trouble reading in data

[Christopher Kedzie]

Hi,

I'm new to stan, so apologies if I am missing something obvious here.

I am trying to fit a simple poisson regression. My model compiles but when I try to run I get the following error:

Exception: data x value  beyond int range

Diagnostic information: 

stan_2.9.0/src/stan/io/dump.hpp(522): Throw in function bool stan::io::dump_reader::next()

Dynamic exception type: boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<std::invalid_argument> >

std::exception::what: data x value  beyond int range

The model is:

data {
    int<lower=0> N;
    int<lower=0> K;
    matrix[N,K] x;
    int<lower=0> y[N];
}

parameters {
    vector[K] theta;
    vector[1] b;
}


transformed parameters  {
    real lp[N];
    real <lower=0> mu[N];

    for (i in 1:N) {
        lp[i] <- x[i] * theta + b[1];
        mu[i] <- exp(lp[i]);
   }
}

model {
    y ~ poisson(mu);
}

And my data file 'all.data.R' is:

N <- 15
K <- 1
x <- matrix(c(1.0, 1.0, 1.0, 1.0, 1.0, 2.0, 1.0, 1.0, 3.0, 1.0, 4.0, 1.0, 2.0, 2.0, 1.0), nrow=15, ncol=1)
y <- c(0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0)

I am running this with CmdStan:

./model1 optimize data file=all.data.R

Any help would be greatly appreciated!

Thanks,

Chris

[Daniel Lee]

Hi Chris,

The format used to read from the data file isn't quite native R. I believe technical details on what's allowed is in the CmdStan manual, but it's really not worth reading.

The quick fix is to change x to:
x <-
structure(c(1, 1, 1, 1, 1, 2, 1, 1, 3, 1, 4, 1, 2, 2, 1),
.Dim = c(15, 1))

If you're using R to export the data, I'd suggest using rstan's stan_rdump() function. It handles edge cases better than just using dump() in R.

Daniel

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[Christopher Kedzie]

Thanks for the quick reply! That worked.