R/internal.R

In tinyVAST: Multivariate Spatio-Temporal Models using Structural Equations

.onAttach <- function(libname, pkgname) {
}

ivector_minus_one <- function( ivector ){
  if( any(is.na(ivector)) ) stop("Check ivector for NAs")
  if( length(ivector) > 0 ){
    ivector = as.integer( ivector - 1 )
  }
  return(ivector)
}

# Modified from sdmTMB::make_anisotropy_spde
make_anisotropy_spde <-
function( inla_mesh ){

  spde = fm_fem( inla_mesh )
  Dset <- 1:2
  TV <- inla_mesh$graph$tv
  V0 <- inla_mesh$loc[TV[, 1], Dset]
  V1 <- inla_mesh$loc[TV[, 2], Dset]
  V2 <- inla_mesh$loc[TV[, 3], Dset]
  E0 <- V2 - V1
  E1 <- V0 - V2
  E2 <- V1 - V0
  TmpFn <- function(Vec1, Vec2) abs(det(rbind(Vec1, Vec2)))
  Tri_Area <- rep(NA, nrow(E0))
  for (i in seq_len(length(Tri_Area))){
    Tri_Area[i] <- TmpFn(E0[i,], E1[i,])/2
  }
  ret <- list( n_s = inla_mesh$n,
               n_tri = nrow(TV),
               Tri_Area = Tri_Area,
               E0 = E0,
               E1 = E1,
               E2 = E2,
               TV = TV - 1,
               G0 = spde$c0,
               G0_inv = as(Matrix::diag(1/Matrix::diag(spde$c0)),"TsparseMatrix") )
  return(ret)
}


#rm_wsp <- function (x) {
#  # from brms:::rm_wsp()
#  # VIA sdmTMB smoothers.R
#  out <- gsub("[ \t\r\n]+", "", x, perl = TRUE)
#  dim(out) <- dim(x)
#  out
#}

#all_terms <- function (x) {
#  # from brms:::all_terms()
#  # VIA sdmTMB smoothers.R
#  if (!length(x)) {
#    return(character(0))
#  }
#  if (!inherits(x, "terms")) {
#    x <- terms(stats::as.formula(x))
#  }
#  rm_wsp(attr(x, "term.labels"))
#}

#get_smooth_terms <- function(terms) {
#  # from brms:::all_terms()
#  # VIA sdmTMB smoothers.R
#  x1 <- grep("s\\(", terms)
#  x2 <- grep("t2\\(", terms)
#  c(x1, x2)
#}