From fa6d0d143286ca420efb9dfdde23eba5a04fc919 Mon Sep 17 00:00:00 2001
From: Nazmus Salehin <salehinnazmus672@gmail.com>
Date: Wed, 28 Feb 2024 18:37:48 -0500
Subject: [PATCH 1/3] Updated skeleton.RMD with data checks for
 data_version,branch_name, sha and data_hash

---
 .../templates/visc_report/skeleton/skeleton.Rmd       | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd
index 45d7922a..c8e41193 100644
--- a/inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd
@@ -103,14 +103,25 @@ pandoc_markup <- set_pandoc_markup(output_type)
 remotes::install_github("https://github.com/FredHutch/VDCNNNAnalysis.git")
 ```
 
+```{r check_data_version}
+DataPackageR::assert_data_version("VDCNNNAnalysis",version_string = "data_version")
+testthat::expect_equal(packageDescription("VDCNNNAnalysis")$RemoteSha,"commit_sha")
+testthat::expect_equal(packageDescription("VDCNNNAnalysis")$RemoteRef,"branch_name")
+
+```
+
+
 ```{r data-processing}
 # For this template use VISCfunction example data
 data(exampleData_ICS)
 
+testthat::expect_equal(digest::digest(exampleData_ICS),"data_hash")
+
 ICS_adata <- exampleData_ICS %>% 
   filter(Population == "IFNg" & Group != 3)
 ```
 
+
 `r insert_break()` 
 
 # Summary of Main Results

From 0d53b21ae3eecceb1176a31c5167ec224dc97858 Mon Sep 17 00:00:00 2001
From: Valeria Duran <106105256+valduran18@users.noreply.github.com>
Date: Wed, 28 Feb 2024 17:49:28 -0600
Subject: [PATCH 2/3] add data hash and datapackage branch name to
 reproducibility table

---
 .../templates/visc_report/skeleton/skeleton.Rmd  | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd
index c8e41193..e0ec6a6d 100644
--- a/inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd
@@ -364,8 +364,9 @@ if (any(installed.packages()[,1] == 'rmarkdown')) suppressWarnings(library(rmark
 
 my_session_info <- VISCfunctions::get_session_info()
 
-kable(
-  my_session_info$platform_table, 
+my_session_info$platform_table %>%
+     add_row(name = "data hash", value = digest::digest(exampleData_ICS), .before = nrow(.)) %>%
+  kable(
   format = output_type, 
   booktabs = TRUE, 
   linesep = "", 
@@ -375,8 +376,17 @@ kable(
 ```
 
 ```{r Software-Package-Version-Information, results="asis", warning=kable_warnings}
+my_session_info$packages_table %>%
+           left_join(
+             sessioninfo::package_info() %>% filter(str_detect(source, pattern = "git2r")) %>% 
+               pull(package) %>% 
+               packageDescription() %>% 
+               .[c("Package","RemoteRef")] %>% 
+               as_tibble() %>%
+               rename("package" = "Package",
+                      "branch" = "RemoteRef"),
+             by = "package") %>%
 kable(
-  my_session_info$packages_table, 
   format = output_type, booktabs = TRUE, 
   linesep = "", 
   caption = "Reproducibility software package version information"

From 410aacc2ddf3905230ecd0c60372f4b0275e1a1a Mon Sep 17 00:00:00 2001
From: Dave Slager <slager@users.noreply.github.com>
Date: Thu, 8 Aug 2024 11:00:25 -0700
Subject: [PATCH 3/3] fix merge commit in one more place

---
 inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd
index bc9f9eed..d7a19106 100644
--- a/inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd
@@ -135,12 +135,7 @@ ICS_adata <- exampleData_ICS %>%
   filter(Population == "IFNg" & Group != 3)
 ```
 
-<<<<<<< HEAD
-
-`r insert_break()` 
-=======
 `r insert_break()`
->>>>>>> develop
 
 # Summary of Main Results