From eb8741a646684242a56675680564c8d687bd6c9a Mon Sep 17 00:00:00 2001
From: Alexander Sandercock <39815775+alex-sandercock@users.noreply.github.com>
Date: Sat, 10 Jan 2026 12:14:29 -0500
Subject: [PATCH 1/3] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index bc3a1ba..90199ef 100644
--- a/README.md
+++ b/README.md
@@ -133,7 +133,7 @@ BIGapp leverages a powerful suite of R packages:
 
 ## Funding
 
-BIGapp development is supported by [Breeding Insight](https://www.breedinginsight.org/), a USDA-funded initiative based at Cornell University.
+BIGapp development is supported by [Breeding Insight](https://www.breedinginsight.org/), a USDA-funded initiative based at University of Florida - IFAS.
 
 ## Citation
 

From 29903b9929f57f6a6a969986318cf30e7d9722ca Mon Sep 17 00:00:00 2001
From: Alexander Sandercock <39815775+alex-sandercock@users.noreply.github.com>
Date: Tue, 10 Feb 2026 15:56:08 -0500
Subject: [PATCH 2/3] Increase maximum upload size to 1000GB

---
 R/app_server.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/app_server.R b/R/app_server.R
index 2052408..50c4b7d 100644
--- a/R/app_server.R
+++ b/R/app_server.R
@@ -10,7 +10,7 @@ app_server <- function(input, output, session) {
   # Your application server logic
 
   ##Add server configurations
-  options(shiny.maxRequestSize = 10000 * 1024^2)  # Set maximum upload size to 10GB
+  options(shiny.maxRequestSize = 1000000 * 1024^2)  # Set maximum upload size to 1000GB
   #shiny.maxRequestSize = 10000 * 1024^2; # 10 GB <- This is for a future limit when using BI's server remotely
 
   callModule(mod_DosageCall_server,

From e17204352647144287da35459449827dffa832f0 Mon Sep 17 00:00:00 2001
From: Alexander Sandercock <39815775+alex-sandercock@users.noreply.github.com>
Date: Tue, 17 Feb 2026 09:17:44 -0500
Subject: [PATCH 3/3] updated dosage tests

Updated expected bias values in tests to reflect new calculations from the R/Updog changes
---
 tests/testthat/test-DosageCall.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/testthat/test-DosageCall.R b/tests/testthat/test-DosageCall.R
index ef8a912..79ba210 100644
--- a/tests/testthat/test-DosageCall.R
+++ b/tests/testthat/test-DosageCall.R
@@ -29,7 +29,7 @@ test_that("Dosage Calling from MADC file",{
                           model = model_select,
                           nc = cores)
   
-  expect_equal(sum(mout$snpdf$bias), 402.7979, tolerance = 0.01)
+  expect_equal(sum(mout$snpdf$bias), 413, tolerance = 0.5)
   expect_equal(sum(mout$inddf$postmean), 95229.13, tolerance = 0.01)
   
   # Convert updog to VCF
@@ -96,7 +96,7 @@ test_that("Dosage Calling from VCF file",{
                           model = model_select,
                           nc = cores)
   
-  expect_equal(sum(mout$snpdf$bias), 402.79, tolerance = 0.01)
+  expect_equal(sum(mout$snpdf$bias), 413, tolerance = 0.5)
   expect_equal(sum(mout$inddf$postmean), 95229.13, tolerance = 0.01)
   
   # Convert updog to VCF
@@ -221,7 +221,7 @@ test_that("Dosage Calling from VCF file f1 and s1 model",{
                           model = input$updog_model,
                           nc = cores)
   
-  expect_equal(sum(mout$snpdf$bias), 408.5401, tolerance = 0.01)
+  expect_equal(sum(mout$snpdf$bias), 440, tolerance = 0.5)
   expect_equal(sum(mout$inddf$postmean), 94249.05, tolerance = 0.01)
   
   # Convert updog to VCF