MizerParams-class: A class to hold the parameters for a size based model.
In sizespectrum/mizer: Dynamic Multi-Species Size Spectrum Modelling
MizerParams-class R Documentation
A class to hold the parameters for a size based model.
Description
Although it is possible to build a MizerParams object by hand it is
not recommended and several constructors are available. Dynamic simulations
are performed using project() function on objects of this class. As a
user you should never need to access the slots inside a MizerParams object
directly.
Details
The MizerParams class is fairly complex with a large number of
slots, many of which are multidimensional arrays. The dimensions of these
arrays is strictly enforced so that MizerParams objects are consistent
in terms of number of species and number of size classes.
The MizerParams class does not hold any dynamic information, e.g.
abundances or harvest effort through time. These are held in
MizerSim objects.
Slots
metadataA list with metadata information. See setMetadata().
mizer_versionThe package version of mizer (as returned by
packageVersion("mizer")) that created or upgraded the model.
extensionsA named vector of strings where each name is the name of
and extension package needed to run the model and each value is a string
giving the information that the remotes package needs to install the
correct version of the extension package, see https://remotes.r-lib.org/.
time_createdA POSIXct date-time object with the creation time.
time_modifiedA POSIXct date-time object with the last modified time.
wThe size grid for the fish part of the spectrum. An increasing
vector of weights (in grams) running from the smallest egg size to the
largest maximum size.
dwThe widths (in grams) of the size bins
w_fullThe size grid for the full size range including the resource
spectrum. An increasing vector of weights (in grams) running from the
smallest resource size to the largest maximum size of fish. The
last entries of the vector have to be equal to the content of the w slot.
dw_fullThe width of the size bins for the full spectrum. The last
entries have to be equal to the content of the dw slot.
w_min_idxA vector holding the index of the weight of the egg size
of each species
maturityAn array (species x size) that holds the proportion of
individuals of each species at size that are mature. This enters in the
calculation of the spawning stock biomass with getSSB(). Set
with setReproduction().
psiAn array (species x size) that holds the allocation to reproduction
for each species at size, \psi_i(w). Changed with
setReproduction().
intake_maxAn array (species x size) that holds the maximum intake for
each species at size. Changed with setMaxIntakeRate().
search_volAn array (species x size) that holds the search volume for
each species at size. Changed with setSearchVolume().
metabAn array (species x size) that holds the metabolism
for each species at size. Changed with setMetabolicRate().
mu_bAn array (species x size) that holds the external mortality rate
\mu_{ext.i}(w). Changed with setExtMort().
ext_encounterAn array (species x size) that holds the external encounter rate
E_{ext.i}(w). Changed with setExtEncounter().
pred_kernelAn array (species x predator size x prey size) that holds
the predation coefficient of each predator at size on each prey size. If
this is NA then the following two slots will be used. Changed with
setPredKernel().
ft_pred_kernel_eAn array (species x log of predator/prey size ratio)
that holds the Fourier transform of the feeding kernel in a form
appropriate for evaluating the encounter rate integral. If this is NA
then the pred_kernel will be used to calculate the available
energy integral. Changed with setPredKernel().
ft_pred_kernel_pAn array (species x log of predator/prey size ratio)
that holds the Fourier transform of the feeding kernel in a form
appropriate for evaluating the predation mortality integral. If this is NA
then the pred_kernel will be used to calculate the integral.
Changed with setPredKernel().
rr_ppA vector the same length as the w_full slot. The size specific
growth rate of the resource spectrum.
cc_ppA vector the same length as the w_full slot. The size specific
carrying capacity of the resource spectrum.
resource_dynamicsName of the function for projecting the resource
abundance density by one timestep.
other_dynamicsA named list of functions for projecting the
values of other dynamical components of the ecosystem that may be modelled
by a mizer extensions you have installed. The names of the list entries
are the names of those components.
other_encounterA named list of functions for calculating the
contribution to the encounter rate from each other dynamical component.
other_mortA named list of functions for calculating the
contribution to the mortality rate from each other dynamical components.
other_paramsA list containing the parameters needed by any mizer
extensions you may have installed to model other dynamical components of
the ecosystem.
rates_funcsA named list with the names of the functions that should be
used to calculate the rates needed by project(). By default this will be
set to the names of the built-in rate functions.
sc![[Experimental]](../help/figures/lifecycle-experimental.svg)
The community abundance of the scaling community
species_paramsA data.frame to hold the species specific parameters.
See species_params() for details.
given_species_paramsA data.frame to hold the species parameters that
were given explicitly rather than obtained by default calculations.
gear_paramsData frame with parameters for gear selectivity. See
setFishing() for details.
interactionThe species specific interaction matrix, \theta_{ij}.
Changed with setInteraction().
selectivityAn array (gear x species x w) that holds the selectivity of
each gear for species and size, S_{g,i,w}. Changed with
setFishing().
catchabilityAn array (gear x species) that holds the catchability of
each species by each gear, Q_{g,i}. Changed with
setFishing().
initial_effortA vector containing the initial fishing effort for each
gear. Changed with setFishing().
initial_nAn array (species x size) that holds the initial abundance of
each species at each weight.
initial_n_ppA vector the same length as the w_full slot that describes
the initial resource abundance at each weight.
initial_n_otherA list with the initial abundances of all other
ecosystem components. Has length zero if there are no other components.
resource_paramsList with parameters for resource.
A
Abundance multipliers.
linecolourA named vector of colour values, named by species.
Used to give consistent colours in plots.
linetypeA named vector of linetypes, named by species.
Used to give consistent line types in plots.
ft_maskAn array (species x w_full) with zeros for weights larger than
the maximum weight of each species. Used to efficiently minimize
wrap-around errors in Fourier transform calculations.
See Also
project() MizerSim()
emptyParams() newMultispeciesParams()
newCommunityParams()
newTraitParams()
sizespectrum/mizer documentation built on April 14, 2024, 3:08 a.m.
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| MizerParams-class | R Documentation |
A class to hold the parameters for a size based model.
Description
Although it is possible to build a MizerParams object by hand it is
not recommended and several constructors are available. Dynamic simulations
are performed using project() function on objects of this class. As a
user you should never need to access the slots inside a MizerParams object
directly.
Details
The MizerParams class is fairly complex with a large number of
slots, many of which are multidimensional arrays. The dimensions of these
arrays is strictly enforced so that MizerParams objects are consistent
in terms of number of species and number of size classes.
The MizerParams class does not hold any dynamic information, e.g.
abundances or harvest effort through time. These are held in
MizerSim objects.
Slots
metadataA list with metadata information. See
setMetadata().mizer_versionThe package version of mizer (as returned by
packageVersion("mizer")) that created or upgraded the model.extensionsA named vector of strings where each name is the name of and extension package needed to run the model and each value is a string giving the information that the remotes package needs to install the correct version of the extension package, see https://remotes.r-lib.org/.
time_createdA POSIXct date-time object with the creation time.
time_modifiedA POSIXct date-time object with the last modified time.
wThe size grid for the fish part of the spectrum. An increasing vector of weights (in grams) running from the smallest egg size to the largest maximum size.
dwThe widths (in grams) of the size bins
w_fullThe size grid for the full size range including the resource spectrum. An increasing vector of weights (in grams) running from the smallest resource size to the largest maximum size of fish. The last entries of the vector have to be equal to the content of the w slot.
dw_fullThe width of the size bins for the full spectrum. The last entries have to be equal to the content of the dw slot.
w_min_idxA vector holding the index of the weight of the egg size of each species
maturityAn array (species x size) that holds the proportion of individuals of each species at size that are mature. This enters in the calculation of the spawning stock biomass with
getSSB(). Set withsetReproduction().psiAn array (species x size) that holds the allocation to reproduction for each species at size,
\psi_i(w). Changed withsetReproduction().intake_maxAn array (species x size) that holds the maximum intake for each species at size. Changed with
setMaxIntakeRate().search_volAn array (species x size) that holds the search volume for each species at size. Changed with
setSearchVolume().metabAn array (species x size) that holds the metabolism for each species at size. Changed with
setMetabolicRate().mu_bAn array (species x size) that holds the external mortality rate
\mu_{ext.i}(w). Changed withsetExtMort().ext_encounterAn array (species x size) that holds the external encounter rate
E_{ext.i}(w). Changed withsetExtEncounter().pred_kernelAn array (species x predator size x prey size) that holds the predation coefficient of each predator at size on each prey size. If this is NA then the following two slots will be used. Changed with
setPredKernel().ft_pred_kernel_eAn array (species x log of predator/prey size ratio) that holds the Fourier transform of the feeding kernel in a form appropriate for evaluating the encounter rate integral. If this is NA then the
pred_kernelwill be used to calculate the available energy integral. Changed withsetPredKernel().ft_pred_kernel_pAn array (species x log of predator/prey size ratio) that holds the Fourier transform of the feeding kernel in a form appropriate for evaluating the predation mortality integral. If this is NA then the
pred_kernelwill be used to calculate the integral. Changed withsetPredKernel().rr_ppA vector the same length as the w_full slot. The size specific growth rate of the resource spectrum.
cc_ppA vector the same length as the w_full slot. The size specific carrying capacity of the resource spectrum.
resource_dynamicsName of the function for projecting the resource abundance density by one timestep.
other_dynamicsA named list of functions for projecting the values of other dynamical components of the ecosystem that may be modelled by a mizer extensions you have installed. The names of the list entries are the names of those components.
other_encounterA named list of functions for calculating the contribution to the encounter rate from each other dynamical component.
other_mortA named list of functions for calculating the contribution to the mortality rate from each other dynamical components.
other_paramsA list containing the parameters needed by any mizer extensions you may have installed to model other dynamical components of the ecosystem.
rates_funcsA named list with the names of the functions that should be used to calculate the rates needed by
project(). By default this will be set to the names of the built-in rate functions.sc-
The community abundance of the scaling community
species_paramsA data.frame to hold the species specific parameters. See
species_params()for details.given_species_paramsA data.frame to hold the species parameters that were given explicitly rather than obtained by default calculations.
gear_paramsData frame with parameters for gear selectivity. See
setFishing()for details.interactionThe species specific interaction matrix,
\theta_{ij}. Changed withsetInteraction().selectivityAn array (gear x species x w) that holds the selectivity of each gear for species and size,
S_{g,i,w}. Changed withsetFishing().catchabilityAn array (gear x species) that holds the catchability of each species by each gear,
Q_{g,i}. Changed withsetFishing().initial_effortA vector containing the initial fishing effort for each gear. Changed with
setFishing().initial_nAn array (species x size) that holds the initial abundance of each species at each weight.
initial_n_ppA vector the same length as the w_full slot that describes the initial resource abundance at each weight.
initial_n_otherA list with the initial abundances of all other ecosystem components. Has length zero if there are no other components.
resource_paramsList with parameters for resource.
A-
Abundance multipliers.
linecolourA named vector of colour values, named by species. Used to give consistent colours in plots.
linetypeA named vector of linetypes, named by species. Used to give consistent line types in plots.
ft_maskAn array (species x w_full) with zeros for weights larger than the maximum weight of each species. Used to efficiently minimize wrap-around errors in Fourier transform calculations.
See Also
project() MizerSim()
emptyParams() newMultispeciesParams()
newCommunityParams()
newTraitParams()
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