[R-sig-ME] A three-level GLMM with binomial link in R
Hedyeh Ahmadi
hedyeh@h @end|ng |rom u@c@edu
Tue Mar 16 17:44:43 CET 2021
Hello all,
I am just forwarding my previous email again just in case and taking out some parts that I already figured out - thank you for all your help:
I'll think more about how to share a data set that would create the same error. Sorry, I am not very simulation savvy, but I'll try harder next time.
On the bright side, I was able to run the following model by implicitly defining the group structure (slightly different from what was suggested in the previous email) and it does give me the same estimation as lme() with random = ~1|site/family/id random structure - so the memory issue resolved for this model! Thank you for the suggestion.
dd$site_family <- interaction(dd$site, dd$family)
m2.1 <- lmer(cbcl_scr_syn_internal_r ~ 1 + X1 + X2 + X3+ (1|site) +(1|site_family/id), data=dd, REML = FALSE)
But now getting to my last question: My data has 22945 rows, and some individuals have only baseline measurement, some individuals have baseline and 1 year measurement. A variable called eventname is the indicator of that. I am now confused as my "id" variable does not have this information (i.e. the order of measurement). How would the model recognize that which repeated measure is measurment1 (i.e. baseline) and which one is measurment2 (i.e. 1 year)? Or maybe because I don't have a random slope, I don't need to define the repeated measure structure and adding eventname as a fixed effect is sufficient?
OR do I need to run a model with additional random intercept of eventname (i.e. (1|site/family/id/eventname)) but in doing so lme() gives me the number of observation equal to number of grouping for eventname %in% id %in% family %in% site as follows. Would that be okay?
Number of Observations: 13388
Number of Groups:
site family %in% site
21 9393
id %in% family %in% site eventname %in% id %in% family %in% abcd_site
11111 13388
Again, thank you so much for your time.
Best,
Hedyeh Ahmadi, Ph.D.
Statistician
Keck School of Medicine
Department of Preventive Medicine
University of Southern California
Postdoctoral Scholar
Institute for Interdisciplinary Salivary Bioscience Research (IISBR)
University of California, Irvine
LinkedIn
www.linkedin.com/in/hedyeh-ahmadi<http://www.linkedin.com/in/hedyeh-ahmadi>
<http://www.linkedin.com/in/hedyeh-ahmadi><http://www.linkedin.com/in/hedyeh-ahmadi>
________________________________
From: Hedyeh Ahmadi <hedyehah using usc.edu>
Sent: Friday, March 12, 2021 12:54 PM
To: r-sig-mixed-models using r-project.org <r-sig-mixed-models using r-project.org>; Ben Bolker <bbolker using gmail.com>
Subject: Re: [R-sig-ME] A three-level GLMM with binomial link in R
I'll think more about how to share a data set that would create the same error. Sorry, I am not very simulation savvy but I'll try harder next time.
On the bright side, I was able to run the following model by implicitly defining the group structure (slightly different from what was suggested in the previous email) and it does give me the same estimation as lme() with random = ~1|site/family/id random structure - so the memory issue resolved for this model! Thank you for the suggestion.
dd$site_family <- interaction(dd$site, dd$family)
m2.1 <- lmer(cbcl_scr_syn_internal_r ~ 1 + X1 + X2 + X3+ (1|site) +(1|site_family/id), data=dd, REML = FALSE)
But now getting to my last question: My data has 22945 rows, and some individuals have only baseline measurement, some individuals have baseline and 1 year measurement. A variable called eventname is the indicator of that. I am now confused as my "id" variable does not have this information (i.e. the order of measurement). How would the model recognize that which repeated measure is measurment1 (i.e. baseline) and which one is measurment2 (i.e. 1 year)? Or maybe because I don't have a random slope, I don't need to define the repeated measure structure and adding eventname as a fixed effect is sufficient?
OR do I need to run a model with additional random intercept of eventname but in doing so lme() gives me the number of observation equal to umber of grouping for eventname %in% id %in% family %in% site as follows. Would that be okay?
Number of Observations: 13388
Number of Groups:
site family %in% site
21 9393
id %in% family %in% site eventname %in% id %in% family %in% abcd_site
11111 13388
The model formula with eventname as random slope in lme() would be as follows but I have not been able to reproduce this in lmer() similar to implicit formatting of m2.1 shown above - any help would be appreciated here. Keep in mind created an implicit three-way and four-way interaction takes too much memory on my personal PC so I am trying to find a way around it as I did in m2.1.
m3 <- lme(cbcl_scr_syn_internal_r ~ 1 +X1+ X2 + X3, random = ~1|site/family/id//eventname ,
data=dd, na.action=na.exclude,method="ML")
Again, thank you so much for your time.
Best,
Hedyeh Ahmadi, Ph.D.
Statistician
Keck School of Medicine
Department of Preventive Medicine
University of Southern California
Postdoctoral Scholar
Institute for Interdisciplinary Salivary Bioscience Research (IISBR)
University of California, Irvine
LinkedIn
www.linkedin.com/in/hedyeh-ahmadi<http://www.linkedin.com/in/hedyeh-ahmadi>
<http://www.linkedin.com/in/hedyeh-ahmadi><http://www.linkedin.com/in/hedyeh-ahmadi>
________________________________
From: Ben Bolker <bbolker using gmail.com>
Sent: Friday, March 12, 2021 11:45 AM
To: Hedyeh Ahmadi <hedyehah using usc.edu>; r-sig-mixed-models using r-project.org <r-sig-mixed-models using r-project.org>
Subject: Re: [R-sig-ME] A three-level GLMM with binomial link in R
On 3/12/21 12:13 PM, Hedyeh Ahmadi wrote:
> Here are my comments/questions:
>
> 1. I have tried changing the site, family, and id to factor and I get
> the same results.
> 2. Unfortunately, I can't share my data due to privacy issues but if
> you tell me what other information you need, I can provide it.
We know you can't share the data. Part of the art of getting
software help is figuring out how you can create a shareable version of
your data set, *or* a shareable version of something that will generate
the same errors you're experiencing. We need to do a bisection search
between the private data you have, which causes problems with factor
expansion in the grouping variables and is surprisingly memory-hungry,
and the reproducible examples that I have constructed that mimic some
aspects of your data set but don't show either problem. Since we can't
look at your data, the burden falls on you to create a
reproducible/shareable example we can work with.
Assuming that
lmer(y ~ 1 +(1|site/family/id) , data =dd)
does show problems with your actual data set, can you anonymize the
levels of site, family, and id, something like
anon_fac <- function(x, prefix="S") {
factor(x, levels=levels(x), labels=paste0(prefix,
seq(length(levels(x))))
}
anon_dd <- transform(dd, select=c(family, site, id))
anon_dd <- transform(anon_dd,
site=anon_fac(site,"S"),
family=anon_fac(family,"F"),
id=anon_fac(id,"I")
)
This should provide a data set that contains *no* information other than
the pattern of co-occurrence of grouping levels. I don't know who's in
charge of data privacy for your group, but it's hard to imagine how
sharing this would present a risk of personal identification ...
https://urldefense.com/v3/__https://stackoverflow.com/questions/10454973/how-to-create-example-data-set-from-private-data-replacing-variable-names-and-l__;!!LIr3w8kk_Xxm!86i5mS45OmW-JeD4GGs4ZQyanE9ePtf5QzjgYVkL_Rg284MkmW9z-lQGP70cEP4$
https://urldefense.com/v3/__https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example/6699112*6699112__;Iw!!LIr3w8kk_Xxm!86i5mS45OmW-JeD4GGs4ZQyanE9ePtf5QzjgYVkL_Rg284MkmW9z-lQGfDnxgGI$
> 3. Note that when I run the three-way interaction code in my PC it
> again runs out of memory and the error says the following. When I
> tried to run it on interactive HPC, it kicks me out as it takes too
> much memory/time so I will have to submit a batch script.
> "Error: cannot allocate vector of size 18.1 Gb
> In addition: Warning message:
> In ans * length(l) :
> Error: cannot allocate vector of size 18.1 Gb"
> 4. When I take out all the fixed effects, the problem still exists.
That's good in one sense, as it simplifies the problem.
> 5. *Question:* Also note that my data has 22945 rows, and some
> individuals have only baseline measurement only, some individuals
> have baseline and 1 year measurement. A variable called eventname is
> the indicator of that. I am now confused as my "id" variable does
> not have this information (i.e. the order of measurement). How would
> the model recognize that which repeated measure is measurment1 (i.e.
> baseline) and which one is measurment2(i.e. 1 year)? Or maybe
> because I don't have a random slope, I don't need to define the
> repeated measure structure and adding eventname as a fixed effect is
> sufficient?
Let's deal with this after we have the basic problems sorted. If
you want to account for the possible effects of ordering, then you'd
need to add this variable ...
>
> Thanks again for all your help on this.
>
> Best,
>
> Hedyeh Ahmadi, Ph.D.
> Statistician
> Keck School of Medicine
> Department of Preventive Medicine
> University of Southern California
>
> Postdoctoral Scholar
> Institute for Interdisciplinary Salivary Bioscience Research (IISBR)
> University of California, Irvine
>
> LinkedIn
> https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!86i5mS45OmW-JeD4GGs4ZQyanE9ePtf5QzjgYVkL_Rg284MkmW9z-lQGJrML1Sk$ <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!86i5mS45OmW-JeD4GGs4ZQyanE9ePtf5QzjgYVkL_Rg284MkmW9z-lQGJrML1Sk$ >
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!86i5mS45OmW-JeD4GGs4ZQyanE9ePtf5QzjgYVkL_Rg284MkmW9z-lQGJrML1Sk$ ><https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!86i5mS45OmW-JeD4GGs4ZQyanE9ePtf5QzjgYVkL_Rg284MkmW9z-lQGJrML1Sk$ >
>
>
>
>
> ------------------------------------------------------------------------
> *From:* Ben Bolker <bbolker using gmail.com>
> *Sent:* Thursday, March 11, 2021 3:55 PM
> *To:* Hedyeh Ahmadi <hedyehah using usc.edu>; r-sig-mixed-models using r-project.org
> <r-sig-mixed-models using r-project.org>; Megan M. Herting <herting using usc.edu>;
> Elisabeth Burnor <burnor using usc.edu>
> *Subject:* Re: [R-sig-ME] A three-level GLMM with binomial link in R
>
>
> On 3/11/21 1:11 PM, Hedyeh Ahmadi wrote:
>> Hi Ben,
>> Thank you for all the help and informative replies. Here is some info
>> about my data and my answers:
>>
>> * Yes, I am running the exact model however this is just my toy model
>> to get the code to work.
>> * Reminder, I am trying to get lmer with a continuous outcome (but
>> same data structure, with 3 random intercept) work before moving to
>> glmer() with a logit link with a categorical 0/1 outcome.
>> * Here are some information about my data:
>> o X1: num [1:22945] 9.25 NA 9.22 NA 9.22 NA 9.42 NA 9.25 NA ...
>> o X2: int [1:22945] 117 140 128 125 113 138 126 130 120 121 ...
>> o X3: chr [1:22945] "Female" "Male" "Male" "Male" "Male"
>> o site: chr [1:22945] "site15" "site15" "site15" "site15" "site15"
>> ... (I have 21 sites)
>> o family: int [1:22945] 0 1 1 1 1 3 3 4 4 5 ...
>> o id: chr [1:22945] "id1" "id2" "id2" "id3" "id3"...
>> * The following model gives me the error that "Error: couldn't
>> evaluate grouping factor id:(family:site) within model frame: try
>> adding grouping factor to data frame explicitly if possible" - I ran
>> this same model on a supercomputer and it *gave me the same error*,
>> so this is not a memory limit issue.
>
> So far I can't replicate this. It seemed fishy to me that family was an
> integer (I would try explicitly converting it to a factor), but doesn't
> actually cause any problems in my example.
>
> (This differs from your example but not in ways I would expect to be
> important: in particular, the types of the grouping variables are the
> same [chr, int, chr]
>
> n <- 10000
> set.seed(101)
> dd <- data.frame(y=rnorm(n),
> x1=rnorm(n),
> x2=rnorm(n),
> x3=rnorm(n),
> site=sample(paste0("s",1:15),size=n,replace=TRUE),
> family=sample(1:100,size=n,replace=TRUE),
> id=sample(paste0("id",1:20),size=n,replace=TRUE))
> library(lme4)
> lmer(y~1 + x1 + x2 + x3 + (1|site/family/id), data=dd)
>
> ###
>
> What is meant by "adding grouping factor to data frame explicitly" would
> be in this case expanding out the nested terms:
>
> dd <- within(dd,
> {
> site_family <- interaction(site,family)
> site_family_id <- interaction(site,family,id)
> })
>
> lmer(y~1 + x1 + x2 + x3 + (1|site) + (1|site_family) +
> (1|site_family_id), data =dd)
>
>
>
>> o m2 <- lmer(cbcl_scr_syn_internal_r ~ 1 + X1 + X2 + X3 +
>> (1|site/family/id), data=dd, REML = FALSE)
>> * The following *model ran on a supercomputer*. This is the model
>> that previously would give me the error "Error: cannot allocate
>> vector of size 2.3 Gb". Here I am*reducing the number of sites to
>> see if it runs, and it did* run on a supercomputer.
>> o m11 <- lmer(cbcl_scr_syn_internal_r ~ 1 + X1 +X2 + X3
>> +(1|site/family/id) ,
>> data=dd[-which(dd$abcd_site %in% c("site01","site02",
>> "site04", "site05", "site06", "site07", "site08","site09")),],
>> na.action=na.exclude, REML=FALSE)
>>
>> Questions:
>>
>> 1. What I don't understand is that in m2, why lmer() does not
>> recognizes the grouping factor that it does recognize in m11?
>
> I'm not sure either.
>
>> 2. At this point I don't think this is a memory issue as *m2 did not
>> run on a supercompute*r and it's giving me *the same error as my
>> personal computer*. However, in m11, the same grouping structure is
>> being recognized when I reduce the number of sites from 21 to 13 -
>> could this be because of severe imbalance in my family/id nesting,
>> meaning most families have only one kid but some have 2 and a few
>> have 3 kids?
>
> It seems surprising.
> Is there any way we can get a reproducible example? For example,
> suppose you randomize your X1, X2, X3 and anonymize all of your grouping
> variables: would you then be able to share the data set?
>
> Does the problem (let's say just the first problem) still occur if
> you leave out the fixed effects? (I would expect so, and that would
> simplify things somewhat - we're trying to get to the *simplest* example
> that still demonstrates the problem.)
>
>
>>
>> Sorry about the long email and thank you for your help in advance.
>>
>> Best,
>>
>> Hedyeh Ahmadi, Ph.D.
>> Statistician
>> Keck School of Medicine
>> Department of Preventive Medicine
>> University of Southern California
>>
>> Postdoctoral Scholar
>> Institute for Interdisciplinary Salivary Bioscience Research (IISBR)
>> University of California, Irvine
>>
>> LinkedIn
>> https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!51-zg2ISp-lS-4HEW0ZNNEVE1ZD8ujdJZYx90xVOnZ-x6A7l6eu2KhSgMhYCJq4$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!51-zg2ISp-lS-4HEW0ZNNEVE1ZD8ujdJZYx90xVOnZ-x6A7l6eu2KhSgMhYCJq4$>
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!51-zg2ISp-lS-4HEW0ZNNEVE1ZD8ujdJZYx90xVOnZ-x6A7l6eu2KhSgMhYCJq4$
> >
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!51-zg2ISp-lS-4HEW0ZNNEVE1ZD8ujdJZYx90xVOnZ-x6A7l6eu2KhSgMhYCJq4$
> ><https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!51-zg2ISp-lS-4HEW0ZNNEVE1ZD8ujdJZYx90xVOnZ-x6A7l6eu2KhSgMhYCJq4$ >
>>
>>
>>
>>
>> ------------------------------------------------------------------------
>> *From:* Ben Bolker <bbolker using gmail.com>
>> *Sent:* Tuesday, March 9, 2021 4:12 PM
>> *To:* Hedyeh Ahmadi <hedyehah using usc.edu>; r-sig-mixed-models using r-project.org
>> <r-sig-mixed-models using r-project.org>
>> *Subject:* Re: [R-sig-ME] A three-level GLMM with binomial link in R
>> OK, then it would be very helpful to have more details about your
>> data set. Are one or more of X1, X2, X3 categorical predictors with many
>> levels ... ? Any chance we can see str() or summary() ? Are you using
>> exactly the formula you told us about, or something slightly different?
>>
>> The computational burden of a large number of fixed effect parameters
>> will be much worse for glmer than for lmer, unless you use nAGQ=0.
>> glmmTMB would be able to help in two ways: (1) it doesn't scale as badly
>> for large numbers of fixed effects; (2) it allows sparse fixed-effect
>> model matrices (something we keep meaning to (re)implement in lme4) ...
>>
>> Making X1 into a 1000-level factor brings the required memory up by
>> about a factor of 10 and increases the run time from seconds to minutes.
>>
>>
>> Base model:
>>
>> Function_Call Elapsed_Time_sec Total_RAM_Used_MiB
>> 1 m<-lmer(form,data=dd,REML=FALSE) 1.903 10.4
>> Peak_RAM_Used_MiB
>> 1 107.7
>>
>> With X=1000-level factor (no derivative calculations):
>>
>> Function_Call
>> 1
>> m2<-lmer(form,data=dd2,REML=FALSE,control=lmerControl(calc.derivs=FALSE),verbose=10)
>> Elapsed_Time_sec Total_RAM_Used_MiB Peak_RAM_Used_MiB
>> 1 559.735 608.8 984.5
>>
>>
>> With derivative calculation at the end:
>>
>> Function_Call Elapsed_Time_sec
>> 1 m3<-lmer(form,data=dd2,REML=FALSE,verbose=10) 677.975
>> Total_RAM_Used_MiB Peak_RAM_Used_MiB
>> 1 608.7 1148.7
>> >
>> >
>>
>> ---
>> ibrary(lme4)
>> set.seed(101)
>> N <- 22945
>> ns <- 100
>> nf <- 100
>> nid <- 100
>> dd <- data.frame(X1=rnorm(N),
>> X2=rnorm(N),
>> X3=rnorm(N),
>> site=sample(ns, replace=TRUE, size=N),
>> family=sample(nf, replace=TRUE, size=N),
>> id=sample(nid, replace=TRUE, size=N))
>> form <- Y ~ 1 + X1 + X2 + X3 + (1|site/family/id)
>> dd$Y <- simulate(form[-2], newdata=dd, family=gaussian,
>>
>> newparams=list(beta=rep(1,4),theta=rep(1,3),sigma=1))[[1]]
>> library(peakRAM)
>> system.time(mem <- peakRAM(
>> m <- lmer(form, data=dd, REML=FALSE)
>> ))
>> print(mem)
>>
>> dd2 <- transform(dd,
>> X1=factor(sample(1000,size=N,replace=TRUE)))
>>
>> system.time(mem2 <- peakRAM(
>> m2 <- lmer(form, data=dd2, REML=FALSE,
>> control=lmerControl(calc.derivs=FALSE), verbose=10)
>> ))
>> print(mem2)
>>
>> system.time(mem3 <- peakRAM(
>> m3 <- lmer(form, data=dd2, REML=FALSE, verbose=10)
>> ))
>> print(mem3)
>>
>>
>> On 3/8/21 11:29 AM, Hedyeh Ahmadi wrote:
>>> Thank you for the toy example. This same example in my PC gives the
>>> following memory use output:
>>>
>>>
>>> > mem
>>> Function_Call
>>> Elapsed_Time_sec Total_RAM_Used_MiB Peak_RAM_Used_MiB
>>> m<-lmer(form,data=dd,REML=FALSE) 2.64
>>> 10.3 130.1
>>>
>>> When I run peakRAM() for my actual data, it take one hour plus then my
>>> PC slows down, then I have to stop R to be able to use my PC.
>>>
>>> Best,
>>>
>>> Hedyeh Ahmadi, Ph.D.
>>> Statistician
>>> Keck School of Medicine
>>> Department of Preventive Medicine
>>> University of Southern California
>>>
>>> Postdoctoral Scholar
>>> Institute for Interdisciplinary Salivary Bioscience Research (IISBR)
>>> University of California, Irvine
>>>
>>> LinkedIn
>>> https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5O8KlsAUILt44__IHSzbCUgVs7dWxAB8FS9wiKC3j5P6hGrnuJSGckmCIR91AZs$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5O8KlsAUILt44__IHSzbCUgVs7dWxAB8FS9wiKC3j5P6hGrnuJSGckmCIR91AZs$>
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5O8KlsAUILt44__IHSzbCUgVs7dWxAB8FS9wiKC3j5P6hGrnuJSGckmCIR91AZs$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5O8KlsAUILt44__IHSzbCUgVs7dWxAB8FS9wiKC3j5P6hGrnuJSGckmCIR91AZs$>>
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5O8KlsAUILt44__IHSzbCUgVs7dWxAB8FS9wiKC3j5P6hGrnuJSGckmCIR91AZs$
>
>> >
>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5O8KlsAUILt44__IHSzbCUgVs7dWxAB8FS9wiKC3j5P6hGrnuJSGckmCIR91AZs$
>
>> ><https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5O8KlsAUILt44__IHSzbCUgVs7dWxAB8FS9wiKC3j5P6hGrnuJSGckmCIR91AZs$
> >
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>> *From:* R-sig-mixed-models <r-sig-mixed-models-bounces using r-project.org> on
>>> behalf of Ben Bolker <bbolker using gmail.com>
>>> *Sent:* Friday, March 5, 2021 5:44 PM
>>> *To:* r-sig-mixed-models using r-project.org <r-sig-mixed-models using r-project.org>
>>> *Subject:* Re: [R-sig-ME] A three-level GLMM with binomial link in R
>>> Here's an example that conforms approximately to the structure of
>>> your data: on my machine the peak RAM usage is 121 Mb, far short of your
>>> 2.3 Gb ... so I still suspect there is something going on that we don't
>>> know about/haven't guessed yet.
>>>
>>> set.seed(101)
>>> N <- 22945
>>> ns <- 100
>>> nf <- 100
>>> nid <- 100
>>> dd <- data.frame(X1=rnorm(N),
>>> X2=rnorm(N),
>>> X3=rnorm(N),
>>> site=sample(ns, replace=TRUE, size=N),
>>> family=sample(nf, replace=TRUE, size=N),
>>> id=sample(nid, replace=TRUE, size=N))
>>> form <- Y ~ 1 + X1 + X2 + X3 + (1|site/family/id)
>>> dd$Y <- simulate(form[-2], newdata=dd, family=gaussian,
>>>
>>> newparams=list(beta=rep(1,4),theta=rep(1,3),sigma=1))[[1]]
>>> library(peakRAM)
>>> mem <- peakRAM(
>>> m <- lmer(form, data=dd, REML=FALSE)
>>> )
>>>
>>> mem
>>> Function_Call Elapsed_Time_sec Total_RAM_Used_MiB
>>> 1 m<-lmer(form,data=dd,REML=FALSE) 1.754 10.3
>>> Peak_RAM_Used_MiB
>>> 1 120.7
>>>
>>>
>>> On 3/5/21 4:52 PM, Robert Long wrote:
>>>> Perhaps because of the different ways they store objects internally while
>>>> fitting the models.
>>>>
>>>> On Fri, 5 Mar 2021, 21:47 Hedyeh Ahmadi, <hedyehah using usc.edu> wrote:
>>>>
>>>>> Thank you for the reply Robert - If I am running out of memory in lmer(),
>>>>> do you know why lme() runs just fine?
>>>>>
>>>>> Best,
>>>>>
>>>>> Hedyeh Ahmadi, Ph.D.
>>>>> Statistician
>>>>> Keck School of Medicine
>>>>> Department of Preventive Medicine
>>>>> University of Southern California
>>>>>
>>>>> Postdoctoral Scholar
>>>>> Institute for Interdisciplinary Salivary Bioscience Research (IISBR)
>>>>> University of California, Irvine
>>>>>
>>>>> LinkedIn
>>>>> https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$>
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$>>
>
>>
>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$>>>
>
>>
>>>
>>>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$
>
>>
>>> >
>>>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$
>
>>
>>> >
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------
>>>>> *From:* Robert Long <longrob604 using gmail.com>
>>>>> *Sent:* Friday, March 5, 2021 1:43 PM
>>>>> *To:* Hedyeh Ahmadi <hedyehah using usc.edu>
>>>>> *Cc:* Dexter Locke <dexter.locke using gmail.com>; R-mixed models mailing list <
>>>>> r-sig-mixed-models using r-project.org>; Megan M. Herting <herting using usc.edu>;
>>>>> Elisabeth Burnor <burnor using usc.edu>
>>>>> *Subject:* Re: [R-sig-ME] A three-level GLMM with binomial link in R
>>>>>
>>>>> You've run out of memory. Try running it on a machine with much larger RAM.
>>>>>
>>>>> On Fri, 5 Mar 2021, 21:18 Hedyeh Ahmadi, <hedyehah using usc.edu> wrote:
>>>>>
>>>>> Hi - Thank you for the informative replies.
>>>>>
>>>>> I will try those other packages. If MASS::glmmPQL uses lme() then this
>>>>> should work for me.
>>>>>
>>>>> My data structure is complex so it's hard to give reproducible example but
>>>>> for example for two of my models I get the following errors in lmer() while
>>>>> lme() runs smoothly.
>>>>>
>>>>> 1- Error: cannot allocate vector of size 2.3 Gb.
>>>>>
>>>>> 2- Error: couldn't evaluate grouping factor id:(family:site) within model
>>>>> frame: try adding grouping factor to data frame explicitly if possible.
>>>>> (note that the id variable works for simpler lmer() models so the variable
>>>>> itself is not an issue)
>>>>>
>>>>> My model looks like the following nested structure:
>>>>> lmer(Y ~ 1 + X1 + X2 + X3 + (1|site/family/id), data=dd, REML = FALSE)
>>>>>
>>>>> Best,
>>>>>
>>>>> Hedyeh Ahmadi, Ph.D.
>>>>> Statistician
>>>>> Keck School of Medicine
>>>>> Department of Preventive Medicine
>>>>> University of Southern California
>>>>>
>>>>> Postdoctoral Scholar
>>>>> Institute for Interdisciplinary Salivary Bioscience Research (IISBR)
>>>>> University of California, Irvine
>>>>>
>>>>> LinkedIn
>>>>> https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$>
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$>>
>
>>
>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$>>>
>
>>
>>>
>>>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
>
>>
>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$>>>>
>>>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$
>
>>
>>>
>>>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
>
>>
>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$>>>>
>>>>>>
>>>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$
>
>>
>>>
>>>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
>
>>
>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$>>>>
>>>>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$
>
>>
>>>
>>>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
>
>>
>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ________________________________
>>>>> From: Dexter Locke <dexter.locke using gmail.com>
>>>>> Sent: Friday, March 5, 2021 1:01 PM
>>>>> To: Hedyeh Ahmadi <hedyehah using usc.edu>
>>>>> Cc: r-sig-mixed-models using r-project.org <r-sig-mixed-models using r-project.org>;
>>>>> Megan M. Herting <herting using usc.edu>; Elisabeth Burnor <burnor using usc.edu>
>>>>> Subject: Re: [R-sig-ME] A three-level GLMM with binomial link in R
>>>>>
>>>>> Hi Hedyeh,
>>>>>
>>>>> What is the problem you are having? Specifically, what is the estimation
>>>>> issue with lmer and lme?
>>>>>
>>>>> Can you provide a reproducible example? Can you provide the complete
>>>>> errors you are seeing?
>>>>>
>>>>> The current questions are vague, so it will be challenging for list
>>>>> members to provide much guidance.
>>>>>
>>>>> -Dexter
>>>>>
>>>>>
>>>>> On Fri, Mar 5, 2021 at 3:27 PM Hedyeh Ahmadi <hedyehah using usc.edu<mailto:
>>>>> hedyehah using usc.edu>> wrote:
>>>>> Hi All,
>>>>> I was wondering what would be a powerful package in R to run GLMM with
>>>>> logit link that can handle a data set with N=22945 and 3 nested random
>>>>> intercepts. So far, I have tried glmer() from lme4 and it's giving me a lot
>>>>> of estimation issues. Any other package I should try?
>>>>>
>>>>> I am asking for another package as I am having the same issue with lmer()
>>>>> for similar LMM with continuous outcome, while lme() from nlme package runs
>>>>> the models with no problem.
>>>>>
>>>>> Thank you in advance.
>>>>>
>>>>> Best,
>>>>>
>>>>> Hedyeh Ahmadi, Ph.D.
>>>>> Statistician
>>>>> Keck School of Medicine
>>>>> Department of Preventive Medicine
>>>>> University of Southern California
>>>>>
>>>>> Postdoctoral Scholar
>>>>> Institute for Interdisciplinary Salivary Bioscience Research (IISBR)
>>>>> University of California, Irvine
>>>>>
>>>>> LinkedIn
>>>>> https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$>
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$>>
>
>>
>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$>>>
>
>>
>>>
>>>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
>
>>
>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$>>>>
>>>>> <
>>>>> https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$>
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$>>
>
>>
>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$>>>
>>>>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$
>
>>
>>>
>>>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
>
>>
>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$>>>>
>>>>> <
>>>>> https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$>
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$>>
>
>>
>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$>>>
>>>>>>>
>>>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$
>
>>
>>>
>>>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
>
>>
>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$>>>>
>>>>> <
>>>>> https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$>
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$>>
>
>>
>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$>>>
>>>>>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k70OXW4fU$
>
>>
>>>
>>>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
>
>>
>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKGGuIvhag$>>>>
>>>>> <
>>>>> https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$>
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$>>
>
>>
>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$
>
>> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$
> <https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$>>>
>>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
>>>>> R-sig-mixed-models using r-project.org<mailto:R-sig-mixed-models using r-project.org>
>>>>> mailing list
>>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$
> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$>
>
>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$
> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$>>
>
>>
>>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$
>
>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$
> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$>>>
>
>>
>>>
>>>>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKG8rJcsmY$
>
>>
>>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKG8rJcsmY$
>
>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKG8rJcsmY$
> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKG8rJcsmY$>>>>
>>>>> <
>>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQM6wKtNs$
> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQM6wKtNs$>
>
>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQM6wKtNs$
> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQM6wKtNs$>>
>
>>
>>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQM6wKtNs$
>
>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQM6wKtNs$
> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQM6wKtNs$>>>
>>>>>>
>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
>>>>> R-sig-mixed-models using r-project.org mailing list
>>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$
> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$>
>
>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$
> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$>>
>
>>
>>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$
>
>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$
> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$>>>
>
>>
>>>
>>>>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKG8rJcsmY$
>
>>
>>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKG8rJcsmY$
>
>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKG8rJcsmY$
> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!5uCe7IsPHtgAoEp8Qsbn8bXOUBLGi7pVfXIjHwMUHVDbmnOSRCu7OHKG8rJcsmY$>>>>
>>>>>
>>>>>
>>>>
>>>> [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
>>>> R-sig-mixed-models using r-project.org mailing list
>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$
> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$>
>
>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$
> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$>>
>
>>
>>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$
>
>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$
> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$>>>
>
>>
>>>
>>>>
>>>
>>> _______________________________________________
>>> R-sig-mixed-models using r-project.org mailing list
>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$
> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$>
>
>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$
> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$>>
>
>>
>>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$
>
>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$
> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models__;!!LIr3w8kk_Xxm!7bcqr_mYJEwUBwSQ-hoyGUZPrR-Wz2RGDxVbFlFtbA0oveGsE7tg-2k7pcSE0ic$>>>
>
>>
>>>
[[alternative HTML version deleted]]
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