Mcmc.Settings

Creation date: Mon Nov 16 11:13:01 2020.

Data types

newtype AnalysisName

Analysis name of the MCMC sampler.

Constructors

AnalysisName

Fields

• fromAnalysisName :: String

Instances

Eq AnalysisName

Defined in Mcmc.Settings

Methods

(==) :: AnalysisName -> AnalysisName -> Bool

(/=) :: AnalysisName -> AnalysisName -> Bool

Read AnalysisName

Defined in Mcmc.Settings

Methods

readsPrec :: Int -> ReadS AnalysisName

readList :: ReadS [AnalysisName]

readPrec :: ReadPrec AnalysisName

readListPrec :: ReadPrec [AnalysisName]

Show AnalysisName

Defined in Mcmc.Settings

Methods

showsPrec :: Int -> AnalysisName -> ShowS

show :: AnalysisName -> String

showList :: [AnalysisName] -> ShowS

ToJSON AnalysisName

Defined in Mcmc.Settings

Methods

toJSON :: AnalysisName -> Value

toEncoding :: AnalysisName -> Encoding

toJSONList :: [AnalysisName] -> Value

toEncodingList :: [AnalysisName] -> Encoding

FromJSON AnalysisName

Defined in Mcmc.Settings

Methods

parseJSON :: Value -> Parser AnalysisName

parseJSONList :: Value -> Parser [AnalysisName]

data BurnInSpecification

Burn in specification.

Constructors

NoBurnIn

No burn in.

BurnInWithoutAutoTuning Int

Burn in for a given number of iterations.

BurnInWithAutoTuning Int Int

Burn in for a given number of iterations. Enable auto tuning with a given period.

Instances

Eq BurnInSpecification

Defined in Mcmc.Settings

Methods

(==) :: BurnInSpecification -> BurnInSpecification -> Bool

(/=) :: BurnInSpecification -> BurnInSpecification -> Bool

Read BurnInSpecification

Defined in Mcmc.Settings

Methods

readsPrec :: Int -> ReadS BurnInSpecification

readList :: ReadS [BurnInSpecification]

readPrec :: ReadPrec BurnInSpecification

readListPrec :: ReadPrec [BurnInSpecification]

Show BurnInSpecification

Defined in Mcmc.Settings

Methods

showsPrec :: Int -> BurnInSpecification -> ShowS

show :: BurnInSpecification -> String

showList :: [BurnInSpecification] -> ShowS

ToJSON BurnInSpecification

Defined in Mcmc.Settings

Methods

toJSON :: BurnInSpecification -> Value

toEncoding :: BurnInSpecification -> Encoding

toJSONList :: [BurnInSpecification] -> Value

toEncodingList :: [BurnInSpecification] -> Encoding

FromJSON BurnInSpecification

Defined in Mcmc.Settings

Methods

parseJSON :: Value -> Parser BurnInSpecification

parseJSONList :: Value -> Parser [BurnInSpecification]

burnInIterations :: BurnInSpecification -> Int

Get the number of burn in iterations.

newtype Iterations

Number of normal iterations after burn in.

Note that auto tuning only happens during burn in.

Constructors

Iterations

Fields

• fromIterations :: Int

Instances

Eq Iterations

Defined in Mcmc.Settings

Methods

(==) :: Iterations -> Iterations -> Bool

(/=) :: Iterations -> Iterations -> Bool

Read Iterations

Defined in Mcmc.Settings

Methods

readsPrec :: Int -> ReadS Iterations

readList :: ReadS [Iterations]

readPrec :: ReadPrec Iterations

readListPrec :: ReadPrec [Iterations]

Show Iterations

Defined in Mcmc.Settings

Methods

showsPrec :: Int -> Iterations -> ShowS

show :: Iterations -> String

showList :: [Iterations] -> ShowS

ToJSON Iterations

Defined in Mcmc.Settings

Methods

toJSON :: Iterations -> Value

toEncoding :: Iterations -> Encoding

toJSONList :: [Iterations] -> Value

toEncodingList :: [Iterations] -> Encoding

FromJSON Iterations

Defined in Mcmc.Settings

Methods

parseJSON :: Value -> Parser Iterations

parseJSONList :: Value -> Parser [Iterations]

data ExecutionMode

Execution mode.

Constructors

Fail

Perform new run.

Call error if an output files exists.

Overwrite

Perform new run.

Overwrite existing output files.

Continue

Continue a previous run and append to output files.

Call error if an output file does not exist.

Instances

Eq ExecutionMode

Defined in Mcmc.Settings

Methods

(==) :: ExecutionMode -> ExecutionMode -> Bool

(/=) :: ExecutionMode -> ExecutionMode -> Bool

Read ExecutionMode

Defined in Mcmc.Settings

Methods

readsPrec :: Int -> ReadS ExecutionMode

readList :: ReadS [ExecutionMode]

readPrec :: ReadPrec ExecutionMode

readListPrec :: ReadPrec [ExecutionMode]

Show ExecutionMode

Defined in Mcmc.Settings

Methods

showsPrec :: Int -> ExecutionMode -> ShowS

show :: ExecutionMode -> String

showList :: [ExecutionMode] -> ShowS

ToJSON ExecutionMode

Defined in Mcmc.Settings

Methods

toJSON :: ExecutionMode -> Value

toEncoding :: ExecutionMode -> Encoding

toJSONList :: [ExecutionMode] -> Value

toEncodingList :: [ExecutionMode] -> Encoding

FromJSON ExecutionMode

Defined in Mcmc.Settings

Methods

parseJSON :: Value -> Parser ExecutionMode

parseJSONList :: Value -> Parser [ExecutionMode]

openWithExecutionMode :: ExecutionMode -> FilePath -> IO Handle

Open a file honoring the execution mode.

Call error if execution mode is

• Continue and file does not exist.
• Fail and file exists.

data ParallelizationMode

Parallelization mode.

Parallel execution of the chains is only beneficial when the algorithm allows for parallelization, and if computation of the next iteration takes a long time. If the calculation of the next state is fast, sequential execution is usually beneficial, even for algorithms involving parallel chains. If the calculation of the next state is slow, parallel execution may be beneficial.

• The Mcmc.Algorithm.Metropolis algorithm is inherently sequential.
• The Mcmc.Algorithm.MC3 algorithm works well with parallelization.

Of course, also the prior or likelihood functions can be computed in parallel. However, this library is not aware of how these functions are computed.

Constructors

Sequential

Parallel

Instances

Eq ParallelizationMode

Defined in Mcmc.Settings

Methods

(==) :: ParallelizationMode -> ParallelizationMode -> Bool

(/=) :: ParallelizationMode -> ParallelizationMode -> Bool

Read ParallelizationMode

Defined in Mcmc.Settings

Methods

readsPrec :: Int -> ReadS ParallelizationMode

readList :: ReadS [ParallelizationMode]

readPrec :: ReadPrec ParallelizationMode

readListPrec :: ReadPrec [ParallelizationMode]

Show ParallelizationMode

Defined in Mcmc.Settings

Methods

showsPrec :: Int -> ParallelizationMode -> ShowS

show :: ParallelizationMode -> String

showList :: [ParallelizationMode] -> ShowS

ToJSON ParallelizationMode

Defined in Mcmc.Settings

Methods

toJSON :: ParallelizationMode -> Value

toEncoding :: ParallelizationMode -> Encoding

toJSONList :: [ParallelizationMode] -> Value

toEncodingList :: [ParallelizationMode] -> Encoding

FromJSON ParallelizationMode

Defined in Mcmc.Settings

Methods

parseJSON :: Value -> Parser ParallelizationMode

parseJSONList :: Value -> Parser [ParallelizationMode]

data SaveMode

Should the MCMC run be saved at the end of the run?

Constructors

NoSave

Save

Instances

Eq SaveMode

Defined in Mcmc.Settings

Methods

(==) :: SaveMode -> SaveMode -> Bool

(/=) :: SaveMode -> SaveMode -> Bool

Read SaveMode

Defined in Mcmc.Settings

Methods

readsPrec :: Int -> ReadS SaveMode

readList :: ReadS [SaveMode]

readPrec :: ReadPrec SaveMode

readListPrec :: ReadPrec [SaveMode]

Show SaveMode

Defined in Mcmc.Settings

Methods

showsPrec :: Int -> SaveMode -> ShowS

show :: SaveMode -> String

showList :: [SaveMode] -> ShowS

ToJSON SaveMode

Defined in Mcmc.Settings

Methods

toJSON :: SaveMode -> Value

toEncoding :: SaveMode -> Encoding

toJSONList :: [SaveMode] -> Value

toEncodingList :: [SaveMode] -> Encoding

FromJSON SaveMode

Defined in Mcmc.Settings

Methods

parseJSON :: Value -> Parser SaveMode

parseJSONList :: Value -> Parser [SaveMode]

data Verbosity

Not much to say here.

Constructors

Quiet

Warn

Info

Debug

Instances

Eq Verbosity

Defined in Mcmc.Settings

Methods

(==) :: Verbosity -> Verbosity -> Bool

(/=) :: Verbosity -> Verbosity -> Bool

Ord Verbosity

Defined in Mcmc.Settings

Methods

compare :: Verbosity -> Verbosity -> Ordering

(<) :: Verbosity -> Verbosity -> Bool

(<=) :: Verbosity -> Verbosity -> Bool

(>) :: Verbosity -> Verbosity -> Bool

(>=) :: Verbosity -> Verbosity -> Bool

max :: Verbosity -> Verbosity -> Verbosity

min :: Verbosity -> Verbosity -> Verbosity

Read Verbosity

Defined in Mcmc.Settings

Methods

readsPrec :: Int -> ReadS Verbosity

readList :: ReadS [Verbosity]

readPrec :: ReadPrec Verbosity

readListPrec :: ReadPrec [Verbosity]

Show Verbosity

Defined in Mcmc.Settings

Methods

showsPrec :: Int -> Verbosity -> ShowS

show :: Verbosity -> String

showList :: [Verbosity] -> ShowS

ToJSON Verbosity

Defined in Mcmc.Settings

Methods

toJSON :: Verbosity -> Value

toEncoding :: Verbosity -> Encoding

toJSONList :: [Verbosity] -> Value

toEncodingList :: [Verbosity] -> Encoding

FromJSON Verbosity

Defined in Mcmc.Settings

Methods

parseJSON :: Value -> Parser Verbosity

parseJSONList :: Value -> Parser [Verbosity]

Settings

data Settings

Settings of an MCMC sampler.

Constructors

Settings

Fields

• sAnalysisName :: AnalysisName
• sBurnIn :: BurnInSpecification
• sIterations :: Iterations
• sExecutionMode :: ExecutionMode
• sParallelizationMode :: ParallelizationMode
• sSaveMode :: SaveMode
• sVerbosity :: Verbosity

Instances

Eq Settings

Defined in Mcmc.Settings

Methods

(==) :: Settings -> Settings -> Bool

(/=) :: Settings -> Settings -> Bool

Show Settings

Defined in Mcmc.Settings

Methods

showsPrec :: Int -> Settings -> ShowS

show :: Settings -> String

showList :: [Settings] -> ShowS

ToJSON Settings

Defined in Mcmc.Settings

Methods

toJSON :: Settings -> Value

toEncoding :: Settings -> Encoding

toJSONList :: [Settings] -> Value

toEncodingList :: [Settings] -> Encoding

FromJSON Settings

Defined in Mcmc.Settings

Methods

parseJSON :: Value -> Parser Settings

parseJSONList :: Value -> Parser [Settings]

settingsSave :: Settings -> IO ()

Save settings to a file determined by the analysis name.

settingsLoad :: AnalysisName -> IO Settings

Load settings.

settingsCheck

Arguments

:: Settings

-> Int

Current iteration.

-> IO ()

Check settings.

Call error if:

• The analysis name is the empty string.
• The number of burn in iterations is negative.
• Auto tuning period is zero or negative.
• The number of iterations is negative.
• The current iteration is larger than the total number of iterations.
• The current iteration is non-zero but the execution mode is not Continue.
• The current iteration is zero but the execution mode is Continue.