gadgetFitHelpers: gadget.fit helper functions

Description Usage Arguments Value Author(s)

Description

read.gadget.wgts reads the output from iterative weighting likelihood output

merge.formula merges txt to gadget.formula

eval.gadget.formula Evaluate gadget formulas, which are in reverse polish notation, ie '(* x y)' which is equivalent to 'x*y'. The evaluation supports the following symbols '*','/','+','-','exp','log','sqrt'. The evaluation uses a gadget parameter object for its evaluation.

get.gadget.growth get gadget growth

get.gadget.recruitment gets gadget recruitment

get.gadget.catches gets gadget catches

read.gadget.grouping reads the the likelihood grouping from the WGTS folder

Usage

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read.gadget.wgts(params.file = "params.in", wgts = "WGTS",
  likelihood = "likelihood", lik.pre = "lik.", params.pre = "params.",
  parallel = FALSE)

## S3 method for class 'formula'
merge(txt)

eval.gadget.formula(gad.for, par = data.frame())

get.gadget.growth(stocks, params, dt = 0.25, age.based = FALSE,
  recl = FALSE)

get.gadget.recruitment(stocks, params, collapse = TRUE)

get.gadget.catches(fleets, params)

read.gadget.grouping(lik = read.gadget.likelihood(), wgts = "WGTS")

Arguments

params.file

base parameter file

wgts

location of the reweighting folder

likelihood

likelihood file

lik.pre

strings matching the likelihood output

params.pre

strings matching the parameter estimates

parallel

should the files be read in parallel

txt

gadget formula text

gad.for

gadget formula

par

gadget parameters object

stocks

gadget.stock

params

gadget.parms

dt

delta t

age.based

logical

recl

recruitment length

fleets

gadget.fleet

lik

old style gadget likelihood object

stocks

gadget.stock

params

gadget.params

params

gadget.params

wgts

logcation of the WGTS folder

Value

data.frame with parameter estimates and likelihood output from the iterative reweighting folder.

txt where the formula has been properly compiled

a vector of evaluated gadget formulas

growth matrix

recruitment by year

catches by year + step

list of wgts groupings

Author(s)

Bjarki Thor Elvarsson


bthe/rgadget documentation built on Sept. 22, 2018, 1:22 p.m.