diff --git a/vignettes/GettingStarted.Rmd b/vignettes/GettingStarted.Rmd new file mode 100644 index 0000000..4e81695 --- /dev/null +++ b/vignettes/GettingStarted.Rmd @@ -0,0 +1,87 @@ +--- +title: "GettingStarted_CommonDataModel" +author: "Aedin Culhane" +date: "11/9/2021" +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{Vignette Title} + %\VignetteEngine{knitr::rmarkdown} + \usepackage[utf8]{inputenc} +--- +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 + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +``` + +Before we start we'll make a local folder for output +```{r} +currentfolder= here::here() +outputfolder = paste0(currentfolder,"out") +``` + +To install this package from Github, we'll check if you already have devtools (you likely do if not this code will install it) +```{r message=FALSE} +if (!"devtools" %in% installed.packages()) + install.packages("devtools") else + print("Found devtools") + +``` + +Now install the R package CommonDataModel from the OHDSI repository on github +```{r message=FALSE} +devtools::install_github("OHDSI/CommonDataModel") +``` + +## Introduction to the CommonDataModel package + +List the currently supported SQL dialets +```{r} +CommonDataModel::listSupportedDialects() +``` + +List the currently supported Common Data Model (CDM) +```{r} +CommonDataModel::listSupportedVersions() +``` + + +## To generate DDLs +There are multiple way to generate DDLs + +1. Use the buildRelease function to generate text files in the dialect of your choice +This function will put the output files in the folder you specify + + + +```{r} +CommonDataModel::buildRelease(cdmVersions = "5.4", + targetDialects = "postgresql", + outputfolder = outputfolder) +``` + +2. If you have an empty schema ready to go, the package will connect and instantiate the tables for you + +2a. To start you need to download DatabaseConnector in order to connect to your database + +to install DatabaseConnector +```{r message=FALSE} +devtools::install_github("OHDSI/DatabaseConnector") +``` + +```{r} +library(DatabaseConnector) +``` + +Please replace with your own username/password and path to the file DatabaseConnector_Jars +```{r, eval=FALSE} +cd<- DatabaseConnector::createConnectionDetails(dbms = "postgresql", + server="localhost/ohdsi", + user="postgres", + password = "postgres", + pathToDriver = "~/Documents/DatabaseConnector_Jars") + +CommonDataModel::executeDdl(connectionDetails = cdm, + cdmVersion = "5.4", + cdmDatabaseSchema = "ohdsi_demo") +``` \ No newline at end of file