From 0cdf690601174ba23f4001bd193230c5154a5938 Mon Sep 17 00:00:00 2001
From: iww312 <iweidling2@kumc.edu>
Date: Wed, 21 Jan 2026 08:49:35 -0600
Subject: [PATCH] Update read_abcds.R

Incorporates the read cognitive function into the ABCDS reader
---
 R/read_abcds.R | 134 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 134 insertions(+)

diff --git a/R/read_abcds.R b/R/read_abcds.R
index 340532f..cd34e3f 100644
--- a/R/read_abcds.R
+++ b/R/read_abcds.R
@@ -454,3 +454,137 @@ read_athropometrics <- new_abcds_reader(
     data[, c("subject_label", "event_sequence", demovars, "ht", "wt", "bmi")]
   }
 )
+
+#' @title read_cognitive
+#' @description Reads the files containing the cognitive function results from the directory
+#'   for the participants and controls. The cognitive function assessments are identified as those
+#'   starting with `cog` using the `dd_crf_name` variable in the data dictionary.
+#' @param directory A path name containing the downloaded ABC-DS data from the
+#'   University of South Carolina Laboratory of Neuro Imaging's (LONI) Image
+#'   and Data Archive
+#' @param person The specific group for which to read in the data, Default: c("participants", "controls")
+#' @param include_demographics An optional parameter to merge demographic information
+#'   before returning the data, Default: FALSE
+#' @return OUTPUT_DESCRIPTION
+#' @details Reads the files containing the cognitive function results from the
+#'   directory for the participants and controls. The cognitive function
+#'   assessments are identified as those starting with `cog` using the
+#'   `dd_crf_name` variable in the data dictionary. End users also have an
+#'   option to include the demographics with the `include_demographics` argument.
+#' @rdname read_cognitive
+#' @export
+
+read_cognitive <- new_abcds_reader("cog")
+
+load(system.file("extdata/data_dictionary.RData", package = "abcds"))
+
+cog_labels <- gsub(
+    "\u2013| |:|/",
+    "_",
+    unique(data_dictionary[
+      startsWith(data_dictionary$dd_crf_name, "cog"),
+      "dd_crf_label"
+    ])
+  )
+
+  if ("participants" %in% person) {
+    participants <- data.frame()
+    for (i in cog_labels[!grepl("Montreal", cog_labels)]) {
+      file <- list.files(directory, pattern = i, full.names = TRUE)
+      if (length(file) != 0) {
+        temp_df <- utils::read.csv(file)
+      }
+      if ("update_stamp" %in% colnames(temp_df)) {
+        temp_df$update_stamp <- NULL
+      }
+      if (all(dim(participants) == 0)) {
+        participants <- temp_df
+      } else {
+        participants <- merge(
+          participants,
+          temp_df,
+          by = c(
+            "subject_label",
+            "event_sequence",
+            "language_code",
+            "language_label"
+          ),
+          all = TRUE
+        )
+      }
+    }
+    if (include_demographics) {
+      participants <- merge(
+        read_demographics(directory),
+        participants,
+        by = c(
+          "subject_label",
+          "event_sequence",
+          "language_code",
+          "language_label"
+        )
+      )
+    }
+    participants <- add_latency(
+      directory,
+      data = participants,
+      person = "participants",
+      visit = "clinical"
+    )
+    participants <- participants[
+      order(participants$subject_label, participants$event_sequence),
+    ]
+    class(participants) <- c("tbl_df", "tbl", "data.frame")
+  }
+
+  if ("controls" %in% person) {
+    controls <- utils::read.csv(
+      list.files(
+        directory,
+        pattern = cog_labels[grepl("Montreal", cog_labels)],
+        full.names = TRUE
+      )
+    )
+    if ("update_stamp" %in% colnames(controls)) {
+      controls$update_stamp <- NULL
+    }
+    if (include_demographics) {
+      controls <- merge(
+        read_demographics(
+          directory,
+          controls = TRUE
+        ),
+        controls,
+        by = c(
+          "subject_label",
+          "event_sequence",
+          "language_code",
+          "language_label"
+        )
+      )
+    }
+    controls <- add_latency(
+      directory,
+      data = controls,
+      person = "controls",
+      visit = "clinical"
+    )
+    controls <- controls[
+      order(controls$subject_label, controls$event_sequence),
+    ]
+    class(controls) <- c("tbl_df", "tbl", "data.frame")
+  }
+
+  if (
+    exists("participants", inherits = FALSE) &
+      exists("controls", inherits = FALSE)
+  ) {
+    return(list(participants = participants, controls = controls))
+  } else if (exists("participants", inherits = FALSE)) {
+    return(participants)
+  } else if (exists("controls", inherits = FALSE)) {
+    return(controls)
+  } else {
+    stop("Did not find any cognitive files")
+  }
+}