Miscellaneous operators

class NoneOp

class NoneOp

This operator does nothing when it is applied to a population. It is usually used as a placeholder when an operator is needed syntactically.

NoneOp(output=">", begin=0, end=0, step=1, at=[], reps=ALL_AVAIL, subPops=ALL_AVAIL, infoFields=[])

Create a NoneOp.

class Dumper

class Dumper

This operator dumps the content of a population in a human readable format. Because this output format is not structured and can not be imported back to simuPOP, this operator is usually used to dump a small population to a terminal for demonstration and debugging purposes.

Dumper(genotype=True, structure=True, ancGens=UNSPECIFIED, width=1, max=100, loci=[], output=">", begin=0, end=-1, step=1, at=[], reps=ALL_AVAIL, subPops=ALL_AVAIL, infoFields=ALL_AVAIL)

Create a operator that dumps the genotype structure (if structure is True) and genotype (if genotype is True) to an output ( default to standard terminal output). Because a population can be large, this operator will only output the first 100 (parameter max) individuals of the present generation (parameter ancGens). All loci will be outputed unless parameter loci are used to specify a subset of loci. This operator by default output values of all information fields unless parameter infoFields is used to specify a subset of info fields to display. If a list of (virtual) subpopulations are specified, this operator will only output individuals in these outputs. Please refer to class BaseOperator for a detailed explanation for common parameters such as output and stage.

class SavePopulation

class SavePopulation

An operator that save populations to specified files.

SavePopulation(output="", begin=0, end=-1, step=1, at=[], reps=ALL_AVAIL, subPops=ALL_AVAIL, infoFields=[])

Create an operator that saves a population to output when it is applied to the population. This operator supports all output specifications ('', 'filename', 'filename' prefixed by one or more ‘>’ characters, and '!expr') but output from different operators will always replace existing files (effectively ignore ‘>’ specification). Parameter subPops is ignored. Please refer to class BaseOperator for a detailed description about common operator parameters such as stage and begin.

class Pause

class Pause

This operator pauses the evolution of a simulator at given generations or at a key stroke. When a simulator is stopped, you can go to a Python shell to examine the status of an evolutionary process, resume or stop the evolution.

Pause(stopOnKeyStroke=False, prompt=True, output=">", begin=0, end=-1, step=1, at=[], reps=ALL_AVAIL, subPops=ALL_AVAIL, infoFields=[])

Create an operator that pause the evolution of a population when it is applied to this population. If stopOnKeyStroke is False (default), it will always pause a population when it is applied, if this parameter is set to True, the operator will pause a population if any key has been pressed. If a specific character is set, the operator will stop when this key has been pressed. This allows, for example, the use of several pause operators to pause different populations.

After a population has been paused, a message will be displayed (unless prompt is set to False) and tells you how to proceed. You can press 's' to stop the evolution of this population, 'S' to stop the evolution of all populations, or 'p' to enter a Python shell. The current population will be available in this Python shell as "pop_X_Y" when X is generation number and Y is replicate number. The evolution will continue after you exit this interactive Python shell.

Note

Ctrl-C will be intercepted even if a specific character is specified in parameter stopOnKeyStroke.

class TicToc

class TicToc

This operator, when called, output the difference between current and the last called clock time. This can be used to estimate execution time of each generation. Similar information can also be obtained from turnOnDebug("DBG_PROFILE"), but this operator has the advantage of measuring the duration between several generations by setting step parameter. As an advanced feature that mainly used for performance testing, this operator accepts a parameter stopAfter (seconds), and will stop the evolution of a population if the overall time exceeds stopAfter. Note that elapsed time is only checked when this operator is applied to a population so it might not be able to stop the evolution process right after stopAfter seconds. This operator can also be applied during mating. Note that to avoid excessive time checking, this operator does not always check system time accurately.

TicToc(output=">", stopAfter=0, begin=0, end=-1, step=1, at=[], reps=ALL_AVAIL, subPops=ALL_AVAIL, infoFields=[])

Create a TicToc operator that outputs the elapsed since the last time it was applied, and the overall time since the first time this operator is applied.