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-directoryNn/anoDirectory that contains results written by the bdval ant scripts.
(-c|--model-conditions) model-conditionsnoThe model condition file where models which are be processed are described.
--survivalsurvivalnoSurvival 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-methodaggregation-methodnoType 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-filenoThe 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-measuresother-measuresnoA 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: )
--labellabelyesA string that the type of model construction process used to generate the models. (default: auto)
--binarybinarynoIndicates 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)