update intrinsic implementation and vignette

davidbolin · Dec 19, 2024 · d7a2b75 · d7a2b75
1 parent 74e2e05
commit d7a2b75
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Showing 4 changed files with 215 additions and 159 deletions.
diff --git a/R/intrinsic.R b/R/intrinsic.R
@@ -55,17 +55,15 @@
 #'     col = 2, lty = 2
 #'   )
 #' }
-intrinsic.operators <- function(tau,
-                                alpha,
-                                beta = 1,
+intrinsic.operators <- function(tau = NULL,
+                                beta = NULL,
                                 G = NULL,
                                 C = NULL,
                                 d = NULL,
                                 mesh = NULL,
                                 graph = NULL,
                                 loc_mesh = NULL,
-                                m_alpha = 2,
-                                m_beta = 2,
+                                m = 2,
                                 compute_higher_order = FALSE,
                                 return_block_list = FALSE,
                                 type_rational_approximation = c(
@@ -74,8 +72,12 @@ intrinsic.operators <- function(tau,
                                            ),
                                 fem_mesh_matrices = NULL,
                                 scaling = NULL) {
+
+    if(is.null(tau) || is.null(beta)) {
+        stop("tau and beta must be provided.")
+    }
  return(intrinsic.matern.operators(tau = tau,
-                                  kappa = 0, 
+                                  kappa = 1, 
                                   alpha = 0, 
                                   beta = beta, 
                                   G = G,
@@ -906,8 +908,8 @@ simulate.intrinsicCBrSPDEobj <- function(object, nsim = 1, seed = NULL,
 #' }
 variogram.intrinsic.spde <- function(s0 = NULL,
                                      s = NULL,
-                                     kappa = NULL,
-                                     alpha = NULL,
+                                     kappa = 0,
+                                     alpha = 0,
                                      beta = NULL,
                                      tau = 1,
                                      L = NULL,

diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
@@ -78,8 +78,10 @@ reference:
   - title: Intrinsic models
     contents:
     - intrinsic.matern.operators
+    - intrinsic.operators
     - variogram.intrinsic.spde
     - rspde.matern.intrinsic
+    - rspde.intrinsic
     - simulate.intrinsicCBrSPDEobj
   - title: Log-likelihood
     contents:
@@ -132,7 +134,6 @@ reference:
   - title: Functions and methods for rSPDE interface for inlabru
     contents:
     - cross_validation
-    - group_predict
     - predict.inla_rspde_matern1d
     - bru_get_mapper.inla_rspde
     - bru_get_mapper.inla_rspde_spacetime

diff --git a/src/cgeneric_aux_intrinsic.cpp b/src/cgeneric_aux_intrinsic.cpp
@@ -154,9 +154,10 @@ void compute_Q_fintrinsic( double tau, double nu,
             if(compute_mean){
                 Qidiag_perm = intrinsic_mean(Lq);
                 Qidiag = R.permutationPinv() * Qidiag_perm;
-                for(int i = 0; i < n; i++){
+                for(int i = 0; i < n - 1; i++){
                     mean_out[i] = Qidiag[i];
                 }
+                mean_out[n-1] = 0;
             }
         } else {
             int start;
@@ -174,9 +175,10 @@ void compute_Q_fintrinsic( double tau, double nu,
                 if(compute_mean){
                     Qidiag_perm = intrinsic_mean(Lq);
                     Qidiag = R.permutationPinv() * Qidiag_perm;
-                    for(int i = 0; i < n; i++){
+                    for(int i = 0; i < n - 1; i++){
                         mean_out[start + i] = Qidiag[i];
                     }
+                    mean_out[start + n - 1] = 0;
                 }
             }    
         }