createSummary error in Large_scale_pop_evidence package

[chandryou]

Hi all, I have another error in Large_scale_pop_evidence package.

The code below worked well! fetchAllDataFromServer(connectionDetails = connectionDetails, cdmDatabaseSchema = cdmDatabaseSchema, workDatabaseSchema = workDatabaseSchema, oracleTempSchema = NULL, studyCohortTable = studyCohortTable, workFolder = workFolder) generateAllPopulations(workFolder) fitAllPredictionModels(workFolder)

But the code below made an error createSummary(workFolder)

Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file 'E:/OHDSI/Large_scale_pop_evidence/models/knnModels/2556/20170121131455/evaluation/testEvaluationStatistics.csv': No such file or directory

In this folder, 'testEvaluationStatistics.csv' does not exist.(but other summaries and statitics, distributions exist)

How can I fix this? Thank you!

[schuemie]

Hi @chandryou ,

I'm getting a bit confused. Are you running the Large scale patient-level prediction study or the Large scale population-level estimation study?

Cheers, Martijn

[chandryou]

Hi @schuemie

Sorry for confusing (actually I'm confused too (Too similar names..))

I was running the LargeScalePrediction package for the 'Patient Level Prediction for therapeutically treated depression'

Thanks! Chan

[schuemie]

No problem, I realize they're very similar (even in terms of code to run).

Pulling in @jreps and @PRijnbeek who developed the prediction study package. They should be able to help you further.

[chandryou]

Hi all, I think the error was caused by the dependency for 'gtable' and 'data.table' packages. Below is the error messages from the files named 'plplog'

Training Lasso Logistic Regression model Error for 2822: Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘gtable’ Error for 2556: Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘gtable’

Training KNN model Error for 2551: Error in read.table(file = file, header = header, sep = sep, quote = quote, : first five rows are empty: giving up

I'll execute the code again after installing those packages.

[jreps]

Thanks for running the study. Did the code run OK after adding the libraries?

[chandryou]

More packages are needed in addition to packages I mentioned. I'm struggling to run it! ^^

[PRijnbeek]

I am closing this issue since you were able to run.