estimateParam: Estimates parameters using the given data and maybe some...

In alko989/s6model: Data-poor stock assessment using a single-sepcies steady-state size-based (s6) model

Estimates parameters using the given data and maybe some parameters

Description

Parameter estimation minimizing the negative log likelihood, using the nlminb function. estimateParam uses data from commercial catches or surveys. estimateMultidata uses both sources

Usage

estimateParam(names = c("Fm", "Winf", "Wfs"),
  data = simulateData3(parameters(), samplesize = 1000), start = rep(0.5,
  length(names)), lower = rep(-Inf, length(names)), upper = rep(Inf,
  length(names)), fixed.names = c(), fixed.vals = numeric(0),
  fixed.transformed = TRUE, plotFit = FALSE, isSurvey = FALSE,
  verbose = getOption("verbose"), useTMB = TRUE, ...)

estimateMultidata(names = c("Fm", "Winf", "Wfs"),
  surdata = simulateData3(parameters(), samplesize = 1000, isSurvey =
  TRUE)$sample, comdata = simulateData3(parameters(), samplesize =
  1000)$sample, start = rep(0.5, length(names)), lower = rep(0.1,
  length(names)), fixed.names = c(), fixed.vals = numeric(0),
  plotFit = FALSE, ...)

Arguments

names	string vector, the parameters to be estimated.
data	numeric vector, or data.frame with columns Weight and Freq, or list with a numeric vector named 'sample' or a data.frame named 'df'. Weight of individual fish (vector) or frequencies per weight class data.frame.
start	numeric vector, initial values of the parameters.
lower	The lower bound for the parameter estimation.
upper	The upper bound for the parameter estimation.
fixed.names	String vector. Names of constants.
fixed.vals	Numeric vector. Transformed values of constants.
fixed.transformed	Logical. If FALSE the constants are not transformed.
plotFit	logical, if TRUE a plot is produced with the fited pdf and the kernel density estimate of the data.
isSurvey	logical, if TRUE the data are assumed to be from a survey.
verbose	logical, if TRUE the estimated confidence intervals are printed.
useTMB	logical, if TRUE TMB is used for parameter estimation
...	Additional named arguments passed to plotFit
surdata	Same as data. Survey data.
comdata	Same as data. Commercial data.

Value

link{Parameters} object, containing the estimated parameters.

Note

If data is a list containing both sample and df, the data.frame df will be used.

Author(s)

alko

Examples

## Simulate some data
sam <- simulateData3(params=parameters("a", 0.5, transformed=FALSE))

## Estimate the a parameter and see the fitted plot
estimateParam(names="a", data=sam$sample, plotFit=TRUE)

alko989/s6model documentation built on Nov. 2, 2023, 10:04 p.m.