Add chapters and reorganize some of the content

.gitignore

@@ -8,3 +8,6 @@ spell_check_results.tsv
 .RData
 .httr-oauth
 docker/git_token.txt
+.Rproj.user/
+docs/*
+*.Rproj

01-data_types.Rmd

@@ -72,12 +72,6 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/1ivDTcLjb2078O0Ge
 
 When used in EHR research, both structured data and clinical notes are generally de-identified to protect patient privacy. Patient ID numbers might be replaced with new identifiers, with linkages maintained by institutional “honest brokers” [@Dhir2008] charged with providing clinical data for research purposes. In some cases, dates may be changed as well. Clinical notes are generally “de-identified” through specialized software designed to remove names, dates, locations, and other sensitive details. Researchers working with institutions to access clinical data should be sure to understand local data de-identification practices.
 
-
-## How to acquire clinical data
-
-### Secondary Sources
-
-
 ## Description of data
 
 ### File types

01d-how_to_acquire_data.Rmd

@@ -0,0 +1,19 @@
+# How to Acquire Clinical Data
+
+## Learning Objectives
+
+## Electronic Health Records
+
+## Medical Databases (?)
+
+## Registries (?)
+
+## Secondary Sources
+
+## Retrospective Analyses
+
+Does this belong in collecting data or acquiring data? 
+
+Retrospective analysis involves the examination of pre-existing clinical data to answer specific research questions, explore hypotheses, and identify patterns or trends. This method leverages historical data collected from medical records, administrative databases, registries, electronic health records (EHRs), or other sources of clinical information.
+
+## Summary

_bookdown.yml

@@ -5,6 +5,8 @@ rmd_files: ["index.Rmd",
             "00-intro.Rmd",
             "01-data_types.Rmd",
             "01b-specific_data_types.Rmd",
+            "01c-how_to_collect_data.Rmd",
+            "01d-how_to_acquire_data.Rmd",
             "02-data_uses.Rmd",
             "03-data_management.Rmd",
             "04-appendixI.Rmd",

packages.bib

@@ -3,32 +3,32 @@ @Manual{R-base
   author = {{R Core Team}},
   organization = {R Foundation for Statistical Computing},
   address = {Vienna, Austria},
-  year = {2020},
+  year = {2025},
   url = {https://www.R-project.org/},
 }
 
 @Manual{R-bookdown,
   title = {bookdown: Authoring Books and Technical Documents with R Markdown},
   author = {Yihui Xie},
-  year = {2021},
-  note = {https://github.com/rstudio/bookdown,
-https://pkgs.rstudio.com/bookdown/},
+  year = {2025},
+  note = {R package version 0.46},
+  url = {https://github.com/rstudio/bookdown},
 }
 
 @Manual{R-knitr,
   title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
   author = {Yihui Xie},
-  year = {2021},
-  note = {R package version 1.33},
+  year = {2025},
+  note = {R package version 1.51},
   url = {https://yihui.org/knitr/},
 }
 
 @Manual{R-rmarkdown,
   title = {rmarkdown: Dynamic Documents for R},
-  author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
-  year = {2021},
-  note = {https://github.com/rstudio/rmarkdown,
-https://pkgs.rstudio.com/rmarkdown/},
+  author = {JJ Allaire and Yihui Xie and Christophe Dervieux and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
+  year = {2026},
+  note = {R package version 2.31},
+  url = {https://github.com/rstudio/rmarkdown},
 }
 
 @Book{bookdown2016,
@@ -37,7 +37,7 @@ @Book{bookdown2016
   publisher = {Chapman and Hall/CRC},
   address = {Boca Raton, Florida},
   year = {2016},
-  note = {ISBN 978-1138700109},
+  isbn = {978-1138700109},
   url = {https://bookdown.org/yihui/bookdown},
 }
 
@@ -60,7 +60,6 @@ @InCollection{knitr2014
   publisher = {Chapman and Hall/CRC},
   year = {2014},
   note = {ISBN 978-1466561595},
-  url = {http://www.crcpress.com/product/isbn/9781466561595},
 }
 
 @Book{rmarkdown2018,
@@ -69,8 +68,8 @@ @Book{rmarkdown2018
   publisher = {Chapman and Hall/CRC},
   address = {Boca Raton, Florida},
   year = {2018},
-  note = {ISBN 9781138359338},
-  url = {https://bookdown.org/yihui/rmarkdown},
+  isbn = {9781138359338},
+  url = {https://yihui.org/rmarkdown/},
 }
 
 @Book{rmarkdown2020,
@@ -79,7 +78,7 @@ @Book{rmarkdown2020
   publisher = {Chapman and Hall/CRC},
   address = {Boca Raton, Florida},
   year = {2020},
-  note = {ISBN 9780367563837},
-  url = {https://bookdown.org/yihui/rmarkdown-cookbook},
+  isbn = {9780367563837},
+  url = {https://yihui.org/rmarkdown-cookbook},
 }
 

resources/dictionary.txt

@@ -16,6 +16,7 @@ colorectal
 comorbidities
 Comorbidities
 CPT
+CRF
 CRFs
 CUIs
 customizations
@@ -48,9 +49,12 @@ McGrady
 MEM
 Modi
 Multivariable
+ncbi
 NCI
 NDC
+nih
 NIH's
+nlm
 NLP
 OMOP
 ontologies
@@ -60,6 +64,8 @@ Permanente
 personalization
 Ph
 PHM
+pmc
+PMC
 polypharmacy
 pre
 PROMs