time |
Numeric defining the length of the simulation in time units.
For example, if an island is known to be 4 million years old, setting
time = 4 will simulate the entire life span of the island; setting time = 2
will stop the simulation at the mid-life of the island.
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mainland_n |
A numeric stating the number of mainland species, that
is the number of species that can potentially colonize the island.
If using a clade-specific diversity dependence, this value is set to 1.
If using an island-wide diversity dependence, this value is set to the
number of mainland species.
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pars |
A numeric vector containing the model parameters:
pars[1] : lambda^c (cladogenesis rate)
pars[2] : mu (extinction rate)
pars[3] : K (carrying capacity), set K=Inf for diversity
independence.
pars[4] : gamma (immigration rate)
pars[5] : lambda^a (anagenesis rate)
pars[6] : lambda^c (cladogenesis rate) for either type 2 species
or rate set 2 in rate shift model
pars[7] : mu (extinction rate) for either type 2 species or rate
set 2 in rate shift model
pars[8] : K (carrying capacity) for either type 2 species or rate
set 2 in rate shift model, set K=Inf for diversity independence.
pars[9] : gamma (immigration rate) for either type 2 species
or rate set 2 in rate shift model
pars[10] : lambda^a (anagenesis rate) for either type 2
species or rate set 2 in rate shift model
Elements 6:10 are required only when type 2 species are included
or in the rate shift model. For DAISIE_sim_relaxed_rate()
pars[6] is the standard deviation of the gamma distribution for the
relaxed parameter and the parameter chosen by the relaxed_par
argument is the mean of the gamma distribution for the relaxed parameter.
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island_ontogeny |
In DAISIE_sim_time_dep() ,
DAISIE_ML_CS and plotting a string describing the type of
island ontogeny. Can be "const" , "beta" for a beta function
describing area through time. In all other functions a
numeric describing the type of island ontogeny. Can be 0 for
constant, 1 for a beta function describing area through time. In ML
functions island_ontogeny = NA assumes constant ontogeny. Time
dependent estimation is not yet available as development is still ongoing.
Will return an error if called in that case.
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sea_level |
In DAISIE_sim_time_dep() and plotting a
string describing the type of sea level. Can be "const" or
"sine" for a sine function describing area through time.
In all other functions a numeric describing the type of sea level. Can
be 0 for constant, 1 for a sine function describing area
through time.
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hyper_pars |
A named list of numeric hyperparameters for the rate
calculations as returned by create_hyper_pars() :
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area_pars |
A named list containing area and sea level parameters as
created by create_area_pars() :
[1]: maximum area
[2]: current area
[3]: value from 0 to 1 indicating where in the island's history the
peak area is achieved
[4]: total island age
[5]: amplitude of area fluctuation from sea level
[6]: frequency of sine wave of area change from sea level
[7]: angle of the slope of the island
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extcutoff |
A numeric with the cutoff for the the maximum extinction
rate preventing it from being too large and slowing down simulation.
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trait_pars |
A named list containing diversification rates considering
two trait states created by create_trait_pars :
[1]:A numeric with the per capita transition rate with state 1
[2]:A numeric with the per capita immigration rate with state 2
[3]:A numeric with the per capita extinction rate with state 2
[4]:A numeric with the per capita anagenesis rate with state 2
[5]:A numeric with the per capita cladogenesis rate with state 2
[6]:A numeric with the per capita transition rate with state 2
[7]:A numeric with the number of species with trait state 2 on
mainland
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