Class SpecSimParameters¶
- Defined in File SpecSimParameters.h
Class Documentation¶
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class
SpecSimParameters
¶ Contains the simulation parameters that are read from the command line.
Public Functions
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SpecSimParameters
()¶
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SpecSimParameters
(const string &fragment_config_file)¶
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void
addSpeciationRate
(const double &speciation_rate)¶ Adds a speciation rate to the speciation parameters list.
- Parameters
speciation_rate
: the speciation rate to add
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void
setup
(string file_in, bool use_spatial_in, string sample_file, const string &use_fragments_in)¶ Sets the application arguments for the inputs.
- Parameters
file_in
: the database to apply speciation rates touse_spatial_in
: if true, record full spatial datasample_file
: the sample file to select lineages from the mapuse_fragments_in
: fragment file, or “T”/”F” for automatic detection/no detection
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void
setup
(string file_in, bool use_spatial_in, string sample_file, const vector<double> ×, const string &use_fragments_in, vector<double> speciation_rates)¶ Sets the application arguments for the inputs.
- Parameters
file_in
: the database to apply speciation rates touse_spatial_in
: if true, record full spatial datasample_file
: the sample file to select lineages from the maptimes
: vector of times to applyuse_fragments_in
: fragment file, or “T”/”F” for automatic detection/no detectionspeciation_rates
: the speciation rates to apply
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void
setup
(string file_in, bool use_spatial_in, string sample_file, const vector<double> ×, const string &use_fragments_in)¶ Sets the application arguments for the inputs. Overloaded version without speciation rates.
- Parameters
file_in
: the database to apply speciation rates touse_spatial_in
: if true, record full spatial datasample_file
: the sample file to select lineages from the maptimes
: vector of times to applyuse_fragments_in
: fragment file, or “T”/”F” for automatic detection/no detection
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void
addMetacommunityParameters
(const unsigned long &metacommunity_size_in, const double &metacommunity_speciation_rate_in, const string &metacommunity_option_in, const unsigned long &metacommunity_reference_in)¶ Sets the metacommunity parameters for the simulation.
- Parameters
metacommunity_size_in
: the number of individuals in the metacommunitymetacommunity_speciation_rate_in
: the speciation rate for the metacommunity
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void
importTimeConfig
()¶ Import the time config file, if there is one.
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void
wipe
()¶ Deletes all the parameters.
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void
addTime
(double time)¶ Adds an additional time to the times vector.
- Parameters
time
: a time to calculate speciation rates at
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void
addProtractedParameters
(double proc_spec_min, double proc_spec_max)¶ Adds a set of protracted speciation parameters to the protracted parameters vector.
- Parameters
proc_spec_min
: the minimum protracted speciation generationproc_spec_max
: the maximum protracted speciation generation
Public Members
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bool
use_spatial
¶
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bool
bMultiRun
¶
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bool
use_fragments
¶
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string
filename
¶
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set<double>
all_speciation_rates
¶
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string
samplemask
¶
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string
times_file
¶
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set<double>
all_times
¶
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string
fragment_config_file
¶
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vector<ProtractedSpeciationParameters>
protracted_parameters
¶
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MetacommunitiesArray
metacommunity_parameters
¶
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