R help - Aug 2005 - Treatment-response analysis along time

Dear R people,
I wonder if you could give me a hand with some of my data. I have a very 
typical analysis in biology, however it is difficult for me to find the 
right way to analyse. I had a group of animals, I gave them a treatment, and 
I measure a variable along time -one??s per day- along 5 days,for 
example(fake data):
Animals Time1 Time2 Time3 Time4
1            1         5        3        1
2            2         7        4        1
3            5         5        3        1
4            1         3        7        2
5            2         7        7        1
Please, notice that all the animals get the same treatment, and there are no 
  control -animals which has no received any treatment.
Normally I handle this kind of data with SPSS and Repeated Measurement 
analysis. That tell me if there is a change along the time, but no 
information about when the treatment start to be effective, when the effect 
has pass. Besides, i would like to be able to handle this data with R.
I have been looking at Crawley's S-plus book, and I cannot find similar 
example as I have, not either in the Dalgaard??s introduction to R, because 
he uses an example where different animals are measured as each time -using 
time as a factor in a one way anova (I am hope I am right).
Thanks for your help and time.
Best regards
Felix

you haven't told us what kind of variable you measure, but either way 
look at lmer() function in lme4 package which fits both linear and 
generalized linear mixed-effects models.

I hope it helps.

Best,
Dimitris

----
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven

Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/16/336899
Fax: +32/16/337015
Web: http://www.med.kuleuven.be/biostat/
     http://www.student.kuleuven.be/~m0390867/dimitris.htm


----- Original Message ----- 
From: "Felix Royo" <z319112 at hotmail.com>
To: <r-help at stat.math.ethz.ch>
Sent: Wednesday, August 10, 2005 9:09 AM
Subject: [R] Treatment-response analysis along time


Dear R people,
I wonder if you could give me a hand with some of my data. I have a 
very
typical analysis in biology, however it is difficult for me to find 
the
right way to analyse. I had a group of animals, I gave them a 
treatment, and
I measure a variable along time -one??s per day- along 5 days,for
example(fake data):
Animals Time1 Time2 Time3 Time4
1            1         5        3        1
2            2         7        4        1
3            5         5        3        1
4            1         3        7        2
5            2         7        7        1
Please, notice that all the animals get the same treatment, and there 
are no
  control -animals which has no received any treatment.
Normally I handle this kind of data with SPSS and Repeated Measurement
analysis. That tell me if there is a change along the time, but no
information about when the treatment start to be effective, when the 
effect
has pass. Besides, i would like to be able to handle this data with R.
I have been looking at Crawley's S-plus book, and I cannot find 
similar
example as I have, not either in the Dalgaard??s introduction to R, 
because
he uses an example where different animals are measured as each 
time -using
time as a factor in a one way anova (I am hope I am right).
Thanks for your help and time.
Best regards
Felix

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"Felix Royo" <z319112 at hotmail.com> writes:
> Dear R people,
> I wonder if you could give me a hand with some of my data. I have a very 
> typical analysis in biology, however it is difficult for me to find the 
> right way to analyse. I had a group of animals, I gave them a treatment,
and
> I measure a variable along time -one??s per day- along 5 days,for 
> example(fake data):
> Animals Time1 Time2 Time3 Time4
> 1            1         5        3        1
> 2            2         7        4        1
> 3            5         5        3        1
> 4            1         3        7        2
> 5            2         7        7        1
> Please, notice that all the animals get the same treatment, and there are
no
>   control -animals which has no received any treatment.
> Normally I handle this kind of data with SPSS and Repeated Measurement 
> analysis. That tell me if there is a change along the time, but no 
> information about when the treatment start to be effective, when the effect
> has pass. Besides, i would like to be able to handle this data with R.
> I have been looking at Crawley's S-plus book, and I cannot find similar
> example as I have, not either in the Dalgaard??s introduction to R, because
> he uses an example where different animals are measured as each time -using
> time as a factor in a one way anova (I am hope I am right).
> Thanks for your help and time.
> Best regards
> Felix
ISwR is hardly an extensive treatise on repeated measurements, but
two-way ANOVA *is* in there (Section 6.3 and 10.6 for the replicated
case). Notice that you need a different data layout for that,
basically the result of a reshape(...direction="long"). 

Also, the capabilities of the newer mlm methods are relevant for this
kind of data (see ?anova.mlm, and the examples).

-- 
   O__  ---- Peter Dalgaard             ??ster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907