[R] LMER - generate data and define model (2 fixed effects and 1 random effect or 1 fixed effect and 2 random effects)

Tue Aug 11 23:53:03 CEST 2015

You need to:

1) Re-read ?seq. Your syntax is wrong. ("," not ":" )
2) Note that (n-1) x m  !=  n x m

Cheers,
Bert
Bert Gunter

"Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom."
   -- Clifford Stoll

On Tue, Aug 11, 2015 at 2:21 AM, Rosa Oliveira <rosita21 at gmail.com> wrote:
> Dear Thierry
>
> id.pat                       = rep(seq(1:nsample), each =n.longitudinal.observations)
>
> time                         = rep(seq(1:n.longitudinal.observations)-1, nsample)
>
> age                          = rnorm(nsample, mean = 36, sd = .8)
> f.age                        = table(cut(age, breaks = 8))
> id.age                      = rep(f.age, each =5)
> visit                         = rnorm(nsample, mean = 2, sd = .03)
> f.visit                       = table(cut(visit, breaks = 3))
> id.visit                     = rep(f.visit, each =5)
>
>
> 1.
> I was able to solve the age problem and the number of visits problem. Now the problem is another:
>
> yy~1+id.age+time+(time|id.pat)
>
> or
>
> yy~1+id.age + time+(time|id.pat) + (1|id.visit)
>
> there is no problem, but when I perform LMER, for example:
>
> lmer(yy~1+id.age+time+(time|id.pat)), there are errors:
>
> Error in model.frame.default(drop.unused.levels = TRUE, formula = yy ~  :
>   variable lengths differ (found for 'time’)
>
> or
>
> Error in model.frame.default(drop.unused.levels = TRUE, formula = yy ~  :
>   variable lengths differ (found for 'id.age')
>
>
>
> 2. I wasn’t trying to add the same variable to both random and fixed effects. I’m simulating a model and I’m trying to figure if it makes sense to add some variables into the model.
>
>
> Another doubt,
>
> 3. LMER only accepts categorical variables?
>
>
> Best,
> RO
>
>
> Atenciosamente,
> Rosa Oliveira
>
> --
> ____________________________________________________________________________
>
>
> Rosa Celeste dos Santos Oliveira,
>
> E-mail: rosita21 at gmail.com
> Tlm: +351 939355143
> Linkedin: https://pt.linkedin.com/in/rosacsoliveira
> ____________________________________________________________________________
> "Many admire, few know"
> Hippocrates
>
>> On 11 Aug 2015, at 09:00, Thierry Onkelinx <thierry.onkelinx at inbo.be> wrote:
>>
>> Dear Rosa,
>>
>> 1) use cut() to convert a continuous variable into a factor. See ?cut for the details.
>> 2) The syntax for factors is the same as for continuous variables. Just add the name of the factor variable to the formula
>> fAge <- cut(age)
>> yy~1+fAge+time+(time|id.pat)
>> 3) Add + (1|fAge) to the formula. Note that adding fAge to both the fixed and the random effect doesn't make sense.
>> yy~1+time+(time|id.pat) + (1|fAge)
>>
>> Best regards,
>>
>> ir. Thierry Onkelinx
>> Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest
>> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
>> Kliniekstraat 25
>> 1070 Anderlecht
>> Belgium
>>
>> To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
>> The plural of anecdote is not data. ~ Roger Brinner
>> The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey
>>
>> 2015-08-11 1:44 GMT+02:00 Rosa Oliveira <rosita21 at gmail.com <mailto:rosita21 at gmail.com>>:
>>
>>
>> ###############################################################################
>>
>> # Clear memory and set the working directory and the seed
>>
>> ###############################################################################
>>
>> rm(list = ls())
>>
>> setwd("/Dropbox/LMER/R ")
>>
>> set.seed(7010)
>>
>> ###############################################################################
>>
>> # Load up needed packages and do a require
>>
>> ###############################################################################
>>
>> # install.packages("gdata")
>>
>>
>>
>> library(nlme)
>>
>> library(lme4)
>>
>>
>>
>> nsample                                       = 1000                    # Number of subjects
>>
>> n.longitudinal.observations  = 5                                  # number of observations per subject
>>
>>
>>
>> ###############################################################################
>>
>> # Set the other parameters
>>
>> ###############################################################################
>>
>> id.pat                       = rep(seq(1:nsample), each =n.longitudinal.observations)
>>
>> time                         = rep(seq(1:n.longitudinal.observations)-1, nsample)
>>
>> age                          = rnorm(nsample, mean = 36, sd = .8)
>> id.age                      = rep(seq(1: n.longitudinal.observations), each =age)
>>
>>
>>
>>
>>
>> ############################################################################### MODEL WITHOUT AGE
>>
>> boldBeta_individual_blup = coef(lmer(yy~1+time+(time|id.pat)   ))$id.pat   #mixed model
>>
>>
>>
>>
>>
>> ############################################################################### MODEL WITH AGE
>>
>> boldBeta_individual_blup = coef(lmer(yy~1+age+time+(time|id.pat)   ))$id.pat   #mixed model
>>
>>
>>
>> Dear all,
>>
>>
>>
>>
>>
>> I’m trying to use LMER in my simulation problem, and I’m having problems ate the very begging L I’m new in LMER. Can you please help me?
>>
>>
>>
>>
>>
>> 1st problem:
>>
>> how do I generate age so I can use it as a fixed factor?
>>
>> 2nd problem:
>>
>> how do I insert age as a fixed factor?
>>
>> 3rd problem:
>>
>>  what if I wanted to insert a 2nd random effect based on age?
>>
>>
>>
>> Best,
>>
>> RO
>>
>>
>>
>> Atenciosamente,
>> Rosa Oliveira
>>
>> --
>> ____________________________________________________________________________
>>
>>
>> Rosa Celeste dos Santos Oliveira,
>>
>> E-mail: rosita21 at gmail.com <mailto:rosita21 at gmail.com>
>> Tlm: +351 939355143 <tel:%2B351%20939355143>
>> Linkedin: https://pt.linkedin.com/in/rosacsoliveira <https://pt.linkedin.com/in/rosacsoliveira>
>> ____________________________________________________________________________
>> "Many admire, few know"
>> Hippocrates
>>
>> ______________________________________________
>> R-help at r-project.org <mailto:R-help at r-project.org> mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help <https://stat.ethz.ch/mailman/listinfo/r-help>
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html <http://www.r-project.org/posting-guide.html>
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.