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Today's Topics:

  1. mixed model (Ahmad Rabiee)
  2. Re: mixed model (Ben Bolker)


----------------------------------------------------------------------

Message: 1
Date: Thu, 11 Aug 2011 11:53:20 +1000
From: "Ahmad Rabiee"<ahmadr at sbscibus.com.au>
To:<r-sig-mixed-models at r-project.org>
Subject: [R-sig-ME] mixed model
Message-ID:<005b01cc57c9$724ca390$56e5eab0$@com.au>
Content-Type: text/plain

Hi



I have a binomial dataset (0, 1), and would like to run a "mixed model"
logistic regression and also a "nested mixed model" logistic regression
using glmer:



ket.glm1<- glmer(z_ket_1.4 ~  bcs_pre + bhb_date + lact  + (1 | herdno) ,
family = binomial, data = ket)

#-------------------------------



To account for the overdispersion in the dataset, I used the following codes
(according to lme4 package), but the output is identical to the first model
(above= ket.hlm1). Comments  please?



# Mixed model accounting for overdispersion

ket$obs<- 1:nrow(ket)

ket.glm2<- glmer(z_ket_1.4 ~  bcs_pre + bhb_date + lact  + (1 | herdno)  +
(1|obs), family = binomial, data = ket)

#-------------------------------------------------



#Nest random effect

When I want to run a nested random effects using "glmer" I get an error
message (below);



# herds nested within studies

ket.glm43<- glmer(z_ket_1.4 ~  bcs_pre + bhb_date + lact +
(1|studyid:herdno) + (1|id), family = binomial, data = ket)



#Error message (What does this mean?)

Error: length(f1) == length(f2) is not TRUE

In addition: Warning messages:

1: In study:herdno :

 numerical expression has 2695 elements: only the first used

2: In study:herdno :

 numerical expression has 2695 elements: only the first used

#---------------------------------------------------------------------------
----------



#glmmadmb

I believe my dataset (binomial) is zero-inflated- and Ben suggested that I
should use the "glmmadmb" package to count for the zero-inflation (Please
correct me if I am wrong). I can run this model (below), when I don't have a
random effects term in the model. But I don't understand the outputs:



# first model (without random effects term)

ket.glmm1<- glmmadmb(z_ket_1.4 ~  bcs_pre + bhb_date + lact , family =
"binomial", data = ket)

summary(ket.glmm2)



Initial statistics: 10 variables; iteration 0; function evaluation 0; phase
1

Function value   1.8680316e+03; maximum gradient component mag   1.4283e+01

Var   Value    Gradient   |Var   Value    Gradient   |Var   Value
Gradient

 1  0.00000  1.42834e+01 |  2  0.00000 -1.25533e-01 |  3  0.00000
7.40839e+00

 4  0.00000  9.75790e-01 |  5  0.00000 -1.44553e+00 |  6  0.00000
-1.77029e+00

 7  0.00000 -1.94537e+00 |  8  0.00000 -1.72752e+00 |  9  0.00000
-9.14276e-01

10  0.00000 -1.12861e+00 |



Intermediate statistics: 10 variables; iteration 10; function evaluation 14;
phase 1

Function value   1.2444800e+03; maximum gradient component mag  -4.4890e-02

Var   Value    Gradient   |Var   Value    Gradient   |Var   Value
Gradient

 1-74.45668  1.75306e-02 |  2  3.38165  1.96037e-02 |  3-39.88270
-8.55544e-03

 4 -4.77457 -4.48896e-02 |  5 10.47568 -5.10712e-03 |  6 12.37466
-2.16758e-03

 7 13.04031  3.49481e-03 |  8 10.98531  5.92878e-04 |  9  6.74107
-4.27903e-03

10  6.99462 -1.41183e-04 |

10 variables; iteration 20; function evaluation 24; phase 1

Function value   1.2444697e+03; maximum gradient component mag   1.2294e-04

Var   Value    Gradient   |Var   Value    Gradient   |Var   Value
Gradient

 1-74.57412  6.45335e-05 |  2  3.24452  3.17209e-05 |  3-39.84581
-2.93776e-05

 4 -4.43904  1.22940e-04 |  5 10.55041 -6.38080e-05 |  6 12.43515
-6.09376e-05

 7 13.07189 -2.38280e-05 |  8 11.01902 -1.81564e-05 |  9  6.79542
-2.85983e-05

10  7.02120 -6.17190e-06 |



- final statistics:

10 variables; iteration 21; function evaluation 25

Function value   1.2445e+03; maximum gradient component mag   4.5702e-05

Exit code = 1;  converg criter   1.0000e-04

Var   Value    Gradient   |Var   Value    Gradient   |Var   Value
Gradient

 1-74.57453  9.86716e-06 |  2  3.24432  1.00312e-05 |  3-39.84559
3.57290e-05

 4 -4.43952  4.57024e-05 |  5 10.55069 -2.73803e-05 |  6 12.43544
-2.03976e-05

 7 13.07205 -6.19842e-06 |  8 11.01915 -2.28111e-06 |  9  6.79553
-1.71599e-05

10  7.02125 -2.24921e-06 |

Estimating row 1 out of 10 for hessian

Estimating row 2 out of 10 for hessian

Estimating row 3 out of 10 for hessian

Estimating row 4 out of 10 for hessian

Estimating row 5 out of 10 for hessian

Estimating row 6 out of 10 for hessian

Estimating row 7 out of 10 for hessian

Estimating row 8 out of 10 for hessian

Estimating row 9 out of 10 for hessian

Estimating row 10 out of 10 for hessian

Estimated covariance matrix may not be positive definite

4.44173 4.92261 5.06046 5.06419 5.35787 5.45402 5.62318 6.84209 8.1491
11.1008

Estimated covariance matrix may not be positive definite

4.44173 4.92261 5.06046 5.06419 5.35787 5.45402 5.62318 6.84209 8.1491
11.1008

#-------------------------------------------



When I run "glmmadmb" with a random effects term in the model, I get an
error message. I don't know what I am doing wrong here. Any help would be
greatly appreciated.



# Mixed model (herdno is the random effects term)

ket.glmm2<- glmmadmb(z_ket_1.4 ~  bcs_pre + bhb_date + lact +  (1 |
herdno), family = "binomial", data = ket)

summary(ket.glmm2)



#Error message

Error in process_randformula(formula, random, data = data) :

 all grouping variables must be factors





Thanks.

Ahmad













#---------------------------------------------------------------------------
------------



















"Try not to become a man of success, but rather try to become a man of
value"
Albert Einstein
<http://www.brainyquote.com/quotes/authors/a/albert_einstein.html>



Please note my new email address is mailto:ahmadr at sbscibus.com.au. Please
update your records.




	[[alternative HTML version deleted]]



------------------------------

Message: 2
Date: Thu, 11 Aug 2011 02:34:52 +0000 (UTC)
From: Ben Bolker<bbolker at gmail.com>
To: r-sig-mixed-models at r-project.org
Subject: Re: [R-sig-ME] mixed model
Message-ID:<loom.20110811T042857-460 at post.gmane.org>
Content-Type: text/plain; charset=us-ascii

Ahmad Rabiee<ahmadr at ...>  writes:

# I have a binomial dataset (0, 1),

 this is a key piece of information not stated previously
(or I missed it ...)

and would like to run a "mixed model"
# logistic regression and also a "nested mixed model" logistic regression
# using glmer:
#
# ket.glm1<- glmer(z_ket_1.4 ~  bcs_pre + bhb_date + lact  + (1 | herdno) ,
# family = binomial, data = ket)

 If your data are binomial with values 0/1 (i.e., "binary" or "Bernoulli"),
it makes sense to incorporate neither overdispersion nor zero-inflation.

# To account for the overdispersion in the dataset, I used the following codes
# (according to lme4 package), but the output is identical to the first model
# (above= ket.hlm1). Comments  please?
#
# # Mixed model accounting for overdispersion
#
# ket$obs<- 1:nrow(ket)
#
# ket.glm2<- glmer(z_ket_1.4 ~  bcs_pre + bhb_date + lact  + (1 | herdno)  +
# (1|obs), family = binomial, data = ket)

 As stated above, overdispersion is unidentifiable with binary data.

# #Nest random effect
# When I want to run a nested random effects using "glmer" I get an error
# message (below);
#
# # herds nested within studies
#
# ket.glm43<- glmer(z_ket_1.4 ~  bcs_pre + bhb_date + lact +
# (1|studyid:herdno) + (1|id), family = binomial, data = ket)
#
# #Error message (What does this mean?)
#
# Error: length(f1) == length(f2) is not TRUE
#
# In addition: Warning messages:
#
# 1: In study:herdno :
#
#   numerical expression has 2695 elements: only the first used

[snip]

 It means that you need studyid and herdno to be factors, not
numeric variables, in order for this to work.

# I believe my dataset (binomial) is zero-inflated- and Ben suggested that I
# should use the "glmmadmb" package to count for the zero-inflation (Please
# correct me if I am wrong). I can run this model (below), when I don't have a
# random effects term in the model. But I don't understand the outputs:

 When I suggested that, it was before I knew your data were binary.
Zero-inflation doesn't make sense for binary data.

# # first model (without random effects term)
#
# ket.glmm1<- glmmadmb(z_ket_1.4 ~  bcs_pre + bhb_date + lact , family =
# "binomial", data = ket)
#
# summary(ket.glmm2)
#
# Initial statistics: 10 variables; iteration 0; function evaluation 0; phase
# 1
[snip]

# Estimated covariance matrix may not be positive definite
#
# 4.44173 4.92261 5.06046 5.06419 5.35787 5.45402 5.62318 6.84209 8.1491
# 11.1008
#
# When I run "glmmadmb" with a random effects term in the model, I get an
# error message. I don't know what I am doing wrong here. Any help would be
# greatly appreciated.
#
# # Mixed model (herdno is the random effects term)
#
# ket.glmm2<- glmmadmb(z_ket_1.4 ~  bcs_pre + bhb_date + lact +  (1 |
# herdno), family = "binomial", data = ket)
#
# summary(ket.glmm2)
#
# #Error message
#
# Error in process_randformula(formula, random, data = data) :
#
#   all grouping variables must be factors

 What it says.  herdno must be a factor.

 Ben Bolker



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