Strubbe Diederik
2009-Jan-28 17:09 UTC
[R] Repeated measures design for GAM? - corrected question...
Dear all, I have a question on the use of GAM with repeated measures. My dataset is as follows: - a number of study areas where bird abundance has been determined. Counts have been performed in 3 consecutive years and there were 2 counts per year (i.e. in total 6 counts). - a number of environmental predictors that do not change over year Xi). When using a GLM, a repeated measures design would like: (for example) lme(Bird_abundance = study_area + count +year+ X1 + X2 + X3,random = ~count|study_area). However, I have found no analogue design for a GAM. For now, I have averaged my bird abundances but I wondered whether a more subtle and elegant strategy exists...? Many thanks, Diederik Diederik Strubbe Evolutionary Ecology Group Department of Biology, University of Antwerp Universiteitsplein 1 B-2610 Antwerp, Belgium http://webhost.ua.ac.be/deco tel : 32 3 820 23 85 [[alternative HTML version deleted]]
Simon Wood
2009-Jan-28 17:30 UTC
[R] Repeated measures design for GAM? - corrected question...
`gamm' in package `mgcv' will let you specify random effects as part of a generalized additive mixed model, but I must admit that I'm a bit confused about what `Bird_abundance' is here, and how it differs from `Count'. best, Simon On Wednesday 28 January 2009 17:09, Strubbe Diederik wrote:> Dear all, > > I have a question on the use of GAM with repeated measures. My dataset is > as follows: - a number of study areas where bird abundance has been > determined. Counts have been performed in 3 consecutive years and there > were 2 counts per year (i.e. in total 6 counts). - a number of > environmental predictors that do not change over year Xi). When using a > GLM, a repeated measures design would like: (for example) > > lme(Bird_abundance = study_area + count +year+ X1 + X2 + X3,random > ~count|study_area). > > However, I have found no analogue design for a GAM. For now, I have > averaged my bird abundances but I wondered whether a more subtle and > elegant strategy exists...? > > Many thanks, > > > Diederik > > Diederik Strubbe > Evolutionary Ecology Group > Department of Biology, University of Antwerp > Universiteitsplein 1 > B-2610 Antwerp, Belgium > http://webhost.ua.ac.be/deco > tel : 32 3 820 23 85 > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > 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.--> Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK > +44 1225 386603 www.maths.bath.ac.uk/~sw283
Strubbe Diederik
2009-Jan-28 19:44 UTC
[R] Repeated measures design for GAM? - corrected question...
Dear Simon, Many thanks for pointing me to the GAMM! For clarification, Bird_abundance are breeding densities ( e.g. 1.25 BP/ha, 2.20 BP/ha,...) and count is just the actual survey(e.g. first_survey,...). The dataset looks like Bird_abundance Study_area YEAR COUNT X1 X2 X3 X4 0.15 area_1 2004 first_survey … … … … 1.26 area_1 2004 second_survey … … … … 2.47 area_1 2005 third_survey … … … … 0.00 area_1 2005 fourth_survey … … … … 0.23 area_1 2006 fifht_survey … … … … 2.64 area_1 2006 sixth_survey … … … … 4.14 area_2 2004 first_survey … … … … 5.00 area_2 2004 second_survey … … … … 6.80 area_2 2005 third_survey … … … … 0.15 area_2 2005 fourth_survey … … … … 0.25 area_2 2006 fifht_survey … … … … 2.36 area_2 2006 sixth_survey … … … … 2.59 area_3 2004 first_survey … … … … 6.31 area_3 2004 second_survey … … … … 0.15 area_3 2005 third_survey … … … … 2.85 area_3 2005 fourth_survey … … … … 2.48 area_3 2006 fifht_survey … … … … 1.23 area_3 2006 sixth_survey … … … … … … … … … … … … Am I correct in assuming the following is a valid syntax for this repeated measures design?: model <-gamm(Bird_abundance ~ YEAR + s(X1)+ s(X2)+ s(X3)+ s(X4),random=list(count=~1,park=~1)) best wishes and thanks again, Diederik Diederik Strubbe Evolutionary Ecology Group Department of Biology, University of Antwerp Universiteitsplein 1 B-2610 Antwerp, Belgium http://webhost.ua.ac.be/deco tel : 32 3 820 23 85 -----Original Message----- From: Strubbe Diederik Sent: Wed 28-1-2009 18:09 To: r-help@R-project.org Subject: Repeated measures design for GAM? - corrected question... Dear all, I have a question on the use of GAM with repeated measures. My dataset is as follows: - a number of study areas where bird abundance has been determined. Counts have been performed in 3 consecutive years and there were 2 counts per year (i.e. in total 6 counts). - a number of environmental predictors that do not change over year Xi). When using a GLM, a repeated measures design would like: (for example) lme(Bird_abundance = study_area + count +year+ X1 + X2 + X3,random = ~count|study_area). However, I have found no analogue design for a GAM. For now, I have averaged my bird abundances but I wondered whether a more subtle and elegant strategy exists...? Many thanks, Diederik Diederik Strubbe Evolutionary Ecology Group Department of Biology, University of Antwerp Universiteitsplein 1 B-2610 Antwerp, Belgium http://webhost.ua.ac.be/deco tel : 32 3 820 23 85 [[alternative HTML version deleted]]