From 2bc655d4a270f1f82e5bad4fd2aa2d28394d3d48 Mon Sep 17 00:00:00 2001 From: clairblacketer Date: Wed, 19 Jul 2017 15:58:53 -0400 Subject: [PATCH] Updated R script for CDM v5.2 pdf --- .../.Rproj.user/C9B3802/sdb/prop/INDEX | 2 + .../C9B3802/sdb/s-572B4995/87804256 | 10 +- .../C9B3802/sdb/s-572B4995/C0F9B15 | 12 +-- .../.Rproj.user/shared/notebooks/paths | 1 + .../MD_to_PDF_conversion.R | 3 +- .../OMOP_CDM_PDF.Rmd | 102 +++++++++--------- 6 files changed, 69 insertions(+), 61 deletions(-) diff --git a/Documentation/CommonDataModel_pdf_create/.Rproj.user/C9B3802/sdb/prop/INDEX b/Documentation/CommonDataModel_pdf_create/.Rproj.user/C9B3802/sdb/prop/INDEX index 3d92f32..64ab079 100644 --- a/Documentation/CommonDataModel_pdf_create/.Rproj.user/C9B3802/sdb/prop/INDEX +++ b/Documentation/CommonDataModel_pdf_create/.Rproj.user/C9B3802/sdb/prop/INDEX @@ -1,3 +1,5 @@ +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%2FMD_to_PDF_conversion.R="BC873E69" C%3A%2FGit%2FGitHub%2FCommonDataModel%2FDocumentation%2FCommonDataModel_pdf_create%2FOMOP_CDM_PDF.Rmd="9FB0FECF" diff --git a/Documentation/CommonDataModel_pdf_create/.Rproj.user/C9B3802/sdb/s-572B4995/87804256 b/Documentation/CommonDataModel_pdf_create/.Rproj.user/C9B3802/sdb/s-572B4995/87804256 index db05b80..1729446 100644 --- a/Documentation/CommonDataModel_pdf_create/.Rproj.user/C9B3802/sdb/s-572B4995/87804256 +++ b/Documentation/CommonDataModel_pdf_create/.Rproj.user/C9B3802/sdb/s-572B4995/87804256 @@ -1,15 +1,15 @@ { "collab_server" : "", - "contents" : "---\ntitle: \"OMOP Common Data Model v5.1 Specifications\"\nauthor: \"Christian Reich, Patrick Ryan, Rimma Belenkaya, Karthik Natarajan and Clair Blacketer\"\ndate: \"`r Sys.Date()`\"\noutput:\n pdf_document:\n number_sections: yes\n toc: yes\nlinkcolor: blue\n---\n\n# License\n\n```{r child = '.../CommonDataModel_Wiki_Files/License.md'}\n```\n\n# Background\n```{r child = 'C:/Git/CommonDataModel.wiki/Background/Background.md'}\n```\n\n## The Role of the Common Data Model\n```{r child = 'C:/Git/CommonDataModel.wiki/Background/The-Role-of-the-Common-Data-Model.md'}\n```\n\n## Design Principles\n```{r child = 'C:/Git/CommonDataModel.wiki/Background/Design-Principles.md'}\n```\n\n## Data Model Conventions\n```{r child = 'C:/Git/CommonDataModel.wiki/Background/Data-Model-Conventions.md'}\n```\n\n# Glossary of Terms\n```{r child = 'C:/Git/CommonDataModel.wiki/Glossary-of-Terms.md'}\n```\n\n# Standardized Vocabularies\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/Standardized-Vocabularies.md'}\n```\n\n## CONCEPT\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/CONCEPT.md'}\n```\n\n## VOCABULARY\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/VOCABULARY.md'}\n```\n\n## DOMAIN\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/DOMAIN.md'}\n```\n\n## CONCEPT_CLASS\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/CONCEPT_CLASS.md'}\n```\n\n## CONCEPT_RELATIONSHIP\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/CONCEPT_RELATIONSHIP.md'}\n```\n\n## RELATIONSHIP\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/RELATIONSHIP.md'}\n```\n\n## CONCEPT_SYNONYM\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/CONCEPT_SYNONYM.md'}\n```\n\n## CONCEPT_ANCESTOR\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/CONCEPT_ANCESTOR.md'}\n```\n\n## SOURCE_TO_CONCEPT_MAP\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/SOURCE_TO_CONCEPT_MAP.md'}\n```\n\n## DRUG_STRENGTH\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/DRUG_STRENGTH.md'}\n```\n\n## COHORT_DEFINITION\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/COHORT_DEFINITION.md'}\n```\n\n## ATTRIBUTE_DEFINITION\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/ATTRIBUTE_DEFINITION.md'}\n```\n\n# Standardized Metadata\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedMetadata/Standardized-Metadata.md'}\n```\n\n## CDM_SOURCE\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedMetadata/CDM_SOURCE.md'}\n```\n\n# Standardized Clinical Data Tables\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/Standardized-clinical-Data-Tables.md'}\n```\n\n## PERSON\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/PERSON.md'}\n```\n\n## OBSERVATION_PERIOD\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/OBSERVATION_PERIOD.md'}\n```\n\n## SPECIMEN\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/SPECIMEN.md'}\n```\n\n## DEATH\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/DEATH.md'}\n```\n\n## VISIT_OCCURRENCE\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/VISIT_OCCURRENCE.md'}\n```\n\n## PROCEDURE_OCCURRENCE\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/PROCEDURE_OCCURRENCE.md'}\n```\n\n## DRUG_EXPOSURE\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/DRUG_EXPOSURE.md'}\n```\n\n## DEVICE_EXPOSURE\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/DEVICE_EXPOSURE.md'}\n```\n\n## CONDITION_OCCURRENCE\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/CONDITION_OCCURRENCE.md'}\n```\n\n## MEASUREMENT\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/MEASUREMENT.md'}\n```\n\n## NOTE\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/NOTE.md'}\n```\n\n## OBSERVATION\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/OBSERVATION.md'}\n```\n\n## FACT_RELATIONSHIP\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/FACT_RELATIONSHIP.md'}\n```\n\n# Standardized Health System Data Tables\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthSystemDataTables/Standardized-Health-System-Data-Tables.md'}\n```\n\n## LOCATION\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthSystemDataTables/LOCATION.md'}\n```\n\n## CARE_SITE\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthSystemDataTables/CARE_SITE.md'}\n```\n\n## PROVIDER\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthSystemDataTables/PROVIDER.md'}\n```\n\n# Standardized Health Economics Data Tables\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthEconomicsDataTables/Standardized-Health-Economics-Data-Tables.md'}\n```\n\n## PAYER_PLAN_PERIOD\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthEconomicsDataTables/PAYER_PLAN_PERIOD.md'}\n```\n\n## COST\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthEconomicsDataTables/COST.md'}\n```\n\n# Standardized Derived Elements\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/Standardized-Derived-Elements.md'}\n```\n\n## COHORT\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/COHORT.md'}\n```\n\n## COHORT_ATTRIBUTE\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/COHORT_ATTRIBUTE.md'}\n```\n\n## DRUG_ERA\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/DRUG_ERA.md'}\n```\n\n## DOSE_ERA\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/DOSE_ERA.md'}\n```\n\n## CONDITION_ERA\n```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/CONDITION_ERA.md'}\n```", + "contents" : "---\ntitle: \"OMOP Common Data Model v5.2 Specifications\"\nauthor: \"Christian Reich, Patrick Ryan, Rimma Belenkaya, Karthik Natarajan and Clair Blacketer\"\ndate: \"`r Sys.Date()`\"\noutput:\n pdf_document:\n number_sections: yes\n toc: yes\nlinkcolor: blue\n---\n\n# License\n\n```{r child = '../CommonDataModel_Wiki_Files/License.md'}\n```\n\n# Background\n```{r child = '../CommonDataModel_Wiki_Files/Background/Background.md'}\n```\n\n## The Role of the Common Data Model\n```{r child = '../CommonDataModel_Wiki_Files/Background/The-Role-of-the-Common-Data-Model.md'}\n```\n\n## Design Principles\n```{r child = '../CommonDataModel_Wiki_Files/Background/Design-Principles.md'}\n```\n\n## Data Model Conventions\n```{r child = '../CommonDataModel_Wiki_Files/Background/Data-Model-Conventions.md'}\n```\n\n# Glossary of Terms\n```{r child = '../CommonDataModel_Wiki_Files/Glossary-of-Terms.md'}\n```\n\n# Standardized Vocabularies\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/Standardized-Vocabularies.md'}\n```\n\n## CONCEPT\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT.md'}\n```\n\n## VOCABULARY\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/VOCABULARY.md'}\n```\n\n## DOMAIN\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/DOMAIN.md'}\n```\n\n## CONCEPT_CLASS\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_CLASS.md'}\n```\n\n## CONCEPT_RELATIONSHIP\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_RELATIONSHIP.md'}\n```\n\n## RELATIONSHIP\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/RELATIONSHIP.md'}\n```\n\n## CONCEPT_SYNONYM\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_SYNONYM.md'}\n```\n\n## CONCEPT_ANCESTOR\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_ANCESTOR.md'}\n```\n\n## SOURCE_TO_CONCEPT_MAP\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/SOURCE_TO_CONCEPT_MAP.md'}\n```\n\n## DRUG_STRENGTH\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/DRUG_STRENGTH.md'}\n```\n\n## COHORT_DEFINITION\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/COHORT_DEFINITION.md'}\n```\n\n## ATTRIBUTE_DEFINITION\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/ATTRIBUTE_DEFINITION.md'}\n```\n\n# Standardized Metadata\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedMetadata/Standardized-Metadata.md'}\n```\n\n## CDM_SOURCE\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedMetadata/CDM_SOURCE.md'}\n```\n\n# Standardized Clinical Data Tables\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/Standardized-clinical-Data-Tables.md'}\n```\n\n## PERSON\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/PERSON.md'}\n```\n\n## OBSERVATION_PERIOD\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/OBSERVATION_PERIOD.md'}\n```\n\n## SPECIMEN\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/SPECIMEN.md'}\n```\n\n## DEATH\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/DEATH.md'}\n```\n\n## VISIT_OCCURRENCE\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/VISIT_OCCURRENCE.md'}\n```\n\n## PROCEDURE_OCCURRENCE\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/PROCEDURE_OCCURRENCE.md'}\n```\n\n## DRUG_EXPOSURE\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/DRUG_EXPOSURE.md'}\n```\n\n## DEVICE_EXPOSURE\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/DEVICE_EXPOSURE.md'}\n```\n\n## CONDITION_OCCURRENCE\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/CONDITION_OCCURRENCE.md'}\n```\n\n## MEASUREMENT\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/MEASUREMENT.md'}\n```\n\n## NOTE\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/NOTE.md'}\n```\n\n## NOTE_NLP\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/NOTE_NLP.md'}\n```\n\n## OBSERVATION\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/OBSERVATION.md'}\n```\n\n## FACT_RELATIONSHIP\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/FACT_RELATIONSHIP.md'}\n```\n\n# Standardized Health System Data Tables\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/Standardized-Health-System-Data-Tables.md'}\n```\n\n## LOCATION\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/LOCATION.md'}\n```\n\n## CARE_SITE\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/CARE_SITE.md'}\n```\n\n## PROVIDER\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/PROVIDER.md'}\n```\n\n# Standardized Health Economics Data Tables\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/Standardized-Health-Economics-Data-Tables.md'}\n```\n\n## PAYER_PLAN_PERIOD\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/PAYER_PLAN_PERIOD.md'}\n```\n\n## COST\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/COST.md'}\n```\n\n# Standardized Derived Elements\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/Standardized-Derived-Elements.md'}\n```\n\n## COHORT\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/COHORT.md'}\n```\n\n## COHORT_ATTRIBUTE\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/COHORT_ATTRIBUTE.md'}\n```\n\n## DRUG_ERA\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/DRUG_ERA.md'}\n```\n\n## DOSE_ERA\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/DOSE_ERA.md'}\n```\n\n## CONDITION_ERA\n```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/CONDITION_ERA.md'}\n```", "created" : 1500488103153.000, "dirty" : false, "encoding" : "UTF-8", "folds" : "", - "hash" : "2206750762", + "hash" : "4194078453", "id" : "87804256", - "lastKnownWriteTime" : 1500488177, - "last_content_update" : 1500488177415, - "path" : "C:/Git/GitHub/CommonDataModel/Documentation/CommonDataModel_pdf_create/OMOP_CDM_PDF.Rmd", + "lastKnownWriteTime" : 1500494221, + "last_content_update" : 1500494221444, + "path" : "C:/Git/GitHub/CDM_v5.2/CommonDataModel/Documentation/CommonDataModel_pdf_create/OMOP_CDM_PDF.Rmd", "project_path" : "OMOP_CDM_PDF.Rmd", "properties" : { }, diff --git a/Documentation/CommonDataModel_pdf_create/.Rproj.user/C9B3802/sdb/s-572B4995/C0F9B15 b/Documentation/CommonDataModel_pdf_create/.Rproj.user/C9B3802/sdb/s-572B4995/C0F9B15 index e3aa233..7b55aa0 100644 --- a/Documentation/CommonDataModel_pdf_create/.Rproj.user/C9B3802/sdb/s-572B4995/C0F9B15 +++ b/Documentation/CommonDataModel_pdf_create/.Rproj.user/C9B3802/sdb/s-572B4995/C0F9B15 @@ -1,15 +1,15 @@ { "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, - "dirty" : true, + "dirty" : false, "encoding" : "UTF-8", "folds" : "", - "hash" : "2905752151", + "hash" : "4214385325", "id" : "C0F9B15", - "lastKnownWriteTime" : 1500489695, - "last_content_update" : 1500489714715, - "path" : "C:/Git/GitHub/CommonDataModel/Documentation/CommonDataModel_pdf_create/MD_to_PDF_conversion.R", + "lastKnownWriteTime" : 1500494244, + "last_content_update" : 1500494244700, + "path" : "C:/Git/GitHub/CDM_v5.2/CommonDataModel/Documentation/CommonDataModel_pdf_create/MD_to_PDF_conversion.R", "project_path" : "MD_to_PDF_conversion.R", "properties" : { }, diff --git a/Documentation/CommonDataModel_pdf_create/.Rproj.user/shared/notebooks/paths b/Documentation/CommonDataModel_pdf_create/.Rproj.user/shared/notebooks/paths index c219611..86dc4e6 100644 --- a/Documentation/CommonDataModel_pdf_create/.Rproj.user/shared/notebooks/paths +++ b/Documentation/CommonDataModel_pdf_create/.Rproj.user/shared/notebooks/paths @@ -1,2 +1,3 @@ +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/OMOP_CDM_PDF.Rmd="4CB4ECEA" diff --git a/Documentation/CommonDataModel_pdf_create/MD_to_PDF_conversion.R b/Documentation/CommonDataModel_pdf_create/MD_to_PDF_conversion.R index d84b67f..d76ce6d 100644 --- a/Documentation/CommonDataModel_pdf_create/MD_to_PDF_conversion.R +++ b/Documentation/CommonDataModel_pdf_create/MD_to_PDF_conversion.R @@ -1,3 +1,4 @@ ## 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") diff --git a/Documentation/CommonDataModel_pdf_create/OMOP_CDM_PDF.Rmd b/Documentation/CommonDataModel_pdf_create/OMOP_CDM_PDF.Rmd index b9cc0fb..9e87767 100644 --- a/Documentation/CommonDataModel_pdf_create/OMOP_CDM_PDF.Rmd +++ b/Documentation/CommonDataModel_pdf_create/OMOP_CDM_PDF.Rmd @@ -1,5 +1,5 @@ --- -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" date: "`r Sys.Date()`" output: @@ -11,193 +11,197 @@ linkcolor: blue # License -```{r child = '.../CommonDataModel_Wiki_Files/License.md'} +```{r child = '../CommonDataModel_Wiki_Files/License.md'} ``` # 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 -```{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 -```{r child = 'C:/Git/CommonDataModel.wiki/Background/Design-Principles.md'} +```{r child = '../CommonDataModel_Wiki_Files/Background/Design-Principles.md'} ``` ## 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 -```{r child = 'C:/Git/CommonDataModel.wiki/Glossary-of-Terms.md'} +```{r child = '../CommonDataModel_Wiki_Files/Glossary-of-Terms.md'} ``` # Standardized Vocabularies -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/Standardized-Vocabularies.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/Standardized-Vocabularies.md'} ``` ## CONCEPT -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/CONCEPT.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT.md'} ``` ## VOCABULARY -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/VOCABULARY.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/VOCABULARY.md'} ``` ## DOMAIN -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/DOMAIN.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/DOMAIN.md'} ``` ## CONCEPT_CLASS -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/CONCEPT_CLASS.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_CLASS.md'} ``` ## CONCEPT_RELATIONSHIP -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/CONCEPT_RELATIONSHIP.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_RELATIONSHIP.md'} ``` ## RELATIONSHIP -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/RELATIONSHIP.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/RELATIONSHIP.md'} ``` ## CONCEPT_SYNONYM -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/CONCEPT_SYNONYM.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_SYNONYM.md'} ``` ## 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 -```{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 -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/DRUG_STRENGTH.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/DRUG_STRENGTH.md'} ``` ## COHORT_DEFINITION -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/COHORT_DEFINITION.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/COHORT_DEFINITION.md'} ``` ## ATTRIBUTE_DEFINITION -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedVocabularies/ATTRIBUTE_DEFINITION.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/ATTRIBUTE_DEFINITION.md'} ``` # Standardized Metadata -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedMetadata/Standardized-Metadata.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedMetadata/Standardized-Metadata.md'} ``` ## 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 -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/Standardized-clinical-Data-Tables.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/Standardized-clinical-Data-Tables.md'} ``` ## PERSON -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/PERSON.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/PERSON.md'} ``` ## OBSERVATION_PERIOD -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/OBSERVATION_PERIOD.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/OBSERVATION_PERIOD.md'} ``` ## SPECIMEN -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/SPECIMEN.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/SPECIMEN.md'} ``` ## DEATH -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/DEATH.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/DEATH.md'} ``` ## VISIT_OCCURRENCE -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/VISIT_OCCURRENCE.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/VISIT_OCCURRENCE.md'} ``` ## PROCEDURE_OCCURRENCE -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/PROCEDURE_OCCURRENCE.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/PROCEDURE_OCCURRENCE.md'} ``` ## DRUG_EXPOSURE -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/DRUG_EXPOSURE.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/DRUG_EXPOSURE.md'} ``` ## DEVICE_EXPOSURE -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/DEVICE_EXPOSURE.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/DEVICE_EXPOSURE.md'} ``` ## CONDITION_OCCURRENCE -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/CONDITION_OCCURRENCE.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/CONDITION_OCCURRENCE.md'} ``` ## MEASUREMENT -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/MEASUREMENT.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/MEASUREMENT.md'} ``` ## 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 -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedclinicalDataTables/OBSERVATION.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/OBSERVATION.md'} ``` ## 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 -```{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 -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthSystemDataTables/LOCATION.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/LOCATION.md'} ``` ## CARE_SITE -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthSystemDataTables/CARE_SITE.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/CARE_SITE.md'} ``` ## PROVIDER -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthSystemDataTables/PROVIDER.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/PROVIDER.md'} ``` # 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 -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthEconomicsDataTables/PAYER_PLAN_PERIOD.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/PAYER_PLAN_PERIOD.md'} ``` ## COST -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedHealthEconomicsDataTables/COST.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/COST.md'} ``` # 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 -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/COHORT.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/COHORT.md'} ``` ## COHORT_ATTRIBUTE -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/COHORT_ATTRIBUTE.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/COHORT_ATTRIBUTE.md'} ``` ## DRUG_ERA -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/DRUG_ERA.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/DRUG_ERA.md'} ``` ## DOSE_ERA -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/DOSE_ERA.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/DOSE_ERA.md'} ``` ## CONDITION_ERA -```{r child = 'C:/Git/CommonDataModel.wiki/StandardizedDerivedElements/CONDITION_ERA.md'} +```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/CONDITION_ERA.md'} ``` \ No newline at end of file