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Quickstart

Source: vignettes/Quickstart.Rmd
Quickstart.Rmd

In this vignette we illustrate how to obtain data from the API using scarlet fever data in Ontario as an example.

(Image From: https://www.flickr.com/photos/niaid/52602981880/)

Preliminaries

We use the following packages for this illustration.

We also turn off messages from the API that are not helpful when presenting this material.

options(iidda_api_msgs = FALSE)

Scarlet Fever Data in Ontario

Data from the canmod digitization project provides communicable disease incidence data for all notifiable infectious diseases, including scarlet fever. The name of the main dataset from that project is canmod-cdi-normalized, which we can get and filter using the following ?featured_data command.

scarlet_fever_ontario = featured_data(
    dataset_id = "canmod-cdi-normalized"
  , iso_3166 = "CA"
  , iso_3166_2 = "CA-ON"
  , time_scale = "wk"
  , basal_disease = "scarlet-fever"
  , period_end_date = "1929-08-01..1930-10-01"
)
print(scarlet_fever_ontario)
#> # A tibble: 61 × 21
#>    iso_3166 iso_3166_2 period_start_date period_end_date disease nesting_disease
#>    <chr>    <chr>      <date>            <date>          <chr>   <chr>          
#>  1 CA       CA-ON      1929-07-28        1929-08-03      scarle… ""             
#>  2 CA       CA-ON      1929-08-04        1929-08-10      scarle… ""             
#>  3 CA       CA-ON      1929-08-11        1929-08-17      scarle… ""             
#>  4 CA       CA-ON      1929-08-18        1929-08-24      scarle… ""             
#>  5 CA       CA-ON      1929-08-25        1929-08-31      scarle… ""             
#>  6 CA       CA-ON      1929-09-01        1929-09-07      scarle… ""             
#>  7 CA       CA-ON      1929-09-08        1929-09-14      scarle… ""             
#>  8 CA       CA-ON      1929-09-15        1929-09-21      scarle… ""             
#>  9 CA       CA-ON      1929-09-22        1929-09-28      scarle… ""             
#> 10 CA       CA-ON      1929-09-29        1929-10-05      scarle… ""             
#> # ℹ 51 more rows
#> # ℹ 15 more variables: basal_disease <chr>, cases_this_period <dbl>,
#> #   location <chr>, location_type <chr>, time_scale <chr>,
#> #   historical_disease <chr>, historical_disease_family <chr>,
#> #   historical_disease_subclass <chr>, days_this_period <dbl>,
#> #   period_mid_date <date>, population <dbl>, record_origin <chr>,
#> #   original_dataset_id <chr>, digitization_id <chr>, scan_id <chr>
(scarlet_fever_ontario
  |> ggplot(aes(period_end_date, cases_this_period))
  + geom_line() + geom_point()
  + ggtitle("Scarlet Fever Incidence in Ontario, Canada")
  + theme_bw()
)