Running examples in 'bayesLopod-Ex.R' failed
The error most likely occurred in:

> ### Name: modelLopod
> ### Title: Run a Bayes inference of Landscape Occupancy from Presence-Only
> ###   Data on Stan
> ### Aliases: modelLopod
> 
> ### ** Examples
> 
> data("simSpRecords", package = "bayesLopod")
> data("simSpSamplingEffort", package = "bayesLopod")
> simSpRasters = xyToRaster(xyRecords = simSpRecords,xySamplingEffort = simSpSamplingEffort,
+ basemap = NULL, nrows = 10, extentExpansion = 0)
> ld_Raster = rasterLopodData(rasterN = simSpRasters[["samplingEffort"]],
+ rasterY = simSpRasters[["spDetections"]], Adjacency = FALSE )
Extrapolation into not-sampled cells cannot be performed without an adjacency matrix 
> mLopodRaster = modelLopod(LopodData = ld_Raster, varP = TRUE, q = NULL,
+ pmin = 0, CAR = FALSE, nChains = 1,warmup = 10,sampling = 10,nCores = 1)
Global q estimated. Psi and P for each sampling unit

SAMPLING FOR MODEL 'psiipiq' NOW (CHAIN 1).

Gradient evaluation took 0 seconds
1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
Adjust your expectations accordingly!


WARNING: No variance estimation is
         performed for num_warmup < 20

Iteration:  1 / 20 [  5%]  (Warmup)
Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipiq' at line 108)

Iteration:  2 / 20 [ 10%]  (Warmup)
Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipiq' at line 108)

Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipiq' at line 108)

Iteration:  4 / 20 [ 20%]  (Warmup)
Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipiq' at line 108)

Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipiq' at line 108)

Iteration:  6 / 20 [ 30%]  (Warmup)
Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipiq' at line 108)

Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipiq' at line 108)

Iteration:  8 / 20 [ 40%]  (Warmup)
Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipiq' at line 108)

Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipiq' at line 108)

Iteration: 10 / 20 [ 50%]  (Warmup)
Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipiq' at line 108)

Iteration: 11 / 20 [ 55%]  (Sampling)
Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipiq' at line 108)

Iteration: 12 / 20 [ 60%]  (Sampling)
Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipiq' at line 108)

Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipiq' at line 108)

Iteration: 14 / 20 [ 70%]  (Sampling)
Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipiq' at line 108)

Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipiq' at line 108)

Iteration: 16 / 20 [ 80%]  (Sampling)
Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipiq' at line 108)

Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipiq' at line 108)

Iteration: 18 / 20 [ 90%]  (Sampling)
Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipiq' at line 108)

Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipiq' at line 108)

Iteration: 20 / 20 [100%]  (Sampling)
Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipiq' at line 108)


 Elapsed Time: 1.123 seconds (Warm-up)
               2.983 seconds (Sampling)
               4.106 seconds (Total)

 [1] "Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:"                        
 [2] "Exception: validate transformed params: qRate is nan, but must be greater than or equal to 0  (in 'model_psiipiq' at line 25)"         
 [3] "If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,"
 [4] "but if this warning occurs often then your model may be either severely ill-conditioned or misspecified."                              
 [5] "Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:"                        
 [6] "Exception: validate transformed params: qRate is nan, but must be greater than or equal to 0  (in 'model_psiipiq' at line 25)"         
 [7] "If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,"
 [8] "but if this warning occurs often then your model may be either severely ill-conditioned or misspecified."                              
 [9] "Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:"                        
[10] "Exception: validate transformed params: qRate is nan, but must be greater than or equal to 0  (in 'model_psiipiq' at line 25)"         
[11] "If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,"
[12] "but if this warning occurs often then your model may be either severely ill-conditioned or misspecified."                              
[13] "Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:"                        
[14] "Exception: validate transformed params: qRate is nan, but must be greater than or equal to 0  (in 'model_psiipiq' at line 25)"         
[15] "If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,"
[16] "but if this warning occurs often then your model may be either severely ill-conditioned or misspecified."                              
[17] "Error in sampler$call_sampler(args_list[[i]]) : "                                                                                      
[18] "  Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipiq' at line 108)"          
[1] "error occurred during calling the sampler; sampling not done"
> 
> data("Andropogon_shape", package = "bayesLopod")
> ld_Shape = shapeLopodData(Shapefile = Andropogon_shape, fieldN = "sampEffort",
+ fieldY = "detections",  Adjacency = FALSE, keepFields = FALSE)
> mLopodShape = modelLopod(LopodData = ld_Shape, varP = FALSE, q = NULL,
+ pmin = 0, CAR = FALSE, nChains = 1,warmup = 5,sampling = 5,nCores = 1)
Global p and q estimated. Psi for each sampling unit.

SAMPLING FOR MODEL 'psiipq' NOW (CHAIN 1).

Gradient evaluation took 0.016 seconds
1000 transitions using 10 leapfrog steps per transition would take 160 seconds.
Adjust your expectations accordingly!


WARNING: No variance estimation is
         performed for num_warmup < 20

Iteration: 1 / 10 [ 10%]  (Warmup)
Iteration: 2 / 10 [ 20%]  (Warmup)
Iteration: 4 / 10 [ 40%]  (Warmup)
Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipq' at line 95)

Iteration: 6 / 10 [ 60%]  (Sampling)
Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipq' at line 95)

Iteration: 7 / 10 [ 70%]  (Sampling)
Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipq' at line 95)

Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipq' at line 95)

Iteration: 9 / 10 [ 90%]  (Sampling)
Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipq' at line 95)

Iteration: 10 / 10 [100%]  (Sampling)
Exception: bernoulli_rng: Probability parameter is 1, but must be in the interval [0, 1]  (in 'model_psiipq' at line 95)


 Elapsed Time: 0.047 seconds (Warm-up)
               0.031 seconds (Sampling)
               0.078 seconds (Total)

Error in validObject(.Object) : 
  invalid class "stanfit" object: The following variables have undefined values:  sim_y[1],The following variables have undefined values:  sim_y[2],The following variables have undefined values:  sim_y[3],The following variables have undefined values:  sim_y[4],The following variables have undefined values:  sim_y[5],The following variables have undefined values:  sim_y[6],The following variables have undefined values:  sim_y[7],The following variables have undefined values:  sim_y[8],The following variables have undefined values:  sim_y[9],The following variables have undefined values:  sim_y[10],The following variables have undefined values:  sim_y[11],The following variables have undefined values:  sim_y[12],The following variables have undefined values:  sim_y[13],The following variables have undefined values:  sim_y[14],The following variables have undefined values:  sim_y[15],The following variables have undefined values:  sim_y[16],The following variables have undefined 
Calls: modelLopod ... .local -> new -> initialize -> initialize -> validObject
Execution halted