[R-sig-ME] Curved residuals vs fitted plot

Fri Mar 7 20:20:19 CET 2014

Dear mixed-models group,

Thank you for taking time to read this plea for help.

I wondered if you could give me any advice regarding the curved residuals vs fitted plot with my model:

model3<-glmer(y~Treatment*Distance.m+(1|Field/Field.section/Transect/fffPlot/Bait.ID),
binomial(link=logit),data=dframe1)

My aim is to explain aphid removal from bait trays in response to treatment (presence of absence of a flower strip) and distance (five distances, or plots, moving away from the margins; 1, 5, 10, 15, and 20m). (More experimental details after message in case helpful).

I am using R version 3.0.2 and the latest version of lme4. The resid vs fitted figure is not great, is this because I need to look at a logit fitted scale? (See here to view the figure: <http://imgur.com/CYe5CxC> http://imgur.com/CYe5CxC)

Any help at all would be more than amazing,

Victoria

Experimental setup
There are two fields overall, each contains one treatment (Mit) and one control (Non). Looking at one treatment, in one field section, there are three transects parallel to each other and perpendicular to the margin treatment (T1, T2 and T3). There are five plots along each transect at specific distances from the treatment margins (1, 5, 10, 15, 20m). At each plot, three replica bait trays were placed (a, b and c). Each tray contained 20 aphids glued to foam. In total, I had two farm fields at the largest scale and between them there were 180 bait trays overall (90 per field).

Script attached, also listed below

library(lme4)

Field<-c("L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,"L" ,
"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B")

Treatment<-c("Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,
"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,
"Mit" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,
"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Non" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit" ,"Mit")

Field.section<-c("D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"D" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"C" ,"B" ,"B" ,
"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"B" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A" ,"A")

Transect<-c("T10" ,"T10" ,"T10" ,"T10" ,"T10" ,"T10" ,"T10" ,"T10" ,"T10" ,"T10" ,"T10" ,"T10" ,"T10" ,"T10" ,"T10" ,"T10" ,"T11" ,"T11" ,"T11" ,"T11" ,"T11" ,"T11" ,"T11" ,"T11" ,"T11" ,"T11" ,"T11" ,"T11" ,"T11" ,"T11" ,"T11" ,"T12" ,"T12" ,"T12" ,"T12" ,"T12" ,"T12" ,"T12" ,
"T12" ,"T12" ,"T12" ,"T12" ,"T12" ,"T12" ,"T12" ,"T7" ,"T7" ,"T7" ,"T7" ,"T7" ,"T7" ,"T7" ,"T7" ,"T7" ,"T7" ,"T7" ,"T7" ,"T7" ,"T7" ,"T7" ,"T8" ,"T8" ,"T8" ,"T8" ,"T8" ,"T8" ,"T8" ,"T8" ,"T8" ,"T8" ,"T8" ,"T8" ,"T8" ,"T8" ,"T8" ,"T9" ,"T9" ,"T9" ,"T9" ,"T9" ,"T9" ,"T9" ,"T9" ,"T9" ,
"T9" ,"T9" ,"T9" ,"T9" ,"T9" ,"T9" ,"T4" ,"T4" ,"T4" ,"T4" ,"T4" ,"T4" ,"T4" ,"T4" ,"T4" ,"T4" ,"T4" ,"T4" ,"T4" ,"T4" ,"T4" ,"T5" ,"T5" ,"T5" ,"T5" ,"T5" ,"T5" ,"T5" ,"T5" ,"T5" ,"T5" ,"T5" ,"T5" ,"T5" ,"T5" ,"T5" ,"T6" ,"T6" ,"T6" ,"T6" ,"T6" ,"T6" ,"T6" ,"T6" ,"T6" ,"T6" ,"T6" ,"T6" ,
"T6" ,"T6" ,"T6" ,"T1" ,"T1" ,"T1" ,"T1" ,"T1" ,"T1" ,"T1" ,"T1" ,"T1" ,"T1" ,"T1" ,"T1" ,"T1" ,"T1" ,"T1" ,"T2" ,"T2" ,"T2" ,"T2" ,"T2" ,"T2" ,"T2" ,"T2" ,"T2" ,"T2" ,"T2" ,"T2" ,"T2" ,"T2" ,"T2" ,"T3" ,"T3" ,"T3" ,"T3" ,"T3" ,"T3" ,"T3" ,"T3" ,"T3" ,"T3" ,"T3" ,"T3" ,"T3" ,"T3" ,"T3")

Distance.m<-c(1 ,1 ,1 ,1 ,5 ,5 ,5 ,10 ,10 ,10 ,15 ,15 ,15 ,20 ,20 ,20 ,1 ,1 ,1 ,5 ,5 ,5 ,10 ,10 ,10 ,15 ,15 ,15 ,20 ,20 ,20 ,1 ,1 ,1 ,5 ,5 ,5 ,10 ,10 ,15 ,15 ,15 ,20 ,20 ,20 ,1 ,1 ,1 ,5 ,5 ,5 ,10 ,10 ,10 ,15 ,15 ,15 ,20 ,20 ,20 ,1 ,1 ,1 ,5 ,5 ,5 ,10 ,10 ,10 ,15 ,15 ,15 ,20 ,20 ,20 ,1 ,1 ,1 ,5 ,5 ,5 ,10 ,10 ,10 ,15 ,15 ,15 ,20 ,20 ,20 ,1 ,1 ,1 ,5 ,5 ,5 ,10 ,10 ,10 ,15 ,15 ,15 ,20 ,20 ,20 ,1 ,1 ,1 ,5 ,5 ,5 ,10 ,10 ,10 ,15 ,15 ,15 ,20 ,20 ,20 ,1 ,1 ,1 ,5 ,5 ,5 ,10 ,10 ,10
,15 ,15 ,15 ,20 ,20 ,20 ,1 ,1 ,1 ,5 ,5 ,5 ,10 ,10 ,10 ,15 ,15 ,15 ,20 ,20 ,20 ,1 ,1 ,1 ,5 ,5 ,5 ,10 ,10 ,10 ,15 ,15 ,15 ,20 ,20 ,20 ,1 ,1 ,1 ,5 ,5 ,5 ,10 ,10 ,10 ,15 ,15 ,15 ,20 ,20 ,20)

Aphid.rm.success<-c(3 ,7 ,19 ,19 ,2 ,0 ,0 ,0 ,0 ,0 ,0 ,1 ,1 ,1 ,1 ,1 ,1 ,1 ,0 ,0 ,8 ,16 ,2 ,0 ,2 ,1 ,1 ,3 ,0 ,0 ,9 ,10 ,15 ,18 ,1 ,0 ,14 ,10 ,4 ,1 ,3 ,12 ,2 ,4 ,0 ,20 ,17 ,19 ,11 ,19 ,5 ,0 ,0 ,3 ,0 ,0 ,0 ,3 ,11 ,0 ,19 ,13 ,13 ,10 ,9 ,5 ,19 ,1 ,2 ,0 ,12 ,2 ,0 ,1 ,7 ,15 ,19 ,6 ,19 ,18 ,17 ,1 ,0 ,0 ,1 ,1 ,9 ,18 ,11 ,19 ,1 ,3 ,0 ,0 ,1 ,1 ,0 ,1 ,1 ,3 ,0 ,0 ,0 ,4 ,1 ,0 ,0 ,2 ,1 ,6 ,0 ,0 ,0 ,1 ,0 ,0 ,1 ,1 ,0 ,0 ,2 ,1 ,11 ,1 ,0 ,3 ,3 ,0 ,1 ,3 ,0 ,0 ,1 ,0 ,0 ,8 ,1 ,3 ,2 ,1 ,3 ,0 ,
1 ,2 ,0 ,1 ,1 ,0 ,0 ,0 ,8 ,0 ,0 ,0 ,7 ,1 ,0 ,1 ,1 ,0 ,1 ,0 ,1 ,0 ,1 ,5 ,0 ,20 ,0 ,17 ,0 ,10 ,1 ,0 ,5 ,0 ,0 ,0 ,0 ,0)

Aphid.remain.fail<-c(17 ,13 ,1 ,1 ,18 ,20 ,20 ,20 ,20 ,20 ,20 ,19 ,19 ,19 ,17 ,19 ,19 ,19 ,20 ,20 ,12 ,4 ,18 ,20 ,18 ,19 ,19 ,17 ,20 ,20 ,10 ,9 ,5 ,2 ,19 ,20 ,6 ,10 ,16 ,19 ,17 ,8 ,18 ,16 ,20 ,0 ,3 ,1 ,9 ,2 ,15 ,20 ,20 ,17 ,20 ,20 ,20 ,17 ,9 ,20 ,1 ,7 ,7 ,10 ,11 ,15 ,1 ,19 ,18 ,20 ,8 ,18 ,20 ,19 ,13 ,5 ,1 ,14 ,0 ,1 ,3 ,19 ,20 ,20 ,19 ,18 ,11 ,2 ,9 ,0 ,19 ,18 ,20 ,20 ,19 ,19 ,20 ,19 ,19 ,16 ,20 ,20 ,20 ,16 ,19 ,20 ,20 ,18 ,19 ,14 ,20 ,20 ,20 ,19 ,20 ,20 ,19 ,19 ,20 ,20 ,18 ,19 ,
9 ,19 ,19 ,18 ,17 ,20 ,19 ,17 ,20 ,20 ,19 ,20 ,17 ,12 ,19 ,17 ,18 ,19 ,17 ,20 ,19 ,18 ,20 ,18 ,20 ,20 ,19 ,20 ,12 ,20 ,20 ,20 ,13 ,19 ,20 ,19 ,19 ,20 ,20 ,20 ,19 ,20 ,19 ,15 ,20 ,0 ,20 ,3 ,20 ,10 ,19 ,20 ,15 ,20 ,20 ,20 ,20 ,20)

fffPlot<-c("D T1 1" ,"D T1 1" ,"D T1 1" ,"D T1 1" ,"D T1 5" ,"D T1 5" ,"D T1 5" ,"D T1 10" ,"D T1 10" ,"D T1 10" ,"D T1 15" ,"D T1 15" ,"D T1 15" ,"D T1 20" ,"D T1 20" ,"D T1 20" ,"D T2 1" ,"D T2 1" ,"D T2 1" ,"D T2 5" ,"D T2 5" ,"D T2 5" ,"D T2 10" ,"D T2 10" ,"D T2 10" ,"D T2 15" ,"D T2 15" ,"D T2 15" ,"D T2 20" ,"D T2 20" ,"D T2 20" ,"D T3 1" ,"D T3 1" ,"D T3 1" ,"D T3 5" ,"D T3 5" ,"D T3 5" ,"D T3 10" ,"D T3 10" ,"D T3 15" ,"D T3 15" ,"D T3 15" ,"D T3 20" ,"D T3 20" ,"D T3 20" ,
"C T1 1" ,"C T1 1" ,"C T1 1" ,"C T1 5" ,"C T1 5" ,"C T1 5" ,"C T1 10" ,"C T1 10" ,"C T1 10" ,"C T1 15" ,"C T1 15" ,"C T1 15" ,"C T1 20" ,"C T1 20" ,"C T1 20" ,"C T2 1" ,"C T2 1" ,"C T2 1" ,"C T2 5" ,"C T2 5" ,"C T2 5" ,"C T2 10" ,"C T2 10" ,"C T2 10" ,"C T2 15" ,"C T2 15" ,"C T2 15" ,"C T2 20" ,"C T2 20" ,"C T2 20" ,"C T3 1" ,"C T3 1" ,"C T3 1" ,"C T3 5" ,"C T3 5" ,"C T3 5" ,"C T3 10" ,"C T3 10" ,"C T3 10" ,"C T3 15" ,"C T3 15" ,"C T3 15" ,"C T3 20" ,"C T3 20" ,"C T3 20" ,"B T1 1" ,
"B T1 1" ,"B T1 1" ,"B T1 5" ,"B T1 5" ,"B T1 5" ,"B T1 10" ,"B T1 10" ,"B T1 10" ,"B T1 15" ,"B T1 15" ,"B T1 15" ,"B T1 20" ,"B T1 20" ,"B T1 20" ,"B T2 1" ,"B T2 1" ,"B T2 1" ,"B T2 5" ,"B T2 5" ,"B T2 5" ,"B T2 10" ,"B T2 10" ,"B T2 10" ,"B T2 15" ,"B T2 15" ,"B T2 15" ,"B T2 20" ,"B T2 20" ,"B T2 20" ,"B T3 1" ,"B T3 1" ,"B T3 1" ,"B T3 5" ,"B T3 5" ,"B T3 5" ,"B T3 10" ,"B T3 10" ,"B T3 10" ,"B T3 15" ,"B T3 15" ,"B T3 15" ,"B T3 20" ,"B T3 20" ,"B T3 20" ,"A T1 1" ,"A T1 1" ,"A T1 1" ,
"A T1 5" ,"A T1 5" ,"A T1 5" ,"A T1 10" ,"A T1 10" ,"A T1 10" ,"A T1 15" ,"A T1 15" ,"A T1 15" ,"A T1 20" ,"A T1 20" ,"A T1 20" ,"A T2 1" ,"A T2 1" ,"A T2 1" ,"A T2 5" ,"A T2 5" ,"A T2 5" ,"A T2 10" ,"A T2 10" ,"A T2 10" ,"A T2 15" ,"A T2 15" ,"A T2 15" ,"A T2 20" ,"A T2 20" ,"A T2 20" ,"A T3 1" ,"A T3 1" ,"A T3 1" ,"A T3 5" ,"A T3 5" ,"A T3 5" ,"A T3 10" ,"A T3 10" ,"A T3 10" ,"A T3 15" ,"A T3 15" ,"A T3 15" ,"A T3 20" ,"A T3 20" ,"A T3 20")

Bait.ID<-c("ID1" ,"ID2" ,"ID3" ,"ID3" ,"ID4" ,"ID5" ,"ID6" ,"ID7" ,"ID8" ,"ID9" ,"ID10" ,"ID11" ,"ID12" ,"ID13" ,"ID14" ,"ID15" ,"ID16" ,"ID17" ,"ID18" ,"ID19" ,"ID20" ,"ID21" ,"ID22" ,"ID23" ,"ID24" ,"ID25" ,"ID26" ,"ID27" ,"ID28" ,"ID29" ,"ID30" ,"ID31" ,"ID32" ,"ID33" ,"ID34" ,"ID35" ,"ID36" ,"ID37" ,"ID38" ,"ID39" ,"ID40" ,"ID41" ,"ID42" ,"ID43" ,"ID44" ,"ID45" ,"ID46" ,"ID47" ,"ID48" ,"ID49" ,"ID50" ,"ID51" ,"ID52" ,"ID53" ,"ID54" ,"ID55" ,"ID56" ,"ID57" ,"ID58" ,"ID59" ,"ID60" ,"ID61" ,"ID62" ,
"ID63" ,"ID64" ,"ID65" ,"ID66" ,"ID67" ,"ID68" ,"ID69" ,"ID70" ,"ID71" ,"ID72" ,"ID73" ,"ID74" ,"ID75" ,"ID76" ,"ID77" ,"ID78" ,"ID79" ,"ID80" ,"ID81" ,"ID82" ,"ID83" ,"ID84" ,"ID85" ,"ID86" ,"ID87" ,"ID88" ,"ID89" ,"ID90" ,"ID91" ,"ID92" ,"ID93" ,"ID94" ,"ID95" ,"ID96" ,"ID97" ,"ID98" ,"ID99" ,"ID100" ,"ID101" ,"ID102" ,"ID103" ,"ID104" ,"ID105" ,"ID106" ,"ID107" ,"ID108" ,"ID109" ,"ID110" ,"ID111" ,"ID112" ,"ID113" ,"ID114" ,"ID115" ,"ID116" ,"ID117" ,"ID118" ,"ID119" ,"ID120" ,"ID121" ,"ID122" ,
"ID123" ,"ID124" ,"ID125" ,"ID126" ,"ID127" ,"ID128" ,"ID129" ,"ID130" ,"ID131" ,"ID132" ,"ID133" ,"ID134" ,"ID135" ,"ID136" ,"ID137" ,"ID138" ,"ID139" ,"ID140" ,"ID141" ,"ID142" ,"ID143" ,"ID144" ,"ID145" ,"ID146" ,"ID147" ,"ID148" ,"ID149" ,"ID150" ,"ID151" ,"ID152" ,"ID153" ,"ID154" ,"ID155" ,"ID156" ,"ID157" ,"ID158" ,"ID159" ,"ID160" ,"ID161" ,"ID162" ,"ID163" ,"ID164" ,"ID165" ,"ID166" ,"ID167" ,"ID168" ,"ID169" ,"ID170" ,"ID171" ,"ID172" ,"ID173" ,"ID174" ,"ID175" ,"ID176" ,"ID177" ,"ID178" ,
"ID179")

dframe1<-data.frame(Field,Treatment,Field.section,Transect,Distance.m,Aphid.rm.success,Aphid.remain.fail,fffPlot,Bait.ID)

y<-cbind(Aphid.rm.success,Aphid.remain.fail)

model3<-glmer(y~Treatment*Distance.m+(1|Field/Field.section/Transect/fffPlot/Bait.ID), # Bait.ID to remove overdispersion
binomial(link=logit),data=dframe1) # note I kept fffPlot smallest scale in (better residuals)
summary(model3)

plot(model3) # issue? Or just messy ecological data?

______________
Victoria Wickens
PhD student
Room GU08
Centre for Agri-Environmental Research (CAER)
School of Agriculture, Policy & Development
University of Reading
Reading RG6 7BE
____________

Email: v.j.wickens at pgr.reading.ac.uk<mailto:v.j.wickens at pgr.reading.ac.uk>
http://www.reading.ac.uk/caer/staff_students.html
https://www.facebook.com/UniRdgAPD