mz-health/OMOP
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OMOP
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Fixed .Rmd parameterization

This commit is contained in:
clairblacketer 2017-11-21 08:18:54 -05:00
parent a5b12716dd
commit 70acdf69a6
5 changed files with 70 additions and 301 deletions
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36
DDLGeneratr/R/writePDF.R
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@ -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"))
}

13
DDLGeneratr/codeToRun.R
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@ -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))

102
DDLGeneratr/reports/OMOP_CDM_PDF.Rmd
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@ -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')}
```

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DDLGeneratr/reports/OMOP_CDM_PDF_rendered.Rmd
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@ -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'}
```

11
DDLGeneratr/reports/OMOP_CDM_v5_3.pdf
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@ -304,12 +304,11 @@ endobj
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