Created
May 6, 2014 09:32
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Running the bym2 model in INLA
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| > n <- nrow(CC) | |
| > Q <- INLA:::inla.pc.bym.Q(border, scale.model=TRUE) | |
| > u <- .2/.31 | |
| > alpha <- .01 | |
| > phi.u <- .5 | |
| > phi.alpha <- 2/3 | |
| > formula2 <- agr ~ age + sex + age:sex + | |
| + f(geo, model='bym2', graph=border, | |
| + constr=TRUE, scale.model=TRUE, | |
| + hyper=list(phi=list(prior='pc', | |
| + param=c(phi.u, phi.alpha), | |
| + initial=-3), | |
| + prec=list(prior='pc.prec', | |
| + param=c(u, alpha), | |
| + initial=5))) | |
| > agr_geo <- inla(formula2, family='gaussian', data=CC, verbose=TRUE) | |
| hgid: f4b2fa41b99b date: Thu Apr 03 15:35:52 2014 +0200 | |
| Report bugs to <help@r-inla.org> | |
| Processing file [/tmp/RtmpwnHhDH/file21967666466b/Model.ini] max_threads=[12] | |
| inla_build... | |
| number of sections=[11] | |
| parse section=[0] name=[INLA.Model] type=[PROBLEM] | |
| inla_parse_problem... | |
| name=[INLA.Model] | |
| openmp.strategy=[default] | |
| store results in directory=[/tmp/RtmpwnHhDH/file21967666466b/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=[2] name=[Predictor] type=[PREDICTOR] | |
| inla_parse_predictor ... | |
| section=[Predictor] | |
| dir=[predictor] | |
| PRIOR->name=[loggamma] | |
| PRIOR->from_theta=[function (x) <<NEWLINE>>exp(x)] | |
| PRIOR->to_theta = [function (x) <<NEWLINE>>log(x)] | |
| PRIOR->PARAMETERS=[1, 1e-05] | |
| initialise log_precision[11] | |
| fixed=[1] | |
| user.scale=[1] | |
| n=[14270] | |
| m=[0] | |
| ndata=[14270] | |
| compute=[0] | |
| read offsets from file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] | |
| read n=[28540] entries from file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] 0/14270 (idx,y) = (0, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] 1/14270 (idx,y) = (1, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] 2/14270 (idx,y) = (2, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] 3/14270 (idx,y) = (3, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] 4/14270 (idx,y) = (4, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] 5/14270 (idx,y) = (5, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] 6/14270 (idx,y) = (6, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] 7/14270 (idx,y) = (7, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] 8/14270 (idx,y) = (8, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] 9/14270 (idx,y) = (9, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] 10/14270 (idx,y) = (10, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] 11/14270 (idx,y) = (11, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] 12/14270 (idx,y) = (12, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] 13/14270 (idx,y) = (13, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] 14/14270 (idx,y) = (14, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] 15/14270 (idx,y) = (15, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] 16/14270 (idx,y) = (16, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] 17/14270 (idx,y) = (17, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] 18/14270 (idx,y) = (18, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e5bbe79] 19/14270 (idx,y) = (19, 0) | |
| Aext=[(null)] | |
| AextPrecision=[1e+08] | |
| output: | |
| summary=[1] | |
| return.marginals=[1] | |
| nquantiles=[3] [ 0.025 0.5 0.975 ] | |
| ncdf=[0] [ ] | |
| parse section=[1] name=[INLA.Data1] type=[DATA] | |
| inla_parse_data [section 1]... | |
| tag=[INLA.Data1] | |
| family=[GAUSSIAN] | |
| likelihood=[GAUSSIAN] | |
| file->name=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e46977d] | |
| file->name=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219675645f27] | |
| read n=[42810] entries from file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21961e46977d] | |
| 0/14270 (idx,a,y,d) = (0, 1, 3.88889, 1) | |
| 1/14270 (idx,a,y,d) = (1, 1, 4.5, 1) | |
| 2/14270 (idx,a,y,d) = (2, 1, 3.125, 1) | |
| 3/14270 (idx,a,y,d) = (3, 1, 3.88889, 1) | |
| 4/14270 (idx,a,y,d) = (4, 1, 4.25, 1) | |
| 5/14270 (idx,a,y,d) = (5, 1, 3.625, 1) | |
| 6/14270 (idx,a,y,d) = (6, 1, 4, 1) | |
| 7/14270 (idx,a,y,d) = (7, 1, 3.5, 1) | |
| 8/14270 (idx,a,y,d) = (8, 1, 3.25, 1) | |
| 9/14270 (idx,a,y,d) = (9, 1, 3.875, 1) | |
| 10/14270 (idx,a,y,d) = (10, 1, 3.375, 1) | |
| 11/14270 (idx,a,y,d) = (11, 1, 3.22222, 1) | |
| 12/14270 (idx,a,y,d) = (12, 1, 2.875, 1) | |
| 13/14270 (idx,a,y,d) = (13, 1, 4.22222, 1) | |
| 14/14270 (idx,a,y,d) = (14, 1, 3.875, 1) | |
| 15/14270 (idx,a,y,d) = (15, 1, 3, 1) | |
| 16/14270 (idx,a,y,d) = (16, 1, 2.875, 1) | |
| 17/14270 (idx,a,y,d) = (17, 1, 3.625, 1) | |
| 18/14270 (idx,a,y,d) = (18, 1, 2.625, 1) | |
| 19/14270 (idx,a,y,d) = (19, 1, 2.375, 1) | |
| use variant [0] | |
| bit 0 is off | |
| bit 1 is off | |
| bit 2 is off | |
| bit 3 is off | |
| initialise log_precision[4] | |
| fixed=[0] | |
| PRIOR->name=[loggamma] | |
| PRIOR->from_theta=[function (x) <<NEWLINE>>exp(x)] | |
| PRIOR->to_theta = [function (x) <<NEWLINE>>log(x)] | |
| PRIOR->PARAMETERS=[1, 5e-05] | |
| Link model [IDENTITY] | |
| Link order [-1] | |
| Link ntheta [0] | |
| mix.use[0] | |
| parse section=[9] name=[geo] type=[FFIELD] | |
| inla_parse_ffield... | |
| section=[geo] | |
| dir=[random.effect00000001] | |
| model=[bym2] | |
| PRIOR0->name=[pcprec] | |
| PRIOR0->from_theta=[function (x) <<NEWLINE>>exp(x)] | |
| PRIOR0->to_theta = [function (x) <<NEWLINE>>log(x)] | |
| PRIOR0->PARAMETERS0=[0.645161 0.01] | |
| PRIOR1->name=[table] | |
| PRIOR1->from_theta=[function (x) <<NEWLINE>>exp(x)/(1 + exp(x))] | |
| PRIOR1->to_theta = [function (x) <<NEWLINE>>log(x/(1 - x))] | |
| PRIOR1->table=[table: /tmp/RtmpwnHhDH/file21967666466b/data.files/file2196381dfd82] | |
| constr=[0] | |
| diagonal=[9.99978e-07] | |
| id.names=<not present> | |
| compute=[1] | |
| nrep=[1] | |
| ngroup=[1] | |
| read covariates from file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] | |
| read n=[28540] entries from file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] 0/14270 (idx,y) = (0, 12) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] 1/14270 (idx,y) = (1, 12) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] 2/14270 (idx,y) = (2, 12) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] 3/14270 (idx,y) = (3, 12) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] 4/14270 (idx,y) = (4, 12) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] 5/14270 (idx,y) = (5, 12) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] 6/14270 (idx,y) = (6, 12) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] 7/14270 (idx,y) = (7, 12) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] 8/14270 (idx,y) = (8, 12) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] 9/14270 (idx,y) = (9, 12) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] 10/14270 (idx,y) = (10, 12) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] 11/14270 (idx,y) = (11, 12) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] 12/14270 (idx,y) = (12, 12) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] 13/14270 (idx,y) = (13, 12) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] 14/14270 (idx,y) = (14, 12) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] 15/14270 (idx,y) = (15, 12) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] 16/14270 (idx,y) = (16, 12) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] 17/14270 (idx,y) = (17, 12) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] 18/14270 (idx,y) = (18, 12) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219629a73474] 19/14270 (idx,y) = (19, 12) | |
| read graph from file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962d2afec7] | |
| file for locations=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219650d89607] | |
| nlocations=[249] | |
| 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] | |
| locations[10]=[11] | |
| locations[11]=[12] | |
| locations[12]=[13] | |
| locations[13]=[14] | |
| locations[14]=[15] | |
| locations[15]=[16] | |
| locations[16]=[17] | |
| locations[17]=[18] | |
| locations[18]=[19] | |
| locations[19]=[20] | |
| initialise log_precision [5] | |
| fixed=[0] | |
| initialise phi_intern [-3] | |
| fixed=[0] | |
| adjust.for.con.comp[1] | |
| scale.model[1] | |
| scale.model: prec_scale[0.71926] | |
| read extra constraint from file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196833f0b7] | |
| Constraint[0] | |
| A[249] = 1.000000 | |
| A[250] = 1.000000 | |
| A[251] = 1.000000 | |
| A[252] = 1.000000 | |
| A[253] = 1.000000 | |
| A[254] = 1.000000 | |
| A[255] = 1.000000 | |
| A[256] = 1.000000 | |
| A[257] = 1.000000 | |
| A[258] = 1.000000 | |
| A[259] = 1.000000 | |
| A[260] = 1.000000 | |
| A[261] = 1.000000 | |
| A[262] = 1.000000 | |
| A[263] = 1.000000 | |
| A[264] = 1.000000 | |
| A[265] = 1.000000 | |
| A[266] = 1.000000 | |
| A[267] = 1.000000 | |
| A[268] = 1.000000 | |
| A[269] = 1.000000 | |
| e[0] = 0.000000 | |
| rank-deficiency is *defined* [1] | |
| output: | |
| summary=[1] | |
| return.marginals=[1] | |
| nquantiles=[3] [ 0.025 0.5 0.975 ] | |
| ncdf=[0] [ ] | |
| section=[3] name=[(Intercept)] type=[LINEAR] | |
| inla_parse_linear... | |
| section[(Intercept)] | |
| dir=[fixed.effect00000001] | |
| file for covariates=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] | |
| read n=[28540] entries from file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] 0/14270 (idx,y) = (0, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] 1/14270 (idx,y) = (1, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] 2/14270 (idx,y) = (2, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] 3/14270 (idx,y) = (3, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] 4/14270 (idx,y) = (4, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] 5/14270 (idx,y) = (5, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] 6/14270 (idx,y) = (6, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] 7/14270 (idx,y) = (7, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] 8/14270 (idx,y) = (8, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] 9/14270 (idx,y) = (9, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] 10/14270 (idx,y) = (10, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] 11/14270 (idx,y) = (11, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] 12/14270 (idx,y) = (12, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] 13/14270 (idx,y) = (13, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] 14/14270 (idx,y) = (14, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] 15/14270 (idx,y) = (15, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] 16/14270 (idx,y) = (16, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] 17/14270 (idx,y) = (17, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] 18/14270 (idx,y) = (18, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219689edc8d] 19/14270 (idx,y) = (19, 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] [ ] | |
| section=[4] name=[age] type=[LINEAR] | |
| inla_parse_linear... | |
| section[age] | |
| dir=[fixed.effect00000002] | |
| file for covariates=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] | |
| read n=[28540] entries from file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] 0/14270 (idx,y) = (0, 19) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] 1/14270 (idx,y) = (1, 26) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] 2/14270 (idx,y) = (2, 25) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] 3/14270 (idx,y) = (3, 22) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] 4/14270 (idx,y) = (4, 21) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] 5/14270 (idx,y) = (5, 27) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] 6/14270 (idx,y) = (6, 43) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] 7/14270 (idx,y) = (7, 28) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] 8/14270 (idx,y) = (8, 22) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] 9/14270 (idx,y) = (9, 24) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] 10/14270 (idx,y) = (10, 21) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] 11/14270 (idx,y) = (11, 23) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] 12/14270 (idx,y) = (12, 21) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] 13/14270 (idx,y) = (13, 21) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] 14/14270 (idx,y) = (14, 19) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] 15/14270 (idx,y) = (15, 21) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] 16/14270 (idx,y) = (16, 42) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] 17/14270 (idx,y) = (17, 29) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] 18/14270 (idx,y) = (18, 28) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196684e3c6e] 19/14270 (idx,y) = (19, 22) | |
| prior mean=[0] | |
| prior precision=[0.001] | |
| compute=[1] | |
| output: | |
| summary=[1] | |
| return.marginals=[1] | |
| nquantiles=[3] [ 0.025 0.5 0.975 ] | |
| ncdf=[0] [ ] | |
| section=[5] name=[sexfemale] type=[LINEAR] | |
| inla_parse_linear... | |
| section[sexfemale] | |
| dir=[fixed.effect00000003] | |
| file for covariates=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] | |
| read n=[28540] entries from file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] 0/14270 (idx,y) = (0, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] 1/14270 (idx,y) = (1, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] 2/14270 (idx,y) = (2, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] 3/14270 (idx,y) = (3, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] 4/14270 (idx,y) = (4, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] 5/14270 (idx,y) = (5, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] 6/14270 (idx,y) = (6, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] 7/14270 (idx,y) = (7, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] 8/14270 (idx,y) = (8, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] 9/14270 (idx,y) = (9, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] 10/14270 (idx,y) = (10, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] 11/14270 (idx,y) = (11, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] 12/14270 (idx,y) = (12, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] 13/14270 (idx,y) = (13, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] 14/14270 (idx,y) = (14, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] 15/14270 (idx,y) = (15, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] 16/14270 (idx,y) = (16, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] 17/14270 (idx,y) = (17, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] 18/14270 (idx,y) = (18, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file219673b12b85] 19/14270 (idx,y) = (19, 1) | |
| prior mean=[0] | |
| prior precision=[0.001] | |
| compute=[1] | |
| output: | |
| summary=[1] | |
| return.marginals=[1] | |
| nquantiles=[3] [ 0.025 0.5 0.975 ] | |
| ncdf=[0] [ ] | |
| section=[6] name=[sexmale] type=[LINEAR] | |
| inla_parse_linear... | |
| section[sexmale] | |
| dir=[fixed.effect00000004] | |
| file for covariates=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] | |
| read n=[28540] entries from file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] 0/14270 (idx,y) = (0, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] 1/14270 (idx,y) = (1, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] 2/14270 (idx,y) = (2, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] 3/14270 (idx,y) = (3, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] 4/14270 (idx,y) = (4, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] 5/14270 (idx,y) = (5, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] 6/14270 (idx,y) = (6, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] 7/14270 (idx,y) = (7, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] 8/14270 (idx,y) = (8, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] 9/14270 (idx,y) = (9, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] 10/14270 (idx,y) = (10, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] 11/14270 (idx,y) = (11, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] 12/14270 (idx,y) = (12, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] 13/14270 (idx,y) = (13, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] 14/14270 (idx,y) = (14, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] 15/14270 (idx,y) = (15, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] 16/14270 (idx,y) = (16, 1) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] 17/14270 (idx,y) = (17, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] 18/14270 (idx,y) = (18, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21965f12e2dd] 19/14270 (idx,y) = (19, 0) | |
| prior mean=[0] | |
| prior precision=[0.001] | |
| compute=[1] | |
| output: | |
| summary=[1] | |
| return.marginals=[1] | |
| nquantiles=[3] [ 0.025 0.5 0.975 ] | |
| ncdf=[0] [ ] | |
| section=[7] name=[age:sexfemale] type=[LINEAR] | |
| inla_parse_linear... | |
| section[age:sexfemale] | |
| dir=[fixed.effect00000005] | |
| file for covariates=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] | |
| read n=[28540] entries from file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] 0/14270 (idx,y) = (0, 19) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] 1/14270 (idx,y) = (1, 26) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] 2/14270 (idx,y) = (2, 25) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] 3/14270 (idx,y) = (3, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] 4/14270 (idx,y) = (4, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] 5/14270 (idx,y) = (5, 27) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] 6/14270 (idx,y) = (6, 43) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] 7/14270 (idx,y) = (7, 28) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] 8/14270 (idx,y) = (8, 22) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] 9/14270 (idx,y) = (9, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] 10/14270 (idx,y) = (10, 21) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] 11/14270 (idx,y) = (11, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] 12/14270 (idx,y) = (12, 21) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] 13/14270 (idx,y) = (13, 21) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] 14/14270 (idx,y) = (14, 19) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] 15/14270 (idx,y) = (15, 21) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] 16/14270 (idx,y) = (16, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] 17/14270 (idx,y) = (17, 29) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] 18/14270 (idx,y) = (18, 28) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file2196116b150d] 19/14270 (idx,y) = (19, 22) | |
| prior mean=[0] | |
| prior precision=[0.001] | |
| compute=[1] | |
| output: | |
| summary=[1] | |
| return.marginals=[1] | |
| nquantiles=[3] [ 0.025 0.5 0.975 ] | |
| ncdf=[0] [ ] | |
| section=[8] name=[age:sexmale] type=[LINEAR] | |
| inla_parse_linear... | |
| section[age:sexmale] | |
| dir=[fixed.effect00000006] | |
| file for covariates=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] | |
| read n=[28540] entries from file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] 0/14270 (idx,y) = (0, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] 1/14270 (idx,y) = (1, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] 2/14270 (idx,y) = (2, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] 3/14270 (idx,y) = (3, 22) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] 4/14270 (idx,y) = (4, 21) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] 5/14270 (idx,y) = (5, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] 6/14270 (idx,y) = (6, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] 7/14270 (idx,y) = (7, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] 8/14270 (idx,y) = (8, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] 9/14270 (idx,y) = (9, 24) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] 10/14270 (idx,y) = (10, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] 11/14270 (idx,y) = (11, 23) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] 12/14270 (idx,y) = (12, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] 13/14270 (idx,y) = (13, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] 14/14270 (idx,y) = (14, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] 15/14270 (idx,y) = (15, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] 16/14270 (idx,y) = (16, 42) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] 17/14270 (idx,y) = (17, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] 18/14270 (idx,y) = (18, 0) | |
| file=[/tmp/RtmpwnHhDH/file21967666466b/data.files/file21962fdcc23] 19/14270 (idx,y) = (19, 0) | |
| prior mean=[0] | |
| prior precision=[0.001] | |
| compute=[1] | |
| output: | |
| summary=[1] | |
| return.marginals=[1] | |
| nquantiles=[3] [ 0.025 0.5 0.975 ] | |
| ncdf=[0] [ ] | |
| Index table: number of entries[8], total length[14774] | |
| tag start-index length | |
| Predictor 0 14270 | |
| geo 14270 498 | |
| (Intercept) 14768 1 | |
| age 14769 1 | |
| sexfemale 14770 1 | |
| sexmale 14771 1 | |
| age:sexfemale 14772 1 | |
| age:sexmale 14773 1 | |
| parse section=[10] 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 0x2b1a480 | |
| Optimiser: DEFAULT METHOD | |
| Option for domin-BFGS: epsx = 0.005 | |
| Option for domin-BFGS: epsf = 1e-05 (rounding error) | |
| Option for domin-BFGS: epsg = 0.005 | |
| 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: Yes | |
| Strategy: Use the Gaussian approximation | |
| 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: 3.36941e-05 | |
| 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: Use points from Central Composite Design (CCD) | |
| f0 (CCD only): 1.100000 | |
| dz (GRID only): 1.000000 | |
| Adjust weights (GRID only): On | |
| Difference in log-density limit (GRID only): 2.500000 | |
| 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-05] | |
| Absolute error ....................... [1e-06] | |
| To stabalise the numerical optimisation: | |
| Minimum value of the -Hesssian [0] | |
| CPO manual calculation[No] | |
| inla_build: check for unused entries in[/tmp/RtmpwnHhDH/file21967666466b/Model.ini] | |
| inla_INLA... | |
| Strategy = [DEFAULT] | |
| Size is [14774] and strategy [LARGE] is chosen | |
| Size of graph=[14774] constraints=[1] | |
| Found optimal reordering=[amdc] nnz(L)=[89990] and use_global_nodes(user)=[no] | |
| List of hyperparameters: | |
| theta[0] = [Log precision for the Gaussian observations] | |
| theta[1] = [Log precision for geo] | |
| theta[2] = [Logit phi for geo] | |
| Optimise using DEFAULT METHOD | |
| Max.post.marg(theta): log(dens) = -134498.510159 fn = 1 theta = 4.010000 5.000000 -3.000000 | |
| Max.post.marg(theta): log(dens) = -133082.794441 fn = 2 theta = 4.000000 5.000000 -2.990000 | |
| Max.post.marg(theta): log(dens) = -133081.483067 fn = 3 theta = 4.000000 4.990000 -3.000000 | |
| Max.post.marg(theta): log(dens) = -131682.215581 fn = 5 theta = 3.990000 5.000000 -3.000000 | |
| Max.post.marg(theta): log(dens) = -46591.414039 fn = 7 theta = 3.000001 4.998908 -2.999911 | |
| Max.post.marg(theta): log(dens) = -46590.132335 fn = 9 theta = 3.000001 4.988908 -2.999911 | |
| Max.post.marg(theta): log(dens) = -46119.632601 fn = 13 theta = 2.990001 4.998908 -2.999911 | |
| Max.post.marg(theta): log(dens) = -23767.692837 fn = 15 theta = -1.404464 4.994099 -2.999517 | |
| Max.post.marg(theta): log(dens) = -23703.310817 fn = 16 theta = -1.394464 4.994099 -2.999517 | |
| Iter=1 |grad|=6.43e+03 |x-x.old|=3.12 |f-f.old|=1.09e+05 | |
| Max.post.marg(theta): log(dens) = -23393.482796 fn = 22 theta = -1.344646 4.184838 -3.583914 | |
| Max.post.marg(theta): log(dens) = -23329.742066 fn = 23 theta = -1.334646 4.184838 -3.583914 | |
| Max.post.marg(theta): log(dens) = -20717.796653 fn = 29 theta = -0.806279 -3.098508 -8.843479 | |
| Max.post.marg(theta): log(dens) = -20659.653740 fn = 30 theta = -0.796279 -3.098508 -8.843479 | |
| file: smtp-taucs.c hgid: f4b2fa41b99b date: Thu Apr 03 15:35:52 2014 +0200 | |
| Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 829, Thread: 0 | |
| Fail to factorize Q. I will try to fix it... | |
| *** ERROR *** table-prior returns NAN. Argument is -56.1796 but prior is defined on [-16,16] only. | |
| 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 help; please contact the developers at <help@r-inla.org>. |
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