make_map: Create a tagged list to turn and off and mirror parameters

In James-Thorson/VAST: Vector-Autoregressive Spatio-Temporal (VAST) Model

Create a tagged list to turn and off and mirror parameters

Description

Create map to turn off and mirror parameters

Usage

make_map(
  DataList,
  TmbParams,
  RhoConfig = c(Beta1 = 0, Beta2 = 0, Epsilon1 = 0, Epsilon2 = 0),
  Npool = 0
)

Arguments

DataList	output from make_data
TmbParams	output from make_parameters
RhoConfig	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, e.g. for component Epsilon2 indicated in the 4rd slot: RhoConfig[4]=0 Each year as fixed effect RhoConfig[4]=1 Each year as an independent and identically distributed random effect, thus estimating the variance as fixed effect RhoConfig[4]=2 Each year as a random effect following a random walk, thus estimating the variance as fixed effect RhoConfig[4]=3 Constant among years as fixed effect RhoConfig[4]=4 Each year as a random effect following a first-order autoregressive process, thus estimating the variance as fixed effects and a single first-order autoregression parameter RhoConfig[4]=5 Each year as a random effect following a first-order autoregressive process, estimating the variance as fixed effects and a separate first-order autoregression parameter for each category RhoConfig[4]=6 Only possible for Epsilon2 or Beta2, and specifying that that associated hyperparameters parameters have identical values to the first component Epsilon1 or Beta1 If missing, the default is to assume a value of zero for each element (i.e., RhoConfig[1:4]=0)
Npool	A user-level interface to pool hyperparameters for multiple categories. For categories with few encounters, these hyperparameters are poorly informed leading to converge difficulties. A value Npool=10 indicates that any category with fewer than 10 encounters across all years should have hyperparameters mirrored to the same value.

James-Thorson/VAST documentation built on July 18, 2024, 4:27 a.m.