OMOP/extras/archive/testSpec.Rmd

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