make.tmb.data: make.tmb.data: prepare data inputs for APAM

In SineAndie/APAM: APAM: American plaice assessment model

Description

Prepares data for use in APAM. No inputs need to be changed to run the default model (see details).

Usage

make.tmb.data(
  do.retro = FALSE,
  retro.year = NULL,
  M.split = TRUE,
  M.matrix = NULL,
  C.bounds = NULL,
  sdL = NULL,
  d = NULL
)

Arguments

do.retro	(optional) T/F, turn on/off option to change retro year? Default = F.
retro.year	(optional) numeric, defines end year for retros if needed. Default = NULL.
M.split	(optional) T/F, turn on/off M increase for years 1989-1996? Default = T.
M.matrix	(optional) a matrix to manually define M assumption. Default = NULL See details.
C.bounds	(optional) a vector to manually define landings upper bounds; Default = NULL. See details.
sdL	(optional) a positive scalar to manually defined landings sd ; Default = NULL.
d	(optional) a vector to turn on/off d for use in make.LI(). Default = NULL.

Details

M.matrix

M.matrix has dimensions nrow=nyears and ncol=nages; M = 0.5 for ages 1-3, 0.3 for age 4 and 0.2 for ages 5+.

M.split

if TRUE, M.matrix = M.matrix + 0.33 for years 1989-1996.

C.bounds

vector of length 3; Default C.bounds = (2,1.2,1.5) for high, low, and moderate uncertainty.

sdL

default sd landings = 0.05

d

Numeric vector of length(nyears*nages) of 0's.

Examples

## Not run: 
tmb.data <- make.tmb.data()

#model with no M split
tmb.data.ns = make.tmb.data(M.split=FALSE)

## End(Not run)

SineAndie/APAM documentation built on Dec. 18, 2021, 2:05 p.m.