87 lines
2.6 KiB
Plaintext
87 lines
2.6 KiB
Plaintext
---
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title: "GettingStarted_CommonDataModel"
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author: "Aedin Culhane"
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date: "11/9/2021"
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output: rmarkdown::html_vignette
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vignette: >
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%\VignetteIndexEntry{Vignette Title}
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%\VignetteEngine{knitr::rmarkdown}
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\usepackage[utf8]{inputenc}
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---
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This vignette used the R code presented by Claire, at the OHDSI tutorial session on 9th November 2021 and hopefully presented a useful starter on this package
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```{r setup, include=FALSE}
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knitr::opts_chunk$set(echo = TRUE)
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```
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Before we start we'll make a local folder for output
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```{r}
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currentfolder= here::here()
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outputfolder = paste0(currentfolder,"out")
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```
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To install this package from Github, we'll check if you already have devtools (you likely do if not this code will install it)
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```{r message=FALSE}
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if (!"devtools" %in% installed.packages())
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install.packages("devtools") else
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print("Found devtools")
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```
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Now install the R package CommonDataModel from the OHDSI repository on github
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```{r message=FALSE}
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devtools::install_github("OHDSI/CommonDataModel")
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```
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## Introduction to the CommonDataModel package
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List the currently supported SQL dialets
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```{r}
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CommonDataModel::listSupportedDialects()
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```
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List the currently supported Common Data Model (CDM)
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```{r}
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CommonDataModel::listSupportedVersions()
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```
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## To generate DDLs
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There are multiple way to generate DDLs
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1. Use the buildRelease function to generate text files in the dialect of your choice
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This function will put the output files in the folder you specify
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```{r}
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CommonDataModel::buildRelease(cdmVersions = "5.4",
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targetDialects = "postgresql",
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outputfolder = outputfolder)
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```
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2. If you have an empty schema ready to go, the package will connect and instantiate the tables for you
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2a. To start you need to download DatabaseConnector in order to connect to your database
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to install DatabaseConnector
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```{r message=FALSE}
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devtools::install_github("OHDSI/DatabaseConnector")
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```
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```{r}
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library(DatabaseConnector)
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```
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Please replace with your own username/password and path to the file DatabaseConnector_Jars
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```{r, eval=FALSE}
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cd<- DatabaseConnector::createConnectionDetails(dbms = "postgresql",
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server="localhost/ohdsi",
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user="postgres",
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password = "postgres",
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pathToDriver = "~/Documents/DatabaseConnector_Jars")
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CommonDataModel::executeDdl(connectionDetails = cdm,
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cdmVersion = "5.4",
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cdmDatabaseSchema = "ohdsi_demo")
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``` |