repository·main·Indexed 40 days ago
https://github.com/ohdsi/achillesAn R package for providing automated, large-scale descriptive statistics and characterization for databases following the OMOP Common Data Model (CDM) versions 5.3 and 5.4. It includes tools to execute standard or specific analysis suites via the `achilles()` function and explore analysis metadata using `getAnalysisDetails()`.
Achilles (Automated Characterization of Health Information at Large-Scale Longitudinal Evidence Systems) is an R package used to provide descriptive statistics on an OMOP CDM database.
Key details:
If you have updated the Achilles package and want to find analyses that are missing from your existing results database, use listMissingAnalyses() and runMissingAnalyses().
Note: runMissingAnalyses() does not delete prior data; it only adds the missing pieces.
# List what is missing
Achilles::listMissingAnalyses(connectionDetails, resultsDatabaseSchema)
# Run only the missing analyses
Achilles::runMissingAnalyses(
connectionDetails = connectionDetails,
cdmDatabaseSchema = cdmDatabaseSchema,
resultsDatabaseSchema = resultsDatabaseSchema,
outputFolder = "your output folder"
)Achilles is an R package. Before installing, ensure your R environment is configured with RTools and Java as per the Hades R setup guide.
To install Achilles directly from GitHub, use the remotes package.
install.packages("remotes")
remotes::install_github("OHDSI/Achilles")You can target specific analyses using the analysisIds parameter. This is useful for running a subset of tests or specific non-default analyses. If you provide analysisIds, Achilles will execute only those specific analyses and remove old/other analyses if they exist in the results schema.
# Run specific IDs
onlyThese <- c(402, 702)
Achilles::achilles(
connectionDetails = connectionDetails,
cdmDatabaseSchema = cdmDatabaseSchema,
resultsDatabaseSchema = resultsDatabaseSchema,
analysisIds = onlyThese,
outputFolder = "your output folder"
)
# Run all non-default analyses
details <- Achilles::getAnalysisDetails()
analysisIds <- details[which(details$IS_DEFAULT == 0), ]$ANALYSIS_ID
Achilles::achilles(
connectionDetails = connectionDetails,
cdmDatabaseSchema = cdmDatabaseSchema,
resultsDatabaseSchema = resultsDatabaseSchema,
analysisIds = analysisIds,
outputFolder = "your output folder"
)By default, achilles() only runs the standard suite. To run every available analysis in the package, set the defaultAnalysesOnly parameter to FALSE.
Achilles::achilles(
connectionDetails = connectionDetails,
cdmDatabaseSchema = cdmDatabaseSchema,
resultsDatabaseSchema = resultsDatabaseSchema,
defaultAnalysesOnly = FALSE,
outputFolder = "your output folder"
)To update or re-run specific analyses without wiping out the results of other analyses already present in your database, use the following combination of parameters:
analysisIds: The IDs of the analyses to run.updateGivenAnalysesOnly = TRUE: Ensures only the specified analyses are touched.createTable = FALSE: Prevents the recreation of existing result tables.reRunThese <- c(402, 702)
Achilles::achilles(
connectionDetails = connectionDetails,
cdmDatabaseSchema = cdmDatabaseSchema,
resultsDatabaseSchema = resultsDatabaseSchema,
analysisIds = reRunThese,
updateGivenAnalysesOnly = TRUE,
createTable = FALSE,
outputFolder = "your output folder"
)Use the excludeAnalysisIds parameter to skip certain analyses. You can pass a vector of specific IDs or programmatically generate a list based on a category (e.g., skipping all 'Drug Exposure' analyses).
# Skip specific IDs
skipThese <- c(402, 702)
Achilles::achilles(
connectionDetails = connectionDetails,
cdmDatabaseSchema = cdmDatabaseSchema,
resultsDatabaseSchema = resultsDatabaseSchema,
excludeAnalysisIds = skipThese,
outputFolder = "your output folder"
)
# Skip an entire category
details <- Achilles::getAnalysisDetails()
skipThese <- details[details$CATEGORY == "Drug Exposure", ]$ANALYSIS_ID
Achilles::achilles(
connectionDetails = connectionDetails,
cdmDatabaseSchema = cdmDatabaseSchema,
resultsDatabaseSchema = resultsDatabaseSchema,
excludeAnalysisIds = skipThese,
outputFolder = "your output folder"
)To execute the standard suite of Achilles analyses against your CDM, use Achilles::achilles(). You must provide connectionDetails, cdmDatabaseSchema, and resultsDatabaseSchema. The outputFolder defaults to the current working directory's /output folder if not specified.
Achilles::achilles(
connectionDetails = connectionDetails,
cdmDatabaseSchema = cdmDatabaseSchema,
resultsDatabaseSchema = resultsDatabaseSchema,
outputFolder = "your output folder"
)The Achilles::getAnalysisDetails() function returns a data frame containing metadata for all available Achilles analyses. This is useful for discovering analysis IDs, categories, and whether an analysis is part of the default suite.
Key columns in the returned data frame include:
ANALYSIS_ID: The unique identifier for the analysis.ANALYSIS_NAME: The descriptive name of the analysis.CATEGORY: The functional group (e.g., 'Person', 'Drug Exposure', 'Condition Occurrence').IS_DEFAULT: A flag (1 for default, 0 for non-default) indicating if the analysis runs in a standard execution.details <- Achilles::getAnalysisDetails()
# Example: View all columns
colnames(details)
# Example: Filter for non-default analyses
details[details$IS_DEFAULT == 0, c(1, 5)]To run Achilles, you must have: