Dear all
Nobody responded to my previous post so far so I try with more offending
subject.
I just encountered a strange problem with nls formula. I tried to use nls
in cycle but I was not successful. I traced the problem to some parse
command.
Here is an example
DF<-data.frame(x=1:10, y=3*(1:10)^.5+rnorm(10))
coef(lm(log(DF[,2])~log(DF[,1])))
(Intercept) log(DF[, 1])
0.7437320 0.6831726
# this works
coef(nls(y~a*x^b, data=DF, start=list(a=3, b=.7)))
a b
2.6412881 0.5545907
# OK, this works too
coef(nls(DF[,2]~a*DF[,1]^b, data=DF, start=list(a=3, b=.7)))
Error in parse(text = x) : unexpected end of input in "~ "
coef(nls(DF[,2]~a*DF[,1]^b, start=list(a=3, b=.7)))
Error in parse(text = x) : unexpected end of input in "~ "
# but this does not
Browse[1]>
debug: mf$formula <- as.formula(paste("~",
paste(varNames[varIndex],
collapse = "+")), env = environment(formula))
Browse[1]>
Error in parse(text = x) : unexpected end of input in "~
">
Actually the problem is that with calling nls with DF[,n]~... varNames and
varIndex is not correctly specified.
I am not sure if this behaviour is a bug or feature. If it is a feature,
please help me how to call variables from data frame
when using nls inside cycle
for (i in ....) result[i,] <- coef(nls( ...., ))
Thank you
Petr
> sessionInfo()
R version 2.8.0 Under development (unstable) (2008-05-18 r45723)
i386-pc-mingw32
locale:
LC_COLLATE=Czech_Czech Republic.1250;LC_CTYPE=Czech_Czech
Republic.1250;LC_MONETARY=Czech_Czech
Republic.1250;LC_NUMERIC=C;LC_TIME=Czech_Czech Republic.1250
attached base packages:
[1] stats grDevices datasets utils graphics methods base
other attached packages:
[1] nlme_3.1-88 lattice_0.17-7 fun_0.1
loaded via a namespace (and not attached):
[1] grid_2.8.0 tools_2.8.0
Petr Pikal
petr.pikal at precheza.cz
724008364, 581252140, 581252257
Dear Petr, I think it's a feature. the formula interface also won't let you specify the slots of S4 objects in the model spec. How about coef(nls(y~a*x^b, data=list(x=DF[,1], y=DF[,2]), start=list(a=3, b=.7))) ? On Thu, 26 Jun 2008, Petr PIKAL wrote:> Dear all > > Nobody responded to my previous post so far so I try with more offending > subject. > > I just encountered a strange problem with nls formula. I tried to use nls > in cycle but I was not successful. I traced the problem to some parse > command. > > Here is an example > > DF<-data.frame(x=1:10, y=3*(1:10)^.5+rnorm(10)) > > coef(lm(log(DF[,2])~log(DF[,1]))) > (Intercept) log(DF[, 1]) > 0.7437320 0.6831726 > # this works > > coef(nls(y~a*x^b, data=DF, start=list(a=3, b=.7))) > a b > 2.6412881 0.5545907 > # OK, this works too > > coef(nls(DF[,2]~a*DF[,1]^b, data=DF, start=list(a=3, b=.7))) > Error in parse(text = x) : unexpected end of input in "~ " > coef(nls(DF[,2]~a*DF[,1]^b, start=list(a=3, b=.7))) > Error in parse(text = x) : unexpected end of input in "~ " > # but this does not > > > Browse[1]> > debug: mf$formula <- as.formula(paste("~", paste(varNames[varIndex], > collapse = "+")), env = environment(formula)) > Browse[1]> > Error in parse(text = x) : unexpected end of input in "~ " > > > > Actually the problem is that with calling nls with DF[,n]~... varNames and > varIndex is not correctly specified. > > I am not sure if this behaviour is a bug or feature. If it is a feature, > please help me how to call variables from data frame > when using nls inside cycle > > for (i in ....) result[i,] <- coef(nls( ...., )) > > Thank you > Petr > > > sessionInfo() > R version 2.8.0 Under development (unstable) (2008-05-18 r45723) > i386-pc-mingw32 > > locale: > LC_COLLATE=Czech_Czech Republic.1250;LC_CTYPE=Czech_Czech > Republic.1250;LC_MONETARY=Czech_Czech > Republic.1250;LC_NUMERIC=C;LC_TIME=Czech_Czech Republic.1250 > > attached base packages: > [1] stats grDevices datasets utils graphics methods base > > other attached packages: > [1] nlme_3.1-88 lattice_0.17-7 fun_0.1 > > loaded via a namespace (and not attached): > [1] grid_2.8.0 tools_2.8.0 > > > Petr Pikal > petr.pikal at precheza.cz > 724008364, 581252140, 581252257 > > ______________________________________________ > R-help at 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. >
Try this and note, in particular, that the "model:" line in the output has the correct variables substituted:> nm <- names(DF) > eqn <- sprintf("%s ~ a * %s", nm[2], nm[1]) > nls(eqn, DF, start = c(a = 1))Nonlinear regression model model: y ~ a * x data: DF a 1.133 residual sum-of-squares: 31.51 Number of iterations to convergence: 1 Achieved convergence tolerance: 1.55e-10 On Thu, Jun 26, 2008 at 7:57 AM, Petr PIKAL <petr.pikal at precheza.cz> wrote:> Dear all > > Nobody responded to my previous post so far so I try with more offending > subject. > > I just encountered a strange problem with nls formula. I tried to use nls > in cycle but I was not successful. I traced the problem to some parse > command. > > Here is an example > > DF<-data.frame(x=1:10, y=3*(1:10)^.5+rnorm(10)) > > coef(lm(log(DF[,2])~log(DF[,1]))) > (Intercept) log(DF[, 1]) > 0.7437320 0.6831726 > # this works > > coef(nls(y~a*x^b, data=DF, start=list(a=3, b=.7))) > a b > 2.6412881 0.5545907 > # OK, this works too > > coef(nls(DF[,2]~a*DF[,1]^b, data=DF, start=list(a=3, b=.7))) > Error in parse(text = x) : unexpected end of input in "~ " > coef(nls(DF[,2]~a*DF[,1]^b, start=list(a=3, b=.7))) > Error in parse(text = x) : unexpected end of input in "~ " > # but this does not > > > Browse[1]> > debug: mf$formula <- as.formula(paste("~", paste(varNames[varIndex], > collapse = "+")), env = environment(formula)) > Browse[1]> > Error in parse(text = x) : unexpected end of input in "~ " >> > > Actually the problem is that with calling nls with DF[,n]~... varNames and > varIndex is not correctly specified. > > I am not sure if this behaviour is a bug or feature. If it is a feature, > please help me how to call variables from data frame > when using nls inside cycle > > for (i in ....) result[i,] <- coef(nls( ...., )) > > Thank you > Petr > >> sessionInfo() > R version 2.8.0 Under development (unstable) (2008-05-18 r45723) > i386-pc-mingw32 > > locale: > LC_COLLATE=Czech_Czech Republic.1250;LC_CTYPE=Czech_Czech > Republic.1250;LC_MONETARY=Czech_Czech > Republic.1250;LC_NUMERIC=C;LC_TIME=Czech_Czech Republic.1250 > > attached base packages: > [1] stats grDevices datasets utils graphics methods base > > other attached packages: > [1] nlme_3.1-88 lattice_0.17-7 fun_0.1 > > loaded via a namespace (and not attached): > [1] grid_2.8.0 tools_2.8.0 > > > Petr Pikal > petr.pikal at precheza.cz > 724008364, 581252140, 581252257 > > ______________________________________________ > R-help at 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. >
G'day Petr, On Thu, 26 Jun 2008 13:57:39 +0200 Petr PIKAL <petr.pikal at precheza.cz> wrote:> I just encountered a strange problem with nls formula. I tried to use > nls in cycle but I was not successful. I traced the problem to some > parse command. > > [...] > > > I am not sure if this behaviour is a bug or feature. [...]It is definitely a feature. It is an error to believe that all modelling functions that use modelling formulae use the same syntax for their modelling formulae. This is, perhaps, easiest realised by observing how lm() and nls() interpret "*" and "/" in model formulae. In nls(), "[..]" can be used to index parameters, if the parameter is allowed to change between groups in the data. This seems to be a little known feature, though there is an example that uses that feature in MASS. The contributed documentation "An Introduction to R: Software for Statistical Modelling & Computing" by Petra Kuhnert and Bill Venables, available from CRAN, also has such an example on pages 134 and 230. The fact that nls() allows you to use "[..]" to index parameters in the model formulae seems to conflict with the way you wanted to specify the observed values in the formula. I guess Gabor's solution is a fix for your problem. Cheers, Berwin =========================== Full address ============================Berwin A Turlach Tel.: +65 6515 4416 (secr) Dept of Statistics and Applied Probability +65 6515 6650 (self) Faculty of Science FAX : +65 6872 3919 National University of Singapore 6 Science Drive 2, Blk S16, Level 7 e-mail: statba at nus.edu.sg Singapore 117546 http://www.stat.nus.edu.sg/~statba