From 72d639b8dbd2989720cb1bee23240d48930dde9e Mon Sep 17 00:00:00 2001
From: egillax <egillax@gmail.com>
Date: Mon, 4 Mar 2024 17:00:59 +0100
Subject: [PATCH] fix roxygen issues

---
 .github/workflows/R_CMD_check_Hades.yaml |  3 ---
 DESCRIPTION                              |  2 +-
 R/HelperFunctions.R                      |  2 ++
 R/PatientLevelPrediction.R               |  3 +--
 man/PatientLevelPrediction.Rd            | 23 +++++++++++++++++++++++
 man/createCohortCovariateSettings.Rd     |  4 +++-
 man/getCohortCovariateData.Rd            |  4 ++--
 7 files changed, 32 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/R_CMD_check_Hades.yaml b/.github/workflows/R_CMD_check_Hades.yaml
index cdd53cf3b..8f940f131 100644
--- a/.github/workflows/R_CMD_check_Hades.yaml
+++ b/.github/workflows/R_CMD_check_Hades.yaml
@@ -92,9 +92,6 @@ jobs:
           remotes::install_cran("covr")
         shell: Rscript {0}
         
-      - name: Setup upterm session
-        uses: lhotari/action-upterm@v1
-
       - name: Test coverage
         if: runner.os == 'Linux'
         run: covr::codecov()
diff --git a/DESCRIPTION b/DESCRIPTION
index ac9fde8ac..700eef1c1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -75,5 +75,5 @@ Remotes:
     ohdsi/FeatureExtraction,
     ohdsi/ShinyAppBuilder,
     ohdsi/ResultModelManager,
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Encoding: UTF-8
diff --git a/R/HelperFunctions.R b/R/HelperFunctions.R
index 5c9d1ae3f..c6fd07d13 100644
--- a/R/HelperFunctions.R
+++ b/R/HelperFunctions.R
@@ -1,6 +1,8 @@
 # fix issue with nrow - temp fix for me locally
 nrow <- function(x){UseMethod("nrow",x)}
+#' @exportS3Method NULL
 nrow.default <- base::nrow
+#' @exportS3Method NULL
 nrow.tbl <- function(x){x %>% dplyr::tally() %>% dplyr::pull()}
 
 
diff --git a/R/PatientLevelPrediction.R b/R/PatientLevelPrediction.R
index b4e2a82b5..848c42705 100644
--- a/R/PatientLevelPrediction.R
+++ b/R/PatientLevelPrediction.R
@@ -20,12 +20,11 @@
 #' 
 #' @description A package for running predictions using data in the OMOP CDM
 #'
-#' @docType package
 #' @name PatientLevelPrediction
 #' @keywords internal
 #' @importFrom dplyr %>%
 #' @importFrom rlang .data
-NULL
+"_PACKAGE"
 
 #' A simulation profile
 #' @docType data
diff --git a/man/PatientLevelPrediction.Rd b/man/PatientLevelPrediction.Rd
index c3d7c5c47..8bc15fc71 100644
--- a/man/PatientLevelPrediction.Rd
+++ b/man/PatientLevelPrediction.Rd
@@ -2,9 +2,32 @@
 % Please edit documentation in R/PatientLevelPrediction.R
 \docType{package}
 \name{PatientLevelPrediction}
+\alias{PatientLevelPrediction-package}
 \alias{PatientLevelPrediction}
 \title{PatientLevelPrediction}
 \description{
 A package for running predictions using data in the OMOP CDM
+}
+\seealso{
+Useful links:
+\itemize{
+  \item \url{https://ohdsi.github.io/PatientLevelPrediction}
+  \item \url{https://github.com/OHDSI/PatientLevelPrediction}
+  \item Report bugs at \url{https://github.com/OHDSI/PatientLevelPrediction/issues}
+}
+
+}
+\author{
+\strong{Maintainer}: Jenna Reps \email{jreps@its.jnj.com}
+
+Authors:
+\itemize{
+  \item Martijn Schuemie
+  \item Marc Suchard
+  \item Patrick Ryan
+  \item Peter Rijnbeek
+  \item Egill Fridgeirsson
+}
+
 }
 \keyword{internal}
diff --git a/man/createCohortCovariateSettings.Rd b/man/createCohortCovariateSettings.Rd
index 98d3480eb..eeb9c974e 100644
--- a/man/createCohortCovariateSettings.Rd
+++ b/man/createCohortCovariateSettings.Rd
@@ -27,7 +27,7 @@ createCohortCovariateSettings(
 
 \item{cohortTable}{the table name that contains the covariate cohort}
 
-\item{cohortId}{cohort id for the covariate cohort}
+\item{cohortId}{DEPRECATED cohort id for the covariate cohort}
 
 \item{startDay}{The number of days prior to index to start observing the cohort}
 
@@ -41,6 +41,8 @@ If TRUE then the covariate value is the number of unique cohort_start_dates betw
 \item{lnAgeInteraction}{If TRUE multiple covariate value by the log of the patient's age in years}
 
 \item{analysisId}{The analysisId for the covariate}
+
+\item{cohortIds}{cohortId(s) for the covariate cohorts}
 }
 \value{
 An object of class covariateSettings specifying how to create the cohort covariate with the covariateId
diff --git a/man/getCohortCovariateData.Rd b/man/getCohortCovariateData.Rd
index ff152f84b..d5333d646 100644
--- a/man/getCohortCovariateData.Rd
+++ b/man/getCohortCovariateData.Rd
@@ -12,7 +12,7 @@ getCohortCovariateData(
   cohortTable = "#cohort_person",
   rowIdField = "row_id",
   aggregated,
-  cohortId,
+  cohortIds,
   covariateSettings
 )
 }
@@ -31,7 +31,7 @@ getCohortCovariateData(
 
 \item{aggregated}{whether the covariate should be aggregated}
 
-\item{cohortId}{cohort id for the target cohort}
+\item{cohortIds}{cohort id for the target cohort}
 
 \item{covariateSettings}{settings for the covariate cohorts and time periods}
 }