MakeInput_Fn: Function to generate inputs for TMB based on data that is...

In James-Thorson/length-based-spatial-regression: Package for estimating spatial variation in length distribution at the community level for marine species

Usage

MakeInput_Fn(Options_vec, c_i, s_i, b_i, X_ij)

Arguments

Options_vec
c_i
s_i
b_i
X_ij

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (Options_vec, c_i, s_i, b_i, X_ij) 
{
    Data = list(Options_vec = Options_vec, n_s = max(s_i) + 1, 
        n_b = max(b_i) + 1, c_i = c_i, x_ij = X_ij, s_i = s_i, 
        b_i = b_i)
    Data[["spde"]] = list(n_s = MeshList$spde$n.spde, n_tri = nrow(MeshList$mesh$graph$tv), 
        Tri_Area = MeshList$Tri_Area, E0 = MeshList$E0, E1 = MeshList$E1, 
        E2 = MeshList$E2, TV = MeshList$TV - 1, G0 = MeshList$spde$param.inla$M0, 
        G0_inv = inla.as.dgTMatrix(solve(MeshList$spde$param.inla$M0)))
    Params = list(ln_H_input = rep(0, 2), gamma_j = rep(0, ncol(Data$x_ij)), 
        logeta_vec = rep(0, 3), rho_vec = rep(0, 2), logkappa_vec = rep(0, 
            2), theta_vec = rep(0, 3), Nuinput_b = rnorm(Data$n_b), 
        Omegainput_sb = matrix(rnorm(Data$n_b * Data$spde$n_s), 
            nrow = Data$spde$n_s, ncol = Data$n_b), Deltainput_s = rnorm(Data$spde$n_s))
    Random = c("Nuinput_b", "Omegainput_sb", "Deltainput_s")
    Map = NULL
    Map[["theta_vec"]] = factor(c(1, NA, 2))
    InputList = list(Data = Data, Params = Params, Random = Random, 
        Map = Map)
    return(InputList)
  }

James-Thorson/length-based-spatial-regression documentation built on May 7, 2019, 10:19 a.m.