ecostate: fit EcoState model

In ecostate: State-Space Mass-Balance Model for Marine Ecosystems

fit EcoState model

Description

Estimate parameters for an EcoState model

Usage

ecostate(
  taxa,
  years,
  catch = data.frame(Year = numeric(0), Mass = numeric(0), Taxon = numeric(0)),
  biomass = data.frame(Year = numeric(0), Mass = numeric(0), Taxon = numeric(0)),
  agecomp = list(),
  weight = list(),
  PB,
  QB,
  B,
  DC,
  EE,
  X,
  type,
  U,
  fit_B = vector(),
  fit_Q = vector(),
  fit_B0 = vector(),
  fit_EE = vector(),
  fit_PB = vector(),
  fit_QB = vector(),
  fit_eps = vector(),
  fit_nu = vector(),
  log_prior = function(p) 0,
  settings = stanza_settings(taxa = taxa),
  control = ecostate_control()
)

Arguments

taxa	Character vector of taxa included in model.
years	Integer-vector of years included in model
catch	long-form data frame with columns Mass, Year and Taxon
biomass	long-form data frame with columns Mass, Year and Taxon, where Mass is assumed to have the same units as catch
agecomp	a named list, with names corresponding to stanza_groups, where each list-element is a matrix with rownames for years and colnames for integer ages, where NA excludes the entry from inclusion and the model computes the likelihood across included ages in a given year, and the rowsum is the input-sample size for a given year
weight	a named list, with names corresponding to stanza_groups, where each list-element is a matrix with rownames for years and colnames for integer ages, where NA excludes the entry from inclusion and the model computes the lognormal likelihood for weight-at-age in each specified age-year combination
PB	numeric-vector with names matching taxa, providing the ratio of production to biomass for each taxon
QB	numeric-vector with names matching taxa, providing the ratio of consumption to biomass for each taxon
B	numeric-vector with names matching taxa, providing the starting (or fixed) value for equilibrium biomass for each taxon
DC	numeric-matrix with rownames and colnames matching taxa, where each column provides the diet proportion for a given predator
EE	numeric-vector with names matching taxa, providing the proportion of proportion of production that is subsequently modeled (termed ecotrophic efficiency)
X	numeric-matrix with rownames and colnames matching taxa, where each element gives the vulnerability parameter for a given interaction.
type	character-vector with names matching taxa and elements c("auto","hetero","detritus"), indicating whether each taxon is a primary producer, consumer/predator, or detritus, respectively.
U	numeric-vector with names matching taxa, providing the proportion of consumption that is unassimilated and therefore exported to detritus
fit_B	Character-vector listing taxa for which equilibrium biomass is estimated as a fixed effect
fit_Q	Character-vector listing taxa for which the catchability coefficient is estimated as a fixed effect
fit_B0	Character-vector listing taxa for which the ratio of initial to equilibrium biomass is estimated as a fixed effect
fit_EE	Character-vector listing taxa for which ecotrophic efficiency is estimated.
fit_PB	Character-vector listing taxa for which equilibrium production per biomass is estimated. Note that it is likely a good idea to include a prior for any species for which this is estimated.
fit_QB	Character-vector listing taxa for which equilibrium consumption per biomass is estimated. Note that it is likely a good idea to include a prior for any species for which this is estimated.
fit_eps	Character-vector listing taxa for which the model should estimate annual process errors in dB/dt
fit_nu	Character-vector listing taxa for which the model should estimate annual process errors in consumption Q_ij
log_prior	A user-provided function that takes as input the list of parameters out$obj$env$parList() where out is the output from ecostate(), and returns a numeric vector where the sum is the log-prior probability. For example log_prior = function(p) dnorm( p$logq_i[1], mean=0, sd=0.1, log=TRUE) specifies a lognormal prior probability for the catchability coefficient for the first taxa with logmean of zero and logsd of 0.1
settings	Output from stanza_settings(), used to define age-structured dynamics (called stanza-groups).
control	Output from ecostate_control(), used to define user settings.

Details

All taxa must be included in QB, PB, B, and DC, but additional taxa can be in QB, PB, B, and DC that are not in taxa. So taxa can be used to redefine the set of modeled species without changing other inputs

Value

An object (list) of S3-class ecostate. Elements include:

obj

RTMB object from MakeADFun

tmb_inputs

The list of inputs passed to MakeADFun

opt

The output from nlminb

sdrep

The output from sdreport

interal

Objects useful for package function, i.e., all arguments passed during the call

rep

report file, including matrix B_ti for biomass in each year t and taxon i, g_ti for growth rate per biomass, and see dBdt for other quantities reported by year

derived

derived quantity estimates and standard errors, for rep objects as requested

call

function call record

run_time

Total runtime

This S3 class then has functions summary, print, and logLik

References

Introducing the state-space mass-balance model:

Thorson, J. Kristensen, K., Aydin, K., Gaichas, S., Kimmel, D.G., McHuron, E.A., Nielsen, J.N., Townsend, H., Whitehouse, G.A (In press). The benefits of hierarchical ecosystem models: demonstration using a new state-space mass-balance model EcoState. Fish and Fisheries.

ecostate documentation built on April 3, 2025, 5:25 p.m.