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Updated R script for CDM v5.2 pdf

This commit is contained in:
clairblacketer 2017-07-19 15:58:53 -04:00
parent 068e3783b4
commit 2bc655d4a2
6 changed files with 69 additions and 61 deletions
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Documentation/CommonDataModel_pdf_create/.Rproj.user/C9B3802/sdb/prop/INDEX
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C%3A%2FGit%2FGitHub%2FCDM_v5.2%2FCommonDataModel%2FDocumentation%2FCommonDataModel_pdf_create%2FMD_to_PDF_conversion.R="BBDD195"
C%3A%2FGit%2FGitHub%2FCDM_v5.2%2FCommonDataModel%2FDocumentation%2FCommonDataModel_pdf_create%2FOMOP_CDM_PDF.Rmd="4851A9DE"
C%3A%2FGit%2FGitHub%2FCommonDataModel%2FDocumentation%2FCommonDataModel_pdf_create%2F.Rhistory="49A263C2" C%3A%2FGit%2FGitHub%2FCommonDataModel%2FDocumentation%2FCommonDataModel_pdf_create%2F.Rhistory="49A263C2"
C%3A%2FGit%2FGitHub%2FCommonDataModel%2FDocumentation%2FCommonDataModel_pdf_create%2FMD_to_PDF_conversion.R="BC873E69" C%3A%2FGit%2FGitHub%2FCommonDataModel%2FDocumentation%2FCommonDataModel_pdf_create%2FMD_to_PDF_conversion.R="BC873E69"
C%3A%2FGit%2FGitHub%2FCommonDataModel%2FDocumentation%2FCommonDataModel_pdf_create%2FOMOP_CDM_PDF.Rmd="9FB0FECF" C%3A%2FGit%2FGitHub%2FCommonDataModel%2FDocumentation%2FCommonDataModel_pdf_create%2FOMOP_CDM_PDF.Rmd="9FB0FECF"

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Documentation/CommonDataModel_pdf_create/.Rproj.user/C9B3802/sdb/s-572B4995/87804256
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Documentation/CommonDataModel_pdf_create/.Rproj.user/C9B3802/sdb/s-572B4995/C0F9B15
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{ {
"collab_server" : "", "collab_server" : "",
"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", "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",
"created" : 1500488094416.000, "created" : 1500488094416.000,
"dirty" : true, "dirty" : false,
"encoding" : "UTF-8", "encoding" : "UTF-8",
"folds" : "", "folds" : "",
"hash" : "2905752151", "hash" : "4214385325",
"id" : "C0F9B15", "id" : "C0F9B15",
"lastKnownWriteTime" : 1500489695, "lastKnownWriteTime" : 1500494244,
"last_content_update" : 1500489714715, "last_content_update" : 1500494244700,
"path" : "C:/Git/GitHub/CommonDataModel/Documentation/CommonDataModel_pdf_create/MD_to_PDF_conversion.R", "path" : "C:/Git/GitHub/CDM_v5.2/CommonDataModel/Documentation/CommonDataModel_pdf_create/MD_to_PDF_conversion.R",
"project_path" : "MD_to_PDF_conversion.R", "project_path" : "MD_to_PDF_conversion.R",
"properties" : { "properties" : {
}, },

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Documentation/CommonDataModel_pdf_create/.Rproj.user/shared/notebooks/paths
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C:/Git/GitHub/CDM_v5.2/CommonDataModel/Documentation/CommonDataModel_pdf_create/OMOP_CDM_PDF.Rmd="642ADD90"
C:/Git/GitHub/CommonDataModel/Documentation/CommonDataModel_pdf_create/.Rhistory="F8815F2B" C:/Git/GitHub/CommonDataModel/Documentation/CommonDataModel_pdf_create/.Rhistory="F8815F2B"
C:/Git/GitHub/CommonDataModel/Documentation/CommonDataModel_pdf_create/OMOP_CDM_PDF.Rmd="4CB4ECEA" C:/Git/GitHub/CommonDataModel/Documentation/CommonDataModel_pdf_create/OMOP_CDM_PDF.Rmd="4CB4ECEA"

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Documentation/CommonDataModel_pdf_create/MD_to_PDF_conversion.R
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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 ## Run this code and point it to the .Rmd file so it can convert the markdown files on the wiki to a pdf
install.packages("rmarkdown")
rmarkdown::render(input = "OMOP_CDM_PDF.Rmd", output_format = "pdf_document", output_file = "OMOP_CDM_v5_1_1.pdf") rmarkdown::render(input = "OMOP_CDM_PDF.Rmd", output_format = "pdf_document", output_file = "OMOP_CDM_v5_2.pdf")

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Documentation/CommonDataModel_pdf_create/OMOP_CDM_PDF.Rmd
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--- ---
title: "OMOP Common Data Model v5.1 Specifications" title: "OMOP Common Data Model v5.2 Specifications"
author: "Christian Reich, Patrick Ryan, Rimma Belenkaya, Karthik Natarajan and Clair Blacketer" author: "Christian Reich, Patrick Ryan, Rimma Belenkaya, Karthik Natarajan and Clair Blacketer"
date: "`r Sys.Date()`" date: "`r Sys.Date()`"
output: output:
@ -11,193 +11,197 @@ linkcolor: blue
# License # License
```{r child = '.../CommonDataModel_Wiki_Files/License.md'} ```{r child = '../CommonDataModel_Wiki_Files/License.md'}
``` ```
# Background # Background
```{r child = 'C:/Git/CommonDataModel.wiki/Background/Background.md'} ```{r child = '../CommonDataModel_Wiki_Files/Background/Background.md'}
``` ```
## The Role of the Common Data Model ## The Role of the Common Data Model
```{r child = 'C:/Git/CommonDataModel.wiki/Background/The-Role-of-the-Common-Data-Model.md'} ```{r child = '../CommonDataModel_Wiki_Files/Background/The-Role-of-the-Common-Data-Model.md'}
``` ```
## Design Principles ## Design Principles
```{r child = 'C:/Git/CommonDataModel.wiki/Background/Design-Principles.md'} ```{r child = '../CommonDataModel_Wiki_Files/Background/Design-Principles.md'}
``` ```
## Data Model Conventions ## Data Model Conventions
```{r child = 'C:/Git/CommonDataModel.wiki/Background/Data-Model-Conventions.md'} ```{r child = '../CommonDataModel_Wiki_Files/Background/Data-Model-Conventions.md'}
``` ```
# Glossary of Terms # Glossary of Terms
```{r child = 'C:/Git/CommonDataModel.wiki/Glossary-of-Terms.md'} ```{r child = '../CommonDataModel_Wiki_Files/Glossary-of-Terms.md'}
``` ```
# Standardized Vocabularies # Standardized Vocabularies
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/Standardized-Vocabularies.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/Standardized-Vocabularies.md'}
``` ```
## CONCEPT ## CONCEPT
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/CONCEPT.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT.md'}
``` ```
## VOCABULARY ## VOCABULARY
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/VOCABULARY.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/VOCABULARY.md'}
``` ```
## DOMAIN ## DOMAIN
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/DOMAIN.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/DOMAIN.md'}
``` ```
## CONCEPT_CLASS ## CONCEPT_CLASS
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/CONCEPT_CLASS.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_CLASS.md'}
``` ```
## CONCEPT_RELATIONSHIP ## CONCEPT_RELATIONSHIP
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/CONCEPT_RELATIONSHIP.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_RELATIONSHIP.md'}
``` ```
## RELATIONSHIP ## RELATIONSHIP
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/RELATIONSHIP.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/RELATIONSHIP.md'}
``` ```
## CONCEPT_SYNONYM ## CONCEPT_SYNONYM
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/CONCEPT_SYNONYM.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_SYNONYM.md'}
``` ```
## CONCEPT_ANCESTOR ## CONCEPT_ANCESTOR
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/CONCEPT_ANCESTOR.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_ANCESTOR.md'}
``` ```
## SOURCE_TO_CONCEPT_MAP ## SOURCE_TO_CONCEPT_MAP
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/SOURCE_TO_CONCEPT_MAP.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/SOURCE_TO_CONCEPT_MAP.md'}
``` ```
## DRUG_STRENGTH ## DRUG_STRENGTH
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/DRUG_STRENGTH.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/DRUG_STRENGTH.md'}
``` ```
## COHORT_DEFINITION ## COHORT_DEFINITION
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/COHORT_DEFINITION.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/COHORT_DEFINITION.md'}
``` ```
## ATTRIBUTE_DEFINITION ## ATTRIBUTE_DEFINITION
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/ATTRIBUTE_DEFINITION.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/ATTRIBUTE_DEFINITION.md'}
``` ```
# Standardized Metadata # Standardized Metadata
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedMetadata/Standardized-Metadata.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedMetadata/Standardized-Metadata.md'}
``` ```
## CDM_SOURCE ## CDM_SOURCE
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedMetadata/CDM_SOURCE.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedMetadata/CDM_SOURCE.md'}
``` ```
# Standardized Clinical Data Tables # Standardized Clinical Data Tables
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/Standardized-clinical-Data-Tables.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/Standardized-clinical-Data-Tables.md'}
``` ```
## PERSON ## PERSON
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/PERSON.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/PERSON.md'}
``` ```
## OBSERVATION_PERIOD ## OBSERVATION_PERIOD
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/OBSERVATION_PERIOD.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/OBSERVATION_PERIOD.md'}
``` ```
## SPECIMEN ## SPECIMEN
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/SPECIMEN.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/SPECIMEN.md'}
``` ```
## DEATH ## DEATH
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/DEATH.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/DEATH.md'}
``` ```
## VISIT_OCCURRENCE ## VISIT_OCCURRENCE
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/VISIT_OCCURRENCE.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/VISIT_OCCURRENCE.md'}
``` ```
## PROCEDURE_OCCURRENCE ## PROCEDURE_OCCURRENCE
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/PROCEDURE_OCCURRENCE.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/PROCEDURE_OCCURRENCE.md'}
``` ```
## DRUG_EXPOSURE ## DRUG_EXPOSURE
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/DRUG_EXPOSURE.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/DRUG_EXPOSURE.md'}
``` ```
## DEVICE_EXPOSURE ## DEVICE_EXPOSURE
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/DEVICE_EXPOSURE.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/DEVICE_EXPOSURE.md'}
``` ```
## CONDITION_OCCURRENCE ## CONDITION_OCCURRENCE
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/CONDITION_OCCURRENCE.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/CONDITION_OCCURRENCE.md'}
``` ```
## MEASUREMENT ## MEASUREMENT
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/MEASUREMENT.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/MEASUREMENT.md'}
``` ```
## NOTE ## NOTE
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/NOTE.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/NOTE.md'}
```
## NOTE_NLP
```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/NOTE_NLP.md'}
``` ```
## OBSERVATION ## OBSERVATION
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/OBSERVATION.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/OBSERVATION.md'}
``` ```
## FACT_RELATIONSHIP ## FACT_RELATIONSHIP
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/FACT_RELATIONSHIP.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/FACT_RELATIONSHIP.md'}
``` ```
# Standardized Health System Data Tables # Standardized Health System Data Tables
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthSystemDataTables/Standardized-Health-System-Data-Tables.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/Standardized-Health-System-Data-Tables.md'}
``` ```
## LOCATION ## LOCATION
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthSystemDataTables/LOCATION.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/LOCATION.md'}
``` ```
## CARE_SITE ## CARE_SITE
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthSystemDataTables/CARE_SITE.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/CARE_SITE.md'}
``` ```
## PROVIDER ## PROVIDER
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthSystemDataTables/PROVIDER.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/PROVIDER.md'}
``` ```
# Standardized Health Economics Data Tables # Standardized Health Economics Data Tables
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthEconomicsDataTables/Standardized-Health-Economics-Data-Tables.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/Standardized-Health-Economics-Data-Tables.md'}
``` ```
## PAYER_PLAN_PERIOD ## PAYER_PLAN_PERIOD
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthEconomicsDataTables/PAYER_PLAN_PERIOD.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/PAYER_PLAN_PERIOD.md'}
``` ```
## COST ## COST
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthEconomicsDataTables/COST.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/COST.md'}
``` ```
# Standardized Derived Elements # Standardized Derived Elements
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/Standardized-Derived-Elements.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/Standardized-Derived-Elements.md'}
``` ```
## COHORT ## COHORT
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/COHORT.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/COHORT.md'}
``` ```
## COHORT_ATTRIBUTE ## COHORT_ATTRIBUTE
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/COHORT_ATTRIBUTE.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/COHORT_ATTRIBUTE.md'}
``` ```
## DRUG_ERA ## DRUG_ERA
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/DRUG_ERA.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/DRUG_ERA.md'}
``` ```
## DOSE_ERA ## DOSE_ERA
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/DOSE_ERA.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/DOSE_ERA.md'}
``` ```
## CONDITION_ERA ## CONDITION_ERA
```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/CONDITION_ERA.md'} ```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/CONDITION_ERA.md'}
``` ```