make.parm: make.parm: prepares parameters for use in APAM

In SineAndie/APAM: APAM: American plaice assessment model

Description

Prepares parameters for use in APAM.

Usage

make.parm(
  data,
  map,
  parms = NULL,
  parmsL = NULL,
  parmsU = NULL,
  no.pe = F,
  no.logits = F,
  no.Flogits = F
)

Arguments

data	object returned from make.tmb.data
map	object returned from make.map
parms	(optional) list, can be used to change default starting parameters. See details.
parmsL	(optional) list, can be used to change default parameter lower bounds. See details.
parmsU	(optional) list, can be used to change default parameter upper bounds.. See details.
no.pe	(optional) if no.pe=T make.map set TRUE to fix sdpe=0.01
no.logits	(optional) if no.logits=T make.map set TRUE to fix logits. See details.
no.Flogits	(optional) if no.Flogits=T make.map set TRUE to fix Flogits. See details.

Details

parms

list that contains starting parameter values. Default parm=

• log_R=c(10,10),

• m_q=matrix(c(rep(log(0.1),t1),rep(-30,14-t1)),nrow=length(data$isurvey1), ncol = 14,byrow=T),

• log_cv_index=rep(0.5,length(unique(data$isd))),

• log_std_log_R=log(1),

• log_F_mean = matrix(log(0.1),nrow=Y,ncol=2,byrow=T),

• log_std_log_F = matrix(log(0.1),nrow=Y,ncol=A-4,byrow=T),

• log_std_pe = matrix(log(0.2),nrow=Y-1,ncol=A-1),

• log_std_crl = matrix(log(0.2),nrow=Y,ncol=A-5),

• logit_ar_index_age = rep(0,length(unique(data$isurvey1))),

• logit_ar_logF = c(0, 0, 0),

• logit_ar_crl = c(2.2,-10),

• logit_ar_pe = rep(-10,2),

• logit_ar_logRec = 0,

• log_F_devt=t(matrix(log(0.001),nrow=Y,ncol=A-4,byrow=T)

• log_Nt=t(matrix(log(10000),nrow=Y,ncol=A,byrow=T)),

• h=0

parmsL

list that contains default parameter lower bounds. Default parmL=

• log_R=c(-10,-10),

• m_q=matrix(-30,nrow=length(data$isurvey1), ncol = A-1),

• log_cv_index=rep(log(0.001),length(unique(data$isd))),

• log_std_log_R=-10,

• log_F_mean = matrix(log(0.0001),nrow=Y,ncol=2,byrow=T),

• log_std_log_F =matrix(-Inf,nrow=Y,ncol=A-4,byrow=T),

• log_std_pe = matrix(log(0.001),nrow=Y-1,ncol=A-1),

• log_std_crl = matrix(log(0.001),nrow=Y,ncol=A-5),

• logit_ar_index_age = rep(-5,length(unique(data$isurvey1))),

• logit_ar_logF = rep(-5,3),

• logit_ar_crl = rep(-5,2),

• logit_ar_pe = rep(-5,2),

• logit_ar_logRec = -5

parmsu

list that contains default parameter upper bounds. Default parmU=

• log_R=c(Inf,Inf),

• m_q=matrix(Inf,nrow=length(data$isurvey1), ncol = A-1),

• log_cv_index=rep(log(5),length(unique(data$isd))),

• log_std_log_R=Inf,

• log_F_mean = matrix(Inf,nrow=Y,ncol=2,byrow=T),

• log_std_log_F = matrix(Inf,nrow=Y,ncol=A-4,byrow=T),

• log_std_pe = matrix(10,nrow=Y-1,ncol=A-1),

• log_std_crl = matrix(5,nrow=Y,ncol=A-5),

• logit_ar_index_age = rep(5,length(unique(data$isurvey1))),

• logit_ar_logF = c(5,5,5),

• logit_ar_crl = c(5,5),

• logit_ar_pe = c(10,10),

• logit_ar_logRec = 5

no.logits

if TRUE, fixed all survey logits = 0.73, all F logits = 0.95 and rec logit = 0.32

no.Flogits

if TRUE, fixed all F logits = 0.95

Examples

## Not run: 
params <- make.parm(data,map)

## End(Not run)

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