R help - Mar 2010 - Different results for different order of factor levels?

Dear R community,

I am a newbie to R and I am using lme() to analyzed a two way repeated  
measures ANCOVA on some data I have gathered.  In producing some  
graphs based on the fixed effects I noticed that I get vary different  
results depending on how I order my levels in my factor statement (see  
code below).  Now, I have read that different models treat data from  
the factor class different for ordered vs non-ordered factors but I am  
unsure as to how this works for lme().  Shown below is a set of code  
used to get the coefficients for two different orders of factor levels.

THE CODE USED TO GET THE COEFFICIENTS:

#Abbr = Subject
#PDSI = covariate
#PDSI2 = PDSI^2 (To fit a polynomial)

#Set the Level order
i.levels<-c("Mixed","Short","Tall","NoType")

#I am not interested in this level for my comparison
data.sub <- data[which(data$indep != "NoType"),]

#Convert the data into factors
data$indep<-factor(data$indep,
	levels = i.levels)

#Run the model
F <- lme(response~indep+PDSI+PDSI2+indep:PDSI+indep:PDSI2,
	random = ~PDSI|Abbr, data = data.sub, method = "ML")

#Get the coefficients for the fixed effects
summary(F)$coefficients$fixed


THE OUTCOME:
 >
i.levels<-c("Tall","Short","Mixed","NoType")
 > summary(F)$coefficients$fixed
  (Intercept)       indep1       indep2         PDSI        PDSI2   
indep1:PDSI
115.20850196   2.13074177 -18.64650516   2.32042307  -0.46510460    
0.09965080

  indep2:PDSI indep1:PDSI2 indep2:PDSI2
   0.90607575   0.01106839  -0.28827352

Other order:
 >
i.levels<-c("Mixed","Short","Tall","NoType")
 > summary(F)$coefficients$fixed
  (Intercept)       indep1       indep2         PDSI        PDSI2   
indep1:PDSI
  115.2085020   16.5157634  -18.6465052    2.3204231   -0.4651046    
-1.0057266

  indep2:PDSI indep1:PDSI2 indep2:PDSI2
    0.9060757    0.2772051   -0.2882735

Also, as I am writing this I found another peculiarity.   The order of  
the first declaration of the levels also matters somehow.  To get the  
above results, I ran a program that ran the first order of i.levels  
and immediately following this code is a duplicate code with the  
second order of i.levels specified.  I ran them both at the same  
time.  When I ran the code with Mixed, Short, Tall, NoType first, both  
orders produced the same coefficients.  But if I ran the  
Tall,Short,Mixed,NoType first then I got the above results.  I am even  
more lost now.  Any insight would be greatly appreciated.

Thanks
Jarrod





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