Hello.
I am stuck in error of PLE package (http://atlas-demo.ohdsi.org/#/estimation/cca/494). I cannot figure out and need helps. Thanks in advance
Creating exposure and outcome cohorts
Connecting using SQL Server driver
Creating cohort: ykgcaesystemicDXAusers
|=====================================================================| 100%
Executing SQL took 6.73 secs
Creating cohort: ykgcaesystemicPDSusers
|=====================================================================| 100%
Executing SQL took 7.27 secs
Creating cohort: ykgcaemskRelatedAE
|=====================================================================| 100%
Executing SQL took 10.5 secs
Creating negative control outcome cohorts
|=====================================================================| 100%
Executing SQL took 1.44 mins
Counting cohorts
Running CohortMethod analyses
*** Creating cohortMethodData objects ***
|=====================================================================| 100%
*** Creating study populations ***
|=====================================================================| 100%
*** Fitting shared propensity score models ***
Loading required package: CohortMethod
Loading required package: Cyclops
Loading required package: FeatureExtraction
Loading required package: Andromeda
Loading required package: dplyr
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Fitting propensity model across all outcomes (ignore messages about 'no outcome specified')
Warning: The addExposureDaysToStart argument is deprecated. Please use the startAnchor argument instead.
Warning: The addExposureDaysToEnd argument is deprecated. Please use the endAnchor argument instead.
No outcome specified so skipping removing people with prior outcomes
Removing subjects with less than 1 day(s) at risk (if any)
No outcome specified so not creating outcome and time variables
Creating propensity scores took 0.0256 secs
*** Adding propensity scores to study population objects ***
|=====================================================================| 100%
*** Trimming/Matching/Stratifying ***
|=====================================================================| 100%
*** Prefiltering covariates for outcome models ***
*** Fitting outcome models for outcomes of interest ***
|=====================================================================| 100%
*** Fitting outcome models for other outcomes ***
|=====================================================================| 100%
Summarizing results
|=====================================================================| 100%
Computing covariate balance
|=====================================================================| 100%
Packaging results
Exporting analyses
- cohort_method_analysis table
- covariate_analysis table
Exporting exposures
- exposure_of_interest table
Exporting outcomes
- outcome_of_interest table
- negative_control_outcome table
Exporting metadata
Warning: no non-missing arguments to min; returning Inf
Warning: no non-missing arguments to min; returning Inf
- database table
- exposure_summary table
Error in aggregate.data.frame(lhs, mf[-1L], FUN = FUN, ...) :
no rows to aggregate
An error report has been created at ./output_steroid/errorReportR.txt
And, the errorReportR.txt is followed
Thread: Main
Message: Error in aggregate.data.frame(lhs, mf[-1L], FUN = FUN, ...) : no rows to aggregate
Level: FATAL
Time: 2021-09-25 20:09:25
Stack trace:
7: stop("no rows to aggregate") 6: aggregate.data.frame(lhs, mf[-1], FUN = FUN, ...) 5: aggregate.formula(minDate ~ exposureId, minDates, min) 4: Export.R#253: aggregate(minDate ~ exposureId, minDates, min) 3: Export.R#53: exportMetadata(outputFolder = outputFolder, exportFolder = ex 2: Main.R#134: exportResults(outputFolder = outputFolder, databaseId = databa 1: execute(connectionDetails = connectionDetails, cdmDatabaseSchema = cdmData R version: R version 4.0.5 (2021-03-31) Platform: x86_64-apple-darwin17.0 Attached base packages: - stats - graphics - grDevices - datasets - utils - methods - base Other attached packages: - CohortMethod (4.0.0) - FeatureExtraction (3.0.1) - Andromeda (0.3.2) - dplyr (1.0.2) - Cyclops (3.0.0) - msk01 (0.0.1) - DatabaseConnector (3.0.0)