Hi all,
I want to to a prior preditive check for my model (stan_glmer) and came across an error.
I tried to reduce runtime by setting nreps to 2 and using a small subsample of my data (n = 1000). I further restricted the initial values in the original model fit as suggested in the documentation (r_init = 0.5).
Since the error message says something about a value in the “y” variable (I assume it´s my response variable in the model) contains non-int values, I checked it, but there are only integers.
I have no idea left how to approach this error. Has anyone an idea?
y_sim <- pp_validate(M1,
nreps = 2,
seed = 12345,
prior_PD = TRUE)
The resulting error message:
Error in new_CppObject_xp(fields$.module, fields$.pointer, ...) :
Exception: int variable contained non-int values; processing stage=data initialization; variable name=y; base type=int (in 'model_count' at line 12)
failed to create the sampler; sampling not done
Error in check_stanfit(stanfit) :
Invalid stanfit object produced please report bug
Error in new_CppObject_xp(fields$.module, fields$.pointer, ...) :
Exception: int variable contained non-int values; processing stage=data initialization; variable name=y; base type=int (in 'model_count' at line 12)
failed to create the sampler; sampling not done
Error in check_stanfit(stanfit) :
Invalid stanfit object produced please report bug
Error in new_CppObject_xp(fields$.module, fields$.pointer, ...) :
Exception: int variable contained non-int values; processing stage=data initialization; variable name=y; base type=int (in 'model_count' at line 12)
failed to create the sampler; sampling not done
Error in check_stanfit(stanfit) :
Invalid stanfit object produced please report bug
Error in dimnamesGets(x, value) :
invalid dimnames given for “dgCMatrix” object
Further information:
starting worker pid=2696 on localhost:11075 at 15:14:43.598
starting worker pid=10640 on localhost:11075 at 15:14:43.768
starting worker pid=9360 on localhost:11075 at 15:14:43.943
starting worker pid=12328 on localhost:11075 at 15:14:44.127
SAMPLING FOR MODEL 'count' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.001 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 10 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 2000 [ 0%] (Warmup)
SAMPLING FOR MODEL 'count' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.002 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 20 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: Iteration: 1 / 2000 [ 0%] (Warmup)
SAMPLING FOR MODEL 'count' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 0.001 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 10 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: Iteration: 1 / 2000 [ 0%] (Warmup)
SAMPLING FOR MODEL 'count' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 0.001 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 10 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: Iteration: 1 / 2000 [ 0%] (Warmup)
Chain 4: Iteration: 200 / 2000 [ 10%] (Warmup)
.....
Chain 2: Iteration: 1800 / 2000 [ 90%] (Sampling)
Chain 4: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 52.494 seconds (Warm-up)
Chain 4: 38.552 seconds (Sampling)
Chain 4: 91.046 seconds (Total)
Chain 4:
Chain 3: Iteration: 1800 / 2000 [ 90%] (Sampling)
Chain 2: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 57.577 seconds (Warm-up)
Chain 2: 42.598 seconds (Sampling)
Chain 2: 100.175 seconds (Total)
Chain 2:
Chain 3: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 64.846 seconds (Warm-up)
Chain 3: 37.27 seconds (Sampling)
Chain 3: 102.116 seconds (Total)
Chain 3:
Chain 1: Iteration: 1600 / 2000 [ 80%] (Sampling)
Chain 1: Iteration: 1800 / 2000 [ 90%] (Sampling)
Chain 1: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 59.242 seconds (Warm-up)
Chain 1: 72.455 seconds (Sampling)
Chain 1: 131.697 seconds (Total)
Chain 1:
- Operating System: Windows 10
- rstanarm Version: 2.21.1
- R version: 4.1.0