name |
value |
type |
provided |
enforcement |
description |
errors |
---|---|---|---|---|---|---|
annealSupport |
|
boolean |
false |
default value: true |
|
|
checkIsDAG |
|
boolean |
false |
default value: true |
|
|
engine |
|
PosteriorInferenceEngine: SCM|PT|MCMC|AIS|Forward|Exact|None|fully qualified |
false |
default value: PT |
|
|
engine.adaptFraction |
|
double |
false |
default value: 0.5 |
Set to zero for disabling schedule adaptation |
|
engine.initialization |
|
InitType: COPIES|FORWARD|SCM |
false |
default value: SCM |
|
|
engine.ladder |
|
TemperatureLadder: Geometric|EquallySpaced|Polynomial|UserSpecified|FromAnotherExec|fully qualified |
false |
default value: EquallySpaced |
The annealing schedule to use or if adaptation is used, the initial value |
|
engine.logNormalizationEstimator |
|
LogNormalizationEstimator: thermodynamicIntegration|steppingStone |
false |
default value: steppingStone |
|
|
engine.nChains |
20 |
int |
true |
default value: 8 |
|
|
engine.nPassesPerScan |
|
double |
false |
default value: 3 |
|
|
engine.nScans |
10000 |
int |
true |
default value: 1_000 |
|
|
engine.nThreads |
|
Cores: Single|Max|Dynamic|Fixed|fully qualified |
false |
default value: Dynamic |
|
|
engine.nThreads.fraction |
|
double |
false |
default value: 0.5 |
|
|
engine.nThreads.ignoreUtilizedCores |
|
boolean |
false |
default value: true |
|
|
engine.nThreads.verbose |
|
boolean |
false |
default value: false |
|
|
engine.random |
|
Random |
false |
default value: 1 |
|
|
engine.reversible |
|
boolean |
false |
default value: false |
|
|
engine.scmInit.maxAnnealingParameter |
|
double |
false |
default value: 1.0 |
Use higher values for likelihood maximization |
|
engine.scmInit.nFinalRejuvenations |
|
int |
false |
default value: 5 |
Number of rejuvenation passes to do after the change of measure. |
|
engine.scmInit.nParticles |
|
int |
false |
default value: 1_000 |
|
|
engine.scmInit.nPassesPerScan |
|
double |
false |
default value: 3 |
|
|
engine.scmInit.nThreads |
|
Cores: Single|Max|Dynamic|Fixed|fully qualified |
false |
default value: Dynamic |
|
|
engine.scmInit.nThreads.fraction |
|
double |
false |
default value: 0.5 |
|
|
engine.scmInit.nThreads.ignoreUtilizedCores |
|
boolean |
false |
default value: true |
|
|
engine.scmInit.nThreads.verbose |
|
boolean |
false |
default value: false |
|
|
engine.scmInit.random |
|
Random |
false |
default value: 1 |
Random seed used for proposals and resampling. |
|
engine.scmInit.recordWeights |
|
boolean |
false |
default value: false |
Save log weights over iterations. |
|
engine.scmInit.resamplingESSThreshold |
|
double |
false |
default value: 0.5 |
If the (relative) Effective Sample Size (ESS) falls below, perform a resampling round. |
|
engine.scmInit.resamplingScheme |
|
ResamplingScheme: STRATIFIED|MULTINOMIAL |
false |
default value: STRATIFIED |
|
|
engine.scmInit.temperatureSchedule |
|
TemperatureSchedule: AdaptiveTemperatureSchedule|FixedTemperatureSchedule|fully qualified |
false |
default value: AdaptiveTemperatureSchedule |
Algorithm selecting annealing parameter increments. |
|
engine.scmInit.temperatureSchedule.absoluteAccuracy |
|
double |
false |
default value: 1e-16 |
The absolute accuracy for searching for next annealing parameter. |
|
engine.scmInit.temperatureSchedule.nudgeFromZeroIfOutOfSupport |
|
double |
false |
default value: 1e-10 |
If all particles are out of support at first iteration, nudge the temperature a bit so that support constraints kick in. |
|
engine.scmInit.temperatureSchedule.threshold |
|
double |
false |
default value: 0.9999 |
Annealing parameter is selected to get the (conditional) ESS decrease specified by this parameter. |
|
engine.scmInit.temperatureSchedule.useConditional |
|
boolean |
false |
default value: true |
See Zhou, Johansen and Aston (2013). |
|
engine.scmInit.usePosteriorSamplingScan |
|
boolean |
false |
default value: false |
|
|
engine.statisticRecordedMaxChainIndex |
|
int |
false |
default value: 100 |
Use when huge number of chains are utilized. Statistics like energy, logLikelihood are only recorded for the first so many indices to avoid excessive output size. |
|
engine.targetAccept |
|
Double |
false |
optional |
|
|
engine.thinning |
|
int |
false |
default value: 1 |
Collect statistics every thinning iteration (=1 to always collect, >1 to save hard drive space) |
|
engine.usePriorSamples |
|
boolean |
false |
default value: true |
|
|
excludeFromOutput |
|
List: Space separated items or "file |
false |
optional |
|
|
experimentConfigs.configFile |
|
File |
false |
optional |
If set, use those arguments in provided file that do not appear in the provided arguments. |
|
experimentConfigs.description |
|
String |
false |
optional |
Documentation for this run. |
|
experimentConfigs.managedExecutionFolder |
|
boolean |
false |
default value: true |
Automatically organize results into subdirectories of 'results/all'? |
|
experimentConfigs.maxIndentationToPrint |
|
int |
false |
default value: inf |
Use -1 to silence all output done through blang.System.* |
|
experimentConfigs.recordExecutionInfo |
|
boolean |
false |
default value: true |
Record information such as timing, main class, code version, etc for this run? |
|
experimentConfigs.recordGitInfo |
true |
boolean |
true |
default value: false |
|
|
experimentConfigs.resultsHTMLPage |
|
boolean |
false |
default value: true |
|
|
experimentConfigs.saveStandardStreams |
|
boolean |
false |
default value: true |
Save combined standard out and err into a file? |
|
experimentConfigs.tabularWriter |
|
TabularWriterFactory: CSV|Spark|fully qualified |
false |
default value: CSV |
|
|
experimentConfigs.tabularWriter.compressed |
|
boolean |
false |
default value: false |
|
|
experimentConfigs.uniqueExperimentDirectoryName |
results/all/UnidentifiableProduct-1896176519 |
String |
true |
optional |
|
|
initRandom |
|
Random |
false |
default value: 1 |
|
|
model |
ex.pt.UnidentifiableProduct$Builder |
ModelBuilder: fully qualified |
true |
|
|
|
model.nFails |
|
IntVar: An integer or NA |
false |
optional |
|
|
model.nTrials |
|
IntVar: An integer or NA |
false |
optional |
|
|
model.x |
|
RealVar: A number or NA |
false |
optional |
|
|
model.y |
|
RealVar: A number or NA |
false |
optional |
|
|
postProcessor |
DefaultPostProcessor |
PostProcessor: DefaultPostProcessor|NoPostProcessor|fully qualified |
true |
default value: NoPostProcessor |
|
|
postProcessor.blangExecutionDirectory |
|
File |
false |
optional |
When called from Blang, this will be the latest run, otherwise point to the .exec folder created by Blang |
|
postProcessor.boldTrajectory |
|
Integer |
false |
optional |
|
|
postProcessor.burnInFraction |
|
double |
false |
default value: 0.5 |
|
|
postProcessor.eleDiagnostic |
|
boolean |
false |
default value: false |
|
|
postProcessor.essEstimator |
|
EssEstimator: Batch|ACT|AR|fully qualified |
false |
default value: Batch |
|
|
postProcessor.essEstimator.referenceFile |
|
File |
false |
optional |
csv file containing reference values for the mean and sd |
|
postProcessor.essEstimator.referenceMeanColumn |
|
String |
false |
default value: mean |
Look for this column name for reference mean. |
|
postProcessor.essEstimator.referenceSDColumn |
|
String |
false |
default value: sd |
Look for this column name for reference sd. |
|
postProcessor.experimentConfigs.configFile |
|
File |
false |
optional |
If set, use those arguments in provided file that do not appear in the provided arguments. |
|
postProcessor.experimentConfigs.description |
|
String |
false |
optional |
Documentation for this run. |
|
postProcessor.experimentConfigs.managedExecutionFolder |
|
boolean |
false |
default value: true |
Automatically organize results into subdirectories of 'results/all'? |
|
postProcessor.experimentConfigs.maxIndentationToPrint |
|
int |
false |
default value: inf |
Use -1 to silence all output done through blang.System.* |
|
postProcessor.experimentConfigs.recordExecutionInfo |
|
boolean |
false |
default value: true |
Record information such as timing, main class, code version, etc for this run? |
|
postProcessor.experimentConfigs.recordGitInfo |
|
boolean |
false |
default value: false |
|
|
postProcessor.experimentConfigs.resultsHTMLPage |
|
boolean |
false |
default value: true |
|
|
postProcessor.experimentConfigs.saveStandardStreams |
|
boolean |
false |
default value: true |
Save combined standard out and err into a file? |
|
postProcessor.experimentConfigs.tabularWriter |
|
TabularWriterFactory: CSV|Spark|fully qualified |
false |
default value: CSV |
|
|
postProcessor.experimentConfigs.tabularWriter.compressed |
|
boolean |
false |
default value: false |
|
|
postProcessor.experimentConfigs.uniqueExperimentDirectoryName |
|
String |
false |
optional |
|
|
postProcessor.facetHeight |
|
double |
false |
default value: 2.0 |
In inches |
|
postProcessor.facetWidth |
|
double |
false |
default value: 4.0 |
In inches |
|
postProcessor.highestDensityIntervalValue |
|
double |
false |
default value: 0.9 |
|
|
postProcessor.imageFormat |
|
String |
false |
default value: pdf |
|
|
postProcessor.rCmd |
|
String |
false |
default value: Rscript |
|
|
postProcessor.referenceSamples |
|
File |
false |
optional |
A directory containing means and variance estimates from a long run, used to improve ESS estimates; usually of the form /path/to/[longRunId].exec/summaries |
|
postProcessor.runPxviz |
|
boolean |
false |
default value: false |
Run visualizations based on Processing (may need extra steps to perform in a 'headless' environment) |
|
printAccessibilityGraph |
|
boolean |
false |
default value: false |
|
|
samplers.additional |
|
SamplerSet: Fully qualified instances of blang.mcmc.Sampler |
false |
|
Samplers to be added. |
|
samplers.excluded |
|
SamplerSet: Fully qualified instances of blang.mcmc.Sampler |
false |
|
Samplers to be excluded (only useful if useAnnotation = true). |
|
samplers.useAnnotation |
|
boolean |
false |
default value: true |
If the arguments of the annotations @Samplers should be used to determine a starting set of sampler types. |
|
stripped |
|
boolean |
false |
default value: false |
Stripped means that the construction of forward simulators and annealers is skipped |
|
treatNaNAsNegativeInfinity |
|
boolean |
false |
default value: false |
|
|