[R] eval-parse and lme in a loop

[Connolly, Colm]

Hi everybody,

I'm having trouble getting an eval-parse combination to work with lme in a for loop.

Consider the code below. The call to lme outside the loop works. The call to aov inside the loop works, but the call to to lme inside the loop does not.
The latter fails with 

Error in model.frame.default(formula = ~meanCol + Group + c1 + c3 + Subject,  : 
  variable lengths differ (found for 'Group')

and I don't know why the eval-parse portion of the code is node being replaced as it is in the call to aov. Anybody got any idea what's wrong?

rm(list=ls())

library('nlme')

df=data.frame(
  Group=rep(c("ctrl", "short", "long"), each=9, times=1),
  Subject=paste("S", 1:27, sep=""),
  Mean_1=c(-2.335482,  8.269832,  6.704734, -2.355664,  0.724432, 11.212987,  5.966652, 10.741065,  3.567522,  5.359832,  4.899951,  4.084452,  5.976326, 8.634508,  5.750942,  7.455622,  6.823843,  0.903801, 13.198157,  5.238985,  5.171453, 10.273715, 5.184785,  6.225874,  8.889997, 12.096968, 9.843028),
  Mean_2=c(16.244444, -1.486571,  1.817303,  3.814328, -0.343775, 19.323227, -0.390764,  7.149855,  4.517766, -0.967120, 11.219844, 0.561103,  5.188478, -4.819444,  6.253271,  7.062638,  4.502291, -0.469567, 12.739646,  5.832679,  9.193511,  7.664636, 6.083930,  9.493136,  7.478424,  7.642287, 7.205822),
  Mean_3=c(7.213662,  2.147219, -1.345795, -0.495567,  3.733844,  3.544084,  0.949573,  4.318238,  2.914248,  3.913391,  9.240128,  8.315122, 12.323612, 14.622557, 11.169847, 10.857631, 14.637243,  7.203096,  7.777472, -1.457673,  2.766380,  9.675148, -5.047292,  1.982447,  3.865502,  5.045913, 10.660579),
  c1=rnorm(9, mean=0.1, sd=0.4),
  c2=rnorm(9, mean=0.5, sd=0.7),
  c3=rnorm(9, mean=0.9, sd=1)
  );


## this works
means.lmeNoCovariate=lme(Mean_1 ~ Group, data=df, random = ~ 1 | Subject)
print(summary(means.lmeNoCovariate))
print(anova(means.lmeNoCovariate))


for (meanCol in paste("Mean_", 1:3, sep="")) {
  ## LMEs go here
 
  cat("####################################################################################################\n")
  cat("### AOV\n")
  cat("####################################################################################################\n")
  ## this works
  means.aov<-aov(eval(parse(text=meanCol)) ~ Group, data=df);
  means.aov.summary=summary(means.aov)
  print(means.aov.summary)
  
  cat("####################################################################################################\n")
  cat("### LME\n")
  cat("####################################################################################################\n")

  ## this doe not work
  means.lmeWithCovariate=lme(eval(parse(text=meanCol)) ~ Group + c1 + c1 + c3, data=df, random = ~ 1 | Subject)
  print(summary(means.lmeWithCovariate))
  print(anova(means.lmeWithCovariate))

}

Regards,
--
Colm G. Connolly, Ph. D.
Dept of Psychiatry
University of California, San Diego
9500 Gilman Dr. #0738
La Jolla, CA 92093-0738
Tel: +1-858-246-0684