rexfw.statistics.writers package

Module contents

StatisticsWriter classes which… well… write statistics to stdout / files / …

ATTENTION: some of these classes expect replica objects to be named replica1, replica2, …

class rexfw.statistics.writers.AbstractFileStatisticsWriter(filename, variables_to_write=[], quantities_to_write=[])

Bases: rexfw.statistics.writers.AbstractStatisticsWriter

_write_quantity_class_header(class_name)

_write_single_quantity_stats(elements)

Writes a single line to stdout / file, e.g., all sampler step sizes which would be stored in elements

Parameters:elements (list of LoggedQuantity) – quantities to write

write(step, elements)

Writes quantities in elements for a given step

Parameters:

• step (int) – sampling step
• elements (list of LoggedQuantity) – list of quantities to write

class rexfw.statistics.writers.AbstractStatisticsWriter(separator, variables_to_write=[], quantities_to_write=[])

Bases: object

_write_single_quantity_stats(elements)

Writes a single line to stdout / file, e.g., all sampler step sizes which would be stored in elements

Parameters:elements (list of LoggedQuantity) – quantities to write

write(step, elements)

Writes quantities in elements for a given step

Parameters:

• step (int) – sampling step
• elements (list of LoggedQuantity) – list of quantities to write

class rexfw.statistics.writers.ConsoleStatisticsWriter(variables_to_write=[], quantities_to_write=[])

Bases: rexfw.statistics.writers.AbstractStatisticsWriter

_format(quantity)

Formats the numeric value of a quantity for output

Parameters:quantity (LoggedQuantity) – a quantity whose numeric value will be written Returns:a string representing a formatted numerical value Return type:str

_sort_quantities(quantities)

Sorts quantities for a single line by, e.g., replica name

Parameters:quantities (list of LoggedQuantity objects) – the logged quantitis which will be written out Returns:the sorted quantities list Return type:list

_write_all_but_header(quantities)

Writes all sampling statistics in quantities, but not the line header

Parameters:quantities (list of LoggedQuantity) – a list of similar LoggedQuantity objects, e.g., all step sizes

_write_quantity_class_header(quantity)

Writes a “header” (line beginning) for a given type of quantity, e.g., “myvariable p_acc”

Parameters:quantity (LoggedQuantity) – a quantity containing the information needed Returns:a preface for a line with similar sampling statistics Return type:str

_write_single_quantity_stats(elements)

Writes a single line to stdout / file, e.g., all sampler step sizes which would be stored in elements

Parameters:elements (list of LoggedQuantity) – quantities to write

_write_step_header(step)

Writes a header for a given sampling step, e.g., ### step number ###

Parameters:step (int) – a sampling step Returns:the header prefacing the ouptut for a given sampling step Return type:str

write(step, elements)

Writes quantities in elements for a given step

Parameters:

• step (int) – sampling step
• elements (list of LoggedQuantity) – list of quantities to write

class rexfw.statistics.writers.StandardConsoleMCMCStatisticsWriter(variables_to_write=[], quantities_to_write=[])

Bases: rexfw.statistics.writers.ConsoleStatisticsWriter

Writes only acceptance rate and step sizes to stdout. Remember to set quantity names correctly, that is, to “acceptance rate” and “stepsize”

Parameters:

• variables_to_write (list of str) – list of sampling variable names for which to write statistics
• quantities_to_write (list of LoggedQuantity) – list of LoggedQuantity objects for which to write statistics

_format(quantity)

Formats the numeric value of a quantity for output

Parameters:quantity (LoggedQuantity) – a quantity whose numeric value will be written Returns:a string representing a formatted numerical value Return type:str

_sort_quantities(quantities)

Sorts quantities for a single line by, e.g., replica name

Parameters:quantities (list of LoggedQuantity objects) – the logged quantitis which will be written out Returns:the sorted quantities list Return type:list

_write_all_but_header(elements)

Writes all sampling statistics in quantities, but not the line header

Parameters:quantities (list of LoggedQuantity) – a list of similar LoggedQuantity objects, e.g., all step sizes

_write_quantity_class_header(quantity)

Writes a “header” (line beginning) for a given type of quantity, e.g., “myvariable p_acc”

Parameters:quantity (LoggedQuantity) – a quantity containing the information needed Returns:a preface for a line with similar sampling statistics Return type:str

_write_single_quantity_stats(elements)

Writes a single line to stdout / file, e.g., all sampler step sizes which would be stored in elements

Parameters:elements (list of LoggedQuantity) – quantities to write

_write_step_header(step)

Writes a header for a given sampling step, e.g., ### step number ###

Parameters:step (int) – a sampling step Returns:the header prefacing the ouptut for a given sampling step Return type:str

write(step, elements)

Writes quantities in elements for a given step

Parameters:

• step (int) – sampling step
• elements (list of LoggedQuantity) – list of quantities to write

class rexfw.statistics.writers.StandardConsoleREStatisticsWriter

Bases: rexfw.statistics.writers.ConsoleStatisticsWriter

_format(quantity)

Formats the numeric value of a quantity for output

Parameters:quantity (LoggedQuantity) – a quantity whose numeric value will be written Returns:a string representing a formatted numerical value Return type:str

_sort_quantities(quantities)

Sorts quantities for a single line by, e.g., replica name

Parameters:quantities (list of LoggedQuantity objects) – the logged quantitis which will be written out Returns:the sorted quantities list Return type:list

_write_all_but_header(quantities)

Writes all sampling statistics in quantities, but not the line header

Parameters:quantities (list of LoggedQuantity) – a list of similar LoggedQuantity objects, e.g., all step sizes

_write_quantity_class_header(class_name)

Writes a “header” (line beginning) for a given type of quantity, e.g., “myvariable p_acc”

Parameters:quantity (LoggedQuantity) – a quantity containing the information needed Returns:a preface for a line with similar sampling statistics Return type:str

_write_single_quantity_stats(elements)

Writes a single line to stdout / file, e.g., all sampler step sizes which would be stored in elements

Parameters:elements (list of LoggedQuantity) – quantities to write

_write_step_header(step)

Writes a header for a given sampling step, e.g., ### step number ###

Parameters:step (int) – a sampling step Returns:the header prefacing the ouptut for a given sampling step Return type:str

write(step, elements)

Writes quantities in elements for a given step

Parameters:

• step (int) – sampling step
• elements (list of LoggedQuantity) – list of quantities to write

class rexfw.statistics.writers.StandardFileMCMCStatisticsWriter(filename, variables_to_write=[], quantities_to_write=[])

Bases: rexfw.statistics.writers.AbstractFileStatisticsWriter

_format(quantity)

_sort_quantities(quantities)

_write_all_but_header(quantities)

_write_header()

_write_quantity_class_header(quantity)

_write_single_quantity_stats(elements)

Writes a single line to stdout / file, e.g., all sampler step sizes which would be stored in elements

Parameters:elements (list of LoggedQuantity) – quantities to write

_write_step_header(step)

write(step, elements)

Writes quantities in elements for a given step

Parameters:

• step (int) – sampling step
• elements (list of LoggedQuantity) – list of quantities to write

class rexfw.statistics.writers.StandardFileREHeatsStatisticsWriter(outfolder)

Bases: rexfw.statistics.writers.AbstractStatisticsWriter

Writes heats produced during replica exchange swap trajectories to a file.

Parameters:outfolder (str) – path to folder to write heats to

_write_single_quantity_stats(elements)

Writes a single line to stdout / file, e.g., all sampler step sizes which would be stored in elements

Parameters:elements (list of LoggedQuantity) – quantities to write

write(elements)

Writes quantities in elements for a given step

Parameters:

• step (int) – sampling step
• elements (list of LoggedQuantity) – list of quantities to write

class rexfw.statistics.writers.StandardFileREStatisticsWriter(filename, quantities_to_write=[])

Bases: rexfw.statistics.writers.AbstractFileStatisticsWriter

Writes replica exchange acceptance rates to a file.

Parameters:

• filename (str) – path to file to write sampling statistics to
• variables_to_write (list of str) – list of sampling variable names for which to write statistics
• quantities_to_write (list of LoggedQuantity) – list of LoggedQuantity objects for which to write statistics

_format(quantity)

_sort_quantities(quantities)

_write_all_but_header(quantities)

_write_header()

_write_quantity_class_header(class_name)

_write_single_quantity_stats(elements)

Writes a single line to stdout / file, e.g., all sampler step sizes which would be stored in elements

Parameters:elements (list of LoggedQuantity) – quantities to write

_write_step_header(step)

write(step, elements)

Writes quantities in elements for a given step

Parameters:

• step (int) – sampling step
• elements (list of LoggedQuantity) – list of quantities to write

class rexfw.statistics.writers.StandardFileREWorksStatisticsWriter(outfolder)

Bases: rexfw.statistics.writers.AbstractStatisticsWriter

_write_single_quantity_stats(elements)

Writes a single line to stdout / file, e.g., all sampler step sizes which would be stored in elements

Parameters:elements (list of LoggedQuantity) – quantities to write

write(elements)

Writes quantities in elements for a given step

Parameters:

• step (int) – sampling step
• elements (list of LoggedQuantity) – list of quantities to write