commit readme

README.Rmd

@@ -104,7 +104,7 @@ dbms <- Sys.getenv("dbms")
 user <- Sys.getenv("user")
 password <- Sys.getenv("password")
 server <- Sys.getenv("host")
-port <- Sys.getenv
+port <- Sys.getenv("port")
 connectionString <- Sys.getenv("connectionString")
 
 connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = dbms,

README.knit.md

@@ -0,0 +1,147 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+
+
+# EHDEN Alopecia
+
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/ohdsi-studies/EhdenAlopecia/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ohdsi-studies/EhdenAlopecia/actions/workflows/R-CMD-check.yaml)
+<img src="https://img.shields.io/badge/Study%20Status-Started-blue.svg" alt="Study Status: Started">
+<!-- badges: end -->
+
+Analytic software to perform large-scale distributed analysis of patients with Alopecia as part of the EHDEN study-athon.
+
+- Analytics use case(s): Population-Level Estimation
+- Study type: Clinical Application
+- Tags: -
+- Study lead: 
+- Study lead forums tag: 
+- Study start date: 1 November 2023
+- Study end date: -
+- Protocol: To be added
+- Publications: -
+- Results explorer: -
+
+# Requirements
+
+A database in Common Data Model version 5 in one of these platforms: SQL Server, Oracle, PostgreSQL, IBM Netezza, Apache Impala, Amazon RedShift, Google BigQuery, or Microsoft APS.
+R version 4.0.5
+On Windows: RTools
+Java
+100 GB of free disk space
+
+# How to run
+
+1. See the instructions at https://ohdsi.github.io/Hades/rSetup.html for configuring your R environment, including Java and RStudio.
+
+2. Clone the EhdenAlopecia package into your local R environment.
+
+3. Open your study package in RStudio. Use the following code to install all the dependencies:
+
+```R
+
+install.packages(c("TreatmentPatterns", 
+                   "DBI",
+                   "dplyr",
+                   "glue",
+                   "zip",
+                   "magrittr",
+                   "checkmate",
+                   "lubridate",
+                   "rlang",
+                   "readr",
+                   "here",
+                   "rmarkdown",
+                   "checkmate",
+                   "SqlRender",
+                   "duckdb",
+                   "ParallelLogger",
+                   "DBI",
+                   "glue",
+                   "zip",
+                   "lubridate",
+                   "rlang",
+                   "jsonlite"))
+
+remotes::install_github(c("ohdsi/CirceR",
+                          "ohdsi/CohortGenerator",
+                          "ohdsi/CohortDiagnostics"))
+
+```
+
+In RStudio, select 'Build' then 'Install and Restart' to install the  package.
+
+After succesfully installing the package. Open the extras/CodeTorun.R and run the following code:
+
+```R
+#Load the library
+
+library(EhdenAlopecia)
+library(here)
+
+# database metadata and connection details -----
+# The name/ acronym for the database
+databaseId <- "..."
+
+# Database connection details -----
+#connection details
+#User specified input
+
+# Details for connecting to the server:
+dbms <- Sys.getenv("dbms")
+user <- Sys.getenv("user")
+password <- Sys.getenv("password")
+server <- Sys.getenv("host")
+port <- Sys.getenv("port")
+connectionString <- Sys.getenv("connectionString")
+
+connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = dbms,
+                                                                connectionString = connectionString,
+                                                                user = user,
+                                                                password = password,
+                                                                port = port)
+
+
+cdmDatabaseSchema <- "..."
+cohortDatabaseSchema <- "..."
+
+
+# Name of table prefix to use in the result schema for tables created during the study.
+# Notes:
+# - if there is an existing table in your results schema with the same names it
+#   will be overwritten
+# - name must be lower case
+cohortTable <- "alopecia_ehden"
+
+
+# minimum counts that can be displayed according to data governance
+minCellCount <- 5
+
+#specify where to save the results
+outputFolder <- here::here("results")
+
+
+#choose analysis to run
+instantiateCohorts <- TRUE
+runDiagnostics <- TRUE
+runPatternAnalysis <- TRUE
+
+### Do not edit below here
+EhdenAlopecia::runStudy(
+  connectionDetails = connectionDetails, 
+  cohortTable = cohortTable, 
+  cdmDatabaseSchema = cdmDatabaseSchema, 
+  cohortDatabaseSchema = cohortDatabaseSchema,
+  instantiateCohorts = instantiateCohorts,
+  runDiagnostics = runDiagnostics,
+  runPatternAnalysis = runPatternAnalysis,
+  outputFolder = outputFolder,
+  databaseId = databaseId,
+  minCellCount = minCellCount
+)
+
+```

README.md

@@ -96,7 +96,7 @@ dbms <- Sys.getenv("dbms")
 user <- Sys.getenv("user")
 password <- Sys.getenv("password")
 server <- Sys.getenv("host")
-port <- Sys.getenv
+port <- Sys.getenv("port")
 connectionString <- Sys.getenv("connectionString")
 
 connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = dbms,