Fixed .Rmd parameterization
This commit is contained in:
parent
a5b12716dd
commit
70acdf69a6
|
@ -1,36 +0,0 @@
|
|||
# Copyright 2017 Observational Health Data Sciences and Informatics
|
||||
#
|
||||
# This file is part of DDLGeneratr
|
||||
#
|
||||
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||
# you may not use this file except in compliance with the License.
|
||||
# You may obtain a copy of the License at
|
||||
#
|
||||
# http://www.apache.org/licenses/LICENSE-2.0
|
||||
#
|
||||
# Unless required by applicable law or agreed to in writing, software
|
||||
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
# See the License for the specific language governing permissions and
|
||||
# limitations under the License.
|
||||
|
||||
#' Write PDF of CDM documentation
|
||||
#'
|
||||
#' @param mdFilesLocation The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"
|
||||
#'
|
||||
#' @param cdmVersion The version of the OMOP Common Data Model for which the pdf document is being written. It should be written without a decimal so v5.3 becomes v5_3
|
||||
#'
|
||||
#' @export
|
||||
writePDF <- function(mdFilesLocation, cdmVersion) {
|
||||
|
||||
sql <- SqlRender::loadRenderTranslateSql(sqlFilename = "OMOP_CDM_PDF.sql",
|
||||
packageName = "DDLGeneratr",
|
||||
dbms = "sql server",
|
||||
mdFilesLocation = mdFilesLocation)
|
||||
|
||||
SqlRender::writeSql(sql = sql,
|
||||
targetFile = "reports/OMOP_CDM_PDF_rendered.Rmd")
|
||||
|
||||
rmarkdown::render(input = "reports/OMOP_CDM_PDF_rendered.Rmd", output_format = "pdf_document", output_file = paste0("OMOP_CDM_",cdmVersion,".pdf"))
|
||||
|
||||
}
|
|
@ -1,7 +1,13 @@
|
|||
#This script is meant to create the OMOP Common Data Model DDLs for each dialect as well as the pdf of the documentation.
|
||||
|
||||
|
||||
# Step 1: Update the file inst/sql/sql_server/OMOP CDM ddl.sql with the changes for the new version
|
||||
# Step 1: Update the file inst/sql/sql_server/OMOP CDM ddl.sql with the changes for the new version and set the below variables
|
||||
|
||||
# Step 1.1: The version of the CDM you are writing. This will be used for the name of the pdf so, for example, write v5.3 as v5_3
|
||||
cdmVersion <- "v5_3"
|
||||
|
||||
# Step 1.2: The location of the wiki markdown files. The default is "../../Documentation/CommonDataModel_Wiki_Files"
|
||||
mdFilesLocation <- "../../Documentation/CommonDataModel_Wiki_Files"
|
||||
|
||||
# Step 2: Run the following code to create the DDLs for each dialect:
|
||||
|
||||
|
@ -30,4 +36,7 @@ writeConstraints("sql server")
|
|||
|
||||
# step 5: Run the following code to create the pdf documentation. It will be written to the reports folder.
|
||||
|
||||
writePDF(mdFilesLocation = "../../Documentation/CommonDataModel_Wiki_Files", cdmVersion = "v5_3")
|
||||
rmarkdown::render("reports/OMOP_CDM_PDF.Rmd",
|
||||
output_format = "pdf_document",
|
||||
output_file = paste0("OMOP_CDM_",cdmVersion,".pdf"),
|
||||
params = list(mdFilesLocation = mdFilesLocation))
|
||||
|
|
|
@ -3,7 +3,7 @@ title: "OMOP Common Data Model Specifications"
|
|||
author: "Christian Reich, Patrick Ryan, Rimma Belenkaya, Karthik Natarajan and Clair Blacketer"
|
||||
date: "`r Sys.Date()`"
|
||||
params:
|
||||
mdFilesLocation:"../../Documentation/CommonDataModel_Wiki_Files"
|
||||
mdFilesLocation: "../../Documentation/CommonDataModel_Wiki_Files"
|
||||
output:
|
||||
pdf_document:
|
||||
number_sections: yes
|
||||
|
@ -11,198 +11,202 @@ output:
|
|||
linkcolor: blue
|
||||
---
|
||||
|
||||
```{r, echo=FALSE}
|
||||
mdFilesLocation <- params$mdFilesLocation
|
||||
```
|
||||
|
||||
# License
|
||||
```{r child = paste0(params$mdFilesLocation,'/License.md')}
|
||||
```{r child = paste0(mdFilesLocation,'/License.md')}
|
||||
```
|
||||
|
||||
# Background
|
||||
```{r child = '@mdFilesLocation/Background/Background.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/Background/Background.md')}
|
||||
```
|
||||
|
||||
## The Role of the Common Data Model
|
||||
```{r child = '@mdFilesLocation/Background/The-Role-of-the-Common-Data-Model.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/Background/The-Role-of-the-Common-Data-Model.md')}
|
||||
```
|
||||
|
||||
## Design Principles
|
||||
```{r child = '@mdFilesLocation/Background/Design-Principles.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/Background/Design-Principles.md')}
|
||||
```
|
||||
|
||||
## Data Model Conventions
|
||||
```{r child = '@mdFilesLocation/Background/Data-Model-Conventions.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/Background/Data-Model-Conventions.md')}
|
||||
```
|
||||
|
||||
# Glossary of Terms
|
||||
```{r child = '@mdFilesLocation/Glossary-of-Terms.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/Glossary-of-Terms.md')}
|
||||
```
|
||||
|
||||
# Standardized Vocabularies
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/Standardized-Vocabularies.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/Standardized-Vocabularies.md')}
|
||||
```
|
||||
|
||||
## CONCEPT
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/CONCEPT.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/CONCEPT.md')}
|
||||
```
|
||||
|
||||
## VOCABULARY
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/VOCABULARY.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/VOCABULARY.md')}
|
||||
```
|
||||
|
||||
## DOMAIN
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/DOMAIN.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/DOMAIN.md')}
|
||||
```
|
||||
|
||||
## CONCEPT_CLASS
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/CONCEPT_CLASS.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/CONCEPT_CLASS.md')}
|
||||
```
|
||||
|
||||
## CONCEPT_RELATIONSHIP
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/CONCEPT_RELATIONSHIP.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/CONCEPT_RELATIONSHIP.md')}
|
||||
```
|
||||
|
||||
## RELATIONSHIP
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/RELATIONSHIP.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/RELATIONSHIP.md')}
|
||||
```
|
||||
|
||||
## CONCEPT_SYNONYM
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/CONCEPT_SYNONYM.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/CONCEPT_SYNONYM.md')}
|
||||
```
|
||||
|
||||
## CONCEPT_ANCESTOR
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/CONCEPT_ANCESTOR.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/CONCEPT_ANCESTOR.md')}
|
||||
```
|
||||
|
||||
## SOURCE_TO_CONCEPT_MAP
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/SOURCE_TO_CONCEPT_MAP.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/SOURCE_TO_CONCEPT_MAP.md')}
|
||||
```
|
||||
|
||||
## DRUG_STRENGTH
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/DRUG_STRENGTH.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/DRUG_STRENGTH.md')}
|
||||
```
|
||||
|
||||
## COHORT_DEFINITION
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/COHORT_DEFINITION.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/COHORT_DEFINITION.md')}
|
||||
```
|
||||
|
||||
## ATTRIBUTE_DEFINITION
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/ATTRIBUTE_DEFINITION.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/ATTRIBUTE_DEFINITION.md')}
|
||||
```
|
||||
|
||||
# Standardized Metadata
|
||||
```{r child = '@mdFilesLocation/StandardizedMetadata/Standardized-Metadata.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedMetadata/Standardized-Metadata.md')}
|
||||
```
|
||||
|
||||
## CDM_SOURCE
|
||||
```{r child = '@mdFilesLocation/StandardizedMetadata/CDM_SOURCE.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedMetadata/CDM_SOURCE.md')}
|
||||
```
|
||||
|
||||
# Standardized Clinical Data Tables
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/Standardized-clinical-Data-Tables.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/Standardized-clinical-Data-Tables.md')}
|
||||
```
|
||||
|
||||
## PERSON
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/PERSON.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/PERSON.md')}
|
||||
```
|
||||
|
||||
## OBSERVATION_PERIOD
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/OBSERVATION_PERIOD.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/OBSERVATION_PERIOD.md')}
|
||||
```
|
||||
|
||||
## SPECIMEN
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/SPECIMEN.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/SPECIMEN.md')}
|
||||
```
|
||||
|
||||
## DEATH
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/DEATH.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/DEATH.md')}
|
||||
```
|
||||
|
||||
## VISIT_OCCURRENCE
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/VISIT_OCCURRENCE.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/VISIT_OCCURRENCE.md')}
|
||||
```
|
||||
|
||||
## PROCEDURE_OCCURRENCE
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/PROCEDURE_OCCURRENCE.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/PROCEDURE_OCCURRENCE.md')}
|
||||
```
|
||||
|
||||
## DRUG_EXPOSURE
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/DRUG_EXPOSURE.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/DRUG_EXPOSURE.md')}
|
||||
```
|
||||
|
||||
## DEVICE_EXPOSURE
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/DEVICE_EXPOSURE.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/DEVICE_EXPOSURE.md')}
|
||||
```
|
||||
|
||||
## CONDITION_OCCURRENCE
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/CONDITION_OCCURRENCE.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/CONDITION_OCCURRENCE.md')}
|
||||
```
|
||||
|
||||
## MEASUREMENT
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/MEASUREMENT.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/MEASUREMENT.md')}
|
||||
```
|
||||
|
||||
## NOTE
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/NOTE.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/NOTE.md')}
|
||||
```
|
||||
|
||||
## NOTE_NLP
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/NOTE_NLP.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/NOTE_NLP.md')}
|
||||
```
|
||||
|
||||
## OBSERVATION
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/OBSERVATION.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/OBSERVATION.md')}
|
||||
```
|
||||
|
||||
## FACT_RELATIONSHIP
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/FACT_RELATIONSHIP.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/FACT_RELATIONSHIP.md')}
|
||||
```
|
||||
|
||||
# Standardized Health System Data Tables
|
||||
```{r child = '@mdFilesLocation/StandardizedHealthSystemDataTables/Standardized-Health-System-Data-Tables.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedHealthSystemDataTables/Standardized-Health-System-Data-Tables.md')}
|
||||
```
|
||||
|
||||
## LOCATION
|
||||
```{r child = '@mdFilesLocation/StandardizedHealthSystemDataTables/LOCATION.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedHealthSystemDataTables/LOCATION.md')}
|
||||
```
|
||||
|
||||
## CARE_SITE
|
||||
```{r child = '@mdFilesLocation/StandardizedHealthSystemDataTables/CARE_SITE.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedHealthSystemDataTables/CARE_SITE.md')}
|
||||
```
|
||||
|
||||
## PROVIDER
|
||||
```{r child = '@mdFilesLocation/StandardizedHealthSystemDataTables/PROVIDER.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedHealthSystemDataTables/PROVIDER.md')}
|
||||
```
|
||||
|
||||
# Standardized Health Economics Data Tables
|
||||
```{r child = '@mdFilesLocation/StandardizedHealthEconomicsDataTables/Standardized-Health-Economics-Data-Tables.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedHealthEconomicsDataTables/Standardized-Health-Economics-Data-Tables.md')}
|
||||
```
|
||||
|
||||
## PAYER_PLAN_PERIOD
|
||||
```{r child = '@mdFilesLocation/StandardizedHealthEconomicsDataTables/PAYER_PLAN_PERIOD.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedHealthEconomicsDataTables/PAYER_PLAN_PERIOD.md')}
|
||||
```
|
||||
|
||||
## COST
|
||||
```{r child = '@mdFilesLocation/StandardizedHealthEconomicsDataTables/COST.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedHealthEconomicsDataTables/COST.md')}
|
||||
```
|
||||
|
||||
# Standardized Derived Elements
|
||||
```{r child = '@mdFilesLocation/StandardizedDerivedElements/Standardized-Derived-Elements.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedDerivedElements/Standardized-Derived-Elements.md')}
|
||||
```
|
||||
|
||||
## COHORT
|
||||
```{r child = '@mdFilesLocation/StandardizedDerivedElements/COHORT.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedDerivedElements/COHORT.md')}
|
||||
```
|
||||
|
||||
## COHORT_ATTRIBUTE
|
||||
```{r child = '@mdFilesLocation/StandardizedDerivedElements/COHORT_ATTRIBUTE.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedDerivedElements/COHORT_ATTRIBUTE.md')}
|
||||
```
|
||||
|
||||
## DRUG_ERA
|
||||
```{r child = '@mdFilesLocation/StandardizedDerivedElements/DRUG_ERA.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedDerivedElements/DRUG_ERA.md')}
|
||||
```
|
||||
|
||||
## DOSE_ERA
|
||||
```{r child = '@mdFilesLocation/StandardizedDerivedElements/DOSE_ERA.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedDerivedElements/DOSE_ERA.md')}
|
||||
```
|
||||
|
||||
## CONDITION_ERA
|
||||
```{r child = '@mdFilesLocation/StandardizedDerivedElements/CONDITION_ERA.md'}
|
||||
```{r child = paste0(mdFilesLocation,'/StandardizedDerivedElements/CONDITION_ERA.md')}
|
||||
```
|
||||
|
|
|
@ -1,207 +0,0 @@
|
|||
---
|
||||
title: "OMOP Common Data Model Specifications"
|
||||
author: "Christian Reich, Patrick Ryan, Rimma Belenkaya, Karthik Natarajan and Clair Blacketer"
|
||||
date: "`r Sys.Date()`"
|
||||
output:
|
||||
pdf_document:
|
||||
number_sections: yes
|
||||
toc: yes
|
||||
linkcolor: blue
|
||||
---
|
||||
|
||||
# License
|
||||
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/License.md'}
|
||||
```
|
||||
|
||||
# Background
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/Background/Background.md'}
|
||||
```
|
||||
|
||||
## The Role of the Common Data Model
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/Background/The-Role-of-the-Common-Data-Model.md'}
|
||||
```
|
||||
|
||||
## Design Principles
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/Background/Design-Principles.md'}
|
||||
```
|
||||
|
||||
## Data Model Conventions
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/Background/Data-Model-Conventions.md'}
|
||||
```
|
||||
|
||||
# Glossary of Terms
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/Glossary-of-Terms.md'}
|
||||
```
|
||||
|
||||
# Standardized Vocabularies
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/Standardized-Vocabularies.md'}
|
||||
```
|
||||
|
||||
## CONCEPT
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT.md'}
|
||||
```
|
||||
|
||||
## VOCABULARY
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/VOCABULARY.md'}
|
||||
```
|
||||
|
||||
## DOMAIN
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/DOMAIN.md'}
|
||||
```
|
||||
|
||||
## CONCEPT_CLASS
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_CLASS.md'}
|
||||
```
|
||||
|
||||
## CONCEPT_RELATIONSHIP
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_RELATIONSHIP.md'}
|
||||
```
|
||||
|
||||
## RELATIONSHIP
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/RELATIONSHIP.md'}
|
||||
```
|
||||
|
||||
## CONCEPT_SYNONYM
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_SYNONYM.md'}
|
||||
```
|
||||
|
||||
## CONCEPT_ANCESTOR
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_ANCESTOR.md'}
|
||||
```
|
||||
|
||||
## SOURCE_TO_CONCEPT_MAP
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/SOURCE_TO_CONCEPT_MAP.md'}
|
||||
```
|
||||
|
||||
## DRUG_STRENGTH
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/DRUG_STRENGTH.md'}
|
||||
```
|
||||
|
||||
## COHORT_DEFINITION
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/COHORT_DEFINITION.md'}
|
||||
```
|
||||
|
||||
## ATTRIBUTE_DEFINITION
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedVocabularies/ATTRIBUTE_DEFINITION.md'}
|
||||
```
|
||||
|
||||
# Standardized Metadata
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedMetadata/Standardized-Metadata.md'}
|
||||
```
|
||||
|
||||
## CDM_SOURCE
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedMetadata/CDM_SOURCE.md'}
|
||||
```
|
||||
|
||||
# Standardized Clinical Data Tables
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/Standardized-clinical-Data-Tables.md'}
|
||||
```
|
||||
|
||||
## PERSON
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/PERSON.md'}
|
||||
```
|
||||
|
||||
## OBSERVATION_PERIOD
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/OBSERVATION_PERIOD.md'}
|
||||
```
|
||||
|
||||
## SPECIMEN
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/SPECIMEN.md'}
|
||||
```
|
||||
|
||||
## DEATH
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/DEATH.md'}
|
||||
```
|
||||
|
||||
## VISIT_OCCURRENCE
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/VISIT_OCCURRENCE.md'}
|
||||
```
|
||||
|
||||
## PROCEDURE_OCCURRENCE
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/PROCEDURE_OCCURRENCE.md'}
|
||||
```
|
||||
|
||||
## DRUG_EXPOSURE
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/DRUG_EXPOSURE.md'}
|
||||
```
|
||||
|
||||
## DEVICE_EXPOSURE
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/DEVICE_EXPOSURE.md'}
|
||||
```
|
||||
|
||||
## CONDITION_OCCURRENCE
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/CONDITION_OCCURRENCE.md'}
|
||||
```
|
||||
|
||||
## MEASUREMENT
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/MEASUREMENT.md'}
|
||||
```
|
||||
|
||||
## NOTE
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/NOTE.md'}
|
||||
```
|
||||
|
||||
## NOTE_NLP
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/NOTE_NLP.md'}
|
||||
```
|
||||
|
||||
## OBSERVATION
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/OBSERVATION.md'}
|
||||
```
|
||||
|
||||
## FACT_RELATIONSHIP
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/FACT_RELATIONSHIP.md'}
|
||||
```
|
||||
|
||||
# Standardized Health System Data Tables
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/Standardized-Health-System-Data-Tables.md'}
|
||||
```
|
||||
|
||||
## LOCATION
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/LOCATION.md'}
|
||||
```
|
||||
|
||||
## CARE_SITE
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/CARE_SITE.md'}
|
||||
```
|
||||
|
||||
## PROVIDER
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/PROVIDER.md'}
|
||||
```
|
||||
|
||||
# Standardized Health Economics Data Tables
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/Standardized-Health-Economics-Data-Tables.md'}
|
||||
```
|
||||
|
||||
## PAYER_PLAN_PERIOD
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/PAYER_PLAN_PERIOD.md'}
|
||||
```
|
||||
|
||||
## COST
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/COST.md'}
|
||||
```
|
||||
|
||||
# Standardized Derived Elements
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/Standardized-Derived-Elements.md'}
|
||||
```
|
||||
|
||||
## COHORT
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/COHORT.md'}
|
||||
```
|
||||
|
||||
## COHORT_ATTRIBUTE
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/COHORT_ATTRIBUTE.md'}
|
||||
```
|
||||
|
||||
## DRUG_ERA
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/DRUG_ERA.md'}
|
||||
```
|
||||
|
||||
## DOSE_ERA
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/DOSE_ERA.md'}
|
||||
```
|
||||
|
||||
## CONDITION_ERA
|
||||
```{r child = '../../Documentation/CommonDataModel_Wiki_Files/StandardizedDerivedElements/CONDITION_ERA.md'}
|
||||
```
|
|
@ -304,12 +304,11 @@ endobj
|
|||
>>
|
||||
stream
|
||||
xÚí[]S£H}Ÿ_Ác§j`úxŒ•]R@¬µf·RLDe<44>ÉT’™*÷×oCHb«Ñ•—@ƒôǹ÷ž{û€P»Ô vô ǃèÓ—Cdkœc¦EÂÄàDã¶m@nkѹöø}ØÑ ÄÀ™ßÜÌgò¼¯byÖŸwtÌÁy2•íð{ÞN&éß<C3A9>ÐI¼Jç³eçŸè<C5B8>/‡˜h6c8L§¶aaKÓ‘mؘËÑœ«Eº\¥q6ƒ 舟$<24>\}–ía¼Z¤“ëâæm<û\þf ½¹‰eó ™&³ëø6.nÿ™u/VWiñè@L‘_ü·*ž<>Ëg§‹¢Ÿi<¹NVÉ"›¿ |