Bayesian Estimation Kirmann Model

Modeling
1

Hello Guys!

I am studying engineering in a France (maybe you will forgive my english!). I have a project where i had to use stan to implement a model called Kirmann Model. I can explain it if it is necessary. I made a code to do it but i don’t understand why it isn’t working. It would be great if someone has experienced this kind of result.

Thank you!!
(here is the code)

model_string <- "
functions{
int arrondi(real x){
  int k;
  while (k<x){
    k=k+1;
  }
  k=k-1;
  if (x-k>0.5){
    k=k+1;
  }
  return k;
}
}
data{
  int iteration;
  real N;
  real x[iteration + 2];
  
}

transformed data{

  
}

parameters{
  real<lower=0,upper=1> alpha;
  real<lower=0,upper=1> beta;
  real v;
  real gg;
}

transformed parameters{
  real k[iteration];
  real evolution[iteration-1];
  real plus2[iteration -1];
  real p1[iteration-1];
  real p2[iteration-1];
  real c[iteration-1];
  vector[3] g[iteration-1];
  for (i in 3:iteration){
    k[i]=N*((1+gg)*x[i-1]-x[i]-gg*x[i-2])/((v+gg)*x[i-1]-gg*x[i-2]);
  }
  for (i in 1:(iteration-1)){
    evolution[i]=k[i+1]-k[i];
    plus2[i]=evolution[i]+2;
}
  for (i in 1:(iteration-1)){
    p2[i]=((k[i]/N)*((N-k[i]-1)/(N-1)))*alpha+((N-k[i])/N)*beta;
    p1[i]=(k[i]/(N-1))*((N-k[i])/(N))*alpha+((k[i])/N)*beta;
    c[i]=1-p1[i]-p2[i];
    g[i][1]=p1[i];
    g[i][2]=c[i];
    g[i][3]=p2[i];
    
  }

}

model{
  alpha ~ uniform(0,0.8);
  beta ~ uniform(0,0.19);
  v ~ uniform(0.1,0.8);
  gg ~ uniform (0.4,5);


  for (i in 1:(iteration-1)){
    target += categorical_lpmf(arrondi(plus2[i])|(g[i]));
  }
}

" 

data_list <- list(iteration=96, N=100, x=c(0.37249999999999994,0.21503749999999988,0.08304631249999986,-0.003710859375000125,-0.046161730468750085,-0.05584673339843754,-0.04672755151367189,-0.0306285186315918,-0.014914024796990968,-0.0032456968660817577,0.0033998913158932867,0.00578925723950827,0.005430946000571311,0.00384691064573303,0.0020863769075200674,0.0006988627172226278,-0.00014884840059802647,-0.000507827799815257,-0.0005358448175050636,-0.00040405454491600744,-0.00023503866239640912,-9.331595207714952e-05,-1.0269035838460515e-06,4.262107865772578e-05,5.184104446696721e-05,4.278795649399163e-05,2.719419667578533e-05,1.265866744214526e-05,2.4724218301659355e-06,-2.9703053924583196e-06,-4.810535057278799e-06,-4.443106181500141e-06,-3.1115327139363485e-06,-1.661137014988234e-06,-5.454479994252784e-07,1.066102574200033e-07,3.636650183543263e-07,3.7055403532510217e-07,2.679084125548817e-07,1.4741689718554556e-07,5.359172987885054e-08,-2.697028102173412e-09,-2.613254102489429e-08,-2.8397019555217715e-08,-2.1112964866940412e-08,-1.1963626363903152e-08,-4.651452547095586e-09,-2.3141830537868805e-10,1.7351506355925047e-09,2.086257349066254e-09,1.6287075374960145e-09,9.642114307626695e-10,4.073256549270107e-10,5.884141863092245e-11,-1.0139533674659585e-10,-1.3929012634864073e-10,-1.1588719986815743e-10,-7.279608951912474e-11,-3.352002655609014e-11,-7.07811191349957e-12,6.309173278161753e-12,1.0267591526300023e-11,9.043447788003972e-12,5.939683360955538e-12,2.9135941269180887e-12,8.13387273521899e-13,-2.8764678205949897e-13,-6.5421494414032e-13,-6.18451238413572e-13,-4.240796228684018e-13,-2.194604537075937e-13,-7.082576050792229e-14,1.1008063053780066e-14,4.218593066409883e-14,4.252400683842038e-14,3.0118036052558213e-14,1.6173297867254218e-14,5.684832340439588e-15,-2.924640659840883e-16,-2.65687869315249e-15,-2.805580936074104e-15,-2.0233875524205187e-15,-1.103493933232929e-15,-4.081697721137257e-16,-1.2501568782549998e-17,1.417278348058873e-16,1.5639937937966838e-16,1.1349075871000796e-16,6.200334765543451e-17,2.3217093681511895e-17,1.5527952014842835e-18,-6.952125724593481e-18,-7.909026863995309e-18,-5.7717368234154634e-18,-3.1628424090250505e-18,-1.201256116857707e-18,-9.707351194561253e-20,3.314957496453375e-19));
stan_samples <- stan(model_code = model_string, data=data_list)
print(stan_samples)
plot(stan_samples,show_density = TRUE,pars="alpha")
plot(stan_samples,show_density = TRUE,pars="beta")
2

Hello Guys!

I tried to figure out the problem of my code but I can’t find it…

When I run it, it is said “initialization between (-2,2) failed”

Any idea would be appreciated!
Thanks!!

3

The bounds in the parameters block need to match the support of the distributions specified in the model block. So you need:

parameters {
  real <lower=0,upper=0.8> alpha;
  real <lower=0,upper=0.19> beta;
  real <lower=0.1,upper=0.8>v;
  real <lower=0.4,upper=5>gg;
}

in the parameters block (although I’d be suspicious about the need to constrain the parameters to these intervals). See here for more thoughts about priors: https://github.com/stan-dev/stan/wiki/Prior-Choice-Recommendations

4

Hey!

Thank you for your answer.
I changed the parameters block as you advised, however I stil have the same problem.

I will look the link you sent to see if changing my priors will solve the problem

5

I suspect it’s this part that’s giving you an error.

while (k<x){
k=k+1;
}
k=k-1;
if (x-k>0.5){
k=k+1;

At least when I run your model I get:

DIAGNOSTIC(S) FROM PARSER:
Info: left-hand side variable (name=k) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=k) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=k) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.

See the deep copy warning here

6

Hey Aya!

Thanks for your answer!

When i run my model, I don’t have the same message,

i get this:

SAMPLING FOR MODEL '78a280b77e742b140c0416f111969089' NOW (CHAIN 1).
Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)

Rejecting initial value:
  Error evaluating the log probability at the initial value.
Exception: categorical_lpmf: Number of categories is 2147483647, but must be in the interval [1, 3]  (in 'model148373115d_78a280b77e742b140c0416f111969089' at line 69)


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."
[1] "error occurred during calling the sampler; sampling not done"

But i didn’t know about the problem you highlighted, thanks for that! I’ll try to write my code with the “tmp” thing
thanks again!

1 Like
7

Hmm ok. Let me try and rerun the model and get around the error I am getting.

8

Did you get any solution for this kind of error?

9

I am getting the same error:
Chain 1: Rejecting initial value:
Chain 1: Error evaluating the log probability at the initial value.
Chain 1: Exception: Exception: categorical_lpmf: Number of categories is -2147483648, but must be in the interval [1, 2]

When I export the functions from Stan to R works:

categorical_test_rng( c(1, 0.00000000134757))
[1] 1
categorical_test_lpmf(1, c(1, 0.00000000134757))
[1] 0

Does anyone knows how to solve it ?

10

This indicates an issue with your model specification. Can you post the model that you’re trying to run?

12

Yes, sure, I removed several functions for privacy:post_error.stan (5.1 KB) :

functions{
  int categorical_test_rng(vector theta){
    int selected_index;
    selected_index=categorical_rng(to_vector(theta));
    return(selected_index);
  }
  real categorical_test_lpmf(int y, vector theta){
    real result;
    result= categorical_lpmf( y |  theta);
    return(result);
  }

}
data{
  real<lower=0.0, upper=2.0> K;
  int<lower=1> N;
  int<lower=2> total_sample_size;
  vector<lower = 0.0>[total_sample_size-1] sorted_coalescent_times_in_model_time_oldest_population;//not including the 0.0 at the beginning
  int indexes_father_populations[N];
  simplex[N] pop_sizes_proportion;
  int<lower=0,upper=2*total_sample_size> topology[total_sample_size-1,3];
}
transformed data{
    int number_inmigrants_per_population[N];
    vector<lower=0.0>[N] input_lower_bound_torigin_in_model_time_oldest_population;
    vector<lower=0.0>[N] input_upper_bound_torigin_in_model_time_oldest_population;
    vector<lower=0.0>[N] input_lower_bound_torigin_in_model_time;
    vector<lower=0.0>[N] input_upper_bound_torigin_in_model_time;
    int number_of_tips_below[2*total_sample_size-1];
    matrix  [(total_sample_size-1),(total_sample_size-1)] Q_coeff_hypoexponential= rep_matrix(0.0, (total_sample_size-1), (total_sample_size-1));
    int number_of_coalescent_times_below[2*total_sample_size-1] ;

    //compute transformed data in terms of data
}
parameters{
  vector<lower=0>[N] alphas;
  vector<lower=0>[N] deltaTs;
  real<lower=input_lower_bound_torigin_in_model_time[1], upper = input_upper_bound_torigin_in_model_time[1] > torigins_in_model_time1;
  real<lower=input_lower_bound_torigin_in_model_time[N]> torigin_oldest_population;
}
transformed parameters {
  vector<lower=0>[N] deltas;
  vector<lower=0>[N-1] torigins_in_model_time_oldest_population;
  vector<lower=0>[N] torigins_in_model_time;

  deltas = deltaTs .* pop_sizes_proportion;
  torigins_in_model_time_oldest_population[1] = torigins_in_model_time1* pop_sizes_proportion[1];
  torigins_in_model_time_oldest_population = (1.0/pop_sizes_proportion[N])*
                                             torigins_in_model_time_oldest_population;

  torigins_in_model_time[1]= torigins_in_model_time1;
  torigins_in_model_time[N] = torigin_oldest_population;
}
model{
   vector[N] MRCA_times_in_model_time_oldest_population;
   int selected_indexes[N-1];
   alphas~gamma(rep_vector(0.001,N), rep_vector(0.001,N));
   deltaTs~exponential(alphas);
   torigins_in_model_time1~conditionalDensityTOrigin(deltas[1], total_sample_size);
   torigin_oldest_population~conditionalDensityTOrigin(deltas[N], total_sample_size);

    for(i in 1:(N-1)){
       int idx_first_coal_time_above_torigin=get_index_coal_time_above_MRCA_in_oldest_population_time_less_than( torigins_in_model_time_oldest_population[i],  sorted_coalescent_times_in_model_time_oldest_population);
       vector [idx_first_coal_time_above_torigin-1] candidate_time_MRCAs_in_model_time_oldest_population= get_candidate_time_MRCAs(torigins_in_model_time_oldest_population[i],  sorted_coalescent_times_in_model_time_oldest_population,
                   topology, number_of_tips_below,idx_first_coal_time_above_torigin );
       vector[rows(candidate_time_MRCAs_in_model_time_oldest_population)]   candidate_time_MRCAs_in_model_time= (pop_sizes_proportion[N] / pop_sizes_proportion[i]) * candidate_time_MRCAs_in_model_time_oldest_population;

       int number_candidate_MRCAs= count_valid_elements_vector(candidate_time_MRCAs_in_model_time_oldest_population);
       vector [idx_first_coal_time_above_torigin-1] candidate_time_MRCAs_Kingman_coal =  from_model_time_to_Kingman_coalescent_time(candidate_time_MRCAs_in_model_time_oldest_population, torigins_in_model_time[i], deltas[i], K);
      
       real p= 1.0/number_candidate_MRCAs;
       vector[number_candidate_MRCAs] theta;
       vector[number_candidate_MRCAs] probab;

       probab= compute_probab_vector(total_sample_size, number_candidate_MRCAs,candidate_time_MRCAs_in_model_time, candidate_time_MRCAs_in_model_time_oldest_population,
                     Q_coeff_hypoexponential, deltas[i], torigins_in_model_time[i], number_of_tips_below,
                     sorted_coalescent_times_in_model_time_oldest_population, topology) ;

       print("probab=", to_vector(probab));
       theta = rep_vector(p, number_candidate_MRCAs);

       selected_indexes[i]~categorical_test(to_vector(probab));

       MRCA_times_in_model_time_oldest_population[i]=candidate_time_MRCAs_in_model_time_oldest_population[selected_indexes[i]];
     }

     MRCA_times_in_model_time_oldest_population[N] = max(sorted_coalescent_times_in_model_time_oldest_population);

    target +=log_likelihood(total_sample_size,    N,  K,  deltas,
                [ torigins_in_model_time1, torigin_oldest_population ]', append_row(torigins_in_model_time_oldest_population, torigin_oldest_population),
                sorted_coalescent_times_in_model_time_oldest_population,
                number_inmigrants_per_population, MRCA_times_in_model_time_oldest_population,
               indexes_father_populations, pop_sizes_proportion, torigin_oldest_population, topology, number_of_tips_below, number_of_coalescent_times_below);
}

The error appears in line 82: selected_indexes[i]~categorical_test(to_vector(probab));

EDIT: @maxbiostat edited this post for readability and syntax highlighting.

13

The error occurs because you’re trying to give a prior to an uninitialised array.

You’ve declared the integer array:

   int selected_indexes[N-1];

And then placed a prior on it:

  selected_indexes[i]~categorical_test(to_vector(probab));

But you haven’t put any integers in the array (you haven’t put anything in selected_indexes), so Stan errors

14

Thanks for the quick reply and help!. Yes, selected_indexes vector doesn’t have a prior . What would be a non informative candidate prior for integer array of indexes over the set of indexes
{1,…,rows(sorted_coalescent_times_in_model_time_oldest_population)} where sorted_coalescent_times_in_model_time_oldest_population is an input data vector ?

15

Unfortunately Stan doesn’t support sampling integer values as parameters. You need to either provide the outcomes as data, or marginalise them out of the likelihood. There’s more information in this section of the User’s Guide: 7 Latent Discrete Parameters | Stan User’s Guide

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