chr> "Wuhan City", "Wuhan City", "Wuhan City", "Wuhan …
#> $ location_type <chr> "city", "metropolitan area", "city", "city", "cit…
#> $ start_date <date> 2020-01-18, 2019-12-31, NA, 2020-01-09, 2019-11-…
#> $ end_date <date> 2020-01-18, 2020-01-29, NA, 2020-01-11, 2020-01-…
#> $ value_type <chr> "central estimate, unspecified", "median", NA, NA…
#> $ value <chr> "4000", "31200", NA, "0.3", "2.2", "2.6", "2.24",…
#> $ uncertainty_type <chr> "confidence interval 95%", "confidence interval 9…
#> $ lower_bound <chr> "1000", "23400", "2020-11-19", "0.17", "1.4", "1.…
#> $ upper_bound <chr> "9700", "40400", "2020-12-19", "0.44", "3.8", "3.…
#> $ population <chr> "general population", "general population", "gene…
#> $ age_range <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
#> $ method_description <chr> NA, "mobility model assuming travelers are expose…
#> $ data_description <chr> "7 imported cases internationally as of 9:00 GMT…
#> $ data_URL <chr> NA, NA, NA, NA, "https://github.com/jriou/wcov", …
#> $ date_publication <date> 2020-01-22, 2020-01-29, 2020-01-23, 2020-01-12, …
#> $ title_publication <chr> "Report 3: Transmissibility of 2019-nCoV", "Early…
#> $ type_publication <chr> "report", "report", "executive summary", "report"…
#> $ authors <chr> "Imai N., Dorigatti I., Cori A., Donnelly C., Ril…
#> $ publication_URL <chr> "https://www.imperial.ac.uk/mrc-global-infectious…
#> $ entry_date <date> 2020-01-24, 2020-01-24, 2020-01-24, 2020-01-24, …
#> $ entry_person <chr> "Cecile Viboud", "Cecile Viboud", "Cecile Viboud"…
#> $ entry_email <chr> "viboudc@mail.nih.gov", "viboudc@mail.nih.gov", "…
summary(params)
#> id peer_review peer_review_location name
#> Length:845 Length:845 Length:845 Length:845
#> Class :character Class :character Class :character Class :character
#> Mode :character Mode :character Mode :character Mode :character
#>
#>
#>
#>
#> abbreviation units country location_name
#> Length:845 Length:845 Length:845 Length:845
#> Class :character Class :character Class :character Class :character
#> Mode :character Mode :character Mode :character Mode :character
#>
#>
#>
#>
#> location_type start_date end_date
#> Length:845 Min. :2019-11-01 Min. :2019-02-04
#> Class :character 1st Qu.:2019-12-31 1st Qu.:2020-02-13
#> Mode :character Median :2020-01-14 Median :2020-04-16
#> Mean :2020-01-21 Mean :2020-03-26
#> 3rd Qu.:2020-01-23 3rd Qu.:2020-04-24
#> Max. :2020-12-24 Max. :2020-07-25
#> NA's :324 NA's :131
#> value_type value uncertainty_type lower_bound
#> Length:845 Length:845 Length:845 Length:845
#> Class :character Class :character Class :character Class :character
#> Mode :character Mode :character Mode :character Mode :character
#>
#>
#>
#>
#> upper_bound population age_range method_description
#> Length:845 Length:845 Length:845 Length:845
#> Class :character Class :character Class :character Class :character
#> Mode :character Mode :character Mode :character Mode :character
#>
#>
#>
#>
#> data_description data_URL date_publication title_publication
#> Length:845 Length:845 Min. :2020-01-12 Length:845
#> Class :character Class :character 1st Qu.:2020-03-19 Class :character
#> Mode :character Mode :character Median :2020-04-01 Mode :character
#> Mean :2020-04-04
#> 3rd Qu.:2020-04-26
#> Max. :2020-06-08
#>
#> type_publication authors publication_URL entry_date
#> Length:845 Length:845 Length:845 Min. :2020-01-24
#> Class :character Class :character Class :character 1st Qu.:2020-03-24
#> Mode :character Mode :character Mode :character Median :2020-04-02
#> Mean :2020-04-09
#> 3rd Qu.:2020-04-29
#> Max. :2020-06-19
#>
#> entry_person entry_email
#> Length:845 Length:845
#> Class :character Class :character
#> Mode :character Mode :character
#>
#>
#>
#>
if(require(DT) & interactive()) {
datatable(params)
}
#> Loading required package: DT