Skip to content

Update deprecated syntax for future rstan compatibility #11

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

Open
andrjohns wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Update deprecated syntax for future rstan compatibility #11

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
f1ed971
Update array syntax
andrjohns Sep 9, 2023
54263a7
Bump rstan ver
andrjohns Sep 10, 2023
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
4 changes: 2 additions & 2 deletions DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,11 +18,11 @@ LazyData: true
ByteCompile: true
Depends: R (>= 3.5.0)
Imports: Rcpp (>= 0.12.17), methods,
rstan (>= 2.18.1), rstantools (>= 1.5.0),
rstan (>= 2.26.0), rstantools (>= 1.5.0),
loo (>= 2.0), forestplot (>= 1.6),
metafor (>= 2.0-0), HDInterval, coda
Suggests: testthat, knitr, rmarkdown, ggplot2, shinystan, vdiffr, bayesmeta, metadat
LinkingTo: StanHeaders (>= 2.18.0), rstan (>= 2.18.1), BH (>= 1.66.0-1),
LinkingTo: StanHeaders (>= 2.26.0), rstan (>= 2.26.0), BH (>= 1.66.0-1),
Rcpp (>= 0.12.17), RcppEigen (>= 0.3.3.4.0), RcppParallel (>= 5.0.1),
SystemRequirements: GNU make
NeedsCompilation: yes
Expand Down
32 changes: 16 additions & 16 deletions inst/stan/MBMA.stan
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,14 +12,14 @@ data {
int<lower=1> Nst;

// Study number for each arm
int<lower=1> st[Nobs];
array[Nobs] int<lower=1> st;

// Dose amount for each arm
real<lower=0> dose[Nobs];
array[Nobs] real<lower=0> dose;


// num doses in each trial
int<lower=1> ndose[Nst];
array[Nst] int<lower=1> ndose;

// link function (1=normal, 2=binary, 3=poisson)
int<lower=1,upper=3> link;
Expand All @@ -32,11 +32,11 @@ data {
vector[Nobs] y_se;

// binomial data, link=logit=2
int<lower=0> r[Nobs];
int<lower=1> n[Nobs];
array[Nobs] int<lower=0> r;
array[Nobs] int<lower=1> n;

// count data, link=log=3
int<lower=0> count[Nobs];
array[Nobs] int<lower=0> count;
vector[Nobs] exposure;

// Priors
Expand All @@ -53,13 +53,13 @@ data {
int<lower=1> Npred;

// Prediction points in the dose-response curve
real Pred_doses[Npred];
array[Npred] real Pred_doses;

// Indicator for placebo arm
int<lower=1> b_ndx[Nst];
array[Nst] int<lower=1> b_ndx;

// Indicator for non-placebo arm
int<lower=1> t_ndx[Nobs-Nst];
array[Nobs-Nst] int<lower=1> t_ndx;

// Fixed-effects or Random-effects model: (0: fe, 1: re)
int<lower=0,upper=1> re;
Expand Down Expand Up @@ -101,10 +101,10 @@ transformed data{
parameters {
vector[Nst] mu; // baseline risks
real alpha;
real<lower=0, upper=1.5> ED50_raw[emax];
real<lower=0.5, upper=10> gamma[hill]; // Hill parameter
array[emax] real<lower=0, upper=1.5> ED50_raw;
array[hill] real<lower=0.5, upper=10> gamma; // Hill parameter
vector[Nobs - Nst] u;
real<lower=0> tau[re];
array[re] real<lower=0> tau;
}

transformed parameters{
Expand All @@ -114,7 +114,7 @@ transformed parameters{
vector[Nobs] md;
vector[Nobs] delta;
vector[Nobs] theta;
real<lower=0> ED50[emax];
array[emax] real<lower=0> ED50;

// used for the prior distribution of ED50 (ED50) parameter
if(emax == 1) {ED50[1] = ED50_raw[1] * maxdose;}
Expand Down Expand Up @@ -217,9 +217,9 @@ model {

generated quantities {
real mean_mu;
real md_pred[Npred];
real delta_pred[Npred]; // Predicted delta
real<lower=0, upper=1> Pred_probs[Npred]; // Predicted probabolities
array[Npred] real md_pred;
array[Npred] real delta_pred; // Predicted delta
array[Npred] real<lower=0, upper=1> Pred_probs; // Predicted probabolities
vector[Nobs] log_lik; // pointwise log-likelihood contribution


Expand Down
16 changes: 8 additions & 8 deletions inst/stan/SMA.stan
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ data {
vector[Nobs] t;

// Study number for each observation
int<lower=1> st[Nobs];
array[Nobs] int<lower=1> st;

// link function (1=normal, 2=binary, 3=poisson)
int<lower=1,upper=3> link;
Expand All @@ -23,12 +23,12 @@ data {
vector[Nobs] y_se;

// binomial data, link=logit=2
int<lower=0> r[Nobs];
int<lower=1> n[Nobs];
array[Nobs] int<lower=0> r;
array[Nobs] int<lower=1> n;


// count data, link=log=3
int<lower=0> count[Nobs];
array[Nobs] int<lower=0> count;
vector[Nobs] exposure;

// Priors
Expand Down Expand Up @@ -58,9 +58,9 @@ data {
parameters {
vector[Nobs] mu; // baseline risks (log odds)
real theta; // relative treatment effect (log odds ratio)
vector[Nobs] u[re]; // individual treatment effects
real<lower=0> tau[re]; // heterogeneity stdev.
vector[ncov] beta[mreg]; // beta coeffients in meta-regression
array[re] vector[Nobs] u; // individual treatment effects
array[re] real<lower=0> tau; // heterogeneity stdev.
array[mreg] vector[ncov] beta; // beta coeffients in meta-regression
}

transformed parameters {
Expand Down Expand Up @@ -159,7 +159,7 @@ model {

generated quantities {
vector[Nobs] log_lik; // pointwise log-likelihood contribution
real theta_pred[re]; // predicted log-odds ratio for the new study
array[re] real theta_pred; // predicted log-odds ratio for the new study


for (s in 1:Nobs) {
Expand Down
16 changes: 8 additions & 8 deletions inst/stan/SMA_Higgins.stan
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ data {
vector[Nobs] t;

// Study number for each observation
int<lower=1> st[Nobs];
array[Nobs] int<lower=1> st;

// link function (1=normal, 2=binary, 3=poisson)
int<lower=1,upper=3> link;
Expand All @@ -23,12 +23,12 @@ data {
vector[Nobs] y_se;

// binomial data, link=logit=2
int<lower=0> r[Nobs];
int<lower=1> n[Nobs];
array[Nobs] int<lower=0> r;
array[Nobs] int<lower=1> n;


// count data, link=log=3
int<lower=0> count[Nobs];
array[Nobs] int<lower=0> count;
vector[Nobs] exposure;

// Priors
Expand Down Expand Up @@ -58,9 +58,9 @@ data {
parameters {
vector[Nobs] mu; // baseline risks (log odds)
real theta; // relative treatment effect (log odds ratio)
vector[Nobs] u[re]; // individual treatment effects
real<lower=0> tau[re]; // heterogeneity stdev.
vector[ncov] beta[mreg]; // beta coeffients in meta-regression
array[re] vector[Nobs] u; // individual treatment effects
array[re] real<lower=0> tau; // heterogeneity stdev.
array[mreg] vector[ncov] beta; // beta coeffients in meta-regression
}

transformed parameters {
Expand Down Expand Up @@ -159,7 +159,7 @@ model {

generated quantities {
vector[Nobs] log_lik; // pointwise log-likelihood contribution
real theta_pred[re]; // predicted log-odds ratio for the new study
array[re] real theta_pred; // predicted log-odds ratio for the new study


for (s in 1:Nobs) {
Expand Down