I am trying to plot fitted lme values as a smooth line of a graph
showing the exponential relationship between temperature and soil
respiration.
In the plot, the x-axis has temperature, and the y-axis has soil
respiration. When I try to add a line showing temperature versus the
fitted values, it is jagged and not smooth.
Here is the code I used:
lme.1<-lme(fixed=LnFlux~Temp, random=~1|Plt, data=resp)
fit.1<-exp(fitted(lme.1))
plot(Flux$Temp, Flux$Flux, xlab="Temperature",
ylab=expression("CO"[2]*"Flux"), xlim=c(-10, 25), ylim=c(0,250), pch=16)
ord1<-order(CFlux$Temp)
lines(CFlux$TempC[ord1], fit.1[ord1], lty=1, lwd=2)
This does not produce a straight line, but a jagged one that moves up
and down between points.
If I use fitted values from a simple linear model (lm), I don't have
this problem, and the line is smooth:
lm.1<-lm(LnFlux~Temp, data=resp)
fit.2<-exp(fitted(lm.1))
plot(Flux$Temp, Flux$Flux, xlab="Temperature",
ylab=expression("CO"[2]*"Flux"), xlim=c(-10, 25), ylim=c(0,250), pch=16)
ord2<-order(Flux$Temp)
lines(Flux$Temp[ord2], fit.2[ord2], lty=1, lwd=2)
The only difference I can find between the two is the structure of the
fitted objects. The fit.1 object from lme is "atomic", and lacks
individual data labels. Instead, the labels are: attr(*, "label")=
chr "Fitted values".
In contrast, the fit.2 object from the lm is "Named num", with:
attr(*, "names")= chr [1:460] "1" "2" "3" "4".
Is this difference causing my problem with adding a smooth line to the
graph? If so, is there any way I can change the structure of the lme
fitted object to make it more amenable to adding a smooth line to a
plot? Or is something else at work?
______________________________________________
[email protected] 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.
