95 lines
2.8 KiB
Plaintext
95 lines
2.8 KiB
Plaintext
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---
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title: "omopCdmDocumentation"
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author: "Clair Blacketer"
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date: "8/16/2019"
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output:
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html_document:
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toc: true
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toc_depth: 5
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toc_float: true
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---
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```{r setup, include=FALSE, eval=TRUE}
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#todo figure out how to get the document dynamically without specifying the name
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library(rmarkdown)
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library(knitr)
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library(kableExtra)
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library(magrittr)
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library(dplyr)
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library(stringr)
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```
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## OMOP Common Data Model Documentation
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## CDM v5.3.1
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```{r docLoop53, echo=FALSE, results='asis'}
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cdmSpecs <- readxl::read_excel("../docs/OMOP CDMv5.3.1 Specs v0.1.xlsx", sheet = "FIELD LEVEL")
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tableSpecs <- readxl::read_excel("../docs/OMOP CDMv5.3.1 Specs v0.1.xlsx", sheet = "TABLE LEVEL")
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tables <- tableSpecs$CDM_TABLE
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cdmSpecsClean <- cdmSpecs %>%
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dplyr::select(`CDM Table` = CDM_TABLE,
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`CDM Field` = CDM_FIELD,
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`User Guide` = USER_GUIDANCE,
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`ETL Conventions` = ETL_CONVENTIONS,
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`Datatype` = CDM_DATATYPE,
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`Is Required` = IS_REQUIRED,
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`Is Primary Key` = IS_PRIMARY_KEY,
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`Is Foreign Key (FK)` = IS_FOREIGN_KEY,
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`FK Table` = FK_TABLE,
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`FK Domain` = FK_DOMAIN,
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`FK Class` = FK_CLASS
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)
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for(tb in tables) {
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cat("###", tb, "{.tabset .tabset-pills} \n\n")
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loopTable <- subset(cdmSpecsClean, `CDM Table` == tb)
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loopTable <- subset(loopTable, select = -c(1))
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print(kable(x = loopTable, align = "l", row.names = FALSE) %>% kable_styling(bootstrap_options = c("hover", "condensed", "responsive")))
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}
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```
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## CDM v6.0
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```{r docLoop60, echo=FALSE, results='asis'}
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cdmSpecs <- readxl::read_excel("C:/Git/Github/DDLgeneratr_OHDSI/docs/OMOP CDMv6 DQ Checks v0.1.xlsx", sheet = "FIELD LEVEL")
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tableSpecs <- readxl::read_excel("C:/Git/Github/DDLgeneratr_OHDSI/docs/OMOP CDMv6 DQ Checks v0.1.xlsx", sheet = "TABLE LEVEL")
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tables <- tableSpecs$CDM_TABLE
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cdmSpecsClean <- cdmSpecs %>%
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dplyr::select(`CDM Table` = CDM_TABLE,
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`CDM Field` = CDM_FIELD,
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`User Guide` = USER_GUIDANCE,
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`ETL Conventions` = ETL_CONVENTIONS,
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`Datatype` = CDM_DATATYPE,
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`Is Required` = IS_REQUIRED,
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`Is Primary Key` = IS_PRIMARY_KEY,
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`Is Foreign Key (FK)` = IS_FOREIGN_KEY,
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`FK Table` = FK_TABLE,
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`FK Domain` = FK_DOMAIN,
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`FK Class` = FK_CLASS
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)
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for(tb in tables) {
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cat("###", tb, "{.tabset .tabset-pills} \n\n")
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loopTable <- subset(cdmSpecsClean, `CDM Table` == tb)
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loopTable <- subset(loopTable, select = -c(1))
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print(kable(x = loopTable, align = "l", row.names = FALSE) %>% kable_styling(bootstrap_options = c("hover", "condensed", "responsive")))
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}
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```
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