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add rvdss endpoint and basic tests
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‎R/endpoints.R‎

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@@ -2036,6 +2036,155 @@ pvt_quidel <- function(
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) %>% fetch(fetch_args = fetch_args)
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}
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#' Canadian respiratory virus surveillance report
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#'
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#' @description
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#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/rvdss.html>
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#'
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#' Data is weekly.
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#'
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#' @examples
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#' \dontrun{
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#' pub_rvdss(
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#' geo_type = "province",
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#' geo_values = c("yu", "on"),
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#' time_values = epirange(20200601, 20200801)
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#' )
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#' pub_rvdss(
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#' geo_type = "province",
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#' geo_values = "*",
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#' time_values = epirange(20200601, 20200801)
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#' )
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#' }
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#'
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#' @param geo_type string. The geographic resolution of the data. Levels available:
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#' "nation", "region", "province", "lab".
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#' @param geo_values character. The geographies to return. Defaults to all
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#' ("*") geographies within requested geographic resolution. "nation" and "province"
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#' locations use standard 2-letter abbreviations (e.g. "on"). Available regions are
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#' "atlantic", "bc", "on", "prairies", "qc", and "territories." "lab"s are full
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#' facility names.
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#' @param time_values [`timeset`]. Dates to fetch. Defaults to all ("*") dates.
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#' @param ... not used for values, forces later arguments to bind by name
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#' @param as_of Date. Optionally, the as of date for the issues to fetch. If not
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#' specified, the most recent data is returned. Mutually exclusive with
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#' `issues` or `lag`.
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#' @param issues [`timeset`]. Optionally, the issue of the data to fetch. If not
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#' specified, the most recent issue is returned. Mutually exclusive with
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#' `as_of` or `lag`.
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#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
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#' @return [`tibble::tibble`]
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#'
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#' @seealso [pub_covidcast_meta()], [covidcast_epidata()], [epirange()]
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#' @keywords endpoint
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#' @export
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pub_rvdss <- function(
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geo_type,
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geo_values = "*",
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time_values = "*",
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...,
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as_of = NULL,
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issues = NULL,
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fetch_args = fetch_args_list()) {
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rlang::check_dots_empty()
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# Check parameters
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if (missing(geo_type)) {
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cli::cli_abort(
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"`geo_type` is required",
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class = "epidatr__pub_rvdss__missing_required_args"
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)
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}
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if (sum(!is.null(issues), !is.null(as_of)) > 1) {
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cli::cli_abort(
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"`issues` and `as_of` are mutually exclusive",
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class = "epidatr__pub_rvdss__too_many_issue_params"
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)
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}
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assert_character_param("geo_type", geo_type, len = 1)
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assert_timeset_param("time_values", time_values)
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assert_character_param("geo_values", geo_values)
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assert_date_param("as_of", as_of, len = 1, required = FALSE)
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assert_timeset_param("issues", issues, required = FALSE)
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time_values <- parse_timeset_input(time_values)
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as_of <- parse_timeset_input(as_of)
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issues <- parse_timeset_input(issues)
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create_epidata_call(
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"covidcast/",
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list(
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geo_type = geo_type,
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geo_values = geo_values,
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time_values = time_values,
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as_of = as_of,
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issues = issues
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),
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list(
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# descriptive fields
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create_epidata_field_info(
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"geo_type",
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"categorical",
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categories = c("nation", "region", "province", "lab")
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),
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create_epidata_field_info("geo_value", "text"),
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create_epidata_field_info("region", "text"),
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create_epidata_field_info(
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"time_type",
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"categorical",
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categories = c("week")
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),
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create_epidata_field_info("epiweek", "epiweek"), # Stored as an int in YYYYWW format
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create_epidata_field_info("time_value", "epiweek"), # Stored as a date
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create_epidata_field_info("issue", "epiweek"), # Stored as a date
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create_epidata_field_info("week", "int"),
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create_epidata_field_info("weekorder", "int"),
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create_epidata_field_info("year", "int"),
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# value fields
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create_epidata_field_info("adv_pct_positive", "float"),
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create_epidata_field_info("adv_positive_tests", "float"),
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create_epidata_field_info("adv_tests", "float"),
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create_epidata_field_info("evrv_pct_positive", "float"),
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create_epidata_field_info("evrv_positive_tests", "float"),
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create_epidata_field_info("evrv_tests", "float"),
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create_epidata_field_info("flu_pct_positive", "float"),
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create_epidata_field_info("flu_positive_tests", "float"),
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create_epidata_field_info("flu_tests", "float"),
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create_epidata_field_info("flua_pct_positive", "float"),
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create_epidata_field_info("flua_positive_tests", "float"),
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create_epidata_field_info("flua_tests", "float"),
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create_epidata_field_info("fluah1n1pdm09_positive_tests", "float"),
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create_epidata_field_info("fluah3_positive_tests", "float"),
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create_epidata_field_info("fluauns_positive_tests", "float"),
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create_epidata_field_info("flub_pct_positive", "float"),
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create_epidata_field_info("flub_positive_tests", "float"),
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create_epidata_field_info("flub_tests", "float"),
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create_epidata_field_info("hcov_pct_positive", "float"),
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create_epidata_field_info("hcov_positive_tests", "float"),
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create_epidata_field_info("hcov_tests", "float"),
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create_epidata_field_info("hmpv_pct_positive", "float"),
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create_epidata_field_info("hmpv_positive_tests", "float"),
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create_epidata_field_info("hmpv_tests", "float"),
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create_epidata_field_info("hpiv1_positive_tests", "float"),
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create_epidata_field_info("hpiv2_positive_tests", "float"),
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create_epidata_field_info("hpiv3_positive_tests", "float"),
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create_epidata_field_info("hpiv4_positive_tests", "float"),
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create_epidata_field_info("hpiv_pct_positive", "float"),
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create_epidata_field_info("hpiv_positive_tests", "float"),
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create_epidata_field_info("hpiv_tests", "float"),
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create_epidata_field_info("hpivother_positive_tests", "float"),
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create_epidata_field_info("rsv_pct_positive", "float"),
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create_epidata_field_info("rsv_positive_tests", "float"),
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create_epidata_field_info("rsv_tests", "float"),
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create_epidata_field_info("sarscov2_pct_positive", "float"),
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create_epidata_field_info("sarscov2_positive_tests", "float"),
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create_epidata_field_info("sarscov2_tests", "float")
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)
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) %>% fetch(fetch_args = fetch_args)
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}
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#' Influenza and dengue digital surveillance sensors
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#' @description
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#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/sensors.html>

‎tests/testthat/test-endpoints.R‎

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Original file line numberDiff line numberDiff line change
@@ -127,6 +127,12 @@ test_that("basic_epidata_call", {
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epiweeks = epirange(201201, 202001),
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fetch_args = fetch_args_list(dry_run = TRUE)
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) %>% request_url())
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expect_no_error(pub_rvdss(
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geo_type = "nation",
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time_values = epirange(20200601, 20200801),
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geo_values = "ca",
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fetch_args = fetch_args_list(dry_run = TRUE)
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) %>% request_url())
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expect_no_error(pvt_sensors(
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auth = "yourkey",
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names = "sar3",
@@ -325,6 +331,13 @@ test_that("endoints accept wildcard for date parameter", {
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epiweeks = "*",
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fetch_args = fetch_args_list(dry_run = TRUE)
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))
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expect_no_error(call <- pub_rvdss(
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geo_type = "province",
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time_values = "*",
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geo_values = "*",
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fetch_args = fetch_args_list(dry_run = TRUE)
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))
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expect_identical(call$params$epiweeks$from, 100001)
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expect_identical(call$params$epiweeks$to, 300001)
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