error in model fitting using INLA

[Getachew Dejene]

Hello Dear all,

I was trying to fit a model using INLA for spatial analysis here is my sample code 

# Define the formula
formula <- cases_mu + death_mu ~ 1 + f(idarea, model = "besag", graph = ALB.graph) + f(idarea1, model = "iid")

### Fit the model using INLA
mod <- inla(
  formula = formula,
  family = "poisson",
  data = df_Covid,E=E,
  control.compute=list(dic=TRUE))

when I run the code to fit the model I got error las follows:

Error in inla.inlaprogram.has.crashed() : The inla-program exited with an error. Unless you interupted it yourself, please rerun with verbose=TRUE and check the output carefully. If this does not help, please contact the developers at <he...@r-inla.org>. *** inla.core.safe: inla.program has crashed: rerun to get better initial values. try=1/2 Error in inla.inlaprogram.has.crashed() : The inla-program exited with an error. Unless you interupted it yourself, please rerun with verbose=TRUE and check the output carefully. If this does not help, please contact the developers at <he...@r-inla.org>. *** inla.core.safe: inla.program has crashed: rerun to get better initial values. try=2/2 Error in inla.inlaprogram.has.crashed() : The inla-program exited with an error. Unless you interupted it yourself, please rerun with verbose=TRUE and check the output carefully. If this does not help, please contact the developers at <he...@r-inla.org>. Error in inla.core.safe(formula = formula, family = family, contrasts = contrasts, : *** Fail to get good enough initial values. Maybe it is due to something else.

[INLA help]

Can u add options 

verbose=T,debug=T

And share the output?

—

Haavard Rue

HelpDesk 

help@r-inla. org

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[Getachew Dejene]

Dear  Haavard Rue, thank you for your help here is the out put:

"[1] "head(scale)"

NULL [1] "head(weights)" NULL [1] "head(Ntrials)" NULL [1] "head(offset)" NULL [1] "head(E)" [1] 11367.347 10733.177 9059.453 11311.607 10179.080 [6] 9261.070 [1] "head(strata)" NULL [1] "head(lp.scale)" NULL [1] "head(link.covariates)" NULL [1] "MPredictor 0" [1] "NPredictor 67" [1] "NData 67" [1] "y...fake has length 67" n.family 1 [1] "Entries with same length:" "County" [3] "cases_mu" "rel.cases" [5] "death_mu" "rel.death" [7] "E" "idarea" [9] "idarea1" "y...fake" [1] "prepare problem section" Prepare inla file.....inla.create.data.file: n.data = 67 [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file350039aa2925" [1] 0 201 67 3 0 1 0 1 [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file35001d9d4963" [1] 0 1 1 1 0 1 0 1 [1] "prepare data section" [1] "prepare predictor section" [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file3500433b3991" [1] 0 134 67 2 0 1 0 1 write label[ (Intercept) ] [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file35006a96575b" [1] 0 134 67 2 0 1 0 1 file fixed C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file35006a96575b 1 besag 2 iid [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file3500e9f5940" [1] 0 67 67 1 0 1 0 1 [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file35001dc03b1e" [1] 0 134 67 2 0 0 0 1 [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file350015ed13a9" [1] 0 134 67 2 0 0 0 1 [1] "n 67" [1] "nrep 1" [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file35001bc02c66" [1] 0 67 67 1 0 1 0 1 [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file35006a4ea1" [1] 0 134 67 2 0 0 0 1 [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file350022ef3259" [1] 0 134 67 2 0 0 0 1 [1] "n 67" [1] "nrep 1" ...done Run inla...[1] "all.args: -s -v -t4:1 -B0 -P compact" Read ntt 4 1 with max.threads 8 Found num.threads = 4:1 max_threads = 4 882c43d68fb015d72b699bcc458cf277dfe110c2 - Mon Apr 24 16:19:16 2023 +0100 Report bugs to <he...@r-inla.org> Set reordering to id=[0] and name=[default] Process file[C:\Users\Getachew\AppData\Local\Temp\RtmpGG6BlT\file3500343c6cbd/Model.ini] threads[4] max.threads[8] blas_threads[1] nested[4:1] inla_build... number of sections=[11] parse section=[0] name=[INLA.libR] type=[LIBR] inla_parse_libR... section[INLA.libR] R_HOME=[C:/PROGRA~1/R/R-42~1.2] parse section=[8] name=[INLA.Expert] type=[EXPERT] inla_parse_expert... section[INLA.Expert] disable.gaussian.check=[0] Measure dot.product.gain=[No] cpo.manual=[0] jp.file=[(null)] jp.model=[(null)] parse section=[1] name=[INLA.Model] type=[PROBLEM] inla_parse_problem... name=[INLA.Model] R-INLA version = [23.04.24] R-INLA build date = [Mon Apr 24 10:06:18 PM +03 2023 (Version_23.04.24)] Build tag = [Version_23.04.24] System memory = [7.7Gb] Cores = (Physical= 8, Logical= 8) 'char' is signed openmp.strategy=[default] pardiso-library installed and working? = [no] smtp = [taucs] strategy = [default] store results in directory=[C:\Users\Getachew\AppData\Local\Temp\RtmpGG6BlT\file3500343c6cbd/results.files] output: gcpo=[0] num.level.sets=[-1] size.max=[32] strategy=[Posterior] correct.hyperpar=[1] epsilon=[0.005] prior.diagonal=[0.0001] keep=[] remove.fixed=[1] remove=[] cpo=[0] po=[0] dic=[1] kld=[1] mlik=[1] q=[0] graph=[0] hyperparameters=[1] config=[0] likelihood.info=[0] internal.opt=[1] summary=[1] return.marginals=[1] return.marginals.predictor=[0] 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-05] initialise log_precision[13.8155] fixed=[1] user.scale=[1] n=[67] m=[0] ndata=[67] compute=[1] read offsets from file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file3500433b3991] read n=[134] entries from file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file3500433b3991] file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file3500433b3991] 0/67 (idx,y) = (0, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file3500433b3991] 1/67 (idx,y) = (1, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file3500433b3991] 2/67 (idx,y) = (2, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file3500433b3991] 3/67 (idx,y) = (3, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file3500433b3991] 4/67 (idx,y) = (4, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file3500433b3991] 5/67 (idx,y) = (5, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file3500433b3991] 6/67 (idx,y) = (6, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file3500433b3991] 7/67 (idx,y) = (7, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file3500433b3991] 8/67 (idx,y) = (8, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file3500433b3991] 9/67 (idx,y) = (9, 0) A=[(null)] Aext=[(null)] AextPrecision=[1e+08] output: summary=[1] return.marginals=[1] return.marginals.predictor=[0] 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=[POISSON] likelihood=[POISSON] file->name=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file350039aa2925] file->name=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file35003ff60c] file->name=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file35001d9d4963] file->name=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file35003c9fa0d] read n=[201] entries from file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500343c6cbd/data.files/file350039aa2925] mdata.nattributes = 0 0/67 (idx,a,y,d) = (0, 11367.3, 129.265, 1) 1/67 (idx,a,y,d) = (1, 10733.2, 459.391, 1) 2/67 (idx,a,y,d) = (2, 9059.45, 48.28, 1) 3/67 (idx,a,y,d) = (3, 11311.6, 52.657, 1) 4/67 (idx,a,y,d) = (4, 10179.1, 120.926, 1) 5/67 (idx,a,y,d) = (5, 9261.07, 20.076, 1) 6/67 (idx,a,y,d) = (6, 10221.3, 42.517, 1) 7/67 (idx,a,y,d) = (7, 11345, 268.806, 1) 8/67 (idx,a,y,d) = (8, 10142.4, 70.87, 1) 9/67 (idx,a,y,d) = (9, 8280.63, 44.252, 1) *** ERROR *** INLA.Data1: POISSON likelihood is defined on integers, but y[0] = 129.265 ..done Error in inla.inlaprogram.has.crashed() : The inla-program exited with an error. Unless you interupted it yourself, please rerun with verbose=TRUE and check the output carefully. If this does not help, please contact the developers at <he...@r-inla.org>. *** inla.core.safe: inla.program has crashed: rerun to get better initial values. try=1/2 [1] "MPredictor 0" [1] "NPredictor 67" [1] "NData 67" [1] "y...fake has length 67" n.family 1 [1] "Entries with same length:" "County" [3] "cases_mu" "rel.cases" [5] "death_mu" "rel.death" [7] "E" "idarea" [9] "idarea1" "y...fake" [1] "prepare problem section" Prepare inla file.....inla.create.data.file: n.data = 67 [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file35001689517" [1] 0 201 67 3 0 1 0 1 [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file3500e0f6f25" [1] 0 1 1 1 0 1 0 1 [1] "prepare data section" [1] "prepare predictor section" [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file35003d5c4cf1" [1] 0 134 67 2 0 1 0 1 write label[ (Intercept) ] [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file3500426c2516" [1] 0 134 67 2 0 1 0 1 file fixed C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file3500426c2516 1 besag 2 iid [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file350018b82e8b" [1] 0 67 67 1 0 1 0 1 [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file3500165a1dc4" [1] 0 134 67 2 0 0 0 1 [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file3500584e5e17" [1] 0 134 67 2 0 0 0 1 [1] "n 67" [1] "nrep 1" [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file35007b3f92" [1] 0 67 67 1 0 1 0 1 [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file3500c92791" [1] 0 134 67 2 0 0 0 1 [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file3500fb325e6" [1] 0 134 67 2 0 0 0 1 [1] "n 67" [1] "nrep 1" ...done Run inla...[1] "all.args: -s -v -t4:1 -B0 -P compact" Read ntt 4 1 with max.threads 8 Found num.threads = 4:1 max_threads = 4 882c43d68fb015d72b699bcc458cf277dfe110c2 - Mon Apr 24 16:19:16 2023 +0100 Report bugs to <he...@r-inla.org> Set reordering to id=[0] and name=[default] Process file[C:\Users\Getachew\AppData\Local\Temp\RtmpGG6BlT\file350034702943/Model.ini] threads[4] max.threads[8] blas_threads[1] nested[4:1] inla_build... number of sections=[11] parse section=[0] name=[INLA.libR] type=[LIBR] inla_parse_libR... section[INLA.libR] R_HOME=[C:/PROGRA~1/R/R-42~1.2] parse section=[8] name=[INLA.Expert] type=[EXPERT] inla_parse_expert... section[INLA.Expert] disable.gaussian.check=[0] Measure dot.product.gain=[No] cpo.manual=[0] jp.file=[(null)] jp.model=[(null)] parse section=[1] name=[INLA.Model] type=[PROBLEM] inla_parse_problem... name=[INLA.Model] R-INLA version = [23.04.24] R-INLA build date = [Mon Apr 24 10:06:18 PM +03 2023 (Version_23.04.24)] Build tag = [Version_23.04.24] System memory = [7.7Gb] Cores = (Physical= 8, Logical= 8) 'char' is signed openmp.strategy=[default] pardiso-library installed and working? = [no] smtp = [taucs] strategy = [default] store results in directory=[C:\Users\Getachew\AppData\Local\Temp\RtmpGG6BlT\file350034702943/results.files] output: gcpo=[0] num.level.sets=[-1] size.max=[32] strategy=[Posterior] correct.hyperpar=[1] epsilon=[0.005] prior.diagonal=[0.0001] keep=[] remove.fixed=[1] remove=[] cpo=[0] po=[0] dic=[0] kld=[1] mlik=[1] q=[0] graph=[0] hyperparameters=[1] config=[0] likelihood.info=[0] internal.opt=[1] summary=[1] return.marginals=[0] return.marginals.predictor=[0] 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-05] initialise log_precision[13.8155] fixed=[1] user.scale=[1] n=[67] m=[0] ndata=[67] compute=[0] read offsets from file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file35003d5c4cf1] read n=[134] entries from file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file35003d5c4cf1] file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file35003d5c4cf1] 0/67 (idx,y) = (0, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file35003d5c4cf1] 1/67 (idx,y) = (1, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file35003d5c4cf1] 2/67 (idx,y) = (2, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file35003d5c4cf1] 3/67 (idx,y) = (3, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file35003d5c4cf1] 4/67 (idx,y) = (4, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file35003d5c4cf1] 5/67 (idx,y) = (5, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file35003d5c4cf1] 6/67 (idx,y) = (6, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file35003d5c4cf1] 7/67 (idx,y) = (7, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file35003d5c4cf1] 8/67 (idx,y) = (8, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file35003d5c4cf1] 9/67 (idx,y) = (9, 0) A=[(null)] Aext=[(null)] AextPrecision=[1e+08] output: summary=[1] return.marginals=[0] return.marginals.predictor=[0] 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=[POISSON] likelihood=[POISSON] file->name=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file35001689517] file->name=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file350060b6a31] file->name=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file3500e0f6f25] file->name=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file350070aac5f] read n=[201] entries from file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file350034702943/data.files/file35001689517] mdata.nattributes = 0 0/67 (idx,a,y,d) = (0, 11367.3, 129.265, 1) 1/67 (idx,a,y,d) = (1, 10733.2, 459.391, 1) 2/67 (idx,a,y,d) = (2, 9059.45, 48.28, 1) 3/67 (idx,a,y,d) = (3, 11311.6, 52.657, 1) 4/67 (idx,a,y,d) = (4, 10179.1, 120.926, 1) 5/67 (idx,a,y,d) = (5, 9261.07, 20.076, 1) 6/67 (idx,a,y,d) = (6, 10221.3, 42.517, 1) 7/67 (idx,a,y,d) = (7, 11345, 268.806, 1) 8/67 (idx,a,y,d) = (8, 10142.4, 70.87, 1) 9/67 (idx,a,y,d) = (9, 8280.63, 44.252, 1) *** ERROR *** INLA.Data1: POISSON likelihood is defined on integers, but y[0] = 129.265 ..done Error in inla.inlaprogram.has.crashed() : The inla-program exited with an error. Unless you interupted it yourself, please rerun with verbose=TRUE and check the output carefully. If this does not help, please contact the developers at <he...@r-inla.org>. *** inla.core.safe: inla.program has crashed: rerun to get better initial values. try=2/2 [1] "MPredictor 0" [1] "NPredictor 67" [1] "NData 67" [1] "y...fake has length 67" n.family 1 [1] "Entries with same length:" "County" [3] "cases_mu" "rel.cases" [5] "death_mu" "rel.death" [7] "E" "idarea" [9] "idarea1" "y...fake" [1] "prepare problem section" Prepare inla file.....inla.create.data.file: n.data = 67 [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file350077ce3c46" [1] 0 201 67 3 0 1 0 1 [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file3500200b75e0" [1] 0 1 1 1 0 1 0 1 [1] "prepare data section" [1] "prepare predictor section" [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file35005462475b" [1] 0 134 67 2 0 1 0 1 write label[ (Intercept) ] [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file350079a1713" [1] 0 134 67 2 0 1 0 1 file fixed C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file350079a1713 1 besag 2 iid [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file350046db7a46" [1] 0 67 67 1 0 1 0 1 [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file35001e812f44" [1] 0 134 67 2 0 0 0 1 [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file35001f7c5e90" [1] 0 134 67 2 0 0 0 1 [1] "n 67" [1] "nrep 1" [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file35002b7e4792" [1] 0 67 67 1 0 1 0 1 [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file350068145867" [1] 0 134 67 2 0 0 0 1 [1] "\nOpen file to write C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file350060bd5483" [1] 0 134 67 2 0 0 0 1 [1] "n 67" [1] "nrep 1" ...done Run inla...[1] "all.args: -s -v -t4:1 -B0 -P compact" Read ntt 4 1 with max.threads 8 Found num.threads = 4:1 max_threads = 4 882c43d68fb015d72b699bcc458cf277dfe110c2 - Mon Apr 24 16:19:16 2023 +0100 Report bugs to <he...@r-inla.org> Set reordering to id=[0] and name=[default] Process file[C:\Users\Getachew\AppData\Local\Temp\RtmpGG6BlT\file3500161b4490/Model.ini] threads[4] max.threads[8] blas_threads[1] nested[4:1] inla_build... number of sections=[11] parse section=[0] name=[INLA.libR] type=[LIBR] inla_parse_libR... section[INLA.libR] R_HOME=[C:/PROGRA~1/R/R-42~1.2] parse section=[8] name=[INLA.Expert] type=[EXPERT] inla_parse_expert... section[INLA.Expert] disable.gaussian.check=[0] Measure dot.product.gain=[No] cpo.manual=[0] jp.file=[(null)] jp.model=[(null)] parse section=[1] name=[INLA.Model] type=[PROBLEM] inla_parse_problem... name=[INLA.Model] R-INLA version = [23.04.24] R-INLA build date = [Mon Apr 24 10:06:18 PM +03 2023 (Version_23.04.24)] Build tag = [Version_23.04.24] System memory = [7.7Gb] Cores = (Physical= 8, Logical= 8) 'char' is signed openmp.strategy=[default] pardiso-library installed and working? = [no] smtp = [taucs] strategy = [default] store results in directory=[C:\Users\Getachew\AppData\Local\Temp\RtmpGG6BlT\file3500161b4490/results.files] output: gcpo=[0] num.level.sets=[-1] size.max=[32] strategy=[Posterior] correct.hyperpar=[1] epsilon=[0.005] prior.diagonal=[0.0001] keep=[] remove.fixed=[1] remove=[] cpo=[0] po=[0] dic=[0] kld=[1] mlik=[1] q=[0] graph=[0] hyperparameters=[1] config=[0] likelihood.info=[0] internal.opt=[1] summary=[1] return.marginals=[0] return.marginals.predictor=[0] 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-05] initialise log_precision[13.8155] fixed=[1] user.scale=[1] n=[67] m=[0] ndata=[67] compute=[0] read offsets from file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file35005462475b] read n=[134] entries from file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file35005462475b] file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file35005462475b] 0/67 (idx,y) = (0, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file35005462475b] 1/67 (idx,y) = (1, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file35005462475b] 2/67 (idx,y) = (2, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file35005462475b] 3/67 (idx,y) = (3, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file35005462475b] 4/67 (idx,y) = (4, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file35005462475b] 5/67 (idx,y) = (5, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file35005462475b] 6/67 (idx,y) = (6, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file35005462475b] 7/67 (idx,y) = (7, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file35005462475b] 8/67 (idx,y) = (8, 0) file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file35005462475b] 9/67 (idx,y) = (9, 0) A=[(null)] Aext=[(null)] AextPrecision=[1e+08] output: summary=[1] return.marginals=[0] return.marginals.predictor=[0] 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=[POISSON] likelihood=[POISSON] file->name=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file350077ce3c46] file->name=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file35002a0a7fcb] file->name=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file3500200b75e0] file->name=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file3500771c4ede] read n=[201] entries from file=[C:/Users/Getachew/AppData/Local/Temp/RtmpGG6BlT/file3500161b4490/data.files/file350077ce3c46] mdata.nattributes = 0 0/67 (idx,a,y,d) = (0, 11367.3, 129.265, 1) 1/67 (idx,a,y,d) = (1, 10733.2, 459.391, 1) 2/67 (idx,a,y,d) = (2, 9059.45, 48.28, 1) 3/67 (idx,a,y,d) = (3, 11311.6, 52.657, 1) 4/67 (idx,a,y,d) = (4, 10179.1, 120.926, 1) 5/67 (idx,a,y,d) = (5, 9261.07, 20.076, 1) 6/67 (idx,a,y,d) = (6, 10221.3, 42.517, 1) 7/67 (idx,a,y,d) = (7, 11345, 268.806, 1) 8/67 (idx,a,y,d) = (8, 10142.4, 70.87, 1) 9/67 (idx,a,y,d) = (9, 8280.63, 44.252, 1) *** ERROR *** INLA.Data1: POISSON likelihood is defined on integers, but y[0] = 129.265 ..done Error in inla.inlaprogram.has.crashed() : The inla-program exited with an error. Unless you interupted it yourself, please rerun with verbose=TRUE and check the output carefully. If this does not help, please contact the developers at <he...@r-inla.org>. Error in inla.core.safe(formula = formula, family = family, contrasts = contrasts, :  

*** Fail to get good enough initial values. Maybe it is due to something else."

Thank you

[INLA help]

If you really have non integer observations use familiarly xpoisson 

To view this discussion on the web, visit https://groups.google.com/d/msgid/r-inla-discussion-group/78986f1b-663d-4464-ac5f-9f348fc09177n%40googlegroups.com.

[Havard Rue]

Your observations are not integers which poisson require 

-- 

Håvard Rue 

hr...@r-inla.org

To view this discussion on the web, visit https://groups.google.com/d/msgid/r-inla-discussion-group/78986f1b-663d-4464-ac5f-9f348fc09177n%40googlegroups.com.

[Håvard Rue]

it is not clear what is going on,

can you rerun with arguments

verbose=TRUE,debug=TRUE,safe=FALSE

and send me the output?

thx
H

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--

Håvard Rue
hr...@r-inla.org