From 828136284f1348db4899857a8d26a04307b0e643 Mon Sep 17 00:00:00 2001
From: araikes <adam.raikes@gmail.com>
Date: Thu, 26 Mar 2026 12:08:00 -0700
Subject: [PATCH 1/2] Update ModelArray roxygen

This should fix the duplicate documentation of "usage" in ModelArray by separating the class and function roxygen.
---
 R/ModelArray_Constructor.R | 37 +++++++++++++++++++------------------
 1 file changed, 19 insertions(+), 18 deletions(-)

diff --git a/R/ModelArray_Constructor.R b/R/ModelArray_Constructor.R
index f16d709..e0e2203 100644
--- a/R/ModelArray_Constructor.R
+++ b/R/ModelArray_Constructor.R
@@ -1,16 +1,22 @@
 # Exported Functions
 
-### setClass of "ModelArray" #####
+#' ModelArray class
+#'
 #' An S4 class to represent element-wise scalar data and statistics.
 #'
 #' @slot sources A list of source filenames
-#' @slot scalars A list of element-wise scalar matrix
-#' @slot results A list of statistical result matrix
+#' @slot scalars A list of element-wise scalar matrices
+#' @slot results A list of statistical result matrices
 #' @slot path Path to the h5 file on disk
+#'
+#' @name ModelArray-class
+#' @rdname ModelArray-class
+#' @keywords internal
 #' @importClassesFrom DelayedArray DelayedArray
-ModelArray <- setClass(
+NULL
+
+setClass(
   "ModelArray",
-  # contains="DelayedArray",
   slots = c(
     results = "list",
     sources = "list",
@@ -43,21 +49,16 @@ ModelArraySeed <- function(filepath, name, type = NA) {
 
 
 
-#' Load element-wise data from .h5 file as an ModelArray object
+#' Construct a ModelArray object
+#'
+#' Load element-wise data from an .h5 file as a `ModelArray` object.
 #'
-#' @details:
-#' Tips for debugging:
-#' if you run into this error: "Error in h(simpleError(msg, call)) :
-#' error in evaluating the argument 'seed' in selecting a method for
-#' function 'DelayedArray': HDF5. Symbol table. Can't open object."
-#' Then please check if you give correct "scalar_types" - check via
-#' rhdf5::h5ls(filename_for_h5)
+#' @param filepath Path to an .h5 file
+#' @param scalar_types Expected scalars
+#' @param analysis_names The subfolder names for results in the .h5 file.
+#'   If empty (default), results are not read.
 #'
-#' @param filepath file
-#' @param scalar_types expected scalars
-#' @param analysis_names the subfolder names for results in .h5 file. If empty
-#' (default), results are not read.
-#' @return ModelArray object
+#' @return A `ModelArray` object
 #' @export
 #' @import methods
 #' @importFrom dplyr %>%

From b17ec967a8a50dd644163891072cea7f5d8575c9 Mon Sep 17 00:00:00 2001
From: araikes <adam.raikes@gmail.com>
Date: Thu, 26 Mar 2026 12:48:26 -0700
Subject: [PATCH 2/2] Update Rd files

---
 DESCRIPTION             |  2 +-
 man/ModelArray-class.Rd | 21 +++++++++++++++++++++
 man/ModelArray.Rd       | 39 +++++++--------------------------------
 3 files changed, 29 insertions(+), 33 deletions(-)
 create mode 100644 man/ModelArray-class.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 3d74ee8..77882dd 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -40,7 +40,7 @@ Imports:
     rlang,
     tibble,
     tidyr
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Suggests:
     rmarkdown,
     knitr,
diff --git a/man/ModelArray-class.Rd b/man/ModelArray-class.Rd
new file mode 100644
index 0000000..2f89cd0
--- /dev/null
+++ b/man/ModelArray-class.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ModelArray_Constructor.R
+\name{ModelArray-class}
+\alias{ModelArray-class}
+\title{ModelArray class}
+\description{
+An S4 class to represent element-wise scalar data and statistics.
+}
+\section{Slots}{
+
+\describe{
+\item{\code{sources}}{A list of source filenames}
+
+\item{\code{scalars}}{A list of element-wise scalar matrices}
+
+\item{\code{results}}{A list of statistical result matrices}
+
+\item{\code{path}}{Path to the h5 file on disk}
+}}
+
+\keyword{internal}
diff --git a/man/ModelArray.Rd b/man/ModelArray.Rd
index defb99a..6d13363 100644
--- a/man/ModelArray.Rd
+++ b/man/ModelArray.Rd
@@ -2,46 +2,21 @@
 % Please edit documentation in R/ModelArray_Constructor.R
 \name{ModelArray}
 \alias{ModelArray}
-\title{An S4 class to represent element-wise scalar data and statistics.}
+\title{Construct a ModelArray object}
 \usage{
-ModelArray(filepath, scalar_types = c("FD"), analysis_names = character(0))
-
 ModelArray(filepath, scalar_types = c("FD"), analysis_names = character(0))
 }
 \arguments{
-\item{filepath}{file}
+\item{filepath}{Path to an .h5 file}
 
-\item{scalar_types}{expected scalars}
+\item{scalar_types}{Expected scalars}
 
-\item{analysis_names}{the subfolder names for results in .h5 file. If empty
-(default), results are not read.}
+\item{analysis_names}{The subfolder names for results in the .h5 file.
+If empty (default), results are not read.}
 }
 \value{
-ModelArray object
+A `ModelArray` object
 }
 \description{
-An S4 class to represent element-wise scalar data and statistics.
-
-Load element-wise data from .h5 file as an ModelArray object
+Load element-wise data from an .h5 file as a `ModelArray` object.
 }
-\details{
-:
-Tips for debugging:
-if you run into this error: "Error in h(simpleError(msg, call)) :
-error in evaluating the argument 'seed' in selecting a method for
-function 'DelayedArray': HDF5. Symbol table. Can't open object."
-Then please check if you give correct "scalar_types" - check via
-rhdf5::h5ls(filename_for_h5)
-}
-\section{Slots}{
-
-\describe{
-\item{\code{sources}}{A list of source filenames}
-
-\item{\code{scalars}}{A list of element-wise scalar matrix}
-
-\item{\code{results}}{A list of statistical result matrix}
-
-\item{\code{path}}{Path to the h5 file on disk}
-}}
-