-
Notifications
You must be signed in to change notification settings - Fork 2
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #2 from ohdsi-studies/develop
v1.0.0 release
- Loading branch information
Showing
14 changed files
with
6,008 additions
and
113 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,5 +1,5 @@ | ||
Package: EhdenAlopecia | ||
Version: 0.1 | ||
Version: 1.0.0 | ||
Authors@R: person("Ross", "Williams", , "[email protected]", role = c("aut", "cre")) | ||
Description: This package creates the cohorts for this EHDEN Alopecia study study. Based on this cohort diagnostics, incidence and prevalence rates and treatment patterns are analysis are performed. | ||
License: Apache License (>= 2) | ||
|
@@ -15,12 +15,13 @@ Imports: | |
zip, | ||
magrittr, | ||
checkmate, | ||
duckdb, | ||
log4r, | ||
lubridate, | ||
rlang | ||
rlang, | ||
readr | ||
Suggests: | ||
testthat (>= 3.0.0), | ||
rmarkdown, | ||
checkmate | ||
checkmate, | ||
duckdb, | ||
Config/testthat/edition: 3 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,4 +1,6 @@ | ||
# Generated by roxygen2: do not edit by hand | ||
|
||
export("%>%") | ||
export(createCohorts) | ||
export(runStudy) | ||
importFrom(magrittr,"%>%") |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1 +1,115 @@ | ||
# EhdenAlopecia | ||
# EHDEN Alopecia | ||
|
||
Analytic software to perform large-scale distributed analysis of patients with Alopecia as part of the EHDEN study-athon | ||
|
||
<img src="https://img.shields.io/badge/Study%20Status-Started-blue.svg" alt="Study Status: Started"> | ||
|
||
- 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 | ||
See the instructions at https://ohdsi.github.io/Hades/rSetup.html for configuring your R environment, including Java and RStudio. | ||
|
||
Clone the EhdenAlopecia package into your local R environment. | ||
|
||
Open your study package in RStudio. Use the following code to install all the dependencies: | ||
```R | ||
install.packages(c("DBI", | ||
"dplyr", | ||
"glue", | ||
"zip", | ||
"magrittr", | ||
"checkmate", | ||
"log4r", | ||
"lubridate", | ||
"rlang", | ||
"readr") | ||
) | ||
``` | ||
|
||
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) | ||
# 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 <- "" | ||
user <- "" | ||
pw <- "" | ||
server <- "" | ||
port <- "" | ||
|
||
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = dbms, | ||
server = server, | ||
user = user, | ||
password = pw, | ||
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 <- "results" | ||
|
||
|
||
#choose analysis to run | ||
instantiateCohorts <- TRUE | ||
runDiagnostics <- TRUE | ||
|
||
|
||
### Do not edit below here | ||
|
||
EhdenAlopecia::runStudy( | ||
connectionDetails = connectionDetails, | ||
cohortTable = cohortTable, | ||
cdmDatabaseSchema = cdmDatabaseSchema, | ||
cohortDatabaseSchema = cohortDatabaseSchema, | ||
instantiateCohorts = instantiateCohorts, | ||
runDiagnostics = runDiagnostics, | ||
outputFolder = outputFolder, | ||
databaseId = databaseId, | ||
minCellCount = minCellCount | ||
) | ||
``` |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Binary file not shown.
Oops, something went wrong.