Dear all,
I am writing as I would really need your help on the problem with gamm4. I have
tried to find a solution online but I wasn't very successful.
I am running a gamm4 model with an interaction between two variable using the
tensor term, t2. I have a group variable (super end group) with six factors; I
would like to run the model to see the how the interaction term varies across
the factor levels and get the plot for each factor in one page. Here is my code
but I get the following message
dat<-read.table("dat.txt", header=TRUE)
str(dat)
#'data.frame': 11744 obs. of 11 variables:
#$ WATERBODY_ID : Factor w/ 1994 levels "GB102021072830",..: 1 1 2 2 2
3 3 3 4 4 5 5 5 5 5 6 ...
#$ SITE_ID : int 157166 157166 1636 1636 1636 1635 1635 1635
134261 1631 65383 65383 65383 111828 ...
#$ Year : int 2011 2014 2013 2006 2003 2002 2013 2005 2013
2006 2011 2005 2004 ...
#$ ResidualQ95 : num 100 100 80 80 80 98 98 98 105 105 101 101 130
120 120 ...
#$ LIFE.OE_spring : num 1.02 1.03 1.02 1.06 1.06 1.07 1.12 1.05 1.14
1.05 1.09 1.14 1.04 0.97 0.98 ...
#$ super.end.group : Factor w/ 6 levels "B","C","D","E",..: 1 1 3 3 3 2 2
2 4 4 ...
#$ X.urban.suburban : num 0 0 0.07 0.07 0.07 0.53 0.53 0.53 8.07 8.07
0.27 0.27 0.27 0.27 0.27 0.72 ...
#$ X.broadleaved_woodland: num 2.83 2.83 10.39 10.39 10.39 7.72 7.72 21.15
21.15 14.44 14.44 ...
#$ X.CapWks : num 0 0 0 0 0 0 0 0 0 0 8.11 8.11 8.11 0 0 0 42.06
42.06 7.08 0.2 ...
#$ Hms_Poaching : num 0 0 10 10 10 0 0 0 0 10 10 20 40 5 30 15 15 0 0
0 50 50 ...
#$ Hms_Rsctned : num 0 0 0 0 0 0 0 0 0 0 2480 800 1960 1160 740 0 0
960 ...
library(gamm4)
model<-gamm4(LIFE.OE_spring~s(ResidualQ95, by=super.end.group)+t2(ResidualQ95,
Hms_Rsctned, by=super.end.group)+Year +Hms_Poaching +X.broadleaved_woodland
+X.urban.suburban +X.CapWks, data=dat, random=~(1|WATERBODY_ID/SITE_ID))
#Warning messages:
#1: In optwrap(optimizer, devfun, getStart(start, rho$lower, rho$pp), :
# convergence code 1 from bobyqa: bobyqa -- maximum number of function
evaluations exceeded
#2: In optwrap(optimizer, devfun, opt$par, lower = rho$lower, control =
control, :
# convergence code 1 from bobyqa: bobyqa -- maximum number of function
evaluations exceeded
I also tried the following but I got the same message as before.
model<-gamm4(LIFE.OE_spring~s(ResidualQ95)+t2(ResidualQ95, Hms_Rsctned,
by=super.end.group)+Year+ Hms_Poaching +X.broadleaved_woodland
+X.urban.suburban +X.CapWks, data=dat, random=~(1|WATERBODY_ID/SITE_ID))
#fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
#Warning messages:
#1: In optwrap(optimizer, devfun, getStart(start, rho$lower, rho$pp), :
# convergence code 1 from bobyqa: bobyqa -- maximum number of function
evaluations exceeded
#2: In optwrap(optimizer, devfun, opt$par, lower = rho$lower, control =
control, :
# convergence code 1 from bobyqa: bobyqa -- maximum number of function
evaluations exceeded
When I tried to plot, I got the following error:
plot(model$gam, page=1)
#Error in plot.window(...) : need finite 'ylim' values
#In addition: Warning messages:
# 1: In min(ll, na.rm = TRUE) :
# no non-missing arguments to min; returning Inf
# 2: In max(ul, na.rm = TRUE) :
# no non-missing arguments to max; returning -Inf
I would really appreciate your help. My dataset is quite large that is why I
have used the str() for you to get an idea; I have attached a txt file as well
as a sample of my dataset but I have trimmed it a lot so it is even smaller to
fit the email size.
Thank you very much.
Best,
MariaWATERBODY_ID SITE_ID Year ResidualQ95 LIFE.OE_spring super.end.group
X.urban.suburban X.broadleaved_woodland X.CapWks Hms_Poaching
Hms_Rsctned
GB102021072830 157166 2011 100 1.02 B 0 2.83 0
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GB102021072830 157166 2014 100 1.03 B 0 2.83 0
0 0
GB102076070960 65383 2007 101 1.03 B 0.27 7.72 0
0 0
GB102076074040 65126 2006 61 1.04 B 0.33 32.18 0
0 0
GB102076074040 65126 2007 61 1.06 B 0.33 32.18 0
0 0
GB102076074070 65380 2007 100 0.94 B 3.56 1.89 0
0 0
GB102076074070 65380 2005 100 0.99 B 3.56 1.89 0
0 0
GB102076074070 65380 2002 100 1.03 B 3.56 1.89 0
0 0
GB102076074100 63432 2013 100 1.04 B 0.23 3.23 0
0 0
GB102077074270 67618 2013 100 1.05 B 0 4.06 0
5 0
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0 0
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0 0
GB103022076790 1688 2013 100 1.1 B 0.15 6.65 0
0 0
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0 0
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0 0
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0 0
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0 0
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0 0
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0 0
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0 0
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5 500
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GB103024077380 1898 2013 100 1.1 B 0.78 1.2 0
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GB103025072240 2010 2014 124 1 B 0.53 2.78 0
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GB103025072240 2010 2006 124 1.07 B 0.53 2.78 0
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GB103025072240 2010 2003 124 1 B 0.53 2.78 0
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GB103025072240 2010 2006 124 1.05 B 0.53 2.78 0
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GB103025072351 2016 2013 100 1.1 B 0.12 0.23 0
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GB103025072351 2016 2004 100 1.02 B 0.12 0.23 0
0 0
GB103025072351 2016 2014 100 1.17 B 0.12 0.23 0
0 0
GB103025072352 2017 2013 100 1.08 B 0.62 0 0
0 760
GB103025072440 2024 2012 100 1.11 B 0 0 0
0 0
GB103025072480 2018 2013 100 1.1 B 0.98 3.02 0
0 0
GB103025072490 2013 2013 100 1.14 B 0.25 2.38 0
10 140
GB103025072490 2013 2007 100 1.02 B 0.25 2.38 0
10 140
GB103025072490 2013 2004 100 1.04 B 0.25 2.38 0
10 140
GB103025072530 2097 2012 100 1.02 B 0.37 0 0
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GB103025076050 1924 2014 100 1 B 0.17 0 0
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0 280
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0 280
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0 1120
GB104027062600 212 2009 131 1.02 B 5.94 6 8.11
0 1120
GB104027062600 212 2004 131 0.95 B 5.94 6 8.11
0 1120
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0 1120
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0 100
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0 100
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0 100
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0 100
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0 100
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0 1480
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0 1480
GB104027062641 57 2007 127 1.02 B 37.03 14.93 42.06
0 1480
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0 1480
GB104027062641 57 2013 127 1.1 B 37.03 14.93 42.06
0 1480
GB104027062641 57 2010 127 1 B 37.03 14.93 42.06
0 1480
GB104027062641 57 2004 127 0.97 B 37.03 14.93 42.06
0 1480
GB104027062641 57 2005 127 1.01 B 37.03 14.93 42.06
0 1480
GB104027062660 60 2004 100 1 B 13.39 9.69 4.19
0 1120
GB104027062660 60 2013 100 1 B 13.39 9.69 4.19
0 1120
GB104027062660 60 2014 100 0.99 B 13.39 9.69 4.19
0 1120
GB104027062690 396 2006 100 0.99 B 2.48 9.01 0
0 600
GB104027062690 396 2003 100 1.01 B 2.48 9.01 0
0 600
GB104027062690 396 2013 100 1.04 B 2.48 9.01 0
0 600
GB104027063880 421 2010 99 1.04 B 0 16.6 0
10 0
GB104027063880 421 2009 99 1.01 B 0 16.6 0
10 0
GB104027063880 421 2013 99 0.99 B 0 16.6 0
10 0
GB104027063890 22 2013 64 1.1 B 0.95 5.58 0
0 0
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GB104027068020 568 2013 85 1.03 B 0.8 4.73 0
0 0
GB104027068230 747 2013 100 1 B 0 14.16 0
0 0
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10 1160
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10 1160
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50 80
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GB104027069593 237 2008 91 1.03 G 5.64 3.62 6.29
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GB104027069593 77327 2002 91 0.96 G 5.64 3.62 6.29
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GB104029061940 55247 2002 91 1.02 G 0.13 1.63 28.88
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GB104029061940 55247 2009 91 1.08 G 0.13 1.63 28.88
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GB104029061990 55198 2014 22 0.98 G 3.98 1.35 17.62
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GB104029062100 55397 2009 114 1.02 G 0.86 2.47 23.01
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GB104029062100 55397 2010 114 1.04 G 0.86 2.47 23.01
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GB104029062100 55397 2004 114 0.99 G 0.86 2.47 23.01
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GB104029062100 55397 2013 114 0.96 G 0.86 2.47 23.01
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GB104029062100 55397 2005 114 1.05 G 0.86 2.47 23.01
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GB104029062100 55397 2003 114 1.04 G 0.86 2.47 23.01
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GB104029062110 55057 2013 98 1.03 G 19.08 1.1 44.29
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GB105033037920 56457 2010 143 1 G 2.16 5.07 24.5
30 220
GB105033037920 56457 2013 143 0.98 G 2.16 5.07 24.5
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GB105033037920 56457 2014 143 1.04 G 2.16 5.07 24.5
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GB105033037920 56457 2007 143 1 G 2.16 5.07 24.5
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GB105033037920 56457 2004 143 1.07 G 2.16 5.07 24.5
30 220
GB105033038000 56441 2009 139 1.07 G 5.23 9.63 52.57
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25 40
GB105033038000 56441 2006 139 1.01 G 5.23 9.63 52.57
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GB105033042750 56063 2006 93 0.99 G 19.69 6.66 3.98
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