Description Usage Arguments Value

`Param_Fn`

generates the `parameters`

input for `TMB::MakeADFun`

1 2 |

`Version` |
a version number (see example for current default). |

`DataList` |
list outputted from |

`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 |

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

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.