On 08/02/2015 3:49 PM, Rolf Turner wrote: > On 09/02/15 06:46, Ravi Varadhan wrote: >> Hi, >> >> I would like to run lme() on a number of response variables in a >> dataframe in an automatic manner. Bu, when I use >> eval(parse(text=yname)) to denote the LHS of the formula in lme(), I >> get the following error message: >> >> >> >>> require(nlme) >> >> >> >>> mod2 <- with(subset(labdata2, Transplant_type!=0 & time >0), >>> lme(eval(parse(text=yname)) ~ time + as.factor(gvhd), random = >>> ~1|Patient, correlation = corAR1(), method="ML", >>> na.action=na.omit)) >> Error in model.frame.default(formula = ~Patient + yname + time + >> gvhd, : variable lengths differ (found for 'yname') >> >> The same usage works well in lme4::lmer without any problems. >> >> >> >> It seems that there is a problem in how the formula object is >> evaluated in lme(). Is there an alternative way to do this? > > What about trying some'at lahk: > > fmla <- as.formula(paste(yname,"~ time + as.factor(gvhd)")) > mod2 <- with(...., lme(fmla, random = ....)) > > Also you would probably be better off using the data argument rather > then using with(); this could have some impact on the environment in > which the formula is evaluated.
Formulas are a little tricky: effectively they are evaluated twice. If you type something like y ~ x (or eval(parse(text="y ~ x")), or as.formula("y ~ x")) then a formula object is created. That object remembers the environment in which it was created, so later when the modelling function uses it, the x and y variables are evaluated in the original context. In your example, as.formula() will convert the string to a formula, and attach the current environment. So you'd better hope that whatever variable yname names, as well as time and gvhd, are all available there. Duncan Murdoch > > Just stabbing in the dark here since you did not provide a reproducible > example. > > cheers, > > Rolf Turner > ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.