Param_Fn: Calculate parameter inputs for TMB

In nwfsc-assess/geostatistical_delta-GLMM: Package for conducting spatial estimation of CPUE index standardization (fisheries, ecology, etc)

Calculate parameter inputs for TMB

Description

Param_Fn generates the parameters input for TMB::MakeADFun

Usage

Param_Fn(Version, DataList, RhoConfig = c(Beta1 = 0, Beta2 = 0, Epsilon1 = 0,
  Epsilon2 = 0))

Arguments

Version	a version number (see example for current default).
DataList	list outputted from SpatialDeltaGLMM::Data_Fn
RhoConfig	OPTIONAL, vector of form c("Beta1"=0,"Beta2"=0,"Epsilon1"=0,"Epsilon2"=0) specifying whether either intercepts (Beta1 and Beta2) or spatio-temporal variation (Epsilon1 and Epsilon2) is structured among time intervals

Value

Tagged list containing starting values for all fixed effects (parameters) and random effects (coefficients)

ln_H_input

two parameters governing geometric anisotropy (rotation matrix H)

hyperparameters_z

parameters for estimating relationships among derived quantities (generally turned off)

beta1_t

intercepts for encounter probability

gamma1_j

effect of density covariates that are static over time on encounter prob

gamma1_tp

effect of density covariates that change over time on encounter prob

lambda1_k

effect of catchability covariates on encounter prob

logetaE1

reciprocal of pointwise variance in spatio-temporal variation in encounter prob

logetaO1

reciprocal of pointwise variance in spatial variation in encounter prob

logkappa1

governs decorrelation distance in encounter prob

logsigmaV1

log-SD of vessel effects that are static over time on encounter prob

logsigmaVT1

log-SD of vessel effects that vary over time on encounter prob

Beta_mean1

average intercept of encounter prob (used with RhoConfig options)

logsigmaB1

SD for intercept of encounter prob (used with RhoConfig options)

Beta_rho1

first-order autoregressive coefficient for intercept of encounter prob (used with RhoConfig options)

Epsilon_rho1

first-order autoregressive coefficient for spatio-temporal variation of encounter prob (used with RhoConfig options)

nu1_v

vessel effects that are static over time on encounter prob

nu1_vt

vessel effects that are static over time on encounter prob

Omegainput1_s

Spatial variation in encounter prob

Epsiloninput1_st

Spatio-temporal variation in encounter prob

beta2_t

intercepts for positive catch-rate

gamma2_j

effect of density covariates that are static over time on positive catch-rate

gamma2_tp

effect of density covariates that change over time on positive catch-rate

lambda2_k

effect of catchability covariates on positive catch-rate

logetaE2

reciprocal of pointwise variance in spatio-temporal variation in positive catch-rate

logetaO2

reciprocal of pointwise variance in spatial variation in positive catch-rate

logkappa2

governs decorrelation distance in positive catch-rate

logsigmaV2

log-SD of vessel effects that are static over time on positive catch-rate

logsigmaVT2

log-SD of vessel effects that vary over time on positive catch-rate

Beta_mean2

average intercept of positive catch-rate (used with RhoConfig options)

logsigmaB2

SD for intercept of positive catch-rate (used with RhoConfig options)

Beta_rho2

first-order autoregressive coefficient for intercept of positive catch-rate (used with RhoConfig options)

Epsilon_rho2

first-order autoregressive coefficient for spatio-temporal variation of positive catch-rate (used with RhoConfig options)

nu2_v

vessel effects that are static over time on positive catch-rate

nu2_vt

vessel effects that are static over time on positive catch-rate

Omegainput2_s

Spatial variation in positive catch-rate

Epsiloninput2_st

Spatio-temporal variation in positive catch-rate

logSigmaM

variance parameters for positive catch ratesA

nwfsc-assess/geostatistical_delta-GLMM documentation built on July 8, 2023, 4:49 a.m.