From 7d154e3d0aeac790e93eb4d014a8384045557c8f Mon Sep 17 00:00:00 2001
From: Douglas Ezra Morrison <demorrison@ucdavis.edu>
Date: Thu, 3 Oct 2024 11:46:21 -0700
Subject: [PATCH] fixes

---
 README.md                                    | 9 +++++++--
 README.qmd                                   | 2 +-
 vignettes/articles/enteric_fever_example.Rmd | 2 +-
 vignettes/articles/scrubTyphus_example.Rmd   | 2 +-
 vignettes/articles/serocalculator.Rmd        | 1 +
 5 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 48e4fe84..293a0d28 100644
--- a/README.md
+++ b/README.md
@@ -11,9 +11,14 @@
 [![codecov](https://codecov.io/gh/UCD-SERG/serocalculator/graph/badge.svg?token=85CXV6GN2T)](https://codecov.io/gh/UCD-SERG/serocalculator)
 <!-- badges: end -->
 
-    #> Warning: package 'qrcode' was built under R version 4.4.1
+<div id="fig-website-QR">
 
-![QR code for {serocalculator} website](man/figures/qr.svg)
+![](man/figures/qr.svg)
+
+
+Figure 1: QR code for `serocalculator` website
+
+</div>
 
 Antibody levels measured in a cross–sectional population sample can be
 translated into an estimate of the frequency with which seroconversions
diff --git a/README.qmd b/README.qmd
index 179427b5..67b1e0df 100644
--- a/README.qmd
+++ b/README.qmd
@@ -29,7 +29,7 @@ code <- qr_code("https://ucd-serg.github.io/serocalculator/")
 generate_svg(code, filename = "man/figures/qr.svg")
 ```
 
-![QR code for {serocalculator} website](man/figures/qr.svg)
+![QR code for `serocalculator` website](man/figures/qr.svg){#fig-website-QR}
 
 Antibody levels measured in a cross–sectional population sample can be translated into an estimate of the frequency with which seroconversions (infections) occur in the sampled population. 
 In other words, the presence of many high antibody titers indicates that many individuals likely experienced infection recently and the burden of disease is high in the population, 
diff --git a/vignettes/articles/enteric_fever_example.Rmd b/vignettes/articles/enteric_fever_example.Rmd
index 86f65164..d884e455 100644
--- a/vignettes/articles/enteric_fever_example.Rmd
+++ b/vignettes/articles/enteric_fever_example.Rmd
@@ -9,7 +9,7 @@ vignette: >
   %\VignetteIndexEntry{Enteric Fever Seroincidence Vignette}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
-bibliography: references.bib
+bibliography: vignettes/references.bib
 ---
 ## Introduction
 
diff --git a/vignettes/articles/scrubTyphus_example.Rmd b/vignettes/articles/scrubTyphus_example.Rmd
index 1d12a61d..59954d93 100644
--- a/vignettes/articles/scrubTyphus_example.Rmd
+++ b/vignettes/articles/scrubTyphus_example.Rmd
@@ -9,7 +9,7 @@ vignette: >
   %\VignetteIndexEntry{Scrub Typhus Seroincidence Vignette}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
-bibliography: references.bib
+bibliography: vignettes/references.bib
 
 ---
 ## Introduction
diff --git a/vignettes/articles/serocalculator.Rmd b/vignettes/articles/serocalculator.Rmd
index ce5259a6..6ae04d48 100644
--- a/vignettes/articles/serocalculator.Rmd
+++ b/vignettes/articles/serocalculator.Rmd
@@ -7,6 +7,7 @@ vignette: >
   %\VignetteIndexEntry{Introduction to serocalculator}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
+bibliography: vignettes/references.bib
 ---
 
 ## Overview