update model examples wrt new stan syntax

Author: Yi Zhang

example-models/FK_coupled/FribergKarlsson.stan

@@ -1,5 +1,5 @@
 functions{
-  vector FK_ODE(real t, vector y, vector y_pk, real[] theta, real[] rdummy, int[] idummy){
+  vector FK_ODE(real t, vector y, vector y_pk, array[] real theta, array[] real rdummy, array[] int idummy){
     /* PK variables */
     real VC = theta[3];
 
@@ -33,16 +33,16 @@ data{
   int<lower = 1> nt;
   int<lower = 1> nObsPK;
   int<lower = 1> nObsPD;
-  int<lower = 1> iObsPK[nObsPK];
-  int<lower = 1> iObsPD[nObsPD];
-  real<lower = 0> amt[nt];
-  int<lower = 1> cmt[nt];
-  int<lower = 0> evid[nt];
-  real<lower = 0> time[nt];
-  real<lower = 0> ii[nt];
-  int<lower = 0> addl[nt];
-  int<lower = 0> ss[nt];
-  real rate[nt];
+  array[nObsPK] int<lower = 1> iObsPK;
+  array[nObsPD] int<lower = 1> iObsPD;
+  array[nt] real<lower = 0> amt;
+  array[nt] int<lower = 1> cmt;
+  array[nt] int<lower = 0> evid;
+  array[nt] real<lower = 0> time;
+  array[nt] real<lower = 0> ii;
+  array[nt] int<lower = 0> addl;
+  array[nt] int<lower = 0> ss;
+  array[nt] real rate;
   vector<lower = 0>[nObsPK] cObs;
   vector<lower = 0>[nObsPD] neutObs;
 
@@ -97,10 +97,10 @@ transformed parameters{
   vector<lower = 0>[nObsPK] cHatObs;
   row_vector[nt] neutHat;
   vector<lower = 0>[nObsPD] neutHatObs;
-  real<lower = 0> theta[nTheta];
+  array[nTheta] real<lower = 0> theta;
   matrix[nOde + 3, nt] x;
-  real biovar[nTheta] = rep_array(1.0, nTheta);
-  real tlag[nTheta] = rep_array(0.0, nTheta);
+  array[nTheta] real biovar = rep_array(1.0, nTheta);
+  array[nTheta] real tlag = rep_array(0.0, nTheta);
 
   theta[1] = CL;
   theta[2] = Q;

example-models/FribergKarlsson/FribergKarlsson.stan

@@ -1,5 +1,6 @@
 functions{
-    vector twoCptNeutModelODE(real t, vector x, real[] parms, real[] rdummy, int[] idummy){
+    vector twoCptNeutModelODE(real t, vector x, array[] real parms,
+                              array[] real rdummy, array[] int idummy){
     real k10;
     real k12;
     real k21;
@@ -64,24 +65,24 @@ data{
   int<lower = 1> nt;
   int<lower = 1> nObsPK;
   int<lower = 1> nObsPD;
-  int<lower = 1> iObsPK[nObsPK];
-  int<lower = 1> iObsPD[nObsPD];
-  real<lower = 0> amt[nt];
-  int<lower = 1> cmt[nt];
-  int<lower = 0> evid[nt];
-  real<lower = 0> time[nt];
-  real<lower = 0> ii[nt];
-  int<lower = 0> addl[nt];
-  int<lower = 0> ss[nt];
-  real rate[nt];
+  array[nObsPK] int<lower = 1> iObsPK;
+  array[nObsPD] int<lower = 1> iObsPD;
+  array[nt] real<lower = 0> amt;
+  array[nt] int<lower = 1> cmt;
+  array[nt] int<lower = 0> evid;
+  array[nt] real<lower = 0> time;
+  array[nt] real<lower = 0> ii;
+  array[nt] int<lower = 0> addl;
+  array[nt] int<lower = 0> ss;
+  array[nt] real rate;
   vector<lower = 0>[nObsPK] cObs;
   vector<lower = 0>[nObsPD] neutObs;
 
   // data for population model
   int<lower = 1> nSubjects;
-  int<lower = 1> start[nSubjects];
-  int<lower = 1> end[nSubjects];
-  real<lower = 0> weight[nSubjects];
+  array[nSubjects] int<lower = 1> start;
+  array[nSubjects] int<lower = 1> end;
+  array[nSubjects] real<lower = 0> weight;
 
   real<lower = 0> circ0HatPrior;
   real<lower = 0> circ0HatPriorCV;
@@ -102,7 +103,7 @@ transformed data{
   int nTheta;
   int nIIV;
 
-  int len[nSubjects];
+  array[nSubjects] int len;
 
   logCObs = log(cObs);
   logNeutObs = log(neutObs);
@@ -143,7 +144,7 @@ transformed parameters{
   row_vector[nt] neutHat;
   vector[nObsPD] neutHatObs;
   matrix[8, nt] x;
-  real<lower = 0> parms[nSubjects, nTheta]; // The [1] indicates the parameters are constant
+  array[nSubjects, nTheta] real<lower = 0> parms; // The [1] indicates the parameters are constant
 
   // variables for Matt's trick
   vector<lower = 0>[nIIV] thetaHat;
@@ -214,7 +215,7 @@ model{
 
 generated quantities {
   matrix[8, nt] xPred;
-  real<lower = 0> parmsPred[nSubjects, nTheta]; // [1] indicates the parameters are constant
+  array[nSubjects, nTheta] real<lower = 0> parmsPred; // [1] indicates the parameters are constant
   row_vector[nt] cHatPred;
   row_vector[nt] neutHatPred;
   vector<lower = 0>[nObsPK] cHatObsCond;

example-models/chemical_reactions/chem.stan

@@ -1,6 +1,7 @@
 functions{
-  real[] reaction(real t, real[] x, real[] p, real[] r, int[] i){
-    real dxdt[3];
+  vector reaction(real t, vector x, array[] real p, array[] real r,
+                  array[] int i){
+    vector[3] dxdt;
     real p1 = p[1];
     real p2 = p[2];
     real p3 = p[3];
@@ -13,19 +14,19 @@ functions{
 
 data {
   int<lower=1> nsub;
-  int<lower=1> len[nsub];  
+  array[nsub] int<lower=1> len;  
   int<lower=1> ntot;  
-  real ts[ntot];
-  real obs[ntot];
+  array[ntot] real ts;
+  array[ntot] real obs;
 }
 
 transformed data {
-  int i1[nsub];
-  int i2[nsub];
+  array[nsub] int i1;
+  array[nsub] int i2;
   real t0 = 0.0;
-  real xr[0];
-  int xi[0];
-  real theta[3] = {0.04, 1.0e4, 3.0e7};
+  array[0] real xr;
+  array[0] int xi;
+  array[3] real theta = {0.04, 1.0e4, 3.0e7};
   i1[1] = 1;
   i2[1] = len[1];
   for (i in 2:nsub) {
@@ -37,19 +38,19 @@ transformed data {
 parameters {
   /*  p1=0.04, p2=1e4, and p3=3e7 */
   real<lower = 0> y0_mu;
-  real<lower = 0> y0_1[nsub];
+  array[nsub] real<lower = 0> y0_1;
   real<lower = 0> sigma;
 }
 
 transformed parameters {
-  real y0[3];
-  real x[ntot, 3];
-  real x3[ntot];
+  vector[3] y0;
+  array[ntot] vector[3] x;
+  array[ntot] real x3;
   for (i in 1:nsub) {
     y0[1] = y0_1[i];
     y0[2] = 0.0;
     y0[3] = 0.0;
-    x[i1[i]:i2[i], ] = pmx_integrate_ode_bdf(reaction, y0, t0, ts[i1[i]:i2[i]], theta, xr, xi, 1.e-4, 1.e-8, 10000);
+    x[i1[i]:i2[i], ] = pmx_ode_bdf_ctrl(reaction, y0, t0, ts[i1[i]:i2[i]], 1.e-4, 1.e-8, 10000, theta, xr, xi);
   }
   x3 = x[ , 3];
 }

example-models/chemical_reactions/chem_group.stan

@@ -1,6 +1,7 @@
 functions{
-  real[] reaction(real t, real[] x, real[] p, real[] r, int[] i){
-    real dxdt[3];
+  array[] real reaction(real t, array[] real x, array[] real p, array[] real r,
+                  array[] int i){
+    array[3] real dxdt;
     real p1 = p[1];
     real p2 = p[2];
     real p3 = p[3];
@@ -13,19 +14,19 @@ functions{
 
 data {
   int<lower=1> nsub;
-  int<lower=1> len[nsub];  
+  array[nsub] int<lower=1> len;  
   int<lower=1> ntot;  
-  real ts[ntot];
-  real obs[ntot];
+  array[ntot] real ts;
+  array[ntot] real obs;
 }
 
 transformed data {
-  int i1[nsub];
-  int i2[nsub];
+  array[nsub] int i1;
+  array[nsub] int i2;
   real t0 = 0.0;
-  real xr[0];
-  int xi[0];
-  real theta[3] = {0.04, 1.0e4, 3.0e7};
+  array[0] real xr;
+  array[0] int xi;
+  array[3] real theta = {0.04, 1.0e4, 3.0e7};
   i1[1] = 1;
   i2[1] = len[1];
   for (i in 2:nsub) {
@@ -37,12 +38,12 @@ transformed data {
 parameters {
   /*  p1=0.04, p2=1e4, and p3=3e7 */
   real<lower = 0> y0_mu;
-  real<lower = 0> y0_1[nsub];
+  array[nsub] real<lower = 0> y0_1;
   real<lower = 0> sigma;
 }
 
 transformed parameters {
-  real y0_pop[nsub, 3];
+  array[nsub, 3] real y0_pop;
   matrix[3, ntot] x;
   row_vector[ntot] x3;
   for (i in 1:nsub) {

example-models/chemical_reactions_with_stiffness_diff/chem_group.stan

@@ -1,6 +1,7 @@
 functions{
-  real[] reaction(real t, real[] x, real[] p, real[] r, int[] i){
-    real dxdt[3];
+  array[] real reaction(real t, array[] real x, array[] real p, array[] real r,
+                  array[] int i){
+    array[3] real dxdt;
     real p1 = p[1];
     real p2 = p[2];
     real p3 = p[3];
@@ -15,21 +16,21 @@ data {
   int<lower=1> nsub;
   int<lower=1> nsub1;
   int<lower=1> nsub2;
-  int<lower=1> len[nsub];  
+  array[nsub] int<lower=1> len;  
   int<lower=1> ntot;  
-  real ts[ntot];
-  real obs[ntot];
+  array[ntot] real ts;
+  array[ntot] real obs;
 }
 
 transformed data {
-  int i1[nsub];
-  int i2[nsub];
+  array[nsub] int i1;
+  array[nsub] int i2;
   real t0 = 0.0;
-  real xr[0];
-  int xi[0];
-  real theta1[3] = {0.04, 1.0e4, 3.0e7};
-  real theta2[3] = {0.04, 0.1, 0.1};
-  real theta[nsub, 3];
+  array[0] real xr;
+  array[0] int xi;
+  array[3] real theta1 = {0.04, 1.0e4, 3.0e7};
+  array[3] real theta2 = {0.04, 0.1, 0.1};
+  array[nsub, 3] real theta;
   i1[1] = 1;
   i2[1] = len[1];
   for (i in 2:nsub) {
@@ -46,12 +47,12 @@ transformed data {
 
 parameters {
   real<lower = 0> y0_mu;
-  real<lower = 0> y0_1[nsub];
+  array[nsub] real<lower = 0> y0_1;
   real<lower = 0> sigma;
 }
 
 transformed parameters {
-  real y0_pop[nsub, 3];
+  array[nsub, 3] real y0_pop;
   matrix[3, ntot] x;
   row_vector[ntot] x3;
   for (i in 1:nsub) {