Dear R community,
I have some questions regarding the analysis of a zero-inflated count dataset
and repeated measures design.
The dataset is arranged as follows :
Unit of analysis: point - these are points were bird were counted during a
certain amount of time. In total we have about 175 points. Each point is
located within a certain habitat fragment (here: "site"= A-B-C-D-..., in
reality we have 25 sites,i.e. forest fragments). All points were counted five
times during three years ( thus in total, each point was counted 15 times). We
want to relate the bird abundance to a number of habitat variables (here:
X1-X2-X3) collected at the site level. Abundance: this is the number of birds
counted at a point. In most cases ( > 90%), no birds were detected and the
abundance dataset is thus zero-inflated.
I have been looking for a code to analyze this zero-inflated poisson
distributed dataset with a repeated measures design, and I have arrived at the
glmmADMB package.
library(glmmADMB)
data <- read.table("D:/Boris/Borisdataset.csv",sep=",",header=TRUE)
count <- data$count
site <- data$site
abundance <- data$abundance
test<-glmm.admb(abundance~data$X1+data$X2+data$year,random=~count,group="site",data=data,family="poisson",zeroInflation=TRUE)
[ for clarity: in the above syntax: count ranges from 1-5 as each site has been
counted 5 times in a year, site refers to one of the 25 forest fragments in
which the point counts were conducted, Xi are the habitat variables].
My questions are:
- does it make sense to analyze these data at the point level, as all habitat
variables are collected at the site level, meaning that for all points
belonging to a certain forest fragment, the habitat variables have the same
value. If it does make sense, is the proposed syntax ok? Is there any option to
include year as a random effect, as I am not especially interested in
differences between years.
-it looks appealing to average the point count values for each forest fragment,
and to analyze the data with "forest fragment" as unit of analysis. However,
also when averaging across fragments, the dataset is still zero-inflated. It is
however impossible to a zero-inflated Poisson distribution for this analysis,
as the averaged forest fragment values are not always discrete values.
Many thanks in advance,
Diederik
{example of dataset reproduced below....}
X1 X2 X3 point site count year abundance
1.23598 0.277765 0.861794 1 A 1 2001 0
1.23598 0.277765 0.861794 1 A 2 2001 0
1.23598 0.277765 0.861794 1 A 3 2001 6
1.23598 0.277765 0.861794 1 A 4 2001 10
1.23598 0.277765 0.861794 1 A 5 2001 0
1.23598 0.277765 0.861794 2 A 1 2001 0
1.23598 0.277765 0.861794 2 A 2 2001 0
1.23598 0.277765 0.861794 2 A 3 2001 0
1.23598 0.277765 0.861794 2 A 4 2001 0
1.23598 0.277765 0.861794 2 A 5 2001 0
1.23598 0.277765 0.861794 3 A 1 2001 9
1.23598 0.277765 0.861794 3 A 2 2001 3
1.23598 0.277765 0.861794 3 A 3 2001 5
1.23598 0.277765 0.861794 3 A 4 2001 0
1.23598 0.277765 0.861794 3 A 5 2001 0
1.23598 0.277765 0.861794 1 A 1 2002 9
1.23598 0.277765 0.861794 1 A 2 2002 0
1.23598 0.277765 0.861794 1 A 3 2002 0
1.23598 0.277765 0.861794 1 A 4 2002 0
1.23598 0.277765 0.861794 1 A 5 2002 0
1.23598 0.277765 0.861794 2 A 1 2002 0
1.23598 0.277765 0.861794 2 A 2 2002 0
1.23598 0.277765 0.861794 2 A 3 2002 0
1.23598 0.277765 0.861794 2 A 4 2002 0
1.23598 0.277765 0.861794 2 A 5 2002 0
1.23598 0.277765 0.861794 3 A 1 2002 0
1.23598 0.277765 0.861794 3 A 2 2002 0
1.23598 0.277765 0.861794 3 A 3 2002 0
1.23598 0.277765 0.861794 3 A 4 2002 0
1.23598 0.277765 0.861794 3 A 5 2002 0
1.23598 0.277765 0.861794 1 A 1 2003 5
1.23598 0.277765 0.861794 1 A 2 2003 5
1.23598 0.277765 0.861794 1 A 3 2003 0
1.23598 0.277765 0.861794 1 A 4 2003 0
1.23598 0.277765 0.861794 1 A 5 2003 0
1.23598 0.277765 0.861794 2 A 1 2003 0
1.23598 0.277765 0.861794 2 A 2 2003 0
1.23598 0.277765 0.861794 2 A 3 2003 0
1.23598 0.277765 0.861794 2 A 4 2003 6
1.23598 0.277765 0.861794 2 A 5 2003 4
1.23598 0.277765 0.861794 3 A 1 2003 0
1.23598 0.277765 0.861794 3 A 2 2003 0
1.23598 0.277765 0.861794 3 A 3 2003 9
1.23598 0.277765 0.861794 3 A 4 2003 0
1.23598 0.277765 0.861794 3 A 5 2003 0
0.47955 0.403671 0.980391 1 B 1 2001 0
0.47955 0.403671 0.980391 1 B 2 2001 0
0.47955 0.403671 0.980391 1 B 3 2001 0
0.47955 0.403671 0.980391 1 B 4 2001 0
0.47955 0.403671 0.980391 1 B 5 2001 9
0.47955 0.403671 0.980391 2 B 1 2001 1
0.47955 0.403671 0.980391 2 B 2 2001 9
0.47955 0.403671 0.980391 2 B 3 2001 0
0.47955 0.403671 0.980391 2 B 4 2001 0
0.47955 0.403671 0.980391 2 B 5 2001 0
0.47955 0.403671 0.980391 3 B 1 2001 0
0.47955 0.403671 0.980391 3 B 2 2001 0
0.47955 0.403671 0.980391 3 B 3 2001 0
0.47955 0.403671 0.980391 3 B 4 2001 7
0.47955 0.403671 0.980391 3 B 5 2001 0
0.47955 0.403671 0.980391 1 B 1 2002 0
0.47955 0.403671 0.980391 1 B 2 2002 0
0.47955 0.403671 0.980391 1 B 3 2002 0
0.47955 0.403671 0.980391 1 B 4 2002 1
0.47955 0.403671 0.980391 1 B 5 2002 0
0.47955 0.403671 0.980391 2 B 1 2002 0
0.47955 0.403671 0.980391 2 B 2 2002 0
0.47955 0.403671 0.980391 2 B 3 2002 0
0.47955 0.403671 0.980391 2 B 4 2002 6
0.47955 0.403671 0.980391 2 B 5 2002 0
0.47955 0.403671 0.980391 3 B 1 2002 0
0.47955 0.403671 0.980391 3 B 2 2002 5
0.47955 0.403671 0.980391 3 B 3 2002 0
0.47955 0.403671 0.980391 3 B 4 2002 2
0.47955 0.403671 0.980391 3 B 5 2002 0
0.47955 0.403671 0.980391 1 B 1 2003 0
0.47955 0.403671 0.980391 1 B 2 2003 0
0.47955 0.403671 0.980391 1 B 3 2003 0
0.47955 0.403671 0.980391 1 B 4 2003 0
0.47955 0.403671 0.980391 1 B 5 2003 0
0.47955 0.403671 0.980391 2 B 1 2003 0
0.47955 0.403671 0.980391 2 B 2 2003 0
0.47955 0.403671 0.980391 2 B 3 2003 0
0.47955 0.403671 0.980391 2 B 4 2003 0
0.47955 0.403671 0.980391 2 B 5 2003 0
0.47955 0.403671 0.980391 3 B 1 2003 0
0.47955 0.403671 0.980391 3 B 2 2003 0
0.47955 0.403671 0.980391 3 B 3 2003 0
0.47955 0.403671 0.980391 3 B 4 2003 0
0.47955 0.403671 0.980391 3 B 5 2003 0
0.036829 0.49832 0.906583 1 C 1 2001 0
0.036829 0.49832 0.906583 1 C 2 2001 0
0.036829 0.49832 0.906583 1 C 3 2001 0
0.036829 0.49832 0.906583 1 C 4 2001 9
0.036829 0.49832 0.906583 1 C 5 2001 0
0.036829 0.49832 0.906583 2 C 1 2001 0
0.036829 0.49832 0.906583 2 C 2 2001 0
0.036829 0.49832 0.906583 2 C 3 2001 0
0.036829 0.49832 0.906583 2 C 4 2001 0
0.036829 0.49832 0.906583 2 C 5 2001 6
0.036829 0.49832 0.906583 3 C 1 2001 0
0.036829 0.49832 0.906583 3 C 2 2001 0
0.036829 0.49832 0.906583 3 C 3 2001 0
0.036829 0.49832 0.906583 3 C 4 2001 0
0.036829 0.49832 0.906583 3 C 5 2001 8
0.036829 0.49832 0.906583 1 C 1 2002 0
0.036829 0.49832 0.906583 1 C 2 2002 0
0.036829 0.49832 0.906583 1 C 3 2002 7
0.036829 0.49832 0.906583 1 C 4 2002 0
0.036829 0.49832 0.906583 1 C 5 2002 0
0.036829 0.49832 0.906583 2 C 1 2002 0
0.036829 0.49832 0.906583 2 C 2 2002 3
0.036829 0.49832 0.906583 2 C 3 2002 0
0.036829 0.49832 0.906583 2 C 4 2002 0
0.036829 0.49832 0.906583 2 C 5 2002 0
0.036829 0.49832 0.906583 3 C 1 2002 0
0.036829 0.49832 0.906583 3 C 2 2002 0
0.036829 0.49832 0.906583 3 C 3 2002 0
0.036829 0.49832 0.906583 3 C 4 2002 0
0.036829 0.49832 0.906583 3 C 5 2002 0
0.036829 0.49832 0.906583 1 C 1 2003 0
0.036829 0.49832 0.906583 1 C 2 2003 0
0.036829 0.49832 0.906583 1 C 3 2003 6
0.036829 0.49832 0.906583 1 C 4 2003 0
0.036829 0.49832 0.906583 1 C 5 2003 0
0.036829 0.49832 0.906583 2 C 1 2003 7
0.036829 0.49832 0.906583 2 C 2 2003 0
0.036829 0.49832 0.906583 2 C 3 2003 2
0.036829 0.49832 0.906583 2 C 4 2003 9
0.036829 0.49832 0.906583 2 C 5 2003 0
0.036829 0.49832 0.906583 3 C 1 2003 0
0.036829 0.49832 0.906583 3 C 2 2003 0
0.036829 0.49832 0.906583 3 C 3 2003 0
0.036829 0.49832 0.906583 3 C 4 2003 0
0.036829 0.49832 0.906583 3 C 5 2003 0
1.23598 0.129 1.30048 1 D 1 2001 0
1.23598 0.129 1.30048 1 D 2 2001 0
1.23598 0.129 1.30048 1 D 3 2001 6
1.23598 0.129 1.30048 1 D 4 2001 10
1.23598 0.129 1.30048 1 D 5 2001 0
1.23598 0.129 1.30048 2 D 1 2001 0
1.23598 0.129 1.30048 2 D 2 2001 0
1.23598 0.129 1.30048 2 D 3 2001 0
1.23598 0.129 1.30048 2 D 4 2001 12
1.23598 0.129 1.30048 2 D 5 2001 0
1.23598 0.129 1.30048 3 D 1 2001 9
1.23598 0.129 1.30048 3 D 2 2001 3
1.23598 0.129 1.30048 3 D 3 2001 5
1.23598 0.129 1.30048 3 D 4 2001 1
1.23598 0.129 1.30048 3 D 5 2001 0
1.23598 0.129 1.30048 1 D 1 2002 9
1.23598 0.129 1.30048 1 D 2 2002 2
1.23598 0.129 1.30048 1 D 3 2002 0
1.23598 0.129 1.30048 1 D 4 2002 3
1.23598 0.129 1.30048 1 D 5 2002 0
1.23598 0.129 1.30048 2 D 1 2002 0
1.23598 0.129 1.30048 2 D 2 2002 0
1.23598 0.129 1.30048 2 D 3 2002 0
1.23598 0.129 1.30048 2 D 4 2002 0
1.23598 0.129 1.30048 2 D 5 2002 0
1.23598 0.129 1.30048 3 D 1 2002 0
1.23598 0.129 1.30048 3 D 2 2002 0
1.23598 0.129 1.30048 3 D 3 2002 0
1.23598 0.129 1.30048 3 D 4 2002 0
1.23598 0.129 1.30048 3 D 5 2002 0
1.23598 0.129 1.30048 1 D 1 2003 5
1.23598 0.129 1.30048 1 D 2 2003 5
1.23598 0.129 1.30048 1 D 3 2003 0
1.23598 0.129 1.30048 1 D 4 2003 0
1.23598 0.129 1.30048 1 D 5 2003 0
1.23598 0.129 1.30048 2 D 1 2003 0
1.23598 0.129 1.30048 2 D 2 2003 0
1.23598 0.129 1.30048 2 D 3 2003 0
1.23598 0.129 1.30048 2 D 4 2003 6
1.23598 0.129 1.30048 2 D 5 2003 4
1.23598 0.129 1.30048 3 D 1 2003 0
0.418671 0.087187 0.504914 1 E 1 2001 0
0.418671 0.087187 0.504914 1 E 2 2001 0
0.418671 0.087187 0.504914 1 E 3 2001
6
0.418671 0.087187 0.504914 1 E 4 2001
10
0.418671 0.087187 0.504914 1 E 5 2001 0
0.418671 0.087187 0.504914 2 E 1 2001 0
0.418671 0.087187 0.504914 2 E 2 2001 0
0.418671 0.087187 0.504914 2 E 3 2001 0
0.418671 0.087187 0.504914 2 E 4 2001 0
0.418671 0.087187 0.504914 2 E 5 2001 0
0.418671 0.087187 0.504914 3 E 1 2001
9
0.418671 0.087187 0.504914 3 E 2 2001
3
0.418671 0.087187 0.504914 3 E 3 2001
5
0.418671 0.087187 0.504914 3 E 4 2001 0
0.418671 0.087187 0.504914 3 E 5 2001 0
0.418671 0.087187 0.504914 1 E 1 2002
9
0.418671 0.087187 0.504914 1 E 2 2002 0
0.418671 0.087187 0.504914 1 E 3 2002 0
0.418671 0.087187 0.504914 1 E 4 2002 0
0.418671 0.087187 0.504914 1 E 5 2002 0
0.418671 0.087187 0.504914 2 E 1 2002 0
0.418671 0.087187 0.504914 2 E 2 2002 0
0.418671 0.087187 0.504914 2 E 3 2002 0
0.418671 0.087187 0.504914 2 E 4 2002 0
0.418671 0.087187 0.504914 2 E 5 2002 0
0.418671 0.087187 0.504914 3 E 1 2002 0
0.418671 0.087187 0.504914 3 E 2 2002 0
0.418671 0.087187 0.504914 3 E 3 2002 0
0.418671 0.087187 0.504914 3 E 4 2002 0
0.418671 0.087187 0.504914 3 E 5 2002 0
0.418671 0.087187 0.504914 1 E 1 2003
5
0.418671 0.087187 0.504914 1 E 2 2003
5
0.418671 0.087187 0.504914 1 E 3 2003 0
0.418671 0.087187 0.504914 1 E 4 2003 0
0.418671 0.087187 0.504914 1 E 5 2003 0
0.418671 0.087187 0.504914 2 E 1 2003 0
0.418671 0.087187 0.504914 2 E 2 2003 0
0.418671 0.087187 0.504914 2 E 3 2003 0
0.418671 0.087187 0.504914 2 E 4 2003
6
0.418671 0.087187 0.504914 2 E 5 2003
4
0.418671 0.087187 0.504914 3 E 1 2003 0
0.418671 0.087187 0.504914 3 E 2 2003 0
0.418671 0.087187 0.504914 3 E 3 2003
9
0.418671 0.087187 0.504914 3 E 4 2003 0
0.418671 0.087187 0.504914 3 E 5 2003 0
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@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.
