chore: merged all into master

miracum · Dec 6, 2024 · 9ee9e59 · 9ee9e59
2 parents 56fee58 + 834bc83
commit 9ee9e59
Show file tree

Hide file tree

Showing 59 changed files with 555 additions and 726 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: DQAstats
 Title: Core Functions for Data Quality Assessment
-Version: 0.3.5
-Date: 2024-06-05
+Version: 0.3.6
+Date: 2024-11-27
 Authors@R: c(
     person("Lorenz A.", "Kapsner", , "[email protected]", role = c("cre", "aut"),
            comment = c(ORCID = "0000-0003-1866-860X")),
@@ -45,4 +45,4 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 SystemRequirements: Quarto command line tools
     (https://github.com/quarto-dev/quarto-cli).
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
diff --git a/NAMESPACE b/NAMESPACE
@@ -4,7 +4,6 @@ export(atemp_plausi_results)
 export(check_date_restriction_requirements)
 export(completeness)
 export(create_helper_vars)
-export(create_markdown)
 export(create_pdf_report)
 export(data_loading)
 export(descriptive_results)

diff --git a/NEWS.md b/NEWS.md
diff --git a/R/DQA.R b/R/DQA.R
@@ -1,6 +1,6 @@
 # DQAstats - Perform data quality assessment (DQA) of electronic health
 # records (EHR)
-# Copyright (C) 2019-2022 Universitätsklinikum Erlangen
+# Copyright (C) 2019-2024 Universitätsklinikum Erlangen
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/calc_cat_stats.R b/R/calc_cat_stats.R
@@ -1,6 +1,6 @@
 # DQAstats - Perform data quality assessment (DQA) of electronic health
 # records (EHR)
-# Copyright (C) 2019-2022 Universitätsklinikum Erlangen
+# Copyright (C) 2019-2024 Universitätsklinikum Erlangen
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/calc_counts.R b/R/calc_counts.R
@@ -1,6 +1,6 @@
 # DQAstats - Perform data quality assessment (DQA) of electronic health
 # records (EHR)
-# Copyright (C) 2019-2022 Universitätsklinikum Erlangen
+# Copyright (C) 2019-2024 Universitätsklinikum Erlangen
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/calc_description.R b/R/calc_description.R
@@ -1,6 +1,6 @@
 # DQAstats - Perform data quality assessment (DQA) of electronic health
 # records (EHR)
-# Copyright (C) 2019-2022 Universitätsklinikum Erlangen
+# Copyright (C) 2019-2024 Universitätsklinikum Erlangen
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/calc_stats.R b/R/calc_stats.R
@@ -1,6 +1,6 @@
 # DQAstats - Perform data quality assessment (DQA) of electronic health
 # records (EHR)
-# Copyright (C) 2019-2022 Universitätsklinikum Erlangen
+# Copyright (C) 2019-2024 Universitätsklinikum Erlangen
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/categorical_analysis.R b/R/categorical_analysis.R
@@ -1,6 +1,6 @@
 # DQAstats - Perform data quality assessment (DQA) of electronic health
 # records (EHR)
-# Copyright (C) 2019-2022 Universitätsklinikum Erlangen
+# Copyright (C) 2019-2024 Universitätsklinikum Erlangen
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/completeness.R b/R/completeness.R
@@ -1,6 +1,6 @@
 # DQAstats - Perform data quality assessment (DQA) of electronic health
 # records (EHR)
-# Copyright (C) 2019-2022 Universitätsklinikum Erlangen
+# Copyright (C) 2019-2024 Universitätsklinikum Erlangen
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/conformance.R b/R/conformance.R
@@ -1,6 +1,6 @@
 # DQAstats - Perform data quality assessment (DQA) of electronic health
 # records (EHR)
-# Copyright (C) 2019-2022 Universitätsklinikum Erlangen
+# Copyright (C) 2019-2024 Universitätsklinikum Erlangen
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/count_uniques.R b/R/count_uniques.R
@@ -1,6 +1,6 @@
 # DQAstats - Perform data quality assessment (DQA) of electronic health
 # records (EHR)
-# Copyright (C) 2019-2022 Universitätsklinikum Erlangen
+# Copyright (C) 2019-2024 Universitätsklinikum Erlangen
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/create_pdf_report.R b/R/create_pdf_report.R
@@ -1,6 +1,6 @@
 # DQAstats - Perform data quality assessment (DQA) of electronic health
 # records (EHR)
-# Copyright (C) 2019-2022 Universitätsklinikum Erlangen
+# Copyright (C) 2019-2024 Universitätsklinikum Erlangen
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -220,9 +220,11 @@ create_pdf_report <- function(rv = rv,
         tmpdir = tempdir(),
         fileext = "-params.yml"
       )
+
       writeLines(
         text = c(paste0("source_system_name: \"", rv$source$system_name, "\""),
                  paste0("target_system_name: \"", rv$target$system_name, "\""),
+                 paste0("sitename: \"", rv$sitename, "\""),
                  paste0("restricting_date: \"", get_restricting_date_info(
                    restricting_date = rv$restricting_date, time = FALSE), "\""
                  )),
@@ -264,145 +266,3 @@ create_pdf_report <- function(rv = rv,
     })
   }
 }
-
-
-#' @title create_markdown helper function
-#'
-#' @description Internal function to generate the final PDF report.
-#'
-#' @param outdir A character string. The directory to store the resulting
-#'   PDF document. Default: \code{tempdir}.
-#' @inheritParams load_csv
-#' @inheritParams dqa
-#'
-#' @return No return value. This function renders the PDF markdown report with
-#'   the data quality assessment results and saves it to `outdir`.
-#'
-#' @examples
-#' \donttest{# runtime > 5 sec.
-#' utils_path <- system.file(
-#'   "demo_data/utilities/",
-#'   package = "DQAstats"
-#' )
-#' mdr_filename <- "mdr_example_data.csv"
-#' rv <- list()
-#' rv$mdr <- read_mdr(
-#'   utils_path = utils_path,
-#'   mdr_filename <- mdr_filename
-#' )
-#'
-#' source_system_name <- "exampleCSV_source"
-#' target_system_name <- "exampleCSV_target"
-#'
-#' rv <- c(rv, create_helper_vars(
-#'   mdr = rv$mdr,
-#'   source_db = source_system_name,
-#'   target_db = target_system_name
-#' ))
-#' # save source/target vars
-#' rv$source$system_name <- source_system_name
-#' rv$target$system_name <- target_system_name
-#' rv$source$system_type <- "csv"
-#' rv$target$system_type <- "csv"
-#'
-#' rv$log$logfile_dir <- tempdir()
-#'
-#' # set headless (without GUI, progressbars, etc.)
-#' rv$headless <- TRUE
-#'
-#' # set configs
-#' demo_files <- system.file("demo_data", package = "DQAstats")
-#' Sys.setenv("EXAMPLECSV_SOURCE_PATH" = demo_files)
-#' Sys.setenv("EXAMPLECSV_TARGET_PATH" = demo_files)
-#'
-#' # get configs
-#' rv$source$settings <- DIZutils::get_config_env(
-#'   system_name = rv$source$system_name,
-#'   logfile_dir = rv$log$logfile_dir,
-#'   headless = rv$headless
-#' )
-#' rv$target$settings <- DIZutils::get_config_env(
-#'   system_name = tolower(rv$target$system_name),
-#'   logfile_dir = rv$log$logfile_dir,
-#'   headless = rv$headless
-#' )
-#'
-#' # set start_time (e.g. when clicking the 'Load Data'-button in shiny
-#' rv$start_time <- format(Sys.time(), usetz = TRUE, tz = "CET")
-#'
-#' # define restricting date
-#' rv$restricting_date$use_it <- FALSE
-#'
-#' # load source data
-#' tempdat <- data_loading(
-#'   rv = rv,
-#'   system = rv$source,
-#'   keys_to_test = rv$keys_source
-#' )
-#' rv$data_source <- tempdat$outdata
-#'
-#' # load target data
-#' tempdat <- data_loading(
-#'   rv = rv,
-#'   system = rv$target,
-#'   keys_to_test = rv$keys_target
-#' )
-#' rv$data_target <- tempdat$outdata
-#'
-#' rv$data_plausibility$atemporal <- get_atemp_plausis(
-#'   rv = rv,
-#'   atemp_vars = rv$pl$atemp_vars,
-#'   mdr = rv$mdr,
-#'   headless = rv$headless
-#' )
-#'
-#' # add the plausibility raw data to data_target and data_source
-#' for (i in names(rv$data_plausibility$atemporal)) {
-#'   for (k in c("source_data", "target_data")) {
-#'     w <- gsub("_data", "", k)
-#'     raw_data <- paste0("data_", w)
-#'     rv[[raw_data]][[i]] <-
-#'       rv$data_plausibility$atemporal[[i]][[k]][[raw_data]]
-#'     rv$data_plausibility$atemporal[[i]][[k]][[raw_data]] <- NULL
-#'   }
-#'   gc()
-#' }
-#'
-#' # calculate descriptive results
-#' rv$results_descriptive <- descriptive_results(
-#'   rv = rv,
-#'   headless = rv$headless
-#' )
-#'
-#' # calculate unique plausibilites
-#' rv$results_plausibility_unique <- uniq_plausi_results(
-#'   rv = rv,
-#'   uniq_vars = rv$pl$uniq_vars,
-#'   mdr = rv$mdr,
-#'   headless = rv$headless
-#' )
-#'
-#' create_markdown(
-#'   rv = rv,
-#'   utils_path = rv$utilspath,
-#'   outdir = output_dir,
-#'   headless = rv$headless
-#' )
-#' }
-#' @export
-#'
-create_markdown <- function(rv = rv,
-                            utils_path,
-                            outdir = tempdir(),
-                            headless = FALSE) {
-  warning(paste0(
-    "'create_markdown()' is deprecated ",
-    "and will be removed in a future version. ",
-    "Use 'create_pdf_report' instead."))
-  create_pdf_report(
-    rv = rv,
-    utils_path,
-    outdir = tempdir(),
-    headless = FALSE
-  )
-}