[Issue 182] Update epi_df examples, check additional_metadata type at construction

R/epi_df.R

@@ -117,7 +117,11 @@ new_epi_df = function(x = tibble::tibble(), geo_type, time_type, as_of,
   if (!is.data.frame(x)) {
     Abort("`x` must be a data frame.")
   }
-
+
+  if (!is.list(additional_metadata)) {
+    Abort("`additional_metadata` must be a list type.")
+  }
+
   # If geo type is missing, then try to guess it
   if (missing(geo_type)) {
     geo_type = guess_geo_type(x$geo_value)
@@ -230,7 +234,7 @@ new_epi_df = function(x = tibble::tibble(), geo_type, time_type, as_of,
 #' 
 #' ex2 <- ex2_input %>% dplyr::rename(geo_value = state, time_value = reported_date) %>%
 #'   as_epi_df(geo_type = "state", as_of = "2020-06-03", 
-#'             additional_metadata = c(other_keys = "pol"))
+#'             additional_metadata = list(other_keys = "pol")) 
 #' 
 #' attr(ex2,"metadata")
 #' 
@@ -244,8 +248,10 @@ new_epi_df = function(x = tibble::tibble(), geo_type, time_type, as_of,
 #' 
 #' ex3 <- ex3_input %>% 
 #'   tsibble::as_tsibble() %>% # needed to add the additional metadata
-#'   dplyr::mutate(state = rep("MA",6)) %>%
-#'   as_epi_df(additional_metadata = c(other_keys = "state"))
+#'   dplyr::mutate(
+#'     state = rep("MA",6),
+#'     pol = rep(c("blue", "swing", "swing"), each = 2)) %>% # 2 extra keys
+#'   as_epi_df(additional_metadata = list(other_keys = "state", "pol")) 
 #' 
 #' attr(ex3,"metadata")
 as_epi_df = function(x, ...) {

tests/testthat/test-epi_df.R

@@ -24,3 +24,18 @@ test_that("new_epi_df works as intended", {
   expect_identical(attributes(epi_tib)$metadata$time_type, "day")
   expect_true(lubridate::is.POSIXt(attributes(epi_tib)$metadata$as_of))
 })
+
+test_that("as_epi_df errors when additional_metadata is not a list", {
+  # This is the 3rd example from as_epi_df
+  ex_input <- jhu_csse_county_level_subset %>%
+    dplyr::filter(time_value > "2021-12-01", state_name == "Massachusetts") %>%
+    dplyr::slice_tail(n = 6) %>%
+    tsibble::as_tsibble() %>%
+    dplyr::mutate(
+      state = rep("MA",6),
+      pol = rep(c("blue", "swing", "swing"), each = 2))
+
+  expect_error(
+    as_epi_df(ex_input, additional_metadata = c(other_keys = "state", "pol")), 
+    "`additional_metadata` must be a list type.")
+})

tests/testthat/test-methods-epi_df.R

@@ -8,7 +8,7 @@ toy_epi_df <- tibble::tibble(
   ), times = 2),
   geo_value = rep(c("ca", "hi"), each = 5),
   indicator_var = as.factor(rep(1:2, times = 5)), 
-) %>% as_epi_df(additional_metadata = c(other_keys = "indicator_var"))
+) %>% as_epi_df(additional_metadata = list(other_keys = "indicator_var"))
 
 att_toy = attr(toy_epi_df, "metadata")
 

vignettes/epiprocess.Rmd

@@ -180,7 +180,7 @@ head(ex2)
 
 ex2 <- ex2 %>% rename(geo_value = state, time_value = reported_date) %>%
   as_epi_df(geo_type = "state", as_of = "2020-06-03", 
-            additional_metadata = c(other_keys = "pol"))
+            additional_metadata = list(other_keys = "pol"))
 
 attr(ex2,"metadata")
 ```
@@ -206,7 +206,7 @@ Now we add state (MA) as a new column and a key to the metadata. Reminder that l
 ex3 <- ex3 %>% 
   as_tibble() %>% # needed to add the additional metadata
   mutate(state = rep(tolower("MA"),6)) %>%
-  as_epi_df(additional_metadata = c(other_keys = "state"))
+  as_epi_df(additional_metadata = list(other_keys = "state"))
 
 attr(ex3,"metadata")
 ```