Hope one of you could help with the following question/problem:
We would like to explain the spatial
distribution of juvenile fish. We have 2135 records, from 75 vessels
(code_tripnr) and 7 to 39 observations for each vessel, hence the random effect
for code_tripnr. The offset (offsetter) accounts for the haul duration and
sub sampling factor. There are no extreme outliers in lat/lon. The model we try
to fit is:
>
gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),family="poisson",
niterPQL=200)
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in MEestimate(lmeSt, grps) :
NA/NaN/Inf in foreign function call (arg 1)
We tried several things. We added some
noise to lon and lat, modelled the density instead of using a count with model
offset, and we normalized the explanatory variables. We also changed several
settings (see models below).
Interestingly, we do manage to fit a more
complex model:
gamm2<-gamm(count~offset(offsetter)+
s(lat,lon,year,dayofyear), random=list(code_tripnr=~1),family="poisson",
correlation = corGaus(0.1, form=~lat + lon))
The models are fitted using mgcv 1.4-1 and
R 2.7.1 on a 64Bits Debian OS.
So there seems to be a convergence problem, correct? And does someone have an
idea what
might cause this? Secondly are there some tricks/solutions. E.g. perhaps we
could use the results from the more complex model (gamm2 above), but I do not
know exactly how. All help/advice would be greatly appreciated.
Kind regards, Geert
>
gamm3<-gamm(count~offset(offsetter)+s(lon,lat),
random=list(code_tripnr=~1),family="poisson", correlation = corExp(1,
form=~X + Y),nite
rPQL=200)
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in recalc.corSpatial(object[[i]],
conLin) :
NA/NaN/Inf in foreign function call (arg 1)
> gamm3<-gamm(count~offset(offsetter)+s(lon,lat,k=c(1,1)),random=list(code_tripnr=~1),family="poisson",
niterPQL=200)
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in lme.formula(fixed = fixed, random
= random, data = data, correlation = correlation, :
nlminb
problem, convergence error code = 1
message = false convergence (8)
In addition: Warning messages:
1: In if (k < M + 1) { :
the
condition has length > 1 and only the first element will be used
.Options$mgcv.vc.logrange=0.001 # we also
tried higher settings
>
gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),family="poisson",
niterPQL=200, control=lmeControl(opt="optim"))
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in optim(c(coef(lmeSt)),
function(lmePars) -logLik(lmeSt, lmePars),
:
initial value in 'vmmin' is not finite
gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),family="poisson",
niterPQL=200,control=lmeControl(minAbsParApV
ar=0.0000000000001))
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in recalc.corSpatial(object[[i]],
conLin) :
NA/NaN/Inf in foreign function call (arg 1)
>
gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),family="poisson",
niterPQL=200)
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in MEestimate(lmeSt, grps) :
NA/NaN/Inf in foreign function call (arg 1)
>
gamm3<-gamm(count~offset(offsetter)+s(lon,lat,k=c(1,1)),random=list(code_tripnr=~1),family="poisson",
niterPQL=200)
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in lme.formula(fixed = fixed, random
= random, data = data, correlation = correlation, :
nlminb problem, convergence
error code = 1
message = false convergence (8)
In addition: Warning messages:
1: In if (k < M + 1) { :
the
condition has length > 1 and only the first element will be used
2: In smooth.construct.tp.smooth.spec(object,
dk$data, dk$knots) :
basis dimension, k, increased to minimum possible
>
gamm3<-gamm(count~offset(offsetter)+s(lon,lat,k=c(8,8)),random=list(code_tripnr=~1),family="poisson",
niterPQL=200)
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in lme.formula(fixed = fixed, random
= random, data = data, correlation = correlation, :
nlminb problem, convergence
error code = 1
message = false convergence (8)
In addition: Warning messages:
1: In if (k < M + 1) { :
the
condition has length > 1 and only the first element will be used
2: In 1:UZ.len : numerical expression has 2
elements: only the first used
3: In if (p.rank > ncol(XZ)) p.rank
<- ncol(XZ) :
the
condition has length > 1 and only the first element will be used
4: In 1:p.rank : numerical expression has 2
elements: only the first used
5: In if (p.rank < k - j) Xf <- XZU[,
(p.rank + 1):(k - j), drop = FALSE] else Xf <- matrix(0, :
the
condition has length > 1 and only the first element will be used
6: In (p.rank + 1):(k - j) :
numerical expression has 2 elements: only the first used
7: In 1:p.rank : numerical expression has 2
elements: only the first used
>
gamm3<-gamm(count~offset(offsetter)+s(lon,lat,k=c(4,4),fx=T),random=list(code_tripnr=~1),family="poisson",
niterPQL=200)
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in MEestimate(lmeSt, grps) :
NA/NaN/Inf in foreign function call (arg 1)
In addition: Warning messages:
1: In if (k < M + 1) { :
the
condition has length > 1 and only the first element will be used
2: In 1:UZ.len : numerical expression has 2
elements: only the first used
>
gamm3<-gamm(count~offset(offsetter)+te(lon,lat),random=list(code_tripnr=~1),family="poisson",
niterPQL=200,control=lmeControl(opt="opti
m"))
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in optim(c(coef(lmeSt)),
function(lmePars) -logLik(lmeSt, lmePars),
:
initial value in 'vmmin' is not finite
>
gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),family="poisson",
niterPQL=200,control=lmeControl(tolerance=
0.00000000000001))
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in MEestimate(lmeSt, grps) :
NA/NaN/Inf in foreign function call (arg 1)
> gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),family="poisson",
niterPQL=200,control=lmeControl(niterEM=200))
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in MEestimate(lmeSt, grps) :
NA/NaN/Inf in foreign function call (arg 1)
>
gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),family="poisson",
niterPQL=200,control=lmeControl(msTol=0.00000000000000001))
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in MEestimate(lmeSt, grps) :
NA/NaN/Inf in foreign function call (arg 1)
>
gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),family="poisson",
niterPQL=200,control=lmeControl(.relStep=0.00000000000000000001))
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in MEestimate(lmeSt, grps) :
NA/NaN/Inf in foreign function call (arg 1)
>
gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),family="poisson",
niterPQL=200,control=lmeControl(nlmStepMax=0.00000000000000000001))
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in MEestimate(lmeSt, grps) :
NA/NaN/Inf in foreign function call (arg 1)
>
gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),family="poisson",
niterPQL=200,control=lmeControl(minAbsParApVar=0.0000000000001))
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in MEestimate(lmeSt, grps) :
NA/NaN/Inf in foreign function call (arg 1)
>
gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),family="poisson",
niterPQL=200, control=lmeControl(returnObject=T))
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in MEestimate(lmeSt, grps) :
Singularity in backsolve at level 0, block 1
In addition: Warning messages:
1: In logLik.reStruct(object, conLin) :
Singular precision matrix in level -1, block 1
2: In logLik.reStruct(object, conLin) :
Singular precision matrix in level -1, block 1
3: In logLik.reStruct(object, conLin) :
Singular precision matrix in level -1, block 1
4: In logLik.reStruct(object, conLin) :
Singular precision matrix in level -1, block 1
5: In logLik.reStruct(object, conLin) :
Singular precision matrix in level -1, block 1
6: In MEestimate(lmeSt, grps) :
Singular precision matrix in level -1, block 1
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