R help - Jul 2011 - GLS - Plotting Graphs with 95% conf interval

Hi, I am trying to plot the original data with the line of the model using
the predict function.  I want to add SE to the graph, but not sure how to
get them out as the predict function for gls does not appear to allow for
SE=TRUE argument.  

Here is my code so far:

f1<-formula(MaxNASC40_50~hu3+flcmax+TidalFlag)

vf1Exp<-varExp(form=~hu3)

B1D<-gls(f1,correlation=corGaus(form=Lat~Lon, nugget=TRUE),weights=vf1Exp ,
data=ocean)

ochu3<-seq(from=2.9,to=4,length=120)
ocflc<-seq(from=0,to=0.8,length=120)
tidal1<-rep(c("1"),length=120)

mydata1<-data.frame(TidalFlag=factor(tidal1),hu3=ochu3,flcmax=ocflc)
lineNASC1<-predict(B1D,newdata=mydata1,type="response")
lineNASC1<-as.data.frame(lineNASC1)

plot(ocean$MaxNASC40_50[ocean$TidalFlag==1]~ocean$flcmax[ocean$TidalFlag==1)
lines(lineNASC1$lineNASC1~mydata1$flcmax)

Tidal Flag is a factor (so i assume i have to plot seperate graphs for each
level).

When I have tried to use the effects package I get the error:  Error in
x$formula : object of type 'symbol' is not subsettable.

Also when i have been trying to predict values from a zero inflated negative
binomial, I am getting the same line of fit regardless of what is on my X
axis (depsite different variables have positive and negative relationships).

any imput on any of these problems would be appreciated.

Thanks

 

 

 


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The Gls function in the rms package is a frontend to gls that allows you to
use all the graphics and other methods available in rms.
Frank

SamiC wrote:
> 
> Hi, I am trying to plot the original data with the line of the model using
> the predict function.  I want to add SE to the graph, but not sure how to
> get them out as the predict function for gls does not appear to allow for
> SE=TRUE argument.  
> 
> Here is my code so far:
> 
> f1<-formula(MaxNASC40_50~hu3+flcmax+TidalFlag)
> 
> vf1Exp<-varExp(form=~hu3)
> 
> B1D<-gls(f1,correlation=corGaus(form=Lat~Lon,
nugget=TRUE),weights=vf1Exp
> , data=ocean)
> 
> ochu3<-seq(from=2.9,to=4,length=120)
> ocflc<-seq(from=0,to=0.8,length=120)
> tidal1<-rep(c("1"),length=120)
> 
> mydata1<-data.frame(TidalFlag=factor(tidal1),hu3=ochu3,flcmax=ocflc)
> lineNASC1<-predict(B1D,newdata=mydata1,type="response")
> lineNASC1<-as.data.frame(lineNASC1)
> 
>
plot(ocean$MaxNASC40_50[ocean$TidalFlag==1]~ocean$flcmax[ocean$TidalFlag==1)
> lines(lineNASC1$lineNASC1~mydata1$flcmax)
> 
> Tidal Flag is a factor (so i assume i have to plot seperate graphs for
> each level).
> 
> When I have tried to use the effects package I get the error:  Error in
> x$formula : object of type 'symbol' is not subsettable.
> 
> Also when i have been trying to predict values from a zero inflated
> negative binomial, I am getting the same line of fit regardless of what is
> on my X axis (depsite different variables have positive and negative
> relationships).
> 
> any imput on any of these problems would be appreciated.
> 
> Thanks
> 

-----
Frank Harrell
Department of Biostatistics, Vanderbilt University
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