Skip to content

Update deprecated syntax for future rstan compatibility #2

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
marcogramatica merged 1 commit into from
Jan 7, 2024
Merged

Update deprecated syntax for future rstan compatibility #2

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Binary file modified .DS_Store
View file
Open in desktop
Binary file not shown.
6 changes: 3 additions & 3 deletions DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ Depends:
Imports:
methods,
Rcpp (>= 0.12.0),
rstan (>= 2.18.1),
rstan (>= 2.26.0),
MASS,
expm,
stats,
Expand All @@ -30,8 +30,8 @@ LinkingTo:
BH (>= 1.66.0),
Rcpp (>= 0.12.0),
RcppEigen (>= 0.3.3.3.0),
rstan (>= 2.18.1),
StanHeaders (>= 2.18.0),
rstan (>= 2.26.0),
StanHeaders (>= 2.26.0),
RcppParallel (>= 5.0.1)
SystemRequirements: GNU make
NeedsCompilation: yes
8 changes: 4 additions & 4 deletions inst/stan/CARMM_COV_P.stan
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
functions {
real sparse_car_lpdf(vector phi,
real alpha,
int[,] W_sparse, vector D_sparse, vector lambda, int n, int W_n) {
array[,] int W_sparse, vector D_sparse, vector lambda, int n, int W_n) {
row_vector[n] phit_D; // phi' * D
row_vector[n] phit_W; // phi' * W
vector[n] ldet_terms;
Expand Down Expand Up @@ -45,7 +45,7 @@ data {
matrix[n, k] X_cov; // predictor matrix

// Outcomes
int<lower = 0> y[m];
array[m] int<lower = 0> y;

// Offsets
vector[m] log_offset;
Expand All @@ -62,7 +62,7 @@ transformed data {
// Adjacency
// Number of directed neighbours per area
vector[n] n_i;
int W_sparse[W_n, 2]; // adjacency pairs
array[W_n, 2] int W_sparse; // adjacency pairs
vector[n] D_sparse; // diagonal of D (number of neigbors for each site)
vector[n] lambda; // eigenvalues of invsqrtD * W * invsqrtD

Expand Down Expand Up @@ -119,7 +119,7 @@ model {
y ~ poisson(exp(log_offset + r_mm));
}
generated quantities {
int<lower = 0> yrep[m];
array[m] int<lower = 0> yrep;
vector[m] log_lik;
vector[m] log_lik_rep;
real sum_ll;
Expand Down