From a251538e64830bea791126fc5d6ca480e4299ca4 Mon Sep 17 00:00:00 2001 From: Andrew Johnson Date: Sun, 10 Sep 2023 20:49:54 +0200 Subject: Update deprecated syntax --- DESCRIPTION | 6 ++--- inst/stan/colext.stan | 32 ++++++++++++------------ inst/stan/include/data.stan | 36 +++++++++++++-------------- inst/stan/include/functions_distsamp.stan | 4 +-- inst/stan/include/functions_keyfuns.stan | 14 +++++------ inst/stan/include/functions_multinomPois.stan | 6 ++--- inst/stan/include/functions_occu.stan | 6 ++--- inst/stan/include/functions_occuRN.stan | 6 ++--- inst/stan/include/functions_occuTTD.stan | 10 ++++---- inst/stan/include/functions_pcount.stan | 6 ++--- inst/stan/include/functions_priors.stan | 4 +-- inst/stan/spatial.stan | 6 ++--- 12 files changed, 68 insertions(+), 68 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index c402cef..a70b815 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -18,7 +18,7 @@ Imports: Rcpp (>= 0.12.0), rlang, RSpectra, - rstan (>= 2.18.1), + rstan (>= 2.26.0), rstantools (>= 2.0.0), stats Suggests: covr, devtools, knitr, pkgdown, raster, rmarkdown, roxygen2, testthat @@ -42,8 +42,8 @@ LinkingTo: Rcpp (>= 0.12.0), RcppArmadillo (>= 0.9.300.2.0), RcppEigen (>= 0.3.3.3.0), - rstan (>= 2.18.1), - StanHeaders (>= 2.18.0), + rstan (>= 2.26.0), + StanHeaders (>= 2.26.0), RcppParallel (>= 5.0.2) SystemRequirements: GNU make Collate: diff --git a/inst/stan/colext.stan b/inst/stan/colext.stan index 8d599da..32d3381 100644 --- a/inst/stan/colext.stan +++ b/inst/stan/colext.stan @@ -3,7 +3,7 @@ functions{ #include /include/functions_priors.stan //can shortcut here I think -vector get_pY(int[] y, vector logit_p, int nd){ +vector get_pY(array[] int y, vector logit_p, int nd){ vector[2] out; out[1] = nd; out[2] = exp(bernoulli_logit_lpmf(y | logit_p)); @@ -29,8 +29,8 @@ matrix get_phi(matrix phi_raw, int Tstart, int Tnext){ } //Ts = indices of primary periods when site was sampled (eg not all NA) -real lp_colext(int[] y, int[] Tsamp, int[] J, row_vector psi, matrix phi_raw, - vector logit_p, int[] nd){ +real lp_colext(array[] int y, array[] int Tsamp, array[] int J, row_vector psi, matrix phi_raw, + vector logit_p, array[] int nd){ int T = size(Tsamp); matrix[2,2] phi_prod = diag_matrix(rep_vector(1, 2)); @@ -56,9 +56,9 @@ real lp_colext(int[] y, int[] Tsamp, int[] J, row_vector psi, matrix phi_raw, } //needs fixed -vector get_loglik_colext(int[] y, int M, int[] Tsamp, int[,] J, int[,] si, +vector get_loglik_colext(array[] int y, int M, array[] int Tsamp, array[,] int J, array[,] int si, matrix psi_raw, matrix phi_raw, vector logit_p, - int[,] nd){ + array[,] int nd){ vector[M] out; for (i in 1:M){ out[i] = lp_colext(y[si[i,1]:si[i,2]], Tsamp[si[i,3]:si[i,4]], J[i,], @@ -82,32 +82,32 @@ int n_fixed_col; int n_fixed_ext; int n_group_vars_col; int n_group_vars_ext; -int n_random_col[has_random_col ? n_group_vars_col : 1]; -int n_random_ext[has_random_ext ? n_group_vars_ext: 1]; +array[has_random_col ? n_group_vars_col : 1] int n_random_col; +array[has_random_ext ? n_group_vars_ext: 1] int n_random_ext; matrix[M*(T-1), n_fixed_col] X_col; matrix[M*(T-1), n_fixed_ext] X_ext; vector[M*(T-1)] offset_col; vector[M*(T-1)] offset_ext; -int Zdim_col[5]; +array[5] int Zdim_col; vector[Zdim_col[3]] Zw_col; -int Zv_col[Zdim_col[4]]; -int Zu_col[Zdim_col[5]]; +array[Zdim_col[4]] int Zv_col; +array[Zdim_col[5]] int Zu_col; -int Zdim_ext[5]; +array[5] int Zdim_ext; vector[Zdim_ext[3]] Zw_ext; -int Zv_ext[Zdim_ext[4]]; -int Zu_ext[Zdim_ext[5]]; +array[Zdim_ext[4]] int Zv_ext; +array[Zdim_ext[5]] int Zu_ext; -int prior_dist_col[3]; -int prior_dist_ext[3]; +array[3] int prior_dist_col; +array[3] int prior_dist_ext; matrix[3, (n_fixed_col+1)] prior_pars_col; matrix[3, (n_fixed_ext+1)] prior_pars_ext; } transformed data{ -int no_detects[M, T]; +array[M, T] int no_detects; int include_scale; int include_shape; diff --git a/inst/stan/include/data.stan b/inst/stan/include/data.stan index bf44ea9..bd5db0c 100644 --- a/inst/stan/include/data.stan +++ b/inst/stan/include/data.stan @@ -3,19 +3,19 @@ int model_code; int M; int T; int Tsamp_size; -int Tsamp[Tsamp_size]; +array[Tsamp_size] int Tsamp; int R; -int J[M,T]; -int y[R]; -int si[M, 6]; +array[M,T] int J; +array[R] int y; +array[M, 6] int si; int K; -int Kmin[M,T]; +array[M,T] int Kmin; int y_dist; int z_dist; int n_aux1; int n_aux2; int n_aux3; -int aux1[n_aux1]; //Used for various auxiliary data +array[n_aux1] int aux1; //Used for various auxiliary data vector[n_aux2] aux2; vector[n_aux3] aux3; @@ -27,28 +27,28 @@ int n_fixed_state; int n_fixed_det; int n_group_vars_state; int n_group_vars_det; -int n_random_state[has_random_state ? n_group_vars_state : 1]; -int n_random_det[has_random_det ? n_group_vars_det: 1]; +array[has_random_state ? n_group_vars_state : 1] int n_random_state; +array[has_random_det ? n_group_vars_det: 1] int n_random_det; matrix[n_obs_state, n_fixed_state] X_state; matrix[n_obs_det, n_fixed_det] X_det; vector[n_obs_state] offset_state; vector[n_obs_det] offset_det; -int Zdim_state[5]; +array[5] int Zdim_state; vector[Zdim_state[3]] Zw_state; -int Zv_state[Zdim_state[4]]; -int Zu_state[Zdim_state[5]]; +array[Zdim_state[4]] int Zv_state; +array[Zdim_state[5]] int Zu_state; -int Zdim_det[5]; +array[5] int Zdim_det; vector[Zdim_det[3]] Zw_det; -int Zv_det[Zdim_det[4]]; -int Zu_det[Zdim_det[5]]; +array[Zdim_det[4]] int Zv_det; +array[Zdim_det[5]] int Zu_det; // Stuff for custom priors -int prior_dist_state[3]; -int prior_dist_det[3]; -int prior_dist_shape[3]; -int prior_dist_scale[3]; +array[3] int prior_dist_state; +array[3] int prior_dist_det; +array[3] int prior_dist_shape; +array[3] int prior_dist_scale; matrix[3, (n_fixed_state+1)] prior_pars_state; matrix[3, (n_fixed_det+1)] prior_pars_det; diff --git a/inst/stan/include/functions_distsamp.stan b/inst/stan/include/functions_distsamp.stan index 22e50d1..a8840d2 100644 --- a/inst/stan/include/functions_distsamp.stan +++ b/inst/stan/include/functions_distsamp.stan @@ -1,4 +1,4 @@ -real lp_distsamp(int[] y, vector db, real log_lambda, real par1, real par2, +real lp_distsamp(array[] int y, vector db, real log_lambda, real par1, real par2, int point, int keyfun, vector conv_const){ real lam = exp(log_lambda); @@ -13,7 +13,7 @@ real lp_distsamp(int[] y, vector db, real log_lambda, real par1, real par2, return loglik; } -vector get_loglik_distsamp(int[] y, int M, vector db, int[,] si, +vector get_loglik_distsamp(array[] int y, int M, vector db, array[,] int si, vector log_lambda, vector trans_par1, int z_dist, real trans_par2, int point, int keyfun, vector conv_const){ diff --git a/inst/stan/include/functions_keyfuns.stan b/inst/stan/include/functions_keyfuns.stan index 12d9b32..1e5b9ef 100644 --- a/inst/stan/include/functions_keyfuns.stan +++ b/inst/stan/include/functions_keyfuns.stan @@ -39,23 +39,23 @@ real int_negexp(real log_rate, real a, real b, int point){ return out; } -//real p_hazard_line(real x, real xc, real[] theta, real[] x_r, int[] x_i){ +//real p_hazard_line(real x, real xc, array[] real theta, array[] real x_r, array[] int x_i){ // return(1 - exp(-1 * pow((x/theta[1]), (-1*theta[2])))); //} -real p_hazard_line(real x, real[] theta){ +real p_hazard_line(real x, array[] real theta){ return(1 - exp(-1 * pow((x/theta[1]), (-1*theta[2])))); } -//real p_hazard_point(real x, real xc, real[] theta, real[] x_r, int[] x_i){ +//real p_hazard_point(real x, real xc, array[] real theta, array[] real x_r, array[] int x_i){ // return((1 - exp(-1 * pow(x/theta[1], -1*theta[2]))) * x); //} -real p_hazard_point(real x, real[] theta){ +real p_hazard_point(real x, array[] real theta){ return((1 - exp(-1 * pow(x/theta[1], -1*theta[2]))) * x); } -real trap_rule_line(real[] theta, real a, real b){ +real trap_rule_line(array[] real theta, real a, real b){ int n = 100; real h = (b - a) / n; @@ -66,7 +66,7 @@ real trap_rule_line(real[] theta, real a, real b){ return h/2 * (p_hazard_line(a, theta) + 2*int_sum + p_hazard_line(b, theta)); } -real trap_rule_point(real[] theta, real a, real b){ +real trap_rule_point(array[] real theta, real a, real b){ int n = 100; real h = (b - a) / n; @@ -83,7 +83,7 @@ real int_hazard(real log_shape, real log_scale, real a, real b, int point){ real out; real shape = exp(log_shape); real scale = exp(log_scale); - real theta[2]; + array[2] real theta; theta[1] = shape; theta[2] = scale; diff --git a/inst/stan/include/functions_multinomPois.stan b/inst/stan/include/functions_multinomPois.stan index 47a8474..c43f71e 100644 --- a/inst/stan/include/functions_multinomPois.stan +++ b/inst/stan/include/functions_multinomPois.stan @@ -32,7 +32,7 @@ vector pi_fun(int pi_type, vector p, int J){ return out; } -real lp_multinomPois(int[] y, real log_lambda, vector logit_p, int pi_type){ +real lp_multinomPois(array[] int y, real log_lambda, vector logit_p, int pi_type){ real loglik = 0.0; real lam = exp(log_lambda); @@ -52,11 +52,11 @@ real lp_multinomPois(int[] y, real log_lambda, vector logit_p, int pi_type){ return loglik; } -vector get_loglik_multinomPois(int[] y, int M, int[,] si, vector log_lambda, +vector get_loglik_multinomPois(array[] int y, int M, array[,] int si, vector log_lambda, vector logit_p, int pi_type){ vector[M] out; - int J = num_elements(logit_p) / M; // use %/% in future version of stan + int J = num_elements(logit_p) %/% M; // use %/% in future version of stan int pstart = 1; int pend; for (i in 1:M){ diff --git a/inst/stan/include/functions_occu.stan b/inst/stan/include/functions_occu.stan index 99ddde3..0b6d153 100644 --- a/inst/stan/include/functions_occu.stan +++ b/inst/stan/include/functions_occu.stan @@ -1,4 +1,4 @@ -real lp_occu(int[] y, real logit_psi, vector logit_p, int Kmin){ +real lp_occu(array[] int y, real logit_psi, vector logit_p, int Kmin){ real out; out = log_inv_logit(logit_psi) + bernoulli_logit_lpmf(y | logit_p); if(Kmin == 1){ @@ -7,8 +7,8 @@ real lp_occu(int[] y, real logit_psi, vector logit_p, int Kmin){ return log_sum_exp(out, log1m_inv_logit(logit_psi)); } -vector get_loglik_occu(int[] y, int M, int[,] J, int[,] si, vector logit_psi, - vector logit_p, int[] Kmin){ +vector get_loglik_occu(array[] int y, int M, array[,] int J, array[,] int si, vector logit_psi, + vector logit_p, array[] int Kmin){ vector[M] out; for (i in 1:M){ out[i] = lp_occu(y[si[i,1]:si[i,2]], logit_psi[i], diff --git a/inst/stan/include/functions_occuRN.stan b/inst/stan/include/functions_occuRN.stan index 05a1253..ddb5270 100644 --- a/inst/stan/include/functions_occuRN.stan +++ b/inst/stan/include/functions_occuRN.stan @@ -1,4 +1,4 @@ -real lp_rn(int[] y, real log_lambda, vector logit_r, int J, int K, int Kmin){ +real lp_rn(array[] int y, real log_lambda, vector logit_r, int J, int K, int Kmin){ int numN = K - Kmin + 1; vector[J] q = 1 - inv_logit(logit_r); @@ -15,8 +15,8 @@ real lp_rn(int[] y, real log_lambda, vector logit_r, int J, int K, int Kmin){ return log_sum_exp(lp); } -vector get_loglik_rn(int[] y, int M, int[,] J, int[,] si, vector log_lambda, - vector logit_p, int K, int[] Kmin){ +vector get_loglik_rn(array[] int y, int M, array[,] int J, array[,] int si, vector log_lambda, + vector logit_p, int K, array[] int Kmin){ vector[M] out; for (i in 1:M){ out[i] = lp_rn(y[si[i,1]:si[i,2]], log_lambda[i], logit_p[si[i,1]:si[i,2]], diff --git a/inst/stan/include/functions_occuTTD.stan b/inst/stan/include/functions_occuTTD.stan index a2404ff..97cb8f2 100644 --- a/inst/stan/include/functions_occuTTD.stan +++ b/inst/stan/include/functions_occuTTD.stan @@ -1,4 +1,4 @@ -vector ttd_prob_exp(vector y, vector log_lam, int[] delta){ +vector ttd_prob_exp(vector y, vector log_lam, array[] int delta){ int J = num_elements(y); vector[J] e_lamt; real lam; @@ -9,7 +9,7 @@ vector ttd_prob_exp(vector y, vector log_lam, int[] delta){ return e_lamt; } -vector ttd_prob_weib(vector y, vector log_lam, int[] delta, real log_k){ +vector ttd_prob_weib(vector y, vector log_lam, array[] int delta, real log_k){ int J = num_elements(y); vector[J] e_lamt; real k = exp(log_k); @@ -23,7 +23,7 @@ vector ttd_prob_weib(vector y, vector log_lam, int[] delta, real log_k){ } real lp_occuTTD(vector y, real logit_psi, vector log_lam, - real log_k, int[] delta, int ydist){ + real log_k, array[] int delta, int ydist){ int J = num_elements(y); vector[J] e_lamt; @@ -40,8 +40,8 @@ real lp_occuTTD(vector y, real logit_psi, vector log_lam, return log(lik); } -vector get_loglik_occuTTD(vector y, int M, int[,] si, vector logit_psi, - vector log_lam, real log_k, int[] delta, int ydist){ +vector get_loglik_occuTTD(vector y, int M, array[,] int si, vector logit_psi, + vector log_lam, real log_k, array[] int delta, int ydist){ vector[M] out; for (i in 1:M){ out[i] = lp_occuTTD(y[si[i,1]:si[i,2]], logit_psi[i], log_lam[si[i,1]:si[i,2]], diff --git a/inst/stan/include/functions_pcount.stan b/inst/stan/include/functions_pcount.stan index 76111ce..71c0325 100644 --- a/inst/stan/include/functions_pcount.stan +++ b/inst/stan/include/functions_pcount.stan @@ -1,4 +1,4 @@ -real lp_pcount_pois(int[] y, real log_lambda, vector logit_p, int K, int Kmin){ +real lp_pcount_pois(array[] int y, real log_lambda, vector logit_p, int K, int Kmin){ real fac = 1; real ff = exp(log_lambda) * prod(1 - inv_logit(logit_p)); @@ -18,8 +18,8 @@ real lp_pcount_pois(int[] y, real log_lambda, vector logit_p, int K, int Kmin){ log(fac); } -vector get_loglik_pcount(int[] y, int M, int[,] J, int[,] si, vector log_lambda, - vector logit_p, int z_dist, real beta_scale, int K, int[] Kmin){ +vector get_loglik_pcount(array[] int y, int M, array[,] int J, array[,] int si, vector log_lambda, + vector logit_p, int z_dist, real beta_scale, int K, array[] int Kmin){ vector[M] out; for (i in 1:M){ out[i] = lp_pcount_pois(y[si[i,1]:si[i,2]], log_lambda[i], diff --git a/inst/stan/include/functions_priors.stan b/inst/stan/include/functions_priors.stan index c910b49..8ac1496 100644 --- a/inst/stan/include/functions_priors.stan +++ b/inst/stan/include/functions_priors.stan @@ -18,7 +18,7 @@ real lp_single_prior(vector x, int dist, row_vector pars1, } -real lp_priors(vector beta, int[] dist, matrix pars){ +real lp_priors(vector beta, array[] int dist, matrix pars){ int idx; real out = 0.0; @@ -42,7 +42,7 @@ real lp_priors(vector beta, int[] dist, matrix pars){ } real lp_random_prior(int has_random, int n_group_vars, vector b, - int[] n_random, vector sigma, int dist, matrix pars){ + array[] int n_random, vector sigma, int dist, matrix pars){ int idx = 1; real out = 0; int par_idx = cols(pars); diff --git a/inst/stan/spatial.stan b/inst/stan/spatial.stan index 4a6f9ea..0f141a9 100644 --- a/inst/stan/spatial.stan +++ b/inst/stan/spatial.stan @@ -16,7 +16,7 @@ real theta_lpdf(vector theta, real tau, matrix Qalpha, int n_eigen){ return 0.5*(n_eigen*log(tau) - tau*quad_form(Qalpha, theta)); } -//real lp_occu_probit(int[] y, real raw_psi, vector raw_p, int Kmin){ +//real lp_occu_probit(array[] int y, real raw_psi, vector raw_p, int Kmin){ // real out; // real psi = Phi(raw_psi); // int J = num_elements(raw_p); @@ -28,8 +28,8 @@ real theta_lpdf(vector theta, real tau, matrix Qalpha, int n_eigen){ // return log(out); //} -//vector get_loglik_occu_probit(int[] y, int M, int[,] J, int[,] si, vector raw_psi, -// vector raw_p, int[] Kmin){ +//vector get_loglik_occu_probit(array[] int y, int M, array[,] int J, array[,] int si, vector raw_psi, +// vector raw_p, array[] int Kmin){ // vector[M] out; // for (i in 1:M){ // out[i] = lp_occu_probit(y[si[i,1]:si[i,2]], raw_psi[i], -- cgit v1.2.3