Updated R script for CDM v5.2 pdf
This commit is contained in:
clairblacketer
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C%3A%2FGit%2FGitHub%2FCDM_v5.2%2FCommonDataModel%2FDocumentation%2FCommonDataModel_pdf_create%2FMD_to_PDF_conversion.R="BBDD195"
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C%3A%2FGit%2FGitHub%2FCDM_v5.2%2FCommonDataModel%2FDocumentation%2FCommonDataModel_pdf_create%2FOMOP_CDM_PDF.Rmd="4851A9DE"
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C%3A%2FGit%2FGitHub%2FCommonDataModel%2FDocumentation%2FCommonDataModel_pdf_create%2F.Rhistory="49A263C2"
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C%3A%2FGit%2FGitHub%2FCommonDataModel%2FDocumentation%2FCommonDataModel_pdf_create%2FMD_to_PDF_conversion.R="BC873E69"
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C%3A%2FGit%2FGitHub%2FCommonDataModel%2FDocumentation%2FCommonDataModel_pdf_create%2FOMOP_CDM_PDF.Rmd="9FB0FECF"
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{
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"collab_server" : "",
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"contents" : "## Run this code and point it to the .Rmd file so it can convert the markdown files on the wiki to a pdf\ninstall.packages(\"rmarkdown\")\n\nrmarkdown::render(input = \"OMOP_CDM_PDF.Rmd\", output_format = \"pdf_document\", output_file = \"OMOP_CDM_v5_1_1.pdf\")\n",
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"contents" : "## Run this code and point it to the .Rmd file so it can convert the markdown files on the wiki to a pdf\ninstall.packages(\"rmarkdown\")\n\nrmarkdown::render(input = \"OMOP_CDM_PDF.Rmd\", output_format = \"pdf_document\", output_file = \"OMOP_CDM_v5_2.pdf\")\n",
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"created" : 1500488094416.000,
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"dirty" : true,
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"dirty" : false,
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"encoding" : "UTF-8",
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"folds" : "",
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"hash" : "2905752151",
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"hash" : "4214385325",
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"id" : "C0F9B15",
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"lastKnownWriteTime" : 1500489695,
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"last_content_update" : 1500489714715,
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"path" : "C:/Git/GitHub/CommonDataModel/Documentation/CommonDataModel_pdf_create/MD_to_PDF_conversion.R",
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"lastKnownWriteTime" : 1500494244,
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"last_content_update" : 1500494244700,
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"path" : "C:/Git/GitHub/CDM_v5.2/CommonDataModel/Documentation/CommonDataModel_pdf_create/MD_to_PDF_conversion.R",
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"project_path" : "MD_to_PDF_conversion.R",
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"properties" : {
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},
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C:/Git/GitHub/CDM_v5.2/CommonDataModel/Documentation/CommonDataModel_pdf_create/OMOP_CDM_PDF.Rmd="642ADD90"
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C:/Git/GitHub/CommonDataModel/Documentation/CommonDataModel_pdf_create/.Rhistory="F8815F2B"
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C:/Git/GitHub/CommonDataModel/Documentation/CommonDataModel_pdf_create/OMOP_CDM_PDF.Rmd="4CB4ECEA"
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## Run this code and point it to the .Rmd file so it can convert the markdown files on the wiki to a pdf
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install.packages("rmarkdown")
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rmarkdown::render(input = "OMOP_CDM_PDF.Rmd", output_format = "pdf_document", output_file = "OMOP_CDM_v5_1_1.pdf")
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rmarkdown::render(input = "OMOP_CDM_PDF.Rmd", output_format = "pdf_document", output_file = "OMOP_CDM_v5_2.pdf")
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---
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title: "OMOP Common Data Model v5.1 Specifications"
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title: "OMOP Common Data Model v5.2 Specifications"
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author: "Christian Reich, Patrick Ryan, Rimma Belenkaya, Karthik Natarajan and Clair Blacketer"
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date: "`r Sys.Date()`"
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output:
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@ -11,193 +11,197 @@ linkcolor: blue
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# License
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```{r child = '.../CommonDataModel_Wiki_Files/License.md'}
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```{r child = '../CommonDataModel_Wiki_Files/License.md'}
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```
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# Background
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```{r child = 'C:/Git/CommonDataModel.wiki/Background/Background.md'}
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```{r child = '../CommonDataModel_Wiki_Files/Background/Background.md'}
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```
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## The Role of the Common Data Model
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```{r child = 'C:/Git/CommonDataModel.wiki/Background/The-Role-of-the-Common-Data-Model.md'}
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```{r child = '../CommonDataModel_Wiki_Files/Background/The-Role-of-the-Common-Data-Model.md'}
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```
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## Design Principles
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```{r child = 'C:/Git/CommonDataModel.wiki/Background/Design-Principles.md'}
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```{r child = '../CommonDataModel_Wiki_Files/Background/Design-Principles.md'}
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```
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## Data Model Conventions
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```{r child = 'C:/Git/CommonDataModel.wiki/Background/Data-Model-Conventions.md'}
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```{r child = '../CommonDataModel_Wiki_Files/Background/Data-Model-Conventions.md'}
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```
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# Glossary of Terms
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```{r child = 'C:/Git/CommonDataModel.wiki/Glossary-of-Terms.md'}
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```{r child = '../CommonDataModel_Wiki_Files/Glossary-of-Terms.md'}
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```
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# Standardized Vocabularies
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/Standardized-Vocabularies.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/Standardized-Vocabularies.md'}
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```
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## CONCEPT
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/CONCEPT.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT.md'}
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```
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## VOCABULARY
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/VOCABULARY.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/VOCABULARY.md'}
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```
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## DOMAIN
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/DOMAIN.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/DOMAIN.md'}
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```
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## CONCEPT_CLASS
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/CONCEPT_CLASS.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_CLASS.md'}
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```
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## CONCEPT_RELATIONSHIP
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/CONCEPT_RELATIONSHIP.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_RELATIONSHIP.md'}
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```
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## RELATIONSHIP
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/RELATIONSHIP.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/RELATIONSHIP.md'}
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```
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## CONCEPT_SYNONYM
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/CONCEPT_SYNONYM.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_SYNONYM.md'}
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```
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## CONCEPT_ANCESTOR
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/CONCEPT_ANCESTOR.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_ANCESTOR.md'}
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```
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## SOURCE_TO_CONCEPT_MAP
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/SOURCE_TO_CONCEPT_MAP.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/SOURCE_TO_CONCEPT_MAP.md'}
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```
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## DRUG_STRENGTH
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/DRUG_STRENGTH.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/DRUG_STRENGTH.md'}
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```
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## COHORT_DEFINITION
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/COHORT_DEFINITION.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/COHORT_DEFINITION.md'}
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```
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## ATTRIBUTE_DEFINITION
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/ATTRIBUTE_DEFINITION.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/ATTRIBUTE_DEFINITION.md'}
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```
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# Standardized Metadata
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedMetadata/Standardized-Metadata.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedMetadata/Standardized-Metadata.md'}
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```
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## CDM_SOURCE
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedMetadata/CDM_SOURCE.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedMetadata/CDM_SOURCE.md'}
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```
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# Standardized Clinical Data Tables
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/Standardized-clinical-Data-Tables.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/Standardized-clinical-Data-Tables.md'}
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```
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## PERSON
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/PERSON.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/PERSON.md'}
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```
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## OBSERVATION_PERIOD
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/OBSERVATION_PERIOD.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/OBSERVATION_PERIOD.md'}
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```
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## SPECIMEN
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/SPECIMEN.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/SPECIMEN.md'}
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```
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## DEATH
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/DEATH.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/DEATH.md'}
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```
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## VISIT_OCCURRENCE
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/VISIT_OCCURRENCE.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/VISIT_OCCURRENCE.md'}
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```
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## PROCEDURE_OCCURRENCE
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/PROCEDURE_OCCURRENCE.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/PROCEDURE_OCCURRENCE.md'}
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```
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## DRUG_EXPOSURE
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/DRUG_EXPOSURE.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/DRUG_EXPOSURE.md'}
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```
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## DEVICE_EXPOSURE
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/DEVICE_EXPOSURE.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/DEVICE_EXPOSURE.md'}
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```
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## CONDITION_OCCURRENCE
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/CONDITION_OCCURRENCE.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/CONDITION_OCCURRENCE.md'}
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```
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## MEASUREMENT
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/MEASUREMENT.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/MEASUREMENT.md'}
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```
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## NOTE
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/NOTE.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/NOTE.md'}
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```
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## NOTE_NLP
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/NOTE_NLP.md'}
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```
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## OBSERVATION
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/OBSERVATION.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/OBSERVATION.md'}
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```
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## FACT_RELATIONSHIP
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/FACT_RELATIONSHIP.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/FACT_RELATIONSHIP.md'}
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```
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# Standardized Health System Data Tables
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthSystemDataTables/Standardized-Health-System-Data-Tables.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/Standardized-Health-System-Data-Tables.md'}
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```
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## LOCATION
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthSystemDataTables/LOCATION.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/LOCATION.md'}
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```
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## CARE_SITE
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthSystemDataTables/CARE_SITE.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/CARE_SITE.md'}
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```
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## PROVIDER
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthSystemDataTables/PROVIDER.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/PROVIDER.md'}
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```
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# Standardized Health Economics Data Tables
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthEconomicsDataTables/Standardized-Health-Economics-Data-Tables.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/Standardized-Health-Economics-Data-Tables.md'}
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```
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## PAYER_PLAN_PERIOD
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthEconomicsDataTables/PAYER_PLAN_PERIOD.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/PAYER_PLAN_PERIOD.md'}
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```
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## COST
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthEconomicsDataTables/COST.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/COST.md'}
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```
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# Standardized Derived Elements
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/Standardized-Derived-Elements.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/Standardized-Derived-Elements.md'}
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```
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## COHORT
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/COHORT.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/COHORT.md'}
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```
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## COHORT_ATTRIBUTE
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/COHORT_ATTRIBUTE.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/COHORT_ATTRIBUTE.md'}
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```
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## DRUG_ERA
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/DRUG_ERA.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/DRUG_ERA.md'}
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```
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## DOSE_ERA
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/DOSE_ERA.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/DOSE_ERA.md'}
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```
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## CONDITION_ERA
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```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/CONDITION_ERA.md'}
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```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/CONDITION_ERA.md'}
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```
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