[R] Issue with formula conversion
A random effect formulation for R package nlme is read in as a string of characters from an input file: ranEff - pdCompSymm(~1+Age) I need to convert 'ranEff' to a formula class. However, as shown below: as.formula(ranEff) ~1 + Age the pdCompSymm is lost in the conversion. Any solutions? Thanks! Gang __ R-help@r-project.org mailing list 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.
Re: [R] Issue with formula conversion
On Aug 27, 2014, at 11:19 AM, Gang Chen wrote: A random effect formulation for R package nlme is read in as a string of characters from an input file: ranEff - pdCompSymm(~1+Age) I need to convert 'ranEff' to a formula class. However, as shown below: as.formula(ranEff) ~1 + Age the pdCompSymm is lost in the conversion. Any solutions? as.formula(paste(~,ranEff)) ~pdCompSymm(~1 + Age) -- David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list 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.
Re: [R] Issue with formula conversion
Thanks for the help! However, I just need to get pdCompSymm(~1 + Age) without a tilde (~) at the beginning. On Wed, Aug 27, 2014 at 3:34 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 27, 2014, at 11:19 AM, Gang Chen wrote: A random effect formulation for R package nlme is read in as a string of characters from an input file: ranEff - pdCompSymm(~1+Age) I need to convert 'ranEff' to a formula class. However, as shown below: as.formula(ranEff) ~1 + Age the pdCompSymm is lost in the conversion. Any solutions? as.formula(paste(~,ranEff)) ~pdCompSymm(~1 + Age) -- David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list 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.
Re: [R] Issue with formula conversion
On Aug 27, 2014, at 12:44 PM, Gang Chen wrote: Thanks for the help! However, I just need to get pdCompSymm(~1 + Age) That's not a formula in the R sense of the word. You should do a better job of posting a use case. Perhaps you want an expression? -- David. without a tilde (~) at the beginning. On Wed, Aug 27, 2014 at 3:34 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 27, 2014, at 11:19 AM, Gang Chen wrote: A random effect formulation for R package nlme is read in as a string of characters from an input file: ranEff - pdCompSymm(~1+Age) I need to convert 'ranEff' to a formula class. However, as shown below: as.formula(ranEff) ~1 + Age the pdCompSymm is lost in the conversion. Any solutions? as.formula(paste(~,ranEff)) ~pdCompSymm(~1 + Age) -- David Winsemius Alameda, CA, USA David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list 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.
Re: [R] Issue with formula conversion
Good point! Here is an example: library(nlme) fm - lme(yield ~ nitro, data=Oats, random=list(Block=pdComSymm(~Variety-1))) Now the problem I'm facing is that the following part pdComSymm(~Variety-1) is read in as a string of characters from an external source: ranEff - 'pdComSymm(~Variety-1)' The following (ranEff1 - as.formula(ranEff)) ~Variety - 1 is not what I want. Even though fm - lme(yield ~ nitro, data=Oats, random=list(Block=pdCompSymm(ranEff1))) works, I don't know the 'pdCompSymm' part in advance and would like to make the process automatic. On Wed, Aug 27, 2014 at 3:49 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 27, 2014, at 12:44 PM, Gang Chen wrote: Thanks for the help! However, I just need to get pdCompSymm(~1 + Age) That's not a formula in the R sense of the word. You should do a better job of posting a use case. Perhaps you want an expression? -- David. without a tilde (~) at the beginning. On Wed, Aug 27, 2014 at 3:34 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 27, 2014, at 11:19 AM, Gang Chen wrote: A random effect formulation for R package nlme is read in as a string of characters from an input file: ranEff - pdCompSymm(~1+Age) I need to convert 'ranEff' to a formula class. However, as shown below: as.formula(ranEff) ~1 + Age the pdCompSymm is lost in the conversion. Any solutions? as.formula(paste(~,ranEff)) ~pdCompSymm(~1 + Age) -- David Winsemius Alameda, CA, USA David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list 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.
Re: [R] Issue with formula conversion
On Aug 27, 2014, at 1:11 PM, Gang Chen wrote: Good point! Here is an example: library(nlme) fm - lme(yield ~ nitro, data=Oats, random=list(Block=pdComSymm(~Variety-1))) One problem is that youa re misspelling the function name. Now the problem I'm facing is that the following part pdComSymm(~Variety-1) is read in as a string of characters from an external source: ranEff - 'pdComSymm(~Variety-1)' The following (ranEff1 - as.formula(ranEff)) ~Variety - 1 is not what I want. Even though fm - lme(yield ~ nitro, data=Oats, random=list(Block=pdCompSymm(ranEff1))) ranEff - 'pdCompSymm(~Variety-1)' tt - parse(text=ranEff) # Returns an unevaluated expression fm - lme(yield ~ nitro, data=Oats, random=list(Block=eval(tt) )) fm Linear mixed-effects model fit by REML Data: Oats Log-restricted-likelihood: -296.5209 Fixed: yield ~ nitro (Intercept) nitro 81.8722273.7 snipped rest of output. -- David works, I don't know the 'pdCompSymm' part in advance and would like to make the process automatic. On Wed, Aug 27, 2014 at 3:49 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 27, 2014, at 12:44 PM, Gang Chen wrote: Thanks for the help! However, I just need to get pdCompSymm(~1 + Age) That's not a formula in the R sense of the word. You should do a better job of posting a use case. Perhaps you want an expression? -- David. without a tilde (~) at the beginning. On Wed, Aug 27, 2014 at 3:34 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 27, 2014, at 11:19 AM, Gang Chen wrote: A random effect formulation for R package nlme is read in as a string of characters from an input file: ranEff - pdCompSymm(~1+Age) I need to convert 'ranEff' to a formula class. However, as shown below: as.formula(ranEff) ~1 + Age the pdCompSymm is lost in the conversion. Any solutions? as.formula(paste(~,ranEff)) ~pdCompSymm(~1 + Age) -- David Winsemius Alameda, CA, USA David Winsemius Alameda, CA, USA David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list 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.
Re: [R] Issue with formula conversion
Sorry for the misspelling! And more importantly, thanks a lot for the nice solution and for the quick help! On Wed, Aug 27, 2014 at 4:22 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 27, 2014, at 1:11 PM, Gang Chen wrote: Good point! Here is an example: library(nlme) fm - lme(yield ~ nitro, data=Oats, random=list(Block=pdComSymm(~Variety-1))) One problem is that youa re misspelling the function name. Now the problem I'm facing is that the following part pdComSymm(~Variety-1) is read in as a string of characters from an external source: ranEff - 'pdComSymm(~Variety-1)' The following (ranEff1 - as.formula(ranEff)) ~Variety - 1 is not what I want. Even though fm - lme(yield ~ nitro, data=Oats, random=list(Block=pdCompSymm(ranEff1))) ranEff - 'pdCompSymm(~Variety-1)' tt - parse(text=ranEff) # Returns an unevaluated expression fm - lme(yield ~ nitro, data=Oats, random=list(Block=eval(tt) )) fm Linear mixed-effects model fit by REML Data: Oats Log-restricted-likelihood: -296.5209 Fixed: yield ~ nitro (Intercept) nitro 81.8722273.7 snipped rest of output. -- David works, I don't know the 'pdCompSymm' part in advance and would like to make the process automatic. On Wed, Aug 27, 2014 at 3:49 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 27, 2014, at 12:44 PM, Gang Chen wrote: Thanks for the help! However, I just need to get pdCompSymm(~1 + Age) That's not a formula in the R sense of the word. You should do a better job of posting a use case. Perhaps you want an expression? -- David. without a tilde (~) at the beginning. On Wed, Aug 27, 2014 at 3:34 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 27, 2014, at 11:19 AM, Gang Chen wrote: A random effect formulation for R package nlme is read in as a string of characters from an input file: ranEff - pdCompSymm(~1+Age) I need to convert 'ranEff' to a formula class. However, as shown below: as.formula(ranEff) ~1 + Age the pdCompSymm is lost in the conversion. Any solutions? as.formula(paste(~,ranEff)) ~pdCompSymm(~1 + Age) -- David Winsemius Alameda, CA, USA David Winsemius Alameda, CA, USA David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list 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.
Re: [R] Issue with formula conversion
do you have control over the external source? if so, then something like BlockFunction - pdComSymm ranEff1 - ~Variety -1 fm - lme(yield ~ nitro, data=Oats, random=list(Block=get(BlockFunction)(ranEff1))) The above is untested. An example if get() is get(sum)(1:4) [1] 10 The main problem with David's solution, which does work, is the use of the eval(parse()) idiom. This is usually strongly discouraged. See, for example, fortunes::fortune(106) If the answer is parse() you should usually rethink the question. -- Thomas Lumley R-help (February 2005) On Wed, Aug 27, 2014 at 4:11 PM, Gang Chen gangch...@gmail.com wrote: Good point! Here is an example: library(nlme) fm - lme(yield ~ nitro, data=Oats, random=list(Block=pdComSymm(~Variety-1))) Now the problem I'm facing is that the following part pdComSymm(~Variety-1) is read in as a string of characters from an external source: ranEff - 'pdComSymm(~Variety-1)' The following (ranEff1 - as.formula(ranEff)) ~Variety - 1 is not what I want. Even though fm - lme(yield ~ nitro, data=Oats, random=list(Block=pdCompSymm(ranEff1))) works, I don't know the 'pdCompSymm' part in advance and would like to make the process automatic. On Wed, Aug 27, 2014 at 3:49 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 27, 2014, at 12:44 PM, Gang Chen wrote: Thanks for the help! However, I just need to get pdCompSymm(~1 + Age) That's not a formula in the R sense of the word. You should do a better job of posting a use case. Perhaps you want an expression? -- David. without a tilde (~) at the beginning. On Wed, Aug 27, 2014 at 3:34 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 27, 2014, at 11:19 AM, Gang Chen wrote: A random effect formulation for R package nlme is read in as a string of characters from an input file: ranEff - pdCompSymm(~1+Age) I need to convert 'ranEff' to a formula class. However, as shown below: as.formula(ranEff) ~1 + Age the pdCompSymm is lost in the conversion. Any solutions? as.formula(paste(~,ranEff)) ~pdCompSymm(~1 + Age) -- David Winsemius Alameda, CA, USA David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list 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. __ R-help@r-project.org mailing list 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.
Re: [R] Issue with formula conversion
On Aug 27, 2014, at 1:33 PM, Richard M. Heiberger wrote: do you have control over the external source? if so, then something like BlockFunction - pdComSymm ranEff1 - ~Variety -1 I doubt that would work, since it is not a formula object. fm - lme(yield ~ nitro, data=Oats, random=list(Block=get(BlockFunction)(ranEff1))) After correcting the misspelling of the function name, I tested this approach: BlockFunction - pdCompSymm ranEff1 - as.formula(~Variety -1) fm - lme(yield ~ nitro, data=Oats, random=list(Block=do.call(BlockFunction, list(form=ranEff1) ) )) fm #-- Linear mixed-effects model fit by REML Data: Oats Log-restricted-likelihood: -296.5209 Fixed: yield ~ nitro snipped -- David. The above is untested. An example if get() is get(sum)(1:4) [1] 10 The main problem with David's solution, which does work, is the use of the eval(parse()) idiom. This is usually strongly discouraged. See, for example, fortunes::fortune(106) If the answer is parse() you should usually rethink the question. -- Thomas Lumley R-help (February 2005) On Wed, Aug 27, 2014 at 4:11 PM, Gang Chen gangch...@gmail.com wrote: Good point! Here is an example: library(nlme) fm - lme(yield ~ nitro, data=Oats, random=list(Block=pdComSymm(~Variety-1))) Now the problem I'm facing is that the following part pdComSymm(~Variety-1) is read in as a string of characters from an external source: ranEff - 'pdComSymm(~Variety-1)' The following (ranEff1 - as.formula(ranEff)) ~Variety - 1 is not what I want. Even though fm - lme(yield ~ nitro, data=Oats, random=list(Block=pdCompSymm(ranEff1))) works, I don't know the 'pdCompSymm' part in advance and would like to make the process automatic. On Wed, Aug 27, 2014 at 3:49 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 27, 2014, at 12:44 PM, Gang Chen wrote: Thanks for the help! However, I just need to get pdCompSymm(~1 + Age) That's not a formula in the R sense of the word. You should do a better job of posting a use case. Perhaps you want an expression? -- David. without a tilde (~) at the beginning. On Wed, Aug 27, 2014 at 3:34 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 27, 2014, at 11:19 AM, Gang Chen wrote: A random effect formulation for R package nlme is read in as a string of characters from an input file: ranEff - pdCompSymm(~1+Age) I need to convert 'ranEff' to a formula class. However, as shown below: as.formula(ranEff) ~1 + Age the pdCompSymm is lost in the conversion. Any solutions? as.formula(paste(~,ranEff)) ~pdCompSymm(~1 + Age) -- David Winsemius Alameda, CA, USA David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list 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. David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list 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.
Re: [R] Issue with formula conversion
David, you caught my typo of excess quotation marks. this should work ranEff1 - ~Variety -1 random=list(Block=get(BlockFunction)(ranEff1))) On Wed, Aug 27, 2014 at 4:41 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 27, 2014, at 1:33 PM, Richard M. Heiberger wrote: do you have control over the external source? if so, then something like BlockFunction - pdComSymm ranEff1 - ~Variety -1 I doubt that would work, since it is not a formula object. fm - lme(yield ~ nitro, data=Oats, random=list(Block=get(BlockFunction)(ranEff1))) After correcting the misspelling of the function name, I tested this approach: BlockFunction - pdCompSymm ranEff1 - as.formula(~Variety -1) fm - lme(yield ~ nitro, data=Oats, random=list(Block=do.call(BlockFunction, list(form=ranEff1) ) )) fm #-- Linear mixed-effects model fit by REML Data: Oats Log-restricted-likelihood: -296.5209 Fixed: yield ~ nitro snipped -- David. The above is untested. An example if get() is get(sum)(1:4) [1] 10 The main problem with David's solution, which does work, is the use of the eval(parse()) idiom. This is usually strongly discouraged. See, for example, fortunes::fortune(106) If the answer is parse() you should usually rethink the question. -- Thomas Lumley R-help (February 2005) On Wed, Aug 27, 2014 at 4:11 PM, Gang Chen gangch...@gmail.com wrote: Good point! Here is an example: library(nlme) fm - lme(yield ~ nitro, data=Oats, random=list(Block=pdComSymm(~Variety-1))) Now the problem I'm facing is that the following part pdComSymm(~Variety-1) is read in as a string of characters from an external source: ranEff - 'pdComSymm(~Variety-1)' The following (ranEff1 - as.formula(ranEff)) ~Variety - 1 is not what I want. Even though fm - lme(yield ~ nitro, data=Oats, random=list(Block=pdCompSymm(ranEff1))) works, I don't know the 'pdCompSymm' part in advance and would like to make the process automatic. On Wed, Aug 27, 2014 at 3:49 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 27, 2014, at 12:44 PM, Gang Chen wrote: Thanks for the help! However, I just need to get pdCompSymm(~1 + Age) That's not a formula in the R sense of the word. You should do a better job of posting a use case. Perhaps you want an expression? -- David. without a tilde (~) at the beginning. On Wed, Aug 27, 2014 at 3:34 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 27, 2014, at 11:19 AM, Gang Chen wrote: A random effect formulation for R package nlme is read in as a string of characters from an input file: ranEff - pdCompSymm(~1+Age) I need to convert 'ranEff' to a formula class. However, as shown below: as.formula(ranEff) ~1 + Age the pdCompSymm is lost in the conversion. Any solutions? as.formula(paste(~,ranEff)) ~pdCompSymm(~1 + Age) -- David Winsemius Alameda, CA, USA David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list 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. David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list 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.
