Closes #237 Removes admiral dependency and corrects site (#240)

* feat: remove admiral from dependencies

* fix: remove redundant parameters

* update ADSL dataset

* fix: updates metadata and vignettes

* chore: lint and styler

* docs: updates news

* docs: Reframe adsl data source

* replace rlang::set_names with dplyr::rename_with

* docs: remove extra note

* docs: simplify example

* revert: bring back abort instead of stop

* fix: remove rlang from vignettes

* chore: explicit use of rlang and haven namespace

* feat: rename adsl to adsl_xportr and ADaM_admiral_spec.xlsx to ADaM_spec.xlsx

* docs: update NAMESPACE

* fix: corrects check errors / notes

* feat: data is non-lazy load and not easily accessible to user

* docs: update spec file

* docs: update news

* fix: updates example after merge

* fix: linter problem

---------

Co-authored-by: Ben Straub <ben.x.straub@gsk.com>

DESCRIPTION

@@ -38,7 +38,6 @@ Imports:
     stringr (>= 1.4.0),
     tidyselect
 Suggests: 
-    admiral,
     DT,
     knitr,
     labelled,
@@ -51,6 +50,5 @@ VignetteBuilder:
     knitr
 Config/testthat/edition: 3
 Encoding: UTF-8
-LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1

NAMESPACE

@@ -12,8 +12,6 @@ export(xportr_split)
 export(xportr_type)
 export(xportr_write)
 export(xpt_validate)
-import(haven)
-import(rlang)
 importFrom(checkmate,assert)
 importFrom(checkmate,assert_character)
 importFrom(checkmate,assert_choice)
@@ -56,6 +54,7 @@ importFrom(dplyr,ungroup)
 importFrom(glue,glue)
 importFrom(glue,glue_collapse)
 importFrom(graphics,stem)
+importFrom(haven,write_xpt)
 importFrom(lifecycle,deprecated)
 importFrom(magrittr,"%>%")
 importFrom(magrittr,extract2)
@@ -68,6 +67,15 @@ importFrom(purrr,pluck)
 importFrom(purrr,walk)
 importFrom(purrr,walk2)
 importFrom(readr,parse_number)
+importFrom(rlang,"%||%")
+importFrom(rlang,":=")
+importFrom(rlang,.data)
+importFrom(rlang,abort)
+importFrom(rlang,inform)
+importFrom(rlang,local_options)
+importFrom(rlang,sym)
+importFrom(rlang,warn)
+importFrom(rlang,with_options)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_extract)
 importFrom(stringr,str_replace)

NEWS.md

@@ -45,6 +45,9 @@ done to make the use of xportr functions more explicit. (#182)
 * The `metacore` argument, which was renamed to `metadata` in the following six xportr functions: (`xportr_df_label()`, `xportr_format()`, `xportr_label()`, `xportr_length()`, `xportr_order()`, and `xportr_type()`) in version `0.3.0` with a soft deprecation warning, has now been hard deprecated. Please update your code to use the new `metadata` argument in place of `metacore`.
 
 * `SASlength` and `SAStype` were removed since they did not have an impact on `xpt_validate` or any other functions (#132)
+* Removes `admiral` from suggested dependencies (#237)
+* `adsl` data object is now called `adsl_xportr` (#237)
+* Data objects are no longer lazy loaded, which means that when needed the user must call `data("name_of_object")` first (#237)
 
 ## Documentation
 

R/data.R

@@ -2,62 +2,70 @@
 #'
 #' An example dataset containing subject level data
 #'
-#' @format ## `adsl`
-#' A data frame with 254 rows and 48 columns:
+#' @source Dataset created by `admiral::use_ad_template("adsl")`
+#' @usage data("adsl_xportr")
+#'
+#' @format ## `adsl_xportr`
+#' A data frame with 306 rows and 51 columns:
 #' \describe{
 #'   \item{STUDYID}{Study Identifier}
 #'   \item{USUBJID}{Unique Subject Identifier}
 #'   \item{SUBJID}{Subject Identifier for the Study}
+#'   \item{RFSTDTC}{Subject Reference Start Date/Time}
+#'   \item{RFENDTC}{Subject Reference End Date/Time}
+#'   \item{RFXSTDTC}{Date/Time of First Study Treatment}
+#'   \item{RFXENDTC}{Date/Time of Last Study Treatment}
+#'   \item{RFICDTC}{Date/Time of Informed Consent}
+#'   \item{RFPENDTC}{Date/Time of End of Participation}
+#'   \item{DTHDTC}{Date/Time of Death}
+#'   \item{DTHFL}{Subject Death Flag}
 #'   \item{SITEID}{Study Site Identifier}
-#'   \item{SITEGR1}{Pooled Site Group 1}
+#'   \item{AGE}{Age}
+#'   \item{AGEU}{Age Units}
+#'   \item{SEX}{Sex}
+#'   \item{RACE}{Race}
+#'   \item{ETHNIC}{Ethnicity}
+#'   \item{ARMCD}{Planned Arm Code}
 #'   \item{ARM}{Description of Planned Arm}
+#'   \item{ACTARMCD}{Actual Arm Code}
+#'   \item{ACTARM}{Description of Actual Arm}
+#'   \item{COUNTRY}{Country}
+#'   \item{DMDTC}{Date/Time of Collection}
+#'   \item{DMDY}{Study Day of Collection}
 #'   \item{TRT01P}{Planned Treatment for Period 01}
-#'   \item{TRT01PN}{Planned Treatment for Period 01 (N)}
 #'   \item{TRT01A}{Actual Treatment for Period 01}
-#'   \item{TRT01AN}{Actual Treatment for Period 01 (N)}
+#'   \item{TRTSDTM}{Datetime of First Exposure to Treatment}
+#'   \item{TRTSTMF}{Time of First Exposure Imputation Flag}
+#'   \item{TRTEDTM}{Datetime of Last Exposure to Treatment}
+#'   \item{TRTETMF}{Time of Last Exposure Imputation Flag}
 #'   \item{TRTSDT}{Date of First Exposure to Treatment}
 #'   \item{TRTEDT}{Date of Last Exposure to Treatment}
-#'   \item{TRTDUR}{Duration of Treatment (days)}
-#'   \item{AVGDD}{Avg Daily Dose (as planned)}
-#'   \item{CUMDOSE}{Cumulative Dose (as planned)}
-#'   \item{AGE}{Age}
-#'   \item{AGEGR1}{Pooled Age Group 1}
-#'   \item{AGEGR1N}{Pooled Age Group 1 (N)}
-#'   \item{AGEU}{Age Units}
-#'   \item{RACE}{Race}
-#'   \item{RACEN}{Race (N)}
-#'   \item{SEX}{Sex}
-#'   \item{ETHNIC}{Ethnicity}
+#'   \item{TRTDURD}{Total Treatment Duration (Days)}
+#'   \item{SCRFDT}{Screen Failure Date}
+#'   \item{EOSDT}{End of Study Date}
+#'   \item{EOSSTT}{End of Study Status}
+#'   \item{FRVDT}{Final Retrieval Visit Date}
+#'   \item{RANDDT}{Date of Randomization}
+#'   \item{DTHDT}{Date of Death}
+#'   \item{DTHDTF}{Date of Death Imputation Flag}
+#'   \item{DTHADY}{Relative Day of Death}
+#'   \item{LDDTHELD}{Elapsed Days from Last Dose to Death}
+#'   \item{LSTALVDT}{Date Last Known Alive}
 #'   \item{SAFFL}{Safety Population Flag}
-#'   \item{ITTFL}{Intent-To-Treat Population Flag}
-#'   \item{EFFFL}{Efficacy Population Flag}
-#'   \item{COMP8FL}{Completers of Week 8 Population Flag}
-#'   \item{COMP16FL}{Completers of Week 16 Population Flag}
-#'   \item{COMP24FL}{Completers of Week 24 Population Flag}
-#'   \item{DISCONFL}{Did the Subject Discontinue the Study}
-#'   \item{DSRAEFL}{Discontinued due to AE}
-#'   \item{DTHFL}{Subject Died}
-#'   \item{BMIBL}{Baseline BMI (kg/m^2)}
-#'   \item{BMIBLGR1}{Pooled Baseline BMI Group 1}
-#'   \item{HEIGHTBL}{Baseline Height (cm)}
-#'   \item{WEIGHTBL}{Baseline Weight (kg)}
-#'   \item{EDUCLVL}{Years of Education}
-#'   \item{DISONSDT}{Date of Onset of Disease}
-#'   \item{DURDIS}{Duration of Disease (Months)}
-#'   \item{DURDSGR1}{Pooled Disease Duration Group 1}
-#'   \item{VISIT1DT}{Date of Visit 1}
-#'   \item{RFSTDTC}{Subject Reference Start Date/Time}
-#'   \item{RFENDTC}{Subject Reference End Date/Time}
-#'   \item{VISNUMEN}{End of Trt Visit (Vis 12 or Early Term.)}
-#'   \item{RFENDT}{Date of Discontinuation/Completion}
-#'   \item{DCDECOD}{Standardized Disposition Term}
-#'   \item{DCREASCD}{Reason for Discontinuation}
-#'   \item{MMSETOT}{MMSE Total}
+#'   \item{RACEGR1}{Pooled Race Group 1}
+#'   \item{AGEGR1}{Pooled Age Group 1}
+#'   \item{REGION1}{Geographic Region 1}
+#'   \item{LDDTHGR1}{Last Dose to Death - Days Elapsed Group 1}
+#'   \item{DTH30FL}{Death Within 30 Days of Last Trt Flag}
+#'   \item{DTHA30FL}{Death After 30 Days from Last Trt Flag}
+#'   \item{DTHB30FL}{Death Within 30 Days of First Trt Flag}
 #' }
-"adsl"
+"adsl_xportr"
 
 #' Example Dataset Variable Specification
 #'
+#' @usage data("var_spec")
+#'
 #' @format ## `var_spec`
 #' A data frame with 216 rows and 19 columns:
 #' \describe{
@@ -85,6 +93,7 @@
 
 #' Example Dataset Specification
 #'
+#' @usage data("dataset_spec")
 #' @format ## `dataset_spec`
 #' A data frame with 1 row and 9 columns:
 #' \describe{

R/length.R

@@ -8,12 +8,6 @@
 #' @inheritParams xportr
 #' @param metadata A data frame containing variable level metadata. See
 #'   'Metadata' section for details.
-#' @param domain Appropriate CDISC dataset name, e.g. ADAE, DM. Used to subset
-#'   the metadata object. If none is passed, then name of the dataset passed as
-#'   .df will be used.
-#' @param verbose The action this function takes when an action is taken on the
-#'   dataset or function validation finds an issue. See 'Messaging' section for
-#'   details. Options are 'stop', 'warn', 'message', and 'none'
 #' @param length_source Choose the assigned length from either metadata or data.
 #'
 #'   If `"metadata"` is specified, the assigned length is from the metadata length.
@@ -155,13 +149,14 @@ xportr_length <- function(.df,
       attr(.df[[i]], "width") <- length_data[[i]]
     }
 
+
     length_msg <- left_join(var_length_max, metadata[, c(variable_name, variable_length)], by = variable_name)
     length_msg <- length_msg %>%
       mutate(
         length_df = as.numeric(length_msg[[paste0(variable_length, ".x")]]),
         length_meta = as.numeric(length_msg[[paste0(variable_length, ".y")]])
       ) %>%
-      filter(length_df < length_meta) %>%
+      filter(.data$length_df < .data$length_meta) %>%
       select(any_of(c(variable_name, "length_df", "length_meta")))
 
     max_length_msg(length_msg, verbose)

R/metadata.R

@@ -32,14 +32,12 @@
 #'
 #' xportr_metadata(adlb, metadata, "test")
 #'
-#' if (rlang::is_installed("magrittr")) {
-#'   library(magrittr)
+#' library(magrittr)
 #'
-#'   adlb %>%
-#'     xportr_metadata(metadata, "test") %>%
-#'     xportr_type() %>%
-#'     xportr_order()
-#' }
+#' adlb %>%
+#'   xportr_metadata(metadata, "test") %>%
+#'   xportr_type() %>%
+#'   xportr_order()
 xportr_metadata <- function(.df,
                             metadata = NULL,
                             domain = NULL,

R/split.R

@@ -21,6 +21,8 @@
 #' @export
 #'
 #' @examples
+#' data("adsl_xportr")
+#' adsl <- adsl_xportr
 #'
 #' adlb <- data.frame(
 #'   USUBJID = c(1001, 1002, 1003),

R/support-test.R

@@ -49,7 +49,7 @@ minimal_table <- function(n_rows = 3, cols = c("x", "y")) {
     d = sample(Sys.Date() + c(1, -1, 10, -10), size = n_rows, replace = TRUE),
     e = sample(c(1, 2), replace = TRUE, size = n_rows)
   ) %>%
-    mutate(e = if_else(seq_along(e) %% 2 == 0, NA, e)) %>%
+    mutate(e = if_else(seq_along(.data$e) %% 2 == 0, NA, .data$e)) %>%
     select(all_of(tolower(cols)))
 }
 

R/write.R

@@ -126,7 +126,7 @@ xportr_write <- function(.df,
       }
     },
     error = function(err) {
-      rlang::abort(
+      abort(
         paste0(
           "Error reported by haven::write_xpt, error was: \n",
           err

R/xportr-package.R

@@ -101,7 +101,9 @@
 #' @keywords internal
 #' @aliases xportr-package
 #'
-#' @import rlang haven
+#' @importFrom haven write_xpt
+#' @importFrom rlang abort warn inform with_options local_options .data := sym
+#'   %||%
 #' @importFrom dplyr left_join bind_cols filter select rename rename_with n
 #'   everything arrange group_by summarize mutate ungroup case_when distinct
 #'   tribble if_else across as_tibble

R/xportr.R

@@ -19,6 +19,9 @@
 #' @export
 #'
 #' @examplesIf requireNamespace("magrittr")
+#' data("adsl_xportr", "dataset_spec", "var_spec")
+#' adsl <- adsl_xportr
+#'
 #' library(magrittr)
 #' test_dir <- tempdir()
 #'

README.Rmd

@@ -104,33 +104,34 @@ To do this we will need to do the following:
 
 All of which can be done using a well-defined specification file and the `{xportr}` package! 
 
-First we will start with our `ADSL` dataset created in R.  This example `ADSL` dataset is taken from the [`{admiral}`](https://pharmaverse.github.io/admiral/index.html) package. The script that generates this `ADSL` dataset can be created by using this command `admiral::use_ad_template("adsl")`.  This `ADSL` dataset has 306 observations and 48 variables.
+First we will start with our `ADSL` dataset created in R.
+This example `ADSL` dataset contains 306 observations and 51 variables.
 
 ```{r, eval=TRUE, message=FALSE, warning=FALSE}
 library(dplyr)
-library(admiral)
 library(xportr)
 
-adsl <- admiral::admiral_adsl
+data("adsl_xportr")
+ADSL <- adsl_xportr
 ```
 
-We have created a dummy specification file called `ADaM_admiral_spec.xlsx` found in the `specs` folder of this package.  You can use `system.file(paste0("specs/", "ADaM_admiral_spec.xlsx"), package = "xportr")` to access this file.
+We have created a dummy specification file called `ADaM_spec.xlsx` found in the `specs` folder of this package.  You can use `system.file(file.path("specs/", "ADaM_spec.xlsx"), package = "xportr")` to access this file.
 
 ```{r}
-spec_path <- system.file(paste0("specs/", "ADaM_admiral_spec.xlsx"), package = "xportr")
+spec_path <- system.file(file.path("specs", "ADaM_spec.xlsx"), package = "xportr")
 
 var_spec <- readxl::read_xlsx(spec_path, sheet = "Variables") %>%
   dplyr::rename(type = "Data Type") %>%
-  rlang::set_names(tolower)
+  dplyr::rename_with(tolower)
 dataset_spec <- readxl::read_xlsx(spec_path, sheet = "Datasets") %>%
   dplyr::rename(label = "Description") %>%
-  rlang::set_names(tolower)
+  dplyr::rename_with(tolower)
 ```
 
 Each `xportr_` function has been written in a way to take in a part of the specification file and apply that piece to the dataset. Setting `verbose = "warn"` will send appropriate warning message to the console. We have suppressed the warning for the sake of brevity.
 
 ```{r, warning = FALSE, message=FALSE, eval=TRUE}
-adsl %>%
+ADSL %>%
   xportr_metadata(var_spec, "ADSL") %>%
   xportr_type(verbose = "warn") %>%
   xportr_length(verbose = "warn") %>%
@@ -144,7 +145,7 @@ adsl %>%
 The `xportr_metadata()` function can reduce duplication by setting the variable specification and domain explicitly at the top of a pipeline. If you would like to use the `verbose` argument, you will need to set in each function call.
 
 ```{r, warning=FALSE, message=FALSE, eval=FALSE}
-adsl %>%
+ADSL %>%
   xportr_metadata(var_spec, "ADSL", verbose = "warn") %>%
   xportr_type() %>%
   xportr_length() %>%
@@ -159,7 +160,7 @@ Furthermore, if you're calling all xportr functions at once with common metadata
 
 ```{r, warning=FALSE, message=FALSE, eval=FALSE}
 xportr(
-  .df = adsl,
+  .df = ADSL,
   var_metadata = var_spec,
   df_metadata = dataset_spec,
   domain = "ADSL",