Merge pull request #260 from cmu-delphi/ndefries/nchs-week-parsing

Get NCHS mortality to fetch data by changing expected date col output type to `epiweek`

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: epidatr
 Type: Package
 Title: Client for Delphi's 'Epidata' API
-Version: 1.1.1
+Version: 1.1.2
 Authors@R:
   c(
     person("Logan", "Brooks", email = "[email protected]", role = c("aut")),

NEWS.md

@@ -5,8 +5,10 @@
 ## Features
 
 ## Patches
-- Fixed failure when passing `as_of` values in `Date` format to
-  `pub_covidcast` while caching is enabled (#259)
+- Fix failure when passing `as_of` values in `Date` format to
+  `pub_covidcast` while caching is enabled (#259).
+- For `pub_covidcast` data source `nchs-mortality`, parse dates as `epiweek`
+  and expect `epiweek` inputs from user (#260).
 
 # epidatr 1.1.0
 

R/endpoints.R

@@ -1025,6 +1025,13 @@ pub_covidcast <- function(
   as_of <- parse_timeset_input(as_of)
   issues <- parse_timeset_input(issues)
 
+  if (source == "nchs-mortality" && time_type != "week") {
+    cli::cli_abort(
+      "{source} data is only available at the week level",
+      class = "epidatr__nchs_week_only"
+    )
+  }
+
   create_epidata_call(
     "covidcast/",
     list(
@@ -1051,8 +1058,14 @@ pub_covidcast <- function(
           c("day", "week")
       ),
       create_epidata_field_info("geo_value", "text"),
-      create_epidata_field_info("time_value", "date"),
-      create_epidata_field_info("issue", "date"),
+      create_epidata_field_info("time_value", switch(time_type,
+        day = "date",
+        week = "epiweek"
+      )),
+      create_epidata_field_info("issue", switch(time_type,
+        day = "date",
+        week = "epiweek"
+      )),
       create_epidata_field_info("lag", "int"),
       create_epidata_field_info("value", "float"),
       create_epidata_field_info("stderr", "float"),

tests/testthat/test-endpoints.R

@@ -517,3 +517,14 @@ test_that("pub_covid_hosp_state_timeseries supports versioned queries", {
   expect_identical(epidata_call$params$as_of, 20220101)
   expect_identical(epidata_call$params$lag, NULL)
 })
+
+test_that("nchs-mortality call fails if time_type not week", {
+  expect_error(pub_covidcast(
+    source = "nchs-mortality",
+    signals = "signal",
+    time_type = "day",
+    geo_type = "state",
+    time_values = "*",
+    geo_values = "*"
+  ), class = "epidatr__nchs_week_only")
+})