Model:ZoneTaxon

ZoneTaxon

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Also known as
Model type	Tool
Model part of larger framework	LandLab
Note on status model
Date note status model

Incorporated models or components:

Spatial dimensions	2D
Spatial extent	Regional-Scale
Model domain	Terrestrial, Ecosystems
One-line model description	A zone-based taxon
Extended model description	A ``ZoneTaxon`` is composed of members of a lower taxonomic level that each exists within a ``Zone`` object. Taxonomic rank is not considered by this class despite the use of the term, 'speciation', which is used herein to generally describe creation of a child taxon object. All zones of the taxon can be obtained with the attribute, ``zones`` that are the objects that manage the geographic aspect of taxon member populations. The total geographic extent of all populations is depicted by the ``range_mask`` attribute. The zones of a ZoneTaxon instance are created and updated using a ``ZoneController``. At model time steps, the connectivity of zones over time is obtained using attributes of the ``Zone`` object. The evolution of this taxon type is carried out in two stages during a model time step. In the first stage, the zones of the taxon are updated as the result of zone connectivity between the prior and current step in the method, ``_update_zones``. This method is the primary implementation of taxon dispersal and it is called in a stage prior to other evolutionary processes so that all taxa are positioned in their landscape locations prior to the other processes. In the second stage, processes are carried out in methods that are readily expanded or overridden when needed. The primary methods of second stage macroevolution are ``_evaluate_dispersal``, ``_evaluate_speciation``, and ``_evaluate_extinction``. The evaluate dispersal method is intended to modify dispersal conducted in the first stage and it has no effect unless it is expanded or overridden to have an effect. Processes other than those listed above can be called by expanding or overridding the ``_evolve`` method. The taxon is allopatric when it is associated with/exists within multiple zones (signifying multiple member populations). A timer is started when a taxon becomes allopatric. Allopatric speciation occurs once the timer reaches or exceeds the ``time_to_allopatric_speciation`` initialization parameter. If the initialization parameter, ``persists_post_speciation`` is True (default), a child taxon is created in each zone except one zone (the largest by area) that becomes the sole zone of the taxon. If ``persists_post_speciation`` is set to False, a child taxon is created in each and every zone, and the parent no longer occupies any zones, and therefore the parent taxon is no longer extant. Extinction occurs when the taxon is no longer associated with any zones. This occurs when zones in the prior time step do not overlap zones in the current time step, signifying the geographic range of the taxon is no more. A taxon can become no longer extant also when the taxon speciates and ``persists_post_speciation`` is False signifying that the parent taxon has evolved into multiple taxon distinct from the original taxon.

Keywords:	ecology, evolution,

Name	Nathan Lyons
Type of contact
Institute / Organization
Postal address 1
Postal address 2
Town / City	New Orleans
Postal code	70118
State	Louisiana
Country	United States
Email address	nlyons@tulane.edu
Phone
Fax

Supported platforms	Unix, Linux, Mac OS, Windows
Other platform
Programming language	Python
Other program language
Code optimized	Single Processor
Multiple processors implemented
Nr of distributed processors
Nr of shared processors
Start year development	2017
Does model development still take place?	No
If above answer is no, provide end year model development	2020
Code development status	Only maintenance
When did you indicate the 'code development status'?	2020
Model availability	As code
Source code availability (Or provide future intension)	Through web repository
Source web address	https://github.com/landlab/landlab/tree/master/landlab
Source csdms web address
Program license type	BSD or MIT X11
Program license type other
Memory requirements
Typical run time

Describe input parameters	zones : list of Zones The initial SpeciesEvolver Zones where the taxon is located. parent : Taxon, optional A SpeciesEvolver taxon that is the parent taxon. The default value, 'None' indicates no parent. time_to_allopatric_speciation : float, int, optional The delay in model time to speciate following taxon geographic fragmentation, indicated by multiple objects in the attribute, ``zones``. Speciation occurs at the time step when the delay is reached or exceeded. The default value of 0 indicates speciation occurs at the same time step as geographic fragmentation. persists_post_speciation : boolean, optional When 'True', the default, taxon persists despite speciation. When 'False' and following speciation, the taxon is no longer extant.
Input format	ASCII
Other input format
Describe output parameters	boolean: Indicates if the taxon is still evolving. When `False` is returned, this method will not be called for the taxon in subsequent stages in the current model time step. list of Taxon: The children produced by the taxon at a given stage. The ``evolve`` method of child taxon will be called in stages following the stage the child taxon was produced. An empty list indicates no child taxon.
Output format	ASCII
Other output format
Pre-processing software needed?	No
Describe pre-processing software
Post-processing software needed?	No
Describe post-processing software
Visualization software needed?	No
If above answer is yes
Other visualization software

Describe processes represented by the model
Describe key physical parameters and equations
Describe length scale and resolution constraints
Describe time scale and resolution constraints
Describe any numerical limitations and issues

Describe available calibration data sets
Upload calibration data sets if available:
Describe available test data sets
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Describe ideal data for testing

Do you have current or future plans for collaborating with other researchers?

Is there a manual available?	No
Upload manual if available:
Model website if any	https://landlab.github.io
Model forum / discussion board	https://github.com/landlab/landlab/issues

Comments

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OpenMI compliant	Not yet"Not yet" is not in the list (Yes, No but planned, No but possible, No not possible) of allowed values for the "Code openmi compliant or not" property.
BMI compliant	Not yet"Not yet" is not in the list (Yes, No but planned, No but possible, No not possible) of allowed values for the "Code IRF or not" property.
WMT component	Not yet"Not yet" is not in the list (Yes, In progress, No but possible, No not possible) of allowed values for the "Code CMT compliant or not" property.
PyMT component	Not yet"Not yet" is not in the list (Yes, In progress, No but possible, No not possible) of allowed values for the "Code PyMT compliant or not" property.
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Model info

Authors

Nathan Lyons

Source code

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