Dear all, 

 

I am trying to run glmmADMB for the first time to check the effect of some
fixed effects over the number of seedlings in some plots (my random factors
are site/transect/plot). However I have some errors. I show what I obtained
with the simplest model (just one fixed and random variable). See that very
long assessments, and at the end the error I get. Does anybody understand
what it means or what does it do? 

 

seed_glmmADMB<-glmmadmb(seedling~Tanual+(1|name),data=datos,zeroInflation=TR
UE,family="poisson")

 

Initial statistics: 2 variables; iteration 0; function evaluation 0; phase 1

Function value   4.7879194e+03; maximum gradient component mag   1.2497e+01

Var   Value    Gradient   |Var   Value    Gradient   |Var   Value
Gradient   

  1  0.00000  1.24969e+01 |  2  0.00000  9.04389e-01 |

 

- final statistics:

2 variables; iteration 6; function evaluation 9

Function value   4.7390e+03; maximum gradient component mag   7.8663e-07

Exit code = 1;  converg criter   1.0000e-04

Var   Value    Gradient   |Var   Value    Gradient   |Var   Value
Gradient   

  1 -7.91676  7.86634e-07 |  2 -0.41408  4.40063e-08 |

 

Initial statistics: 3 variables; iteration 0; function evaluation 0; phase 2

Function value   4.7389614e+03; maximum gradient component mag  -2.9509e+02

Var   Value    Gradient   |Var   Value    Gradient   |Var   Value
Gradient   

  1 -0.81924 -2.95094e+02 |  2 -7.91676  7.86634e-07 |  3 -0.41408
4.40063e-08

 

- final statistics:

3 variables; iteration 8; function evaluation 17

Function value   4.0911e+03; maximum gradient component mag  -3.2363e-05

Exit code = 1;  converg criter   1.0000e-04

Var   Value    Gradient   |Var   Value    Gradient   |Var   Value
Gradient   

  1  0.30667 -3.23634e-05 |  2 12.46576  8.22294e-06 |  3 -0.74889
3.49842e-07

Hessian type 4 

 inner maxg = -7.739e-05  Inner f = 3095

f = 3094.890062650702 max g = 7.738900271303528e-05

Newton raphson 1   f = 3094.890062650651 max g = 3.215205879314453e-12

Newton raphson 2   f = 3094.890062650652 max g = 4.67847982577041e-13

 

Initial statistics: 4 variables; iteration 0; function evaluation 0; phase 3

Function value   3.1003811e+03; maximum gradient component mag   5.2192e+02

Var   Value    Gradient   |Var   Value    Gradient   |Var   Value
Gradient   

  1  0.30667  5.21923e+02 |  2 12.46576  1.24754e+01 |  3 -0.74889
-1.73876e-01

  4  0.00000 -9.28148e+00 |

inner maxg = 1.13185043559838e-08  Inner f = 3094.869988088167

f = 3094.869988088167 max g = 1.13185043559838e-08

Newton raphson 1   f = 3094.869988088207 max g = 1.163069640597314e-12

Newton raphson 2   f = 3094.869988088206 max g = 6.403766406037903e-13

inner maxg = 1.128069884170912e-06  Inner f = 3094.669391084265

f = 3094.669391084265 max g = 1.128069884170912e-06

Newton raphson 1   f = 3094.669391084331 max g = 9.93205517829665e-13

Newton raphson 2   f = 3094.669391084331 max g = 5.349054532644004e-13

inner maxg = 0.0001115143807413066  Inner second time =
0.0001115143807413066  Inner f = 3092.678234601511

f = 3092.678234601511 max g = 0.0001115143807413066

Newton raphson 1   f = 3092.678234601386 max g = 7.909584098797495e-11

Newton raphson 2   f = 3092.678234601406 max g = 1.992850329202156e-13

inner maxg = 0.0009823048846091531  Inner second time =
0.0009823048846091531  Inner f = 3074.202875155122

f = 3074.202875155122 max g = 0.0009823048846091531

Newton raphson 1   f = 3074.202875154946 max g = 5.528604241078483e-10

Newton raphson 2   f = 3074.202875154951 max g = 6.274980535181385e-13

inner maxg = 0.003463307678898068  Inner second time = 0.00346328487513741
Inner f = 4103.262910506314

f = 4103.262910506314 max g = 22312718.07549081

Newton raphson 1  matrix not pos definite in sparse choleski

inner maxg = -2.330666920791202e-06  Inner f = 3073.748469359025

f = 3073.748469359025 max g = 2.330666920791202e-06

Newton raphson 1   f = 3073.748469358986 max g = 1.13598019879646e-12

Newton raphson 2   f = 3073.748469358986 max g = 2.688960165642129e-13

inner maxg = -7.021767163273296e-07  Inner f = 3073.340482945362

f = 3073.340482945362 max g = 7.021767163273296e-07

Newton raphson 1   f = 3073.340482945313 max g = 8.877343304902752e-13

Newton raphson 2   f = 3073.340482945312 max g = 5.684341886080801e-14

inner maxg = -5.10335793100225e-05  Inner f = 3069.293714517054

f = 3069.293714517054 max g = 5.10335793100225e-05

Newton raphson 1   f = 3069.293714517018 max g = 2.364108908636808e-12

Newton raphson 2   f = 3069.293714517019 max g = 3.632649736573512e-13

inner maxg = 3.120669105349805e-07  Inner f = 3032.10210954915

f = 3032.10210954915 max g = 3.120669105349805e-07

Newton raphson 1   f = 3032.102109549179 max g = 1.612709965570502e-12

Newton raphson 2   f = 3032.102109549178 max g = 6.548095399239173e-13

inner maxg = 9.298684347647246e-05  Inner f = 2965.72338753619

f = 2965.72338753619 max g = 9.298684347647246e-05

Newton raphson 1   f = 2965.723387536238 max g = 3.640643342350813e-12

Newton raphson 2   f = 2965.723387536238 max g = 1.148192652067337e-12

inner maxg = 0.0002974090840781596  Inner second time =
0.0002974090840781596  Inner f = 2927.249754587155

f = 2927.249754587155 max g = 0.0002974090840781596

Newton raphson 1   f = 2927.249754587122 max g = 2.789279918147258e-11

Newton raphson 2   f = 2927.249754587125 max g = 9.325873406851315e-14

inner maxg = -3.43840595495859e-05  Inner f = 2927.085841055282

f = 2927.085841055282 max g = 3.43840595495859e-05

Newton raphson 1   f = 2927.085841055307 max g = 6.912248551316225e-13

Newton raphson 2   f = 2927.085841055307 max g = 6.912248551316225e-13

inner maxg = -5.01900131011368e-07  Inner f = 2927.110603336049

f = 2927.110603336049 max g = 5.01900131011368e-07

Newton raphson 1   f = 2927.110603336091 max g = 4.247713292215849e-13

Newton raphson 2   f = 2927.110603336091 max g = 4.247713292215849e-13

inner maxg = 0.0001766011291963743  Inner second time =
0.0001766011291963743  Inner f = 2927.114505918551

f = 2927.114505918551 max g = 0.0001766011291963743

Newton raphson 1   f = 2927.11450591854 max g = 1.01401109731114e-11

Newton raphson 2   f = 2927.114505918538 max g = 1.740829702612245e-13

inner maxg = 6.0772079679694e-07  Inner f = 2927.113662140426

f = 2927.113662140426 max g = 6.0772079679694e-07

Newton raphson 1   f = 2927.113662140507 max g = 4.919398222114069e-13

Newton raphson 2   f = 2927.113662140507 max g = 3.199662756969701e-13

inner maxg = 8.193470357742427e-07  Inner f = 2927.113869102554

f = 2927.113869102554 max g = 8.193470357742427e-07

Newton raphson 1   f = 2927.113869102639 max g = 2.94098079223204e-13

Newton raphson 2   f = 2927.113869102639 max g = 1.234568003383174e-13

 

Intermediate statistics: 4 variables; iteration 10; function evaluation 16;
phase 3

Function value   2.9338236e+03; maximum gradient component mag   6.3296e-04

Var   Value    Gradient   |Var   Value    Gradient   |Var   Value
Gradient   

  1 -0.05319 -3.73679e-04 |  2 -0.00978  3.69469e-06 |  3 -0.74900
-8.15139e-06

  4  0.02047  6.32955e-04 |

inner maxg = 0.0008783207721976272  Inner second time =
0.0008783207721976272  Inner f = 2927.11388749145

f = 2927.11388749145 max g = 0.0008783207721976272

Newton raphson 1   f = 2927.113887487097 max g = 4.341400794416472e-09

Newton raphson 2   f = 2927.113887487017 max g = 7.005507285384738e-13

 

- final statistics:

4 variables; iteration 11; function evaluation 17

Function value   2.9338e+03; maximum gradient component mag   5.7419e-05

Exit code = 1;  converg criter   1.0000e-04

Var   Value    Gradient   |Var   Value    Gradient   |Var   Value
Gradient   

  1 -0.05319 -3.47265e-05 |  2 -0.00978  6.44728e-07 |  3 -0.74899
3.77593e-08

  4  0.02047  5.74186e-05 |

inner maxg = -7.005507285384738e-13  Inner f = 2927.113887487017

f = 2927.113887487017 max g = 7.005507285384738e-13

Newton raphson 1   f = 2927.113887487017 max g = 7.005507285384738e-13

Newton raphson 2   f = 2927.113887487017 max g = 7.005507285384738e-13

Hessian type 4 

 inner maxg = -7.005507285384738e-13  Inner f = 2926.833345932613

f = 2926.833345932613 max g = 7.005507285384738e-13

Newton raphson 1   f = 2926.833345932613 max g = 7.005507285384738e-13

Newton raphson 2   f = 2926.833345932613 max g = 7.005507285384738e-13

 

Initial statistics: 4 variables; iteration 0; function evaluation 0; phase 4

Function value   2.9335431e+03; maximum gradient component mag   7.4899e-01

Var   Value    Gradient   |Var   Value    Gradient   |Var   Value
Gradient   

  1 -0.05319 -3.47264e-05 |  2 -0.00978  9.78413e-03 |  3 -0.74899
7.48991e-01

  4  0.02047  5.74191e-05 |

inner maxg = 6.553251605811994e-07  Inner f = 2926.813728712582

f = 2926.813728712582 max g = 6.553251605811994e-07

Newton raphson 1   f = 2926.813728712566 max g = 2.205124971510486e-12

Newton raphson 2   f = 2926.813728712565 max g = 2.466915560717098e-13

inner maxg = -0.0007456044647558002  Inner second time =
-0.0007456044647558002  Inner f = 2926.648451231914

f = 2926.648451231914 max g = 0.0007456044647558002

Newton raphson 1   f = 2926.648451231907 max g = 1.737932020517974e-10

Newton raphson 2   f = 2926.648451231905 max g = 2.623457007189245e-12

inner maxg = -1.784915065616843e-05  Inner f = 2962.262565785922

f = 2962.262565785922 max g = 1.784915065616843e-05

Newton raphson 1   f = 2962.262565785899 max g = 3.054989594630797e-11

Newton raphson 2   f = 2962.262565785899 max g = 3.054989594630797e-11

inner maxg = -2.07386404138532e-05  Inner f = 2926.642643642231

f = 2926.642643642231 max g = 2.07386404138532e-05

Newton raphson 1   f = 2926.642643642257 max g = 2.501554519085403e-12

Newton raphson 2   f = 2926.642643642258 max g = 4.574118861455645e-13

inner maxg = 0.000463495998217045  Inner second time = 0.000463495998217045
Inner f = 2926.638998525533

f = 2926.638998525533 max g = 0.000463495998217045

Newton raphson 1   f = 2926.638998525564 max g = 6.499267790616159e-11

Newton raphson 2   f = 2926.638998525562 max g = 3.628208844475012e-13

inner maxg = 0.0006646374906422725  Inner second time =
0.0006646374906422725  Inner f = 2926.603272547002

f = 2926.603272547002 max g = 0.0006646374906422725

Newton raphson 1   f = 2926.603272546958 max g = 1.363047452684896e-10

Newton raphson 2   f = 2926.603272546958 max g = 6.379341499496149e-13

inner maxg = -0.0004211633814736881  Inner second time =
-0.0004211633814736881  Inner f = 2926.318178250152

f = 2926.318178250152 max g = 0.0004211633814736881

Newton raphson 1   f = 2926.318178249885 max g = 5.583955520194195e-10

Newton raphson 2   f = 2926.318178249847 max g = 1.422195694544826e-12

inner maxg = -0.0001070381538612608  Inner second time =
-0.0001070381538612608  Inner f = 2928.111663659769

f = 2928.111663659769 max g = 0.0001070381538612608

Newton raphson 1   f = 2928.111663659759 max g = 5.914380096783134e-12

Newton raphson 2   f = 2928.111663659765 max g = 2.575717417130363e-13

inner maxg = 0.0002429445097936744  Inner second time =
0.0002429445097936744  Inner f = 2926.55523874152

f = 2926.55523874152 max g = 0.0002429445097936744

Newton raphson 1   f = 2926.555238741352 max g = 2.016461442266859e-10

Newton raphson 2   f = 2926.55523874129 max g = 5.523359547510154e-13

inner maxg = 0.0001877236726046672  Inner second time =
0.0001877236726046672  Inner f = 2926.475481673395

f = 2926.475481673395 max g = 0.0001877236726046672

Newton raphson 1   f = 2926.475481673358 max g = 1.03113073635086e-11

Newton raphson 2   f = 2926.475481673357 max g = 8.526512829121202e-13

inner maxg = 0.0002508076849150331  Inner second time =
0.0002508076849150331  Inner f = 2926.480394354198

f = 2926.480394354198 max g = 0.0002508076849150331

Newton raphson 1   f = 2926.480394354201 max g = 2.086952832769384e-11

Newton raphson 2   f = 2926.4803943542 max g = 2.747579941342337e-12

inner maxg = -1.287842164909847e-06  Inner f = 2926.485286672633

f = 2926.485286672633 max g = 1.287842164909847e-06

Newton raphson 1   f = 2926.485286672604 max g = 9.743317264110374e-13

Newton raphson 2   f = 2926.485286672601 max g = 1.072253397182976e-12

f = 2926.485286672604 max g = 9.743317264110374e-13

inner maxg = -1.401636462849964e-05  Inner f = 2926.53515063371

f = 2926.53515063371 max g = 1.401636462849964e-05

Newton raphson 1   f = 2926.535150633661 max g = 1.269651050961329e-12

Newton raphson 2   f = 2926.535150633661 max g = 1.387778780781446e-13

inner maxg = -2.25291761233315e-05  Inner f = 2926.53955722584

f = 2926.53955722584 max g = 2.25291761233315e-05

Newton raphson 1   f = 2926.53955722571 max g = 9.294787162161811e-13

Newton raphson 2   f = 2926.53955722571 max g = 9.294787162161811e-13

inner maxg = -1.083530822887369e-05  Inner f = 2926.585075954518

f = 2926.585075954518 max g = 1.083530822887369e-05

Newton raphson 1   f = 2926.585075954516 max g = 5.326850072151501e-13

Newton raphson 2   f = 2926.585075954516 max g = 4.103384299014579e-13

inner maxg = -4.338747421339662e-07  Inner f = 2926.61173612726

f = 2926.61173612726 max g = 4.338747421339662e-07

Newton raphson 1   f = 2926.611736127267 max g = 7.402967128200544e-13

Newton raphson 2   f = 2926.611736127268 max g = 6.579181643928678e-13

inner maxg = 0.0002400253470632441  Inner second time =
0.0002400253470632441  Inner f = 2926.610406863815

f = 2926.610406863815 max g = 0.0002400253470632441

Newton raphson 1   f = 2926.610406863634 max g = 2.058787584857669e-10

Newton raphson 2   f = 2926.610406863614 max g = 2.90656387846866e-13

 

Intermediate statistics: 4 variables; iteration 10; function evaluation 17;
phase 4

Function value   2.9331131e+03; maximum gradient component mag  -4.1946e+00

Var   Value    Gradient   |Var   Value    Gradient   |Var   Value
Gradient   

  1 -0.05344 -7.31256e-02 |  2-11.75476  4.02143e-03 |  3 -1.67178
1.93962e-02

  4  0.01618 -4.19464e+00 |

inner maxg = -9.509682201302994e-05  Inner f = 2926.550400034863

f = 2926.550400034863 max g = 9.509682201302994e-05

Newton raphson 1   f = 2926.550400034756 max g = 3.166478190763655e-11

Newton raphson 2   f = 2926.550400034767 max g = 1.353805956227916e-12

inner maxg = 5.267491322458184e-06  Inner f = 2926.497867123815

f = 2926.497867123815 max g = 5.267491322458184e-06

Newton raphson 1   f = 2926.49786712383 max g = 6.679101716144942e-13

Newton raphson 2   f = 2926.49786712383 max g = 6.183942247162122e-13

inner maxg = 1.009483248104459e-07  Inner f = 2926.480459752548

f = 2926.480459752548 max g = 1.009483248104459e-07

Newton raphson 1   f = 2926.480459752518 max g = 7.37854222165879e-13

Newton raphson 2   f = 2926.480459752516 max g = 4.18776124888609e-13

inner maxg = 0.000936718795431668  Inner second time = 0.000936718795431668
Inner f = 2926.479951042753

f = 2926.479951042753 max g = 0.000936718795431668

Newton raphson 1   f = 2926.479951042718 max g = 2.852946767717413e-10

Newton raphson 2   f = 2926.479951042717 max g = 2.031264045854186e-12

 

- final statistics:

4 variables; iteration 14; function evaluation 21

Function value   2.9331e+03; maximum gradient component mag  -3.7990e-05

Exit code = 1;  converg criter   1.0000e-04

Var   Value    Gradient   |Var   Value    Gradient   |Var   Value
Gradient   

  1 -0.05360 -3.79897e-05 |  2-18.38500 -6.74121e-07 |  3 -1.69565
7.58115e-06

  4  0.01855 -1.76954e-05 |

inner maxg = 2.031264045854186e-12  Inner f = 2926.479951042717

f = 2926.479951042717 max g = 2.031264045854186e-12

Newton raphson 1   f = 2926.479951042718 max g = 1.408206884434549e-12

Newton raphson 2   f = 2926.479951042717 max g = 3.577138585342254e-13

inner maxg = 3.577138585342254e-13  Inner f = 2926.479951042717

f = 2926.479951042717 max g = 3.577138585342254e-13

Newton raphson 1   f = 2926.479951042717 max g = 3.577138585342254e-13

Newton raphson 2   f = 2926.479951042717 max g = 3.577138585342254e-13

3 4

Estimating row 1 out of 4 for hessian

inner maxg = 2.38363824012211e-07  Inner f = 2926.479916505355

f = 2926.479916505355 max g = 2.38363824012211e-07

Newton raphson 1   f = 2926.47991650535 max g = 3.390621117205228e-13

Newton raphson 2   f = 2926.479916505349 max g = 4.224398608698721e-13

f = 2926.47991650535 max g = 3.390621117205228e-13

inner maxg = 6.00488698765389e-08  Inner f = 2926.479927219252

f = 2926.479927219252 max g = 6.00488698765389e-08

Newton raphson 1   f = 2926.479927219282 max g = 1.908917468540494e-12

Newton raphson 2   f = 2926.479927219282 max g = 1.342259636771814e-12

inner maxg = 2.401179890476612e-07  Inner f = 2926.47998797534

f = 2926.47998797534 max g = 2.401179890476612e-07

Newton raphson 1   f = 2926.479987975352 max g = 4.267697306659102e-13

Newton raphson 2   f = 2926.47998797535 max g = 4.267697306659102e-13

inner maxg = 6.034008537270097e-08  Inner f = 2926.480038017215

f = 2926.480038017215 max g = 6.034008537270097e-08

Newton raphson 1   f = 2926.480038017186 max g = 3.836486683894691e-12

Newton raphson 2   f = 2926.480038017185 max g = 1.937339177970898e-12

Estimating row 2 out of 4 for hessian

inner maxg = 6.259960320664781e-07  Inner f = 2926.479951069167

f = 2926.479951069167 max g = 6.259960320664781e-07

Newton raphson 1   f = 2926.47995106913 max g = 1.091793322416379e-12

Newton raphson 2   f = 2926.47995106913 max g = 3.674838211509268e-14

inner maxg = 0.0002630993256712566  Inner second time =
0.0002630993256712566  Inner f = 2926.479951056221

f = 2926.479951056221 max g = 0.0002630993256712566

Newton raphson 1   f = 2926.479951055881 max g = 2.383513941772719e-10

Newton raphson 2   f = 2926.479951055914 max g = 1.969535645685028e-13

inner maxg = 0.0005262150065855065  Inner second time =
0.0005262150065855065  Inner f = 2926.479951030491

f = 2926.479951030491 max g = 0.0005262150065855065

Newton raphson 1   f = 2926.479951029418 max g = 9.535680023375903e-10

Newton raphson 2   f = 2926.479951029398 max g = 1.435740415445252e-12

inner maxg = 0.0002630993328229247  Inner second time =
0.0002630993328229247  Inner f = 2926.47995101648

f = 2926.47995101648 max g = 0.0002630993328229247

Newton raphson 1   f = 2926.47995101619 max g = 2.383747643719403e-10

Newton raphson 2   f = 2926.47995101616 max g = 1.844080443902385e-13

Estimating row 3 out of 4 for hessian

inner maxg = -0.0004919394040759917  Inner second time =
-0.0004919394040759917  Inner f = 2926.479951279448

f = 2926.479951279448 max g = 0.0004919394040759917

Newton raphson 1   f = 2926.479951278098 max g = 1.058444554224991e-09

Newton raphson 2   f = 2926.479951278072 max g = 3.042011087472929e-13

inner maxg = 0.0001152809235651642  Inner second time =
0.0001152809235651642  Inner f = 2926.479951156406

f = 2926.479951156406 max g = 0.0001152809235651642

Newton raphson 1   f = 2926.479951156369 max g = 1.032107732612531e-11

Newton raphson 2   f = 2926.479951156374 max g = 6.048495038157853e-13

inner maxg = 0.00023060371562722  Inner second time = 0.00023060371562722
Inner f = 2926.479950936918

f = 2926.479950936918 max g = 0.00023060371562722

Newton raphson 1   f = 2926.479950936905 max g = 4.130240593980261e-11

Newton raphson 2   f = 2926.479950936917 max g = 1.586730746794274e-12

inner maxg = 0.0001153227366483822  Inner second time =
0.0001153227366483822  Inner f = 2926.479950839088

f = 2926.479950839088 max g = 0.0001153227366483822

Newton raphson 1   f = 2926.479950839035 max g = 1.039268671121363e-11

Newton raphson 2   f = 2926.479950839041 max g = 7.791545186819349e-13

Estimating row 4 out of 4 for hessian

inner maxg = -0.000139362732505921  Inner second time =
-0.000139362732505921  Inner f = 2926.489555138762

f = 2926.489555138762 max g = 0.000139362732505921

Newton raphson 1   f = 2926.489555138726 max g = 6.460387780293786e-12

Newton raphson 2   f = 2926.489555138728 max g = 1.829425499977333e-12

inner maxg = 1.435504278557431e-06  Inner f = 2926.484745391796

f = 2926.484745391796 max g = 1.435504278557431e-06

Newton raphson 1   f = 2926.484745391857 max g = 1.38453692954954e-11

Newton raphson 2   f = 2926.484745391857 max g = 1.38453692954954e-11

inner maxg = 0.0001369117335996428  Inner second time =
0.0001369117335996428  Inner f = 2926.475172042353

f = 2926.475172042353 max g = 0.0001369117335996428

Newton raphson 1   f = 2926.475172042317 max g = 5.3170801095348e-12

Newton raphson 2   f = 2926.475172042315 max g = 1.0618173007515e-12

inner maxg = 6.247216707055969e-06  Inner f = 2926.470408341941

f = 2926.470408341941 max g = 6.247216707055969e-06

Newton raphson 1   f = 2926.470408341923 max g = 1.070254995738651e-12

Newton raphson 2   f = 2926.470408341922 max g = 4.807265696626928e-13

Error in run_bin(platform, bin_loc, file_name, cmdoptions, run, rm_binary =
!use_tmp_dir,  : 

  object 'sys.result' not found

> 

 

Hope somebody could tell me what I am doing wrong!!

Thanks

Raquel

 

 

 


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