This mode calculates performance statistics from a table of predictions generated by Predict Mode.

It is implemented by org.bdval.StatsMode.java.

Mode Parameters

The following options are available in this mode

Flag Arguments Required Description
result-directory1 result-directory2 … result-directoryN n/a no Directory that contains results written by the bdval ant scripts.
(-c|--model-conditions) model-conditions no The model condition file where models which are be processed are described.
--survival survival no Survival filename. This file contains survival data in tab delimited format; column 1: chipID has to match cids and tmm, column 2: time to event, column 3 censor with 1 as event 0 as censor, column 4 and beyond are numerical covariates that will be included in the regression model
--aggregation-method aggregation-method no Type of aggregation method. Predictions can be aggregated by repeat of cross-validation (per-repeat, default value of this option), or by test set (per-test-set).  (default: per-test-set)
--submission-file submission-file no The MAQC-II submission file to create. Please note that this file lacks some columns required for MAQCII submission. These columns must be created manually in excel. (default: -)
--other-measures other-measures no A list of performance measures to evaluate and report in the maqcii file. These measures will be appended at the end of the columns, after the official maqcii submission columns. (default: )
--label label yes A string that the type of model construction process used to generate the models. (default: auto)
--binary binary no Indicates that binary decision values (-1/+1) should be used to evaluate the binary flavor of evaluation measures in addition to the traditional evaluation measures. (default: false)