stan-dev/example-models

`stan_demo` example 500 not working

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#144 aberto em 30 de nov. de 2018

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Description

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

Guia do colaborador

Direção de pesquisa
Investigue os valores iniciais do modelo probit multi good que causam NaN na função Phi. O problema pode ser devido a parâmetros ilimitados ou restrições ausentes. Veja o código Stan no exemplo para verificar se o preditor linear pode produzir valores extremos.
Pilha de tecnologia
None
Domain
machine learning
Tipo Issue
Bug
DifficultyDificuldade de implementação estimada para um novo contribuidor, de 1 para alterações muito pequenas a 5 para trabalho de nível especializado.
2
Tempo estimadoUm intervalo de tempo aproximado para um colaborador experiente investigar, implementar, testar e preparar um pull request.
1-3 horas
Status da atividadeQuão disponível o issue aparece agora: novo, ativo, obsoleto, bloqueado ou aguardando entrada do mantenedor.
Ativo
ClarityCom que clareza o issue explica a mudança esperada, os critérios de aceitação e a próxima etapa.
Principalmente claro
Prerequisites
None
Simpatia para novatosUma pontuação de 1 a 100 que estima o quão acessível este issue é para colaboradores iniciantes.
65