ohdsi-studies / TofacitinibSafetyinRA

OHDSI Community Study-a-thon 2018 (hosted at Columbia University): This study aims to compare the safety of tofacitinib with adalimumab and etanercept in patients with rheumatoid arthritis (RA).
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Error in Diagnostics - Covariate Balance #4

Closed kmkostka closed 4 years ago

kmkostka commented 4 years ago

Unable to generate Diagnostics on Covariate Balance.

Running diagnostics
Warning: Estimate(s) with NA standard error detected. Removing before fitting null distribution
Error in frame[[1]] == ".signalSimpleWarning" : 
  comparison (1) is possible only for atomic and list types

Where R traceback() generates:

27: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
25: withRestarts({
        .Internal(.signalCondition(cond, message, call))
        .Internal(.dfltWarn(message, call))
    }, muffleWarning = function() NULL)
24: warning(cnd)
23: warn(glue_collapse(wrapped, "\n", last = "\n"))
22: warning_wrap("Removed ", sum(missing), " rows containing ", str, 
        " values", name, ".")
21: remove_missing(data, params$na.rm, c(self$required_aes, self$non_missing_aes), 
        snake_class(self))
20: f(..., self = self)
19: self$geom$handle_na(data, self$geom_params)
18: f(..., self = self)
17: l$draw_geom(d, layout)
16: (function (l, d) 
    l$draw_geom(d, layout))(dots[[1L]][[9L]], dots[[2L]][[9L]])
15: mapply(FUN = f, ..., SIMPLIFY = FALSE)
14: Map(function(l, d) l$draw_geom(d, layout), plot$layers, data)
13: ggplot_gtable.ggplot_built(data)
12: ggplot_gtable(data)
11: print.ggplot(x)
10: print(x)
9: grid.draw.ggplot(plot)
8: grid.draw(plot)
7: ggplot2::ggsave(fileName, plot, width = 6, height = 4.5, dpi = 400)
6: EmpiricalCalibration::plotCalibrationEffect(logRrNegatives = negControlSubset$logRr, 
       seLogRrNegatives = negControlSubset$seLogRr, null = null, 
       showCis = TRUE, title = title, fileName = fileName)
5: FUN(X[[i]], ...)
4: lapply(x, fun, ...)
3: ParallelLogger::clusterApply(cluster = cluster, x = subsets, 
       fun = createDiagnosticsForSubset, allControls = allControls, 
       outputFolder = outputFolder, cmOutputFolder = cmOutputFolder, 
       diagnosticsFolder = diagnosticsFolder)
2: generateDiagnostics(outputFolder = outputFolder, maxCores = maxCores)
1: execute(connectionDetails = connectionDetails, cdmDatabaseSchema = cdmDatabaseSchema, 
       cohortDatabaseSchema = cohortDatabaseSchema, cohortTable = cohortTable, 
       oracleTempSchema = oracleTempSchema, outputFolder = outputFolder, 
       databaseId = databaseId, databaseName = databaseName, databaseDescription = databaseDescription, 
       createCohorts = FALSE, synthesizePositiveControls = TRUE, 
       runAnalyses = FALSE, runDiagnostics = TRUE, packageResults = FALSE, 
       maxCores = 1)

In the RShiny app, this manifests as this: image

@schuemie or @jamieweaver, any idea how to debug?

kmkostka commented 4 years ago

Relates to #5. This is an error because of the versioning of ggplot being incompatible with ParallelLogger.

If you revert ggplot to be v3.2.0, it can be compatible with ParallelLogger v1.1.1.