stan_demo example 500 not working

[caimiao0714]

Hi Ben,

I tried the 500th example of stan_demo, but it seems not to be working. I ran the code from RStudio cloud. Here are my codes:

library(RStan)
stan_demo()
500

Here are the console log:

> K <- 8

> D <- 4

> N <- 500

> y <- 
>+ structure(c(1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 0,
>+ 1, 0, 1, 1, 0, 0, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0, 1, 0,  .... [TRUNCATED] 

> x <- 
+ structure(c(-0.56947710721168, 0.0686981186395276, 0.807151998639757,
+ 0.311832939914023, 0.670993954113173, -0.914759441112067, -0.1375718 .... [TRUNCATED] 


SAMPLING FOR MODEL 'probit-multi-good' NOW (CHAIN 1).
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: Phi: x is nan, but must not be nan!  (in 'model4f66680104f2_probit_multi_good' at line 26)

Rejecting initial value:
  Log probability evaluates to log(0), i.e. negative infinity.
  Stan can't start sampling from this initial value.

Initialization between (-2, 2) failed after 100 attempts. 
 Try specifying initial values, reducing ranges of constrained values, or reparameterizing the model.
[1] "Error in sampler$call_sampler(args_list[[i]]) : Initialization failed."
error occurred during calling the sampler; sampling not done

[bob-carpenter]

Thanks. The set of examples was just scraped and many of them don't work. In my opinion, it should be edited down to a small set of working examples. The decision's up to @bgoodri.

[bob-carpenter]

Also, this is partly an RStan issue for just scraping this repo and partly this repo's fault for not having consistent working examples. So there are two ways to fix it---either by pruning example-models or by cleaning up RStan. Cleaning the example-models repo is probably best.

[bgoodri]

I agree that cleaning up the example-models repo would be best.

…

On Fri, Nov 30, 2018 at 3:30 PM Bob Carpenter ***@***.***> wrote: Also, this is partly an RStan issue for just scraping this repo and partly this repo's fault for not having consistent working examples. So there are two ways to fix it---either by pruning example-models or by cleaning up RStan. Cleaning the example-models repo is probably best. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#144 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADOrqkDvwGuv_KNaiRAMOFhNz80dMu08ks5u0ZVdgaJpZM4Y8IaO> .

[bgoodri]

In this case, I think it is fine if you specify init_r = 1 or thereabouts. But we don't have a way of knowing that in stan_demo. I guess the example-models repo could optionally specify initial values.