Rename linelist -> datatagr

Occurrences of linelist are replaced when not indicative of actual linelist references.

NAMESPACE

@@ -1,24 +1,24 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method("$<-",linelist)
-S3method("[",linelist)
-S3method("[<-",linelist)
-S3method("[[<-",linelist)
-S3method("names<-",linelist)
-S3method(print,linelist)
-S3method(select,linelist)
+S3method("$<-",datatagr)
+S3method("[",datatagr)
+S3method("[<-",datatagr)
+S3method("[[<-",datatagr)
+S3method("names<-",datatagr)
+S3method(print,datatagr)
+S3method(select,datatagr)
 export(get_lost_tags_action)
 export(has_tag)
 export(lost_tags_action)
-export(make_linelist)
+export(make_datatagr)
 export(select_tags)
 export(set_tags)
 export(tags)
 export(tags_defaults)
 export(tags_df)
 export(tags_names)
 export(tags_types)
-export(validate_linelist)
+export(validate_datatagr)
 export(validate_tags)
 export(validate_types)
 importFrom(dplyr,select)

R/datatagr-package.R

@@ -9,7 +9,7 @@
 #'
 #' @section Main functions:
 #'
-#'   * [make_linelist()]: to create `datatagr` objects from a `data.frame` or a
+#'   * [make_datatagr()]: to create `datatagr` objects from a `data.frame` or a
 #'   `tibble`
 #'
 #'   * [set_tags()]: to change or add tagged variables in a `datatagr`
@@ -35,7 +35,7 @@
 #'   * `names() <-` (and related functions, such as [dplyr::rename()]) will
 #'   rename tags as needed
 #'
-#'   * `x[...] <-` and `x[[...]] <-` (see [sub_linelist]): will adopt the
+#'   * `x[...] <-` and `x[[...]] <-` (see [sub_datatagr]): will adopt the
 #'    desired behaviour when tagged variables are lost
 #'
 #'   * `print()`: prints info about the `datatagr` in addition to the
@@ -46,11 +46,11 @@
 #' if (require(outbreaks)) {
 #'   # using base R style
 #'
-#'   ## dataset we'll create a linelist from, only using the first 50 entries
+#'   ## dataset we'll create a datatagr from, only using the first 50 entries
 #'   measles_hagelloch_1861[1:50, ]
 #'
-#'   ## create linelist
-#'   x <- make_linelist(measles_hagelloch_1861[1:50, ],
+#'   ## create datatagr
+#'   x <- make_datatagr(measles_hagelloch_1861[1:50, ],
 #'     id = "case_ID",
 #'     date_onset = "date_of_prodrome",
 #'     age = "age",
@@ -82,13 +82,13 @@
 #'
 #'   # using tidyverse style
 #'
-#'   ## example of creating a linelist, adding a new variable, and adding a tag
+#'   ## example of creating a datatagr, adding a new variable, and adding a tag
 #'   ## for it
 #'
 #'   if (require(dplyr) && require(magrittr)) {
 #'     x <- measles_hagelloch_1861 %>%
 #'       tibble() %>%
-#'       make_linelist(
+#'       make_datatagr(
 #'         id = "case_ID",
 #'         date_onset = "date_of_prodrome",
 #'         age = "age",

R/drop_datatagr.R

@@ -0,0 +1,24 @@
+#' Remove the datatagr class from an object
+#'
+#' Internal function. Used for dispatching to other methods when `NextMethod` is
+#' an issue (typically to pass additional arguments to the `datatagr` method).
+#'
+#' @param x a `datatagr` object
+#'
+#' @param remove_tags a `logical` indicating if tags should be removed from the
+#'   attributes; defaults to `TRUE`
+#'
+#' @noRd
+#'
+#' @return The function returns the same object without the `datatagr` class.
+#'
+#'
+
+drop_datatagr <- function(x, remove_tags = TRUE) {
+  classes <- class(x)
+  class(x) <- setdiff(classes, "datatagr")
+  if (remove_tags) {
+    attr(x, "tags") <- NULL
+  }
+  x
+}

R/has_tag.R

@@ -10,11 +10,11 @@
 #'
 #' @examples
 #' if (require(outbreaks) && require(dplyr)) {
-#'   ## dataset we'll create a linelist from
+#'   ## dataset we'll create a datatagr from
 #'   measles_hagelloch_1861
 #'
-#'   ## create linelist
-#'   x <- make_linelist(measles_hagelloch_1861,
+#'   ## create datatagr
+#'   x <- make_datatagr(measles_hagelloch_1861,
 #'     id = "case_ID",
 #'     date_onset = "date_of_prodrome",
 #'     age = "age",

R/lost_tags_action.R

@@ -1,8 +1,8 @@
 #' Check and set behaviour for lost tags
 #'
 #' This function determines the behaviour to adopt when tagged variables of a
-#' `linelist` are lost e.g. through subsetting. This is achieved using `options`
-#' defined for the `linelist` package.
+#' `datatagr` are lost e.g. through subsetting. This is achieved using `options`
+#' defined for the `datatagr` package.
 #'
 #' @param action a `character` indicating the behaviour to adopt when tagged
 #'   variables have been lost: "error" (default) will issue an error; "warning"
@@ -13,10 +13,10 @@
 #'
 #' @param x deprecated
 #'
-#' @return returns `NULL`; the option itself is set in `options("linelist")`
+#' @return returns `NULL`; the option itself is set in `options("datatagr")`
 #'
-#' @details The errors or warnings generated by linelist in case of tagged
-#' variable loss has a custom class of `linelist_error` and `linelist_warning`
+#' @details The errors or warnings generated by datatagr in case of tagged
+#' variable loss has a custom class of `datatagr_error` and `datatagr_warning`
 #' respectively.
 #'
 #' @export
@@ -46,18 +46,18 @@
 lost_tags_action <- function(action = c("warning", "error", "none"),
                              quiet = FALSE,
                              x) {
-  if (!missing(x) || inherits(action, "linelist")) {
+  if (!missing(x) || inherits(action, "datatagr")) {
     stop(
       "Using `lost_tags_action()` in a pipeline is deprecated",
       call. = FALSE
     )
   }
 
-  linelist_options <- options("linelist")$linelist # nolint
+  datatagr_options <- options("datatagr")$datatagr # nolint
 
   action <- match.arg(action)
-  linelist_options$lost_tags_action <- action
-  options(linelist = linelist_options) # nolint
+  datatagr_options$lost_tags_action <- action
+  options(datatagr = datatagr_options) # nolint
   if (!quiet) {
     if (action == "warning") msg <- "Lost tags will now issue a warning."
     if (action == "error") msg <- "Lost tags will now issue an error."
@@ -74,5 +74,5 @@ lost_tags_action <- function(action = c("warning", "error", "none"),
 #' @rdname lost_tags_action
 
 get_lost_tags_action <- function() {
-  options("linelist")$linelist$lost_tags_action # nolint
+  options("datatagr")$datatagr$lost_tags_action # nolint
 }

R/make_linelist.R → R/make_datatagr.R

@@ -1,12 +1,12 @@
-#' Create a linelist from a data.frame
+#' Create a datatagr from a data.frame
 #'
-#' This function converts a `data.frame` or a `tibble` into a `linelist` object,
+#' This function converts a `data.frame` or a `tibble` into a `datatagr` object,
 #' where different types of epidemiologically relevant data are tagged. This
 #' includes dates of different events (e.g. onset of symptoms, case reporting),
 #' information on the patient (e.g. age, gender, location) as well as other
 #' information such as the type of case (e.g. confirmed, probable) or the
 #' outcome of the disease. The output will seem to be the same `data.frame`, but
-#' `linelist`-aware packages will then be able to automatically use tagged
+#' `datatagr`-aware packages will then be able to automatically use tagged
 #' fields for further data cleaning and analysis.
 #'
 #' @param x a `data.frame` or a `tibble` containing case line list data, with
@@ -18,15 +18,15 @@
 #'   details for a list of known variable types and their expected content
 #'
 #' @param allow_extra a `logical` indicating if additional data tags not
-#'   currently recognized by `linelist` should be allowed; if `FALSE`, unknown
+#'   currently recognized by `datatagr` should be allowed; if `FALSE`, unknown
 #'   tags will trigger an error
 #'
 #' @seealso
 #'
 #' * An overview of the [datatagr] package
 #' * [tags_names()]: for a list of known tag names
 #' * [tags_types()]: for the associated accepted types/classes
-#' * [tags()]: for a list of tagged variables in a `linelist`
+#' * [tags()]: for a list of tagged variables in a `datatagr`
 #' * [set_tags()]: for modifying tags
 #' * [tags_df()]: for selecting variables by tags
 #'
@@ -73,16 +73,16 @@
 #'
 #' @export
 #'
-#' @return The function returns a `linelist` object.
+#' @return The function returns a `datatagr` object.
 #'
 #' @examples
 #'
 #' if (require(outbreaks)) {
-#'   ## dataset we will convert to linelist
+#'   ## dataset we will convert to datatagr
 #'   head(measles_hagelloch_1861)
 #'
-#'   ## create linelist
-#'   x <- make_linelist(measles_hagelloch_1861,
+#'   ## create datatagr
+#'   x <- make_datatagr(measles_hagelloch_1861,
 #'     id = "case_ID",
 #'     date_onset = "date_of_prodrome",
 #'     age = "age",
@@ -102,13 +102,13 @@
 #'     age = "age",
 #'     gender = "gender"
 #'   )
-#'   new_x <- make_linelist(measles_hagelloch_1861, !!!my_tags)
+#'   new_x <- make_datatagr(measles_hagelloch_1861, !!!my_tags)
 #'
 #'   ## The output is strictly equivalent to the previous one
 #'   identical(x, new_x)
 #' }
 #'
-make_linelist <- function(x,
+make_datatagr <- function(x,
                           ...,
                           allow_extra = FALSE) {
   # assert inputs
@@ -139,6 +139,6 @@ make_linelist <- function(x,
   x <- tag_variables(x, tags)
 
   # shape output and return object
-  class(x) <- c("linelist", class(x))
+  class(x) <- c("datatagr", class(x))
   x
 }

R/names.R

@@ -1,23 +1,23 @@
-#' Rename columns of a linelist
+#' Rename columns of a datatagr
 #'
-#' This function can be used to rename the columns a `linelist`, adjusting tags
+#' This function can be used to rename the columns a `datatagr`, adjusting tags
 #' as needed.
 #'
-#' @param x a `linelist` object
+#' @param x a `datatagr` object
 #'
 #' @param value a `character` vector to set the new names of the columns of `x`
 #'
-#' @return a `linelist` with new column names
+#' @return a `datatagr` with new column names
 #'
 #' @export
 #'
 #' @examples
 #' if (require(outbreaks)) {
-#'   ## dataset to create a linelist from
+#'   ## dataset to create a datatagr from
 #'   measles_hagelloch_1861
 #'
-#'   ## create linelist
-#'   x <- make_linelist(measles_hagelloch_1861,
+#'   ## create datatagr
+#'   x <- make_datatagr(measles_hagelloch_1861,
 #'     id = "case_ID",
 #'     date_onset = "date_of_prodrome",
 #'     age = "age",
@@ -41,7 +41,7 @@
 #'     tags(x)
 #'   }
 #' }
-`names<-.linelist` <- function(x, value) {
+`names<-.datatagr` <- function(x, value) {
   # Strategy for renaming
 
   # Since renaming cannot drop columns, we can update tags to match new variable
@@ -50,7 +50,7 @@
   # 1. Storing old names and new names to have define replacement rules
   # 2. Replace all tagged variables using the replacement rules
 
-  out <- drop_linelist(x, remove_tags = TRUE)
+  out <- drop_datatagr(x, remove_tags = TRUE)
   names(out) <- value
 
   # Step 1

R/print.linelist.R → R/print.datatagr.R

@@ -1,8 +1,8 @@
-#' Printing method for linelist objects
+#' Printing method for datatagr objects
 #'
-#' This function prints linelist objects.
+#' This function prints datatagr objects.
 #'
-#' @param x a `linelist` object
+#' @param x a `datatagr` object
 #'
 #' @param ... further arguments to be passed to 'print'
 #'
@@ -12,11 +12,11 @@
 #'
 #' @examples
 #' if (require(outbreaks)) {
-#'   ## dataset we'll create a linelist from
+#'   ## dataset we'll create a datatagr from
 #'   measles_hagelloch_1861
 #'
-#'   ## create linelist
-#'   x <- make_linelist(measles_hagelloch_1861,
+#'   ## create datatagr
+#'   x <- make_datatagr(measles_hagelloch_1861,
 #'     id = "case_ID",
 #'     date_onset = "date_of_prodrome",
 #'     age = "age",
@@ -30,17 +30,17 @@
 #'   if (require(tibble) && require(magrittr)) {
 #'     measles_hagelloch_1861 %>%
 #'       tibble() %>%
-#'       make_linelist(
+#'       make_datatagr(
 #'         id = "case_ID",
 #'         date_onset = "date_of_prodrome",
 #'         age = "age",
 #'         gender = "gender"
 #'       )
 #'   }
 #' }
-print.linelist <- function(x, ...) {
-  cat("\n// linelist object\n")
-  print(drop_linelist(x, remove_tags = TRUE))
+print.datatagr <- function(x, ...) {
+  cat("\n// datatagr object\n")
+  print(drop_datatagr(x, remove_tags = TRUE))
   tags_txt <- paste(names(tags(x)), unlist(tags(x)), sep = ":", collapse = ", ")
   if (tags_txt == "") {
     tags_txt <- "[no tagged variable]"