Remove linelist default values from tags_types

R/make_datatagr.R

@@ -8,12 +8,11 @@
 #' @param x a `data.frame` or a `tibble`
 #'
 #' @param ... <[`dynamic-dots`][rlang::dyn-dots]> A series of tags provided as
-#'   `tag_name = "column_name"`, where `tag_name` indicates any of the known
-#'   variables listed in 'Details' and values indicate their name in `x`; see
-#'   details for a list of known variable types and their expected content
+#'   `tag_name = "column_name"`. When specifying tags, please also see 
+#'   `tag_defaults` to specify default values.
 #'
 #' @param tag_defaults a list of default values for the provided tags. Defaults
-#'   to `list()`
+#'   to `list()`, effectively defaulting to NULL values.
 #'
 #' @param allow_extra a `logical` indicating if additional data tags not
 #'   currently recognized by `datatagr` should be allowed; if `FALSE`, unknown
@@ -27,47 +26,6 @@
 #' * [set_tags()]: for modifying tags
 #' * [tags_df()]: for selecting variables by tags
 #'
-#' @details Known variable types include:
-#'
-#' * `id`: a unique case identifier as `numeric` or `character`
-#'
-#' * `date_onset`: date of symptom onset (see below for date formats)
-#'
-#' * `date_reporting`: date of case notification (see below for date formats)
-#'
-#' * `date_admission`: date of hospital admission (see below for date formats)
-#'
-#' * `date_discharge`: date of hospital discharge (see below for date formats)
-#'
-#' * `date_outcome`: date of disease outcome (see below for date formats)
-#'
-#' * `date_death`: date of death (see below for date formats)
-#'
-#' * `gender`: a `factor` or `character` indicating the gender of the patient
-#'
-#' * `age`: a `numeric` indicating the age of the patient, in years
-#'
-#' * `location`: a `factor` or `character` indicating the location of the
-#'   patient
-#'
-#' * `occupation`: a `factor` or `character` indicating the professional
-#'   activity of the patient
-#'
-#' * `hcw`: a `logical` indicating if the patient is a health care worker
-#'
-#' * `outcome`: a `factor` or `character` indicating the outcome of the disease
-#'   (death or survival)
-#'
-#'   Dates can be provided in the following formats/types:
-#'
-#' * `Date` objects (e.g. using `as.Date` on a `character` with a correct date
-#'   format); this is the recommended format
-#'
-#' * `POSIXct/POSIXlt` objects (when a finer scale than days is needed)
-#'
-#' * `numeric` values, typically indicating the number of days since the first
-#'   case
-#'
 #' @export
 #'
 #' @return The function returns a `datatagr` object.

R/tags_types.R

@@ -24,38 +24,11 @@
 #' # add new types e.g. to allow genetic sequences using ape's format
 #' tags_types(sequence = "DNAbin", allow_extra = TRUE)
 #'
-tags_types <- function(..., allow_extra = FALSE) {
-  defaults <- list(
-    id = c("numeric", "integer", "character"),
-    date_onset = date_types,
-    date_reporting = date_types,
-    date_admission = date_types,
-    date_discharge = date_types,
-    date_outcome = date_types,
-    date_death = date_types,
-    gender = category_types,
-    age = numeric_types,
-    location = category_types,
-    occupation = category_types,
-    hcw = binary_types,
-    outcome = category_types
-  )
+tags_types <- function(..., allow_extra = TRUE) {
+  defaults <- list()
 
   new_values <- rlang::list2(...)
   checkmate::assert_list(new_values, types = "character")
 
   modify_defaults(defaults = defaults, x = new_values, strict = !allow_extra)
 }
-
-
-#' @noRd
-date_types <- c("integer", "numeric", "Date", "POSIXct", "POSIXlt")
-
-#' @noRd
-category_types <- c("character", "factor")
-
-#' @noRd
-numeric_types <- c("numeric", "integer")
-
-#' @noRd
-binary_types <- c("logical", "integer", "character", "factor")

tests/testthat/_snaps/validate_types.md

@@ -2,6 +2,6 @@
 
     Some tags have the wrong class:
       - age: Must inherit from class 'factor', but has class 'numeric'
-      - gender: Must inherit from class 'character'/'factor', but has class 'numeric'
+      - gender: Must inherit from class 'character', but has class 'numeric'
 
 

tests/testthat/test-tags_types.R

@@ -1,8 +1,4 @@
 test_that("tests for tags_types", {
-  # Check errors
-  msg <- "Use only known tags or set `allow_extra = TRUE`"
-  expect_error(tags_types(toto = "ilestbo"), msg, fixed = TRUE)
-
   # Check functionality
   x <- tags_types()
   expect_type(x, "list")

tests/testthat/test-validate_datatagr.R

@@ -4,13 +4,14 @@ test_that("tests for validate_datatagr", {
   expect_error(validate_datatagr(NULL), msg)
 
   x <- make_datatagr(cars, id = "speed", toto = "dist", allow_extra = TRUE)
-  msg <- "Allowed types for tag `toto` are not documented in `ref_types`."
+  msg <- "Allowed types for tag `id`, `toto` are not documented in `ref_types`."
   expect_error(validate_datatagr(x), msg)
   expect_identical(x, validate_datatagr(x, ref_types = list(id = "numeric", toto = "numeric")))
 
   x <- make_datatagr(cars, gender = "speed")
   expect_error(
-    validate_datatagr(x),
+    validate_datatagr(x, ref_types = tags_types(gender = c('character', 
+                                                           'factor'))),
     "- gender: Must inherit from class 'character'/'factor'"
   )
 

tests/testthat/test-validate_types.R

@@ -11,7 +11,7 @@ test_that("validate_types() validates types", {
   expect_silent(
     expect_identical(
       x,
-      validate_types(x)
+      validate_types(x, ref_types = tags_types(age = 'numeric'))
     )
   )
 
@@ -24,7 +24,7 @@ test_that("validate_types() validates types", {
 
   x <- make_datatagr(cars, age = "speed", gender = "dist")
   expect_snapshot_error(
-    validate_types(x, ref_types = tags_types(age = "factor"))
+    validate_types(x, ref_types = tags_types(age = "factor", gender = "character"))
   )
 })
 
@@ -33,7 +33,7 @@ test_that("missing ref_type in validate_types()", {
   x <- make_datatagr(cars, age = "speed", d = "dist", allow_extra = TRUE)
   expect_error(
     validate_types(x),
-    "Allowed types for tag `d` are not documented in `ref_types`."
+    "Allowed types for tag `age`, `d` are not documented in `ref_types`."
   )
 
   # Two missing