Stan model

General
1

hi all.
I am estimating stan, I am facing this error.
what should I do?
can anyone help?

library(rstan)
library(gdata)
library(bayesplot)
write("// Stan model for simple linear regression
 
 data {
   int<lower=0>N;
   int<lower=0>N_edges;
   int<lower+1 , upper=N> node1[N_edges]; / node[i], node2[i]
   neighbors
   int<lower=1, upper=N> node2[N_edges]; /node1[i] , node2[i]
 }
 
 parameters {
   real alpha; // Intercept
   real beta; // Slope (regression coefficients)
   real < lower = 0 > sigma; // Error SD
 }
 
 model {
  vector[N] mu = alpha + beta * x;
   y ~ normal(mu , sigma);
 }
 
 
 generated quantities {
 } // The posterior predictive distribution",
 
 "stan_model1.stan")
stanc=("stan_model1.stan")
stan_model1 <- "stan_model1.stan"
fit <- stan(file = stan_model1, data = hyperlipid_xls, warmup = 500, iter = 1000, chains = 4, cores = 2, thin = 1)
SYNTAX ERROR, MESSAGE(S) FROM PARSER:
 error in 'model383452e55421_stan_model1' at line 6, column 11
  -------------------------------------------------
     4:     int<lower=0>N;
     5:   int<lower=0>N_edges;
     6:   int<lower+1 , upper=N> node1[N_edges]; / node[i], node2[i]
                  ^
     7:   neighbors
  -------------------------------------------------

PARSER EXPECTED: "="
Error in stanc(file = file, model_code = model_code, model_name = model_name,  : 
  failed to parse Stan model 'stan_model1' due to the above error.
2

The error is:

 6:   int<lower+1 , upper=N> node1[N_edges]; / node[i], node2[i]
              ^
PARSER EXPECTED: "="
Error in stanc(file = file, model_code = model_code, model_name = model_name, :
failed to parse Stan model ‘stan_model1’ due to the above error.

Which is because your constraint declaration should be lower=1 not lower+1

3

dear @andrjohns .
i changed it but still got the error.

write("// Stan model for simple linear regression
+

  • data {
  • int<lower=0>N;
  • int<lower=0>N_edges;
  • int<lower=1 , upper=N> node1[N_edges]; / node[i], node2[i]
  • neighbors
  • int<lower=1, upper=N> node2[N_edges]; /node1[i] , node2[i]
  • }
  • parameters {
  • real alpha; // Intercept
  • real beta; // Slope (regression coefficients)
  • real < lower = 0 > sigma; // Error SD
  • }
  • model {
  • vector[N] mu = alpha + beta * x;
  • y ~ normal(mu , sigma);
  • }
  • generated quantities {
  • } // The posterior predictive distribution",
  • “stan_model1.stan”)

stanc=(“stan_model1.stan”)
stan_model1 ← “stan_model1.stan”
fit ← stan(file = stan_model1, data = hyperlipid_xls, warmup = 500, iter = 1000, chains = 4, cores = 2, thin = 1)
SYNTAX ERROR, MESSAGE(S) FROM PARSER:
error in ‘model38345c036fa2_stan_model1’ at line 6, column 41

 4:     int<lower=0>N;
 5:   int<lower=0>N_edges;
 6:   int<lower=1 , upper=N> node1[N_edges]; / node[i], node2[i]
                                            ^
 7:   neighbors

PARSER EXPECTED: <one of the following:
a variable declaration, beginning with type,
(int, real, vector, row_vector, matrix, unit_vector,
simplex, ordered, positive_ordered,
corr_matrix, cov_matrix,
cholesky_corr, cholesky_cov
or ‘}’ to close variable declarations>
Error in stanc(file = file, model_code = model_code, model_name = model_name, :
failed to parse Stan model ‘stan_model1’ due to the above error.

4

This new error is because you have a semicolon followed by other code in your declaration:

int<lower=1 , upper=N> node1[N_edges]; / node[i], node2[i]

The / node[i], node2[i] division does not seem to have any purpose here. If that’s intended to be a comment then it needs to have a double forward-slash:

// node[i], node2[i]
5

dear @andrjohns
in this case , i will encounter this error again.

library(rstan)

library(gdata)
library(bayesplot)
write("// Stan model for simple linear regression

  • data {
  • int<lower=0>N;
  • int<lower=0>N_edges;
  • int<lower=1 , upper=N> node1[N_edges]; // node[i], node2[i]
  • neighbors
  • int<lower=1, upper=N> node2[N_edges]; //node1[i] , node2[i]
  • }
  • parameters {
  • real alpha; // Intercept
  • real beta; // Slope (regression coefficients)
  • real < lower = 0 > sigma; // Error SD
  • }
  • model {
  • vector[N] mu = alpha + beta * x;
  • y ~ normal(mu , sigma);
  • }
  • generated quantities {
  • } // The posterior predictive distribution",
  • “stan_model1.stan”)

stanc=(“stan_model1.stan”)
stan_model1 ← “stan_model1.stan”
fit ← stan(file = ‘stan_model1’, data =Untitled2, warmup = 500, iter = 1000, chains = 4, cores = 2, thin = 1)
Error in file(fname, “rt”) : cannot open the connection
In addition: Warning messages:
1: In normalizePath(path.expand(path), winslash, mustWork) :
path[1]=“stan_model1”: The system cannot find the file specified
2: In file(fname, “rt”) :
cannot open file ‘C:\Users\Uaer\Desktop\Hyperlipid\stan_model1’: No such file or directory
Error in get_model_strcode(file, model_code) :
cannot open model file “C:\Users\Uaer\Desktop\Hyperlipid\stan_model1”

6

Again, this is a different error.

The error message states:

cannot open file ‘C:\Users\Uaer\Desktop\Hyperlipid\stan_model1’: No such file or directory

Which is because the file is called stan_model1.stan, but you’ve told rstan that the file is just called stan_model1 (with no extension).

Please try to take note of the error messages that are being returned throughout this process, they will often indicate the source of the issue

7

yeah dear @andrjohns .
you are right.
but i am a little week in running data in RStudio.
i am facing this error now.
please see it too…thanke you.

write("// Stan model for simple linear regression

  • data {
  • int < lower = 1 > N; // Sample size
  • vector[N] x; // Predictor
  • vector[N] y; // Outcome
  • }
  • parameters {
  • real alpha; // Intercept
  • real beta; // Slope (regression coefficients)
  • real < lower = 0 > sigma; // Error SD
  • }
  • model {
  • y ~ normal(alpha + x * beta , sigma);
  • }
  • generated quantities {
  • } // The posterior predictive distribution",
  • “stan_model1.stan”)

stanc=(“stan_model1.stan”)
stan_model1 ← “stan_model1.stan”
fit ← stan(file = “stan_model1.stan”, data =Untitled2, warmup = 500, iter = 1000, chains = 4, cores = 2, thin = 1)
Error in mod$fit_ptr() :
Exception: variable does not exist; processing stage=data initialization; variable name=N; base type=int (in ‘model383454081ff0_stan_model1’ at line 4)

failed to create the sampler; sampling not done

8

@shayeste I updated your first post to encapsulate code with ``` and the end of your code block. You may highlight R, Python, Stan and a variety of other languages by writing ```stan.

It helps people to see the problem more clearly when the issue is laid out in a more readable format. We’re going to post some notes on how to ask questions on the forum but we don’t have it yet! Right now it’s in discussion at Forum question posting guideline - #4 by yizhang. Feel free to add to it as well with your experience as a new poster.

Thanks and welcome to the Stan community!

1 Like
9

dear @andrjohns
i found the answer .
in the command related to fit , i tried using the stan function instead of data=untitled2 , data= stan_data.
its true :)