Error in inla.inlaprogram.has.crashed()
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Luiz Henrique .Arroyo
Oct 5, 2018, 9:41:03 AM10/5/18
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Hello everybody
I'm performing a BYM model with Zero-inflated Poisson, with this formula:
formula.zip <- Y ~ 1 + f(ZBS, model="bym", graph=LDN.adj,
hyper=list(prec.unstruct=list(prior="gaussian",param=c(0,1)),
prec.spatial=list(prior="gaussian",param=c(0,1))))
The model looks this way:
mod.zip1 <- inla(formula.zip,family="zeroinflatedpoisson0",
data=data.navarra, offset = log(E),
control.predictor=list(compute=TRUE),verbose=TRUE)
However, when I run the model I get this error message:
Error in inla.inlaprogram.has.crashed()
Rerunning with verbose=TRUE, this was reported:
Report bugs to <he...@r-inla.org>
Process file[C:\Users\ricardo\AppData\Local\Temp\Rtmp80k15f\file6c430477f3a/Model.ini] threads[4] blas_threads[1]
inla_build...
number of sections=[8]
parse section=[0] name=[INLA.libR] type=[LIBR]
inla_parse_libR...
section[INLA.libR]
R_HOME=[C:/Users/ricardo/Documents/R/R-3.5.1]
parse section=[7] name=[INLA.Expert] type=[EXPERT]
inla_parse_expert...
section[INLA.Expert]
disable.gaussian.check=[0]
cpo.manual=[0]
jp.file=[(null)]
jp.model=[(null)]
parse section=[1] name=[INLA.Model] type=[PROBLEM]
inla_parse_problem...
name=[INLA.Model]
openmp.strategy=[default]
pardiso-library installed and working? = [no]
smtp = [taucs]
strategy = [default]
store results in directory=[C:\Users\ricardo\AppData\Local\Temp\Rtmp80k15f\file6c430477f3a/results.files]
output:
cpo=[0]
po=[0]
dic=[0]
kld=[1]
mlik=[1]
q=[0]
graph=[0]
gdensity=[0]
hyperparameters=[1]
summary=[1]
return.marginals=[1]
nquantiles=[3] [ 0.025 0.5 0.975 ]
ncdf=[0] [ ]
parse section=[3] name=[Predictor] type=[PREDICTOR]
inla_parse_predictor ...
section=[Predictor]
dir=[predictor]
PRIOR->name=[loggamma]
hyperid=[53001|Predictor]
PRIOR->from_theta=[function (x) <<NEWLINE>>exp(x)]
PRIOR->to_theta = [function (x) <<NEWLINE>>log(x)]
PRIOR->PARAMETERS=[1, 1e-005]
initialise log_precision[12]
fixed=[1]
user.scale=[1]
n=[645]
m=[0]
ndata=[645]
compute=[1]
read offsets from file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c473197c64]
read n=[1290] entries from file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c473197c64]
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c473197c64] 0/645 (idx,y) = (0, -1.#INF)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c473197c64] 1/645 (idx,y) = (1, -1.#INF)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c473197c64] 2/645 (idx,y) = (2, -1.#INF)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c473197c64] 3/645 (idx,y) = (3, -1.#INF)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c473197c64] 4/645 (idx,y) = (4, -1.#INF)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c473197c64] 5/645 (idx,y) = (5, -1.#INF)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c473197c64] 6/645 (idx,y) = (6, -1.#INF)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c473197c64] 7/645 (idx,y) = (7, 0.455471)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c473197c64] 8/645 (idx,y) = (8, -1.#INF)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c473197c64] 9/645 (idx,y) = (9, -1.#INF)
Aext=[(null)]
AextPrecision=[1e+008]
output:
summary=[1]
return.marginals=[1]
nquantiles=[3] [ 0.025 0.5 0.975 ]
ncdf=[0] [ ]
parse section=[2] name=[INLA.Data1] type=[DATA]
inla_parse_data [section 1]...
tag=[INLA.Data1]
family=[ZEROINFLATEDPOISSON0]
likelihood=[ZEROINFLATEDPOISSON0]
file->name=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c4134af0]
file->name=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c45d045c9a]
read n=[1935] entries from file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c4134af0]
0/645 (idx,a,y,d) = (0, 1, 0, 1)
1/645 (idx,a,y,d) = (1, 1, 0, 1)
2/645 (idx,a,y,d) = (2, 1, 0, 1)
3/645 (idx,a,y,d) = (3, 1, 0, 1)
4/645 (idx,a,y,d) = (4, 1, 0, 1)
5/645 (idx,a,y,d) = (5, 1, 0, 1)
6/645 (idx,a,y,d) = (6, 1, 0, 1)
7/645 (idx,a,y,d) = (7, 1, 5, 1)
8/645 (idx,a,y,d) = (8, 1, 0, 1)
9/645 (idx,a,y,d) = (9, 1, 0, 1)
likelihood.variant=[0]
initialise prob_intern[-1]
fixed=[0]
PRIOR->name=[gaussian]
hyperid=[85001|INLA.Data1]
PRIOR->from_theta=[function (x) <<NEWLINE>>exp(x)/(1 + exp(x))]
PRIOR->to_theta = [function (x) <<NEWLINE>>log(x/(1 - x))]
PRIOR->PARAMETERS=[-1, 0.2]
Link model [LOG]
Link order [-1]
Link variant [-1]
Link ntheta [0]
mix.use[0]
parse section=[5] name=[ZBS] type=[FFIELD]
inla_parse_ffield...
section=[ZBS]
dir=[random.effect00000001]
model=[bym]
PRIOR0->name=[gaussian]
hyperid=[10001|ZBS]
PRIOR0->from_theta=[function (x) <<NEWLINE>>exp(x)]
PRIOR0->to_theta = [function (x) <<NEWLINE>>log(x)]
PRIOR0->PARAMETERS0=[0, 1]
PRIOR1->name=[gaussian]
hyperid=[10002|ZBS]
PRIOR1->from_theta=[function (x) <<NEWLINE>>exp(x)]
PRIOR1->to_theta = [function (x) <<NEWLINE>>log(x)]
PRIOR1->PARAMETERS1=[0, 1]
correct=[-1]
constr=[0]
diagonal=[1.01511e-005]
id.names=<not present>
compute=[1]
nrep=[1]
ngroup=[1]
read covariates from file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c45ccc6a2f]
read n=[1290] entries from file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c45ccc6a2f]
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c45ccc6a2f] 0/645 (idx,y) = (0, 0)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c45ccc6a2f] 1/645 (idx,y) = (1, 1)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c45ccc6a2f] 2/645 (idx,y) = (2, 2)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c45ccc6a2f] 3/645 (idx,y) = (3, 3)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c45ccc6a2f] 4/645 (idx,y) = (4, 4)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c45ccc6a2f] 5/645 (idx,y) = (5, 5)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c45ccc6a2f] 6/645 (idx,y) = (6, 6)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c45ccc6a2f] 7/645 (idx,y) = (7, 7)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c45ccc6a2f] 8/645 (idx,y) = (8, 8)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c45ccc6a2f] 9/645 (idx,y) = (9, 9)
read graph from file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c479251a01]
file for locations=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c4136f1c25]
nlocations=[645]
locations[0]=[1]
locations[1]=[2]
locations[2]=[3]
locations[3]=[4]
locations[4]=[5]
locations[5]=[6]
locations[6]=[7]
locations[7]=[8]
locations[8]=[9]
locations[9]=[10]
initialise log_precision (iid component)[4]
fixed=[0]
initialise log_precision (spatial component)[4]
fixed=[0]
adjust.for.con.comp[1]
scale.model[0]
read extra constraint from file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c4125d429e]
Constraint[0]
A[645] = 1.000000
A[646] = 1.000000
A[647] = 1.000000
A[648] = 1.000000
A[649] = 1.000000
A[650] = 1.000000
A[651] = 1.000000
A[652] = 1.000000
A[653] = 1.000000
A[654] = 1.000000
A[655] = 1.000000
e[0] = 0.000000
rank-deficiency is *defined* [2]
output:
summary=[1]
return.marginals=[1]
nquantiles=[3] [ 0.025 0.5 0.975 ]
ncdf=[0] [ ]
section=[4] name=[(Intercept)] type=[LINEAR]
inla_parse_linear...
section[(Intercept)]
dir=[fixed.effect00000001]
file for covariates=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c414652c68]
read n=[1290] entries from file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c414652c68]
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c414652c68] 0/645 (idx,y) = (0, 1)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c414652c68] 1/645 (idx,y) = (1, 1)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c414652c68] 2/645 (idx,y) = (2, 1)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c414652c68] 3/645 (idx,y) = (3, 1)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c414652c68] 4/645 (idx,y) = (4, 1)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c414652c68] 5/645 (idx,y) = (5, 1)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c414652c68] 6/645 (idx,y) = (6, 1)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c414652c68] 7/645 (idx,y) = (7, 1)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c414652c68] 8/645 (idx,y) = (8, 1)
file=[C:/Users/ricardo/AppData/Local/Temp/Rtmp80k15f/file6c430477f3a/data.files/file6c414652c68] 9/645 (idx,y) = (9, 1)
prior mean=[0]
prior precision=[0]
compute=[1]
output:
summary=[1]
return.marginals=[1]
nquantiles=[3] [ 0.025 0.5 0.975 ]
ncdf=[0] [ ]
Index table: number of entries[3], total length[1936]
tag start-index length
Predictor 0 645
ZBS 645 1290
(Intercept) 1935 1
parse section=[6] name=[INLA.Parameters] type=[INLA]
inla_parse_INLA...
section[INLA.Parameters]
lincomb.derived.only = [Yes]
lincomb.derived.correlation.matrix = [No]
global_node.factor = 2.000
global_node.degree = 2147483647
reordering = -1
Contents of ai_param 0000000005C12E30
Optimiser: DEFAULT METHOD
Option for GSL-BFGS2: tol = 0.1
Option for GSL-BFGS2: step_size = 1
Option for GSL-BFGS2: epsx = 0.005
Option for GSL-BFGS2: epsf = 0.000353553
Option for GSL-BFGS2: epsg = 0.005
Restart: 0
Mode known: No
Gaussian approximation:
abserr_func = 0.0005
abserr_step = 0.0005
optpar_fp = 0
optpar_nr_step_factor = -0.1
Gaussian data: No
Strategy: Use a mean-skew corrected Gaussian by fitting a Skew-Normal
Fast mode: On
Use linear approximation to log(|Q +c|)? Yes
Method: Compute the derivative exact
Parameters for improved approximations
Number of points evaluate: 9
Step length to compute derivatives numerically: 0.000100002
Stencil to compute derivatives numerically: 5
Cutoff value to construct local neigborhood: 0.0001
Log calculations: On
Log calculated marginal for the hyperparameters: On
Integration strategy: Automatic (GRID for dim(theta)=1 and 2 and otherwise CCD)
f0 (CCD only): 1.100000
dz (GRID only): 0.750000
Adjust weights (GRID only): On
Difference in log-density limit (GRID only): 6.000000
Skip configurations with (presumed) small density (GRID only): On
Gradient is computed using Central difference with step-length 0.010000
Hessian is computed using Central difference with step-length 0.100000
Hessian matrix is forced to be a diagonal matrix? [No]
Compute effective number of parameters? [Yes]
Perform a Monte Carlo error-test? [No]
Interpolator [Auto]
CPO required diff in log-density [3]
Stupid search mode:
Status [On]
Max iter [1000]
Factor [1.05]
Numerical integration of hyperparameters:
Maximum number of function evaluations [100000]
Relative error ....................... [1e-005]
Absolute error ....................... [1e-006]
To stabilise the numerical optimisation:
Minimum value of the -Hessian [-1.#INF]
CPO manual calculation[No]
Laplace-correction is Disabled.
inla_build: check for unused entries in[C:\Users\ricardo\AppData\Local\Temp\Rtmp80k15f\file6c430477f3a/Model.ini]
inla_INLA...
Strategy = [DEFAULT]
Sparse-matrix library... = [taucs]
OpenMP strategy......... = [medium]
Density-strategy........ = [High]
Size of graph........... = [1936]
Number of constraints... = [1]
Found optimal reordering=[amdc] nnz(L)=[9531] and use_global_nodes(user)=[no]
List of hyperparameters:
theta[0] = [intern zero-probability parameter for zero-inflated poisson_0]
theta[1] = [Log precision for ZBS (idd component)]
theta[2] = [Log precision for ZBS (spatial component)]
Optimise using DEFAULT METHOD
max.logdens= -1.#IND fn= 1 theta= -0.9900 4.0000 4.0000 range=[-1.#J -1.#J]
Is there anything I can do to fix this error?
Thank you very much for your attention.
Luiz Henrique Arroyo
INLA help
Oct 5, 2018, 10:15:14 AM10/5/18
to R-inla discussion group, Luiz Henrique .Arroyo
Looks like there is something going on in the offset and there are cases where E=0
Can u define E in the family instead?
Can u define E in the family instead?
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INLA help
Oct 5, 2018, 6:38:53 PM10/5/18
to R-inla discussion group, Luiz Henrique .Arroyo
Might be in the response itself...
On 5 Oct 2018, 08:41 -0500, Luiz Henrique .Arroyo <luiz....@hotmail.com>, wrote:
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