fix using multiple refs and add ymls

01-BioDIGS_project_overview.Rmd

@@ -3,7 +3,7 @@
 
 # Background
 
-One critical aspect of an undergraduate STEM education is hands-on research. Undergraduate research experiences enhance what students learn in the classroom as well as increase a student's interest in pursuing STEM careers [@Russell2007]. It can also lead to improved scientific reasoning and increased academic performance overall [@Buffalari2020]. However, many students at underresourced institutions like community colleges, Historically Black Colleges and Universities (HBCUs), tribal colleges and universities, and Hispanic-serving institutions have limited access to research opportunities compared to their cohorts at larger four-year colleges and R1 institutions. These students are also more likely to belong to groups that are already under-represented in STEM disciplines, particularly genomics and data science [@Canner2017] [@GDSCN2022].
+One critical aspect of an undergraduate STEM education is hands-on research. Undergraduate research experiences enhance what students learn in the classroom as well as increase a student's interest in pursuing STEM careers [@Russell2007]. It can also lead to improved scientific reasoning and increased academic performance overall [@Buffalari2020]. However, many students at underresourced institutions like community colleges, Historically Black Colleges and Universities (HBCUs), tribal colleges and universities, and Hispanic-serving institutions have limited access to research opportunities compared to their cohorts at larger four-year colleges and R1 institutions. These students are also more likely to belong to groups that are already under-represented in STEM disciplines, particularly genomics and data science [@Canner2017; @GDSCN2022].
 
 The BioDIGS Project aims to be at the intersection of genomics, data science, cloud computing, and education.
 
@@ -32,6 +32,6 @@ It can be challenging to include undergraduates in human genomic and health rese
 
 ## Heavy metals and human health
 
-Human activities that change the landscape can also change what sorts of inorganic and abiotic compounds we find in the soil, particularly increasing the amount of heavy metals [@Yan2020]. When cars drive on roads, compounds from the exhaust, oil, and other fluids might settle onto the roads and be washed into the soil. When we put salt on roads, parking lots, and sidewalks, the salts themselves will eventually be washed away and enter the ecosystem through both water and soil. Chemicals from factories and other businesses also leech into our environment. Previous research has demonstrated that in areas with more human activity, like cities, soils include greater concentrations of heavy metals than found in rural areas with limited human populations [@Khan2023] [@Wang2022]. Increased heavy metal concentrations also disproportionately affect lower-income and predominantly minority areas [@Jones2022].
+Human activities that change the landscape can also change what sorts of inorganic and abiotic compounds we find in the soil, particularly increasing the amount of heavy metals [@Yan2020]. When cars drive on roads, compounds from the exhaust, oil, and other fluids might settle onto the roads and be washed into the soil. When we put salt on roads, parking lots, and sidewalks, the salts themselves will eventually be washed away and enter the ecosystem through both water and soil. Chemicals from factories and other businesses also leech into our environment. Previous research has demonstrated that in areas with more human activity, like cities, soils include greater concentrations of heavy metals than found in rural areas with limited human populations [@Khan2023; @Wang2022]. Increased heavy metal concentrations also disproportionately affect lower-income and predominantly minority areas [@Jones2022].
 
-Research suggests that increased heavy metal concentration in soils has major impacts on the soil microbial community. In particular, increased heavy metal concentration is associated with an increase in soil bacteria that have antibiotic resistance markers [@Gorovtsov2018] [@Nguyen2019] [@Sun2021].
+Research suggests that increased heavy metal concentration in soils has major impacts on the soil microbial community. In particular, increased heavy metal concentration is associated with an increase in soil bacteria that have antibiotic resistance markers [@Gorovtsov2018; @Nguyen2019; @Sun2021].

_bookdown.yml

@@ -9,7 +9,8 @@ rmd_files: ["index.Rmd",
             "05-anvil_onboarding.Rmd",
             "06-using_platforms_modules.Rmd",
             "08-data_exploration.Rmd",
-            "About.Rmd"]
+            "About.Rmd",
+            "References.Rmd"]
 new_session: yes
 bibliography: [book.bib]
 delete_merged_file: true
@@ -19,4 +20,3 @@ language:
 output_dir: "docs"
 output:
     bookdown::html_book
-

_output.yml

@@ -5,6 +5,7 @@ bookdown::gitbook:
     in_header: GA_Script.html
     before_body: assets/GDSCN_style/big-image_gdscn.html
     after_body: assets/GDSCN_style/footer.html
+  split_bib: false
   highlight: tango
   config:
     toc:
@@ -17,5 +18,5 @@ bookdown::gitbook:
        <a href="https://hutchdatascience.org/" target="_blank"><img src="https://raw.githubusercontent.com/jhudsl/OTTR_Template/main/style-sets/fhdasl/copy_to_assets/big-dasl-stacked.png" style="width: 80%; padding-left: 34px; padding-top: 8px;"</a>
        <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
        <p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span><a href="https://docs.google.com/forms/d/e/1FAIpQLScrDVb_utm55pmb_SHx-RgELTEbCCWdLea0T3IzS0Oj00GE4w/viewform?usp=pp_url&entry.1565230805=your+course"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
-       
-# Note: Do not edit the feedback link in this file. This is automatically edited through the render-preview and render-bookdown workflows.
+
+# Note: Do not edit the feedback link in this file. This is automatically edited through the render-preview and render-bookdown workflows.