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Today's Topics:
1. Problem_Downdated VtV is not positive definite (C. AMAL D. GLELE)
2. Re: Problem_Downdated VtV is not positive definite (Ben Bolker)
----------------------------------------------------------------------
Message: 1
Date: Sun, 19 Jan 2020 13:29:54 +0000
From: "C. AMAL D. GLELE" <altessedac2 at gmail.com>
To: R SIG Mixed Models <r-sig-mixed-models at r-project.org>
Subject: [R-sig-ME] Problem_Downdated VtV is not positive definite
Message-ID:
<
CANrzCv0JTGCDDrJ0eRuVQGOKpdtMLvAy3XPBWNotJfkD4nECOw at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hello, everyone.
In the models below, mydata has 32 rows
village and Year are grouping factor variables with respectively 8 and 4
levels.
1)
model1.1 fits well
model1.1<-glmer(cbind(F,L)~village+Year+(1|Year)+(1|village),
family="binomial",data=mydata)
But, when I replace village+Year by village*Year, I get the warning and
error message below
model1.2<-glmer(cbind(F,L)~village*Year+(1|Year)+(1|village),
family="binomial",data=mydata)
Warning:
fixed-effect model matrix is rank deficient so dropping 2 columns /
coefficients
Error message:
Error in (function (fr, X, reTrms, family, nAGQ = 1L, verbose = 0L, maxit =
100L, :
Downdated VtV is not positive definite
I noticed a similar behavior when trying with glmmadmb:
model2.1 fits well
model2.1<-glmmadmb(cbind(F,L)~village+Year+(1|Year)+(1|village),family="binomial",data=na.omit
(mydata))
But, with village*Year, Iget the error message below:
model2.2<-glmmadmb(cbind(F,L)~village*Year+(1|Year)+(1|village),family="binomial",data=na.omit
(mydata))
Error:
Error in glmmadmb(cbind(F, L) ~ village * Year + (1 | Year) + (1 |
village), :
rank of X = 30 < ncol(X) = 32
##
in advance, thanks for helping solve these issues(I'm very interested in
interaction terms).
Kinds regards,
[[alternative HTML version deleted]]
------------------------------
Message: 2
Date: Sun, 19 Jan 2020 19:46:02 -0500
From: Ben Bolker <bbolker at gmail.com>
To: r-sig-mixed-models at r-project.org
Subject: Re: [R-sig-ME] Problem_Downdated VtV is not positive definite
Message-ID: <b102d218-f1b4-1628-7e73-a34664dc55b4 at gmail.com>
Content-Type: text/plain; charset="utf-8"
On 2020-01-19 8:29 a.m., C. AMAL D. GLELE wrote:
Hello, everyone.
In the models below, mydata has 32 rows
village and Year are grouping factor variables with respectively 8 and 4
levels.
1)
model1.1 fits well
model1.1<-glmer(cbind(F,L)~village+Year+(1|Year)+(1|village),
family="binomial",data=mydata)
But, when I replace village+Year by village*Year, I get the warning and
error message below
model1.2<-glmer(cbind(F,L)~village*Year+(1|Year)+(1|village),
family="binomial",data=mydata)
Warning:
fixed-effect model matrix is rank deficient so dropping 2 columns /
coefficients
Error message:
Error in (function (fr, X, reTrms, family, nAGQ = 1L, verbose = 0L,
maxit =
100L, :
Downdated VtV is not positive definite
When you include a fixed effect of village*Year, it expands to (1 +
village + Year + village:Year).
Assuming Year is numeric, the combination of a fixed effect of Year
(treated as the overall slope of a linear relationship) and a random
intercept of Year (Year treated as a categorical grouping variable) is OK.
But ... you also have village as categorical fixed effect *and* a
random intercept, which is redundant.
You could use ~ Year + village:Year + (1|Year) + (1|village) *or*
~ Year + (1+Year|village)
I noticed a similar behavior when trying with glmmadmb:
model2.1 fits well
model2.1<-glmmadmb(cbind(F,L)~village+Year+(1|Year)+(1|village),family="binomial",data=na.omit
(mydata))
But, with village*Year, Iget the error message below:
model2.2<-glmmadmb(cbind(F,L)~village*Year+(1|Year)+(1|village),family="binomial",data=na.omit
(mydata))
Error:
Error in glmmadmb(cbind(F, L) ~ village * Year + (1 | Year) + (1 |
village), :
rank of X = 30 < ncol(X) = 32
##
in advance, thanks for helping solve these issues(I'm very interested in
interaction terms).
Kinds regards,
[[alternative HTML version deleted]]
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