Thanks to Rolf, Duncan, and Ben.
Ben, your suggestion worked (with a minor correction of concatenating the
termlabels into a vector).
Here is the solution to those interested.
ff <- reformulate(termlabels=c("time","as.factor(gvhd)"),
response=yname, intercept=TRUE)
dd <- subset(labdata2, Transplant_type!=0 & time >0)
lme(ff, random=~1|Patient, data=dd, correlation=corAR1(), na.action=na.omit)
Best,
Ravi
Ravi Varadhan, Ph.D. (Biostatistics), Ph.D. (Environmental Engg)
Associate Professor
Department of Oncology
Division of Biostatistics & Bionformatics
Johns Hopkins University
550 N. Broadway
Baltimore, MD 21205
40-502-2619
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> ff <- reformulate(termlabels=c("time","as.factor(gvhd)"), response=yname,intercept=TRUE) If the right hand side of the formula were more complicated than an additive list of terms, say '~ time * as.factor(gvhd)' or the left side were more than a name, say 'log(yname)' you could use bquote() instead of reformulate. E.g., > formulaTemplate <- log(.(responseName)) ~ time * as.factor(gvhd) > lapply(c("y1","y2","y3"), function(yname)do.call(bquote, list(formulaTemplate, list(responseName=as.name(yname))))) [[1]] log(y1) ~ time * as.factor(gvhd) [[2]] log(y2) ~ time * as.factor(gvhd) [[3]] log(y3) ~ time * as.factor(gvhd) I used 'do.call' because bquote does not evaluate its first argument, but we need to evaluate the name 'formulaTemplate'. You could avoid that by putting the template verbatim in the call to bquote, as in lapply(c("y1","y2","y3"), function(yname)bquote(log(.(responseName)) ~ time * as.factor(gvhd), list(responseName=as.name(yname)))) I like the do.call method because I can bury it in a function and forget about it. bquote() retains the environment of the formula template. Bill Dunlap TIBCO Software wdunlap tibco.com On Mon, Feb 9, 2015 at 6:44 AM, Ravi Varadhan <ravi.varadhan at jhu.edu> wrote:> Thanks to Rolf, Duncan, and Ben. > > Ben, your suggestion worked (with a minor correction of concatenating the > termlabels into a vector). > > Here is the solution to those interested. > > ff <- reformulate(termlabels=c("time","as.factor(gvhd)"), response=yname, > intercept=TRUE) > dd <- subset(labdata2, Transplant_type!=0 & time >0) > lme(ff, random=~1|Patient, data=dd, correlation=corAR1(), > na.action=na.omit) > > Best, > Ravi > > Ravi Varadhan, Ph.D. (Biostatistics), Ph.D. (Environmental Engg) > Associate Professor > Department of Oncology > Division of Biostatistics & Bionformatics > Johns Hopkins University > 550 N. Broadway > Baltimore, MD 21205 > 40-502-2619 > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at 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. >[[alternative HTML version deleted]]
Yes, this is a very important point. Thank you, Bill. Best, Ravi ________________________________ From: William Dunlap <wdunlap at tibco.com> Sent: Friday, February 13, 2015 4:56 PM To: Ravi Varadhan Cc: r-help at stat.math.ethz.ch Subject: Re: [R] Unable to use `eval(parse(text))' in nlme::lme> ff <- reformulate(termlabels=c("time","as.factor(gvhd)"), response=yname, intercept=TRUE)If the right hand side of the formula were more complicated than an additive list of terms, say '~ time * as.factor(gvhd)' or the left side were more than a name, say 'log(yname)' you could use bquote() instead of reformulate. E.g., > formulaTemplate <- log(.(responseName)) ~ time * as.factor(gvhd) > lapply(c("y1","y2","y3"), function(yname)do.call(bquote, list(formulaTemplate, list(responseName=as.name<http://as.name>(yname))))) [[1]] log(y1) ~ time * as.factor(gvhd) [[2]] log(y2) ~ time * as.factor(gvhd) [[3]] log(y3) ~ time * as.factor(gvhd) I used 'do.call' because bquote does not evaluate its first argument, but we need to evaluate the name 'formulaTemplate'. You could avoid that by putting the template verbatim in the call to bquote, as in lapply(c("y1","y2","y3"), function(yname)bquote(log(.(responseName)) ~ time * as.factor(gvhd), list(responseName=as.name<http://as.name>(yname)))) I like the do.call method because I can bury it in a function and forget about it. bquote() retains the environment of the formula template. Bill Dunlap TIBCO Software wdunlap tibco.com<http://tibco.com> On Mon, Feb 9, 2015 at 6:44 AM, Ravi Varadhan <ravi.varadhan at jhu.edu<mailto:ravi.varadhan at jhu.edu>> wrote: Thanks to Rolf, Duncan, and Ben. Ben, your suggestion worked (with a minor correction of concatenating the termlabels into a vector). Here is the solution to those interested. ff <- reformulate(termlabels=c("time","as.factor(gvhd)"), response=yname, intercept=TRUE) dd <- subset(labdata2, Transplant_type!=0 & time >0) lme(ff, random=~1|Patient, data=dd, correlation=corAR1(), na.action=na.omit) Best, Ravi Ravi Varadhan, Ph.D. (Biostatistics), Ph.D. (Environmental Engg) Associate Professor Department of Oncology Division of Biostatistics & Bionformatics Johns Hopkins University 550 N. Broadway Baltimore, MD 21205 40-502-2619 [[alternative HTML version deleted]] ______________________________________________ R-help at r-project.org<mailto:R-help at 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. [[alternative HTML version deleted]]