Static

.Rbuildignore

@@ -17,3 +17,7 @@ coverage.*
 init.sh
 workflows.md
 images
+^\_targets\.yaml$
+^README\.Rmd$
+^data-raw$
+^LICENSE\.md$

.gitignore

@@ -31,3 +31,6 @@ coverage.*
 node_modules/
 package-lock.json
 package.json
+data-raw/_targets
+data-raw/mmrm_review.R
+

DESCRIPTION

@@ -1,31 +1,23 @@
 Type: Package
-Package: r.pkg.template
-Title: R Package Template
-Version: 0.1.0.9130
-Date: 2023-07-05
-Authors@R:
-    person("insightsengineering", , , "[email protected]", role = c("aut", "cre"))
-Description: R package template with GitHub Actions workflows included.
-License: Apache License 2.0 | file LICENSE
-URL: https://github.com/insightsengineering/r.pkg.template/
-BugReports: https://github.com/insightsengineering/r.pkg.template/issues
-Depends:
-    R (>= 3.6)
-Imports:
-    plumber,
-    shiny,
-    stringr
-Suggests:
-    future,
-    httr,
+Package: clindata
+Title: Open Clinical Data
+Version: 0.0.1
+Date: 2023-11-09
+Authors@R: person("Jonathan","Sidi" , , "[email protected]", role = c("aut", "cre"))
+Description: Reproducible simulated clinical trials for use in R packages.
+License: MIT + file LICENSE
+URL: https://github.com/openpharma/clindata
+BugReports: https://github.com/openpharma/clindata/issues
+Depends: R (>= 4.0)
+Imports: tools, utils, MASS, clusterGeneration
+Suggests: 
     knitr,
-    shinytest,
-    testthat (>= 2.0)
-VignetteBuilder:
-    knitr
-biocViews:
+    withr,
+    testthat (>= 3.0.0)
+VignetteBuilder: knitr
 Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
+Config/testthat/edition: 3

LICENSE

@@ -1,13 +1,2 @@
-Copyright 2022 F. Hoffmann-La Roche AG
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
-    http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
+YEAR: 2024
+COPYRIGHT HOLDER: clindata authors

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 clindata authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -1,6 +1,15 @@
 # Generated by roxygen2: do not edit by hand
 
-export(hello)
-export(plumber_api)
-export(shiny_app)
-importFrom(utils,packageName)
+export(cache_data)
+export(cache_destroy)
+export(cache_dir)
+export(cache_init)
+export(cache_ls)
+export(cache_rm)
+export(compute_unstructured_matrix)
+export(generate_outcomes)
+export(list_data)
+export(load_data)
+export(mar)
+export(mcar)
+export(read_data)

R/api_cache.R

@@ -0,0 +1,97 @@
+#' @title Data Caching API
+#' @description Functions to manage cache data across sessions.
+#' @param path character, path to cache directory, Default: `cache_dir()`
+#' @param \dots arguments passed to [list.files()]
+#' @param verbose logical, show message on success of [cache_destroy()]
+#' @return character
+#' @details
+#'   If the environment variable CLINDATA_CACHE_DIR is set then [cache_dir()] will use the value.
+#'
+#'   If the environment variable CLINDATA_CACHE_DIR is not set then [cache_dir()] will
+#'   default to the internal mechanism via [R_user_dir][tools::R_user_dir].
+#' @examples
+#'  cache_dir()
+#'  cache_init()
+#'  cache_ls()
+#'  cache_destroy()
+#' @rdname cache_api
+#' @export
+cache_init <- function(path = cache_dir()) {
+
+  dir.create(path = path, recursive = TRUE, showWarnings = FALSE)
+
+}
+
+#' @rdname cache_api
+#' @export
+cache_ls <- function(path = cache_dir(), ...) {
+
+  list.files(path = path, ...)
+
+}
+
+#' @rdname cache_api
+#' @export
+cache_dir <- function() {
+  if (nzchar(Sys.getenv("CLINDATA_CACHE_DIR")))
+    return(Sys.getenv("CLINDATA_CACHE_DIR"))
+
+  tools::R_user_dir(
+    package = "clindata",
+    which = "cache"
+  )
+
+}
+
+#' @title Clear data cache
+#' @description Clear file(s) from the cache path.
+#' @param files character, files to be removed,
+#'   Default: [cache_ls][cache_ls](full.names = TRUE)
+#' @param recursive boolean. Should directories be deleted recursively?
+#' @param force boolean. Should permissions be changed (if possible) to
+#'   allow the file or directory to be removed?
+#' @return NULL
+#' @examples
+#'   # initialize the cache directory
+#'   cache_init()
+#'
+#'   # populate the cache
+#'   cache_data("fev_data")
+#'   cache_data("cars")
+#'
+#'   # list files in the cache
+#'   cache_ls()
+#'
+#'   # clear all the files in the cache
+#'   cache_rm()
+#'   cache_ls()
+#'
+#'  # remove a single file based on a pattern
+#'   cache_data("fev_data")
+#'   cache_data("cars")
+#'   cache_rm(cache_ls(pattern = "fev", full.names = TRUE))
+#'   cache_ls()
+#'
+#'  # cleanup
+#'   cache_destroy()
+#' @export
+cache_rm <- function(
+    files = cache_ls(full.names = TRUE),
+    recursive = FALSE,
+    force = FALSE) {
+
+  invisible(
+    lapply(files,
+           function(f) {
+             unlink(x = f, recursive = recursive, force = force)
+           })
+  )
+}
+
+#' @rdname cache_api
+#' @export
+cache_destroy <- function(path = cache_dir(), verbose = TRUE) {
+  unlink(path, recursive = TRUE, force = TRUE)
+  if (verbose)
+    message(path, " directory removed")
+}

R/api_data.R

@@ -0,0 +1,117 @@
+#' @title Read data
+#' @description Read data directly into a global environment
+#' @param data character, name of data object
+#' @param filetype character, extension type of the data. Default: "rds"
+#' @param use_cache boolean, use the data stored in cache? Default: FALSE
+#' @return data stored in either the local cache directory or within the package.
+#' @details
+#'   Currently only loading of rds files is supported
+#' @examples
+#'  read_data("fev_data")
+#'  read_data("bcva_data")
+#' @rdname data_api
+#' @export
+read_data <- function(data, filetype = "rds", use_cache = FALSE) {
+
+  if(use_cache) {
+    cache_dir <- cache_dir()
+    if(dir.exists(cache_dir)) {
+      items <- tools::file_path_sans_ext(list.files(cache_dir))
+      if(data %in% items){
+        data_path <- file.path(cache_dir, sprintf("%s.%s", data, filetype))
+        message(sprintf("Retrieving %s from cache", data))
+        if(filetype == "rds"){
+          data_out <- readRDS(data_path)
+        }
+      } else {
+        stop(sprintf("%s not in cache", data))
+      }
+    }
+  }else{
+    data_out <- get(data, asNamespace("clindata"))
+  }
+
+  return(data_out)
+
+}
+
+#' @title Load data
+#' @description Load data directly into an enivornment
+#' @param data character, name of data object
+#' @param env environment, Default: parent.frame()
+#' @param ... arguments passed to assign [assign][base::assign]
+#' @return NULL
+#' @details
+#'   By default the data is loaded into the parent frame from which it is called.
+#' @examples
+#'  load_data("fev_data")
+#' @rdname load_data
+#' @export
+load_data <- function(data, env = parent.frame(), ...) {
+
+  invisible(
+    Map(function(x) {
+      assign(x, read_data(x, ...), envir = env)
+    },
+    x = data
+    )
+  )
+
+}
+
+#' @title Store data
+#' @description Store data in the cache
+#' @param data character, name of the object to store
+#' @param filetype character, extension of the
+#'   filetype to save the data. Default: "rds"
+#' @return NULL
+#' @details
+#'   Currently only rds is supported
+#' @examples
+#'   # initialize the cache directory
+#'   cache_init()
+#'
+#'   # populate the cache
+#'   cache_data("fev_data")
+#'   cache_ls()
+#'
+#'   # cleanup
+#'    cache_destroy()
+#' @rdname cache_data
+#' @export
+cache_data <- function(data, filetype = "rds") {
+  cl <- match.call()
+  data_name <- as.character(cl[[2]])
+
+  cache_dir <- cache_dir()
+
+  if(!dir.exists(cache_dir)) {
+    cache_init()
+  }
+
+  if(filetype == "rds") {
+    saveRDS(
+      object = data,
+      file = file.path(cache_dir, sprintf("%s.%s", data_name, filetype))
+    )
+  }
+
+}
+
+#' @title List data
+#' @description List the clinical data stored in the package
+#' @return character
+#' @examples
+#'  list_data()
+#' @rdname list_data
+#' @export
+list_data <- function() {
+
+  utils::data(package = "clindata")[["results"]][, "Item"]
+
+}
+
+test_data <- function(data) {
+  f <- system.file(file.path("benchmark", sprintf("%s.rds", data)), package = "clindata")
+  readRDS(f)
+}

R/clindata-package.R

@@ -0,0 +1,6 @@
+#' `clindata` Package
+#'
+#' `clindata` data package for clinical trials data.
+#'
+#' @aliases clindata-package
+"_PACKAGE"

R/data-bcva.R

@@ -0,0 +1,20 @@
+#' Simulated BCVA Data
+#'
+#' @description `r lifecycle::badge("experimental")`
+#'
+#' @note Measurements of BCVA (best corrected visual acuity) is a measure of how
+#'   how many letters a person can read off of an eye chart using corrective
+#'   lenses or contacts. This a common endpoint in ophthalmology trials.
+#'
+#' @format A `tibble` with 10,000 rows and 7 variables:
+#'   - `USUBJID`: subject ID.
+#'   - `VISITN`: visit number (numeric).
+#'   - `AVISIT`: visit number (factor).
+#'   - `ARMCD`: treatment, `TRT` or `CTL`.
+#'   - `RACE`: 3-category race.
+#'   - `BCVA_BL`: BCVA at baseline.
+#'   - `BCVA_CHG`: Change in BCVA at study visits.
+#'
+#' @source This is an artificial dataset.
+#' @name bcva_data
+NULL

R/data-fev.R

@@ -0,0 +1,21 @@
+#' Simulated FEV1 Data
+#'
+#' @description `r lifecycle::badge("experimental")`
+#'
+#' @note Measurements of FEV1 (forced expired volume in one second) is a measure
+#' of how quickly the lungs can be emptied. Low levels of FEV1 may indicate
+#' chronic obstructive pulmonary disease (COPD).
+#'
+#' @format A `tibble` with 800 rows and 7 variables:
+#'   - `USUBJID`: subject ID.
+#'   - `AVISIT`: visit number.
+#'   - `ARMCD`: treatment, `TRT` or `PBO`.
+#'   - `RACE`: 3-category race.
+#'   - `SEX`: sex.
+#'   - `FEV1_BL`: FEV1 at baseline (%).
+#'   - `FEV1`: FEV1 at study visits.
+#'   - `WEIGHT`: weighting variable.
+#'
+#' @source This is an artificial dataset.
+#' @name fev_data
+NULL