Merge pull request #277 from atorus-research/271_add_hms

Closes #271 add_hms: add hms to xportr.numeric_types and add details to xpor…

NEWS.md

@@ -1,3 +1,11 @@
+# xportr (development version)
+
+* `"hms"` was added to the default value of the `xportr.numeric_types` option.
+This ensures that `{xportr}` works smoothly with variables created by
+`admiral::derive_vars_dtm_to_tm()`. (#271)
+
+* More details were added to the messages of `xportr_type()`. (#271)
+
 # xportr 0.4.1
 
 ## New Feature

R/messages.R

@@ -88,11 +88,39 @@ type_log <- function(meta_ordered, type_mismatch_ind, verbose) {
 
   if (length(type_mismatch_ind) > 0) {
     cli_h2("Variable type mismatches found.")
-    cli_alert_success("{ length(type_mismatch_ind) } variables coerced")
+    cli_alert_success("{ length(type_mismatch_ind) } variable{?s} coerced")
 
+    meta_mismatch <- meta_ordered[type_mismatch_ind, ]
     message <- glue(
       "Variable type(s) in dataframe don't match metadata: ",
-      "{encode_vars(meta_ordered[type_mismatch_ind, 'variable'])}"
+      "{encode_vars(meta_ordered[type_mismatch_ind, 'variable'])}\n",
+      paste0(
+        "- `", meta_mismatch$variable, "` was coerced to ",
+        ifelse(meta_mismatch$type.y == "_character", "<character>", "<numeric>"),
+        ". (type in data: ", meta_mismatch$orig_type_data, ", type in metadata: ",
+        meta_mismatch$orig_type_meta, ")",
+        collapse = "\n"
+      ),
+      paste(
+        "\ni Types in metadata considered as character (xportr.character_metadata_types option):",
+        encode_vals(getOption("xportr.character_metadata_types")),
+        collapse = " "
+      ),
+      paste(
+        "\ni Types in metadata considered as numeric (xportr.numeric_metadata_types option):",
+        encode_vals(getOption("xportr.numeric_metadata_types")),
+        collapse = " "
+      ),
+      paste(
+        "\ni Types in data considered as character (xportr.character_types option):",
+        encode_vals(getOption("xportr.character_types")),
+        collapse = " "
+      ),
+      paste(
+        "\ni Types in data considered as numeric (xportr.numeric_types option):",
+        encode_vals(getOption("xportr.numeric_types")),
+        collapse = " "
+      )
     )
 
     xportr_logger(message, verbose)

R/options.R

@@ -15,42 +15,42 @@
 #' @section Options with `options()`:
 #'
 #' \describe{
-#' \item{xportr.df_domain_name}{defaults to `"dataset"`}:
-#'  The name of the domain "name" column in dataset metadata.
-#' \item{xportr.df_label}{defaults to `"label"`}:
-#'  The column noting the dataset label in dataset metadata.
-#' \item{xportr.domain_name}{defaults to `"dataset"`}:
-#'  The name of the domain "name" column in variable metadata.
-#' \item{xportr.variable_name}{defaults to `"variable"`}:
-#'  The name of the variable "name" in variable metadata.
-#' \item{xportr.type_name}{defaults to `"type"`}:
-#'  The name of the variable type column in variable metadata.
-#' \item{xportr.label}{defaults to `"label"`}:
-#'  The name of the variable label column in variable metadata.
-#' \item{xportr.length}{defaults to `"length"`}:
-#'  The name of the variable length column in variable metadata.
-#' \item{xportr.order_name}{defaults to `"order"`}:
-#'  The name of the variable order column in variable metadata.
-#' \item{xportr.format_name}{defaults to `"format"`}:
-#'  The name of the variable format column in variable metadata.
-#' \item{xportr.format_verbose}{defaults to `"none"`}:
-#'  The default argument for the 'verbose' argument for `xportr_format`.
-#' \item{xportr.label_verbose}{defaults to `"none"`}:
-#'  The default argument for the 'verbose' argument for `xportr_label`.
-#' \item{xportr.length_verbose}{defaults to `"none"`}:
-#'  The default argument for the 'verbose' argument for `xportr_length`.
-#' \item{xportr.type_verbose}{defaults to `"label"`}:
-#'  The default argument for the 'verbose' argument for `xportr_type`.
-#' \item{xportr.character_types}{defaults to `"character"`}:
-#'  The default character vector used to explicitly coerce R classes to character XPT types.
+#' \item{xportr.df_domain_name}{defaults to `"dataset"`\cr
+#'  The name of the domain "name" column in dataset metadata.}
+#' \item{xportr.df_label}{defaults to `"label"`\cr
+#'  The column noting the dataset label in dataset metadata.}
+#' \item{xportr.domain_name}{defaults to `"dataset"`\cr
+#'  The name of the domain "name" column in variable metadata.}
+#' \item{xportr.variable_name}{defaults to `"variable"`\cr
+#'  The name of the variable "name" in variable metadata.}
+#' \item{xportr.type_name}{defaults to `"type"`\cr
+#'  The name of the variable type column in variable metadata.}
+#' \item{xportr.label}{defaults to `"label"`\cr
+#'  The name of the variable label column in variable metadata.}
+#' \item{xportr.length}{defaults to `"length"`\cr
+#'  The name of the variable length column in variable metadata.}
+#' \item{xportr.order_name}{defaults to `"order"`\cr
+#'  The name of the variable order column in variable metadata.}
+#' \item{xportr.format_name}{defaults to `"format"`\cr
+#'  The name of the variable format column in variable metadata.}
+#' \item{xportr.format_verbose}{defaults to `"none"`\cr
+#'  The default argument for the 'verbose' argument for `xportr_format`.}
+#' \item{xportr.label_verbose}{defaults to `"none"`\cr
+#'  The default argument for the 'verbose' argument for `xportr_label`.}
+#' \item{xportr.length_verbose}{defaults to `"none"`\cr
+#'  The default argument for the 'verbose' argument for `xportr_length`.}
+#' \item{xportr.type_verbose}{defaults to `"label"`\cr
+#'  The default argument for the 'verbose' argument for `xportr_type`.}
+#' \item{xportr.character_types}{defaults to `"character"`\cr
+#'  The default character vector used to explicitly coerce R classes to character XPT types.}
 #' \item{xportr.character_metadata_types}{defaults to `c("character", "char", "text", "date", "posixct", "posixt",
 #'                                              "datetime", "time", "partialdate", "partialtime", "partialdatetime",
-#'                                              "incompletedatetime", "durationdatetime", "intervaldatetime")`}:
-#'  The default character vector used to explicitly coerce R classes to character XPT types.
-#' \item{xportr.numeric_metadata_types}{defaults to `c("integer", "numeric", "num", "float")`}:
-#'  The default character vector used to explicitly coerce R classes to numeric XPT types.
-#' \item{xportr.numeric_types}{defaults to `c("integer", "float", "numeric", "posixct", "posixt", "time", "date")`}:
-#'  The default character vector used to explicitly coerce R classes to numeric XPT types.
+#'                                              "incompletedatetime", "durationdatetime", "intervaldatetime")`\cr
+#'  The default character vector used to explicitly coerce R classes to character XPT types.}
+#' \item{xportr.numeric_metadata_types}{defaults to `c("integer", "numeric", "num", "float")`\cr
+#'  The default character vector used to explicitly coerce R classes to numeric XPT types.}
+#' \item{xportr.numeric_types}{defaults to ``r deparse(getOption("xportr.numeric_types"), width.cutoff = 500)``\cr
+#'  The default character vector used to explicitly coerce R classes to numeric XPT types.}
 #' }
 #'
 #' @section Options with `xportr_options()`:

R/split.R

@@ -36,7 +36,7 @@
 #' adlb <- xportr_split(adlb, "LBCAT")
 xportr_split <- function(.df, split_by = NULL) {
   lifecycle::deprecate_warn(
-    when = "0.5.0",
+    when = "0.4.1",
     what = "xportr_split()",
     with = "xportr_write()",
     details = "Please use the argument `max_gb_size` in the

R/type.R

@@ -1,11 +1,12 @@
 #' Coerce variable type
 #'
-#' XPT v5 datasets only have data types of character and numeric. `xportr_type`
+#' XPT v5 datasets only have data types of character and numeric. `xportr_type()`
 #' attempts to collapse R classes to those two XPT types. The
 #' 'xportr.character_types' option is used to explicitly collapse the class of a
-#' column to character using `as.character`. Similarly, 'xportr.numeric_types'
-#' will collapse a column to a numeric type. If no type is passed for a
-#' variable, it is assumed to be numeric and coerced with `as.numeric()`.
+#' column to character using `as.character()`. Similarly, 'xportr.numeric_types'
+#' will collapse a column to a numeric type. (See `xportr_options()` for default
+#' values of these options.) If no type is passed for a variable, it is assumed
+#' to be numeric and coerced with `as.numeric()`.
 #'
 #' Certain care should be taken when using timing variables. R serializes dates
 #' based on a reference date of 01/01/1970 where XPT uses 01/01/1960. This can
@@ -17,7 +18,7 @@
 #'
 #' @section Messaging: `type_log()` is the primary messaging tool for
 #'   `xportr_type()`. The number of column types that mismatch the reported type
-#'   in the metadata, if any, is reported by by `xportr_type()`. If there are any
+#'   in the metadata, if any, is reported by `xportr_type()`. If there are any
 #'   type mismatches, and the 'verbose' argument is 'stop', 'warn', or
 #'   'message', each mismatch will be detailed with the actual type in the data
 #'   and the type noted in the metadata.
@@ -132,6 +133,8 @@ xportr_type <- function(.df,
     by = "variable"
   ) %>%
     mutate(
+      orig_type_data = type.x,
+      orig_type_meta = type.y,
       # _character is used here as a mask of character, in case someone doesn't
       # want 'character' coerced to character
       type.x = if_else(type.x %in% character_types, "_character", type.x),
@@ -154,11 +157,11 @@ xportr_type <- function(.df,
 
   # Check if variable types match
   is_correct <- vapply(meta_ordered[["type.x"]] == meta_ordered[["type.y"]], isTRUE, logical(1))
-  # Use the original variable iff metadata is missing that variable
+  # Use the original variable if metadata is missing that variable
   correct_type <- ifelse(is.na(meta_ordered[["type.y"]]), meta_ordered[["type.x"]], meta_ordered[["type.y"]])
 
   # Walk along the columns and coerce the variables. Modifying the columns
-  # Directly instead of something like map_dfc to preserve any attributes.
+  # directly instead of something like map_dfc to preserve any attributes.
   iwalk(
     correct_type,
     function(x, i, is_correct) {

R/xportr-package.R

@@ -12,82 +12,82 @@
 #' \itemize{
 #'   \item{
 #'   xportr.df_domain_name - The name of the domain "name" column in dataset
-#'   metadata. Default: "dataset"
+#'   metadata. Default: `"dataset"`
 #'   }
 #'   \item {
 #'   xportr.df_label - The column noting the dataset label in dataset metadata.
-#'   Default: "label"
+#'   Default: `"label"`
 #'   }
 #'   \item{
 #'   xportr.domain_name - The name of the domain "name" column in variable
-#'   metadata. Default: "dataset"
+#'   metadata. Default: `"dataset"`
 #'   }
 #'   \item{
 #'   xportr.variable_name - The name of the variable "name" in variable
-#'   metadata. Default: "variable"
+#'   metadata. Default: `"variable"`
 #'   }
 #'   \item{
 #'   xportr.type_name - The name of the variable type column in variable
-#'   metadata. Default: "type"
+#'   metadata. Default: `"type"`
 #'   }
 #'   \item{
 #'   xportr.label - The name of the variable label column in variable metadata.
-#'   Default: "label"
+#'   Default: `"label"`
 #'   }
 #'   \item{
 #'   xportr.length - The name of the variable length column in variable
-#'   metadata. Default: "length"
+#'   metadata. Default: `"length"`
 #'   }
 #'   \item{
 #'   xportr.order_name - The name of the variable order column in variable
-#'   metadata. Default: "order"
+#'   metadata. Default: `"order"`
 #'   }
 #'   \item{
 #'   xportr.format_name - The name of the variable format column in variable
-#'   metadata. Default: "format"
+#'   metadata. Default: `"format"`
 #'   }
 #'   \item{
 #'   xportr.format_verbose - The default argument for the 'verbose' argument for
-#'   `xportr_format`. Default: "none"
+#'   `xportr_format`. Default: `"none"`
 #'   }
 #'   \item{
 #'   xportr.label_verbose - The default argument for the 'verbose' argument for
-#'   `xportr_label`. Default: "none"
+#'   `xportr_label`. Default: `"none"`
 #'   }
 #'   \item{
 #'   xportr.length_verbose - The default argument for the 'verbose' argument for
-#'   `xportr_length`. Default: "none"
+#'   `xportr_length`. Default: `"none"`
 #'   }
 #'   \item{
 #'   xportr.type_verbose - The default argument for the 'verbose' argument for
-#'   `xportr_type`. Default: "none"
+#'   `xportr_type`. Default: `"none"`
 #'   }
 #'   \item{
 #'   xportr.character_types - The default character vector used to explicitly
-#'   coerce R classes to character XPT types. Default:  "character"
+#'   coerce R classes to character XPT types. Default: `"character"`
 #'   }
 #'   \item{
 #'   xportr.character_metadata_types - The default character vector used to explicitly
-#'   coerce R classes to character XPT types. Default: c("character", "char",
+#'   coerce R classes to character XPT types. Default: `c("character", "char",
 #'   "text", "date", "posixct", "posixt", "datetime", "time", "partialdate",
 #'   "partialtime", "partialdatetime", "incompletedatetime", "durationdatetime",
 #'   "intervaldatetime")`
 #'   }
 #'   \item{
 #'   xportr.numeric_metadata_types - The default character vector used to explicitly
-#'   coerce R classes to numeric XPT types. Default: c("integer", "numeric", "num", "float")
+#'   coerce R classes to numeric XPT types. Default: `c("integer", "numeric", "num", "float")`
 #'   }
 #'   \item{
 #'   xportr.numeric_types - The default character vector used to explicitly
-#'   coerce R classes to numeric XPT types. Default: c("integer", "float",
-#'   "numeric", "posixct", "posixt", "time", "date")
+#'   coerce R classes to numeric XPT types. Default:
+#'   ``r deparse(getOption("xportr.numeric_types"), width.cutoff = 500)``
 #'   }
 #' }
 #'
 #' @section Updating Options:
 #' \itemize{
 #'   \item{For a single session, an option can be changed by
-#'   `option(<optionToChange> = <NewValue>)`}
+#'   `options(<optionToChange> = <NewValue>)`.}
 #'   \item{To change an option for a single projects across sessions in that
 #'   projects, place the options update in the `.Rprofile` in that project
 #'   directory.}

R/zzz.R

@@ -33,7 +33,7 @@ xportr_options_list <- list(
   ),
   xportr.numeric_types = getOption(
     "xportr.numeric_types",
-    c("integer", "float", "numeric", "posixct", "posixt", "time", "date")
+    c("integer", "float", "numeric", "posixct", "posixt", "time", "date", "hms")
   )
 )