Girish A.R.
2009-Jun-01 05:45 UTC
[R] Sweave:Figures from plot (LME output) not getting generated (pdf or eps)
Hi,
I seem to be facing a strange problem when I use Sweave for creating a
LaTeX document of the R lme() output --- The EPS and PDF figure files
get created, but are empty. I have attached a reproducible example
below (taken from the R lme() help example).
------------------------------------------------------------------------------------
\documentclass[a4paper,10pt]{article}
\usepackage{Sweave}
\SweaveOpts{keep.source=TRUE}
\begin{document}
<<>>fm1 <- lme(distance ~ age, Orthodont, random = ~ age |
Subject)
@
<<fig=TRUE>>plot(fm1, distance ~ fitted(.) | Subject, abline =
c(0,1))
@
\end{document}
------------------------------------------------------------------------------------
I don't seem to face this problem while plotting other objects. Any
help is appreciated.
Thanks,
-Girish
==========================> sessionInfo()
R version 2.9.0 (2009-04-17)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.
1252;LC_MONETARY=English_United States.
1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] grid splines stats graphics grDevices utils
datasets methods
[9] base
other attached packages:
[1] RWinEdt_1.8-1 coda_0.13-4 verification_1.29
CircStats_0.2-3
[5] boot_1.2-36 fields_5.02 spam_0.15-4
waveslim_1.6.1
[9] lmtest_0.9-23 zoo_1.5-5 psychometric_2.1
multilevel_2.3
[13] MASS_7.2-46 nlme_3.1-92 languageR_0.953
lme4_0.999375-31
[17] Matrix_0.999375-26 zipfR_0.6-5 lattice_0.17-22
gplots_2.7.0
[21] caTools_1.9 bitops_1.0-4.1 gdata_2.4.2
gtools_2.5.0-1
[25] gmodels_2.14.1 ggplot2_0.8.3 reshape_0.8.3
plyr_0.1.8
[29] proto_0.3-8 doBy_3.9 foreign_0.8-34
car_1.2-14
[33] Design_2.1-2 survival_2.35-4 Hmisc_3.6-0
loaded via a namespace (and not attached):
[1] cluster_1.12.0 Formula_0.1-3 kinship_1.1.0-22
plm_1.1-2 sandwich_2.2-1
[6] tools_2.9.0
Girish A.R.
2009-Jun-01 07:00 UTC
[R] [SOLVED] Sweave:Figures from plot (LME output) not getting generated (pdf or eps)
Hi, My problem has been solved. Thanks to Renaud Lancelot! Solution pasted below: ----------------------------------------------------------------- Plotting functions in package nlme are built using functions of package lattice. You need to print() the result: <<fig=TRUE>>print(plot(fm1, distance ~ fitted(.) | Subject, abline = c(0,1))) @ Renaud ------------------------------------------------------------ On Jun 1, 10:45?am, "Girish A.R." <garam... at gmail.com> wrote:> Hi, > > I seem to be facing a strange problem when I use Sweave for creating a > LaTeX document of the R lme() output --- The EPS and PDF figure files > get created, but are empty. I have attached a reproducible example > below (taken from the R lme() help example). > > ------------------------------------------------------------------------------------ > \documentclass[a4paper,10pt]{article} > \usepackage{Sweave} > \SweaveOpts{keep.source=TRUE} > \begin{document} > > <<>>> fm1 <- lme(distance ~ age, Orthodont, random = ~ age | Subject) > @ > > <<fig=TRUE>>> plot(fm1, distance ~ fitted(.) | Subject, abline = c(0,1)) > @ > > \end{document} > > ------------------------------------------------------------------------------------ > > I don't seem to face this problem while plotting other objects. Any > help is appreciated. > > Thanks, > > -Girish > > ===========================> sessionInfo() > > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States. > 1252;LC_MONETARY=English_United States. > 1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] grid ? ? ?splines ? stats ? ? graphics ?grDevices utils > datasets ?methods > [9] base > > other attached packages: > ?[1] RWinEdt_1.8-1 ? ? ?coda_0.13-4 ? ? ? ?verification_1.29 > CircStats_0.2-3 > ?[5] boot_1.2-36 ? ? ? ?fields_5.02 ? ? ? ?spam_0.15-4 > waveslim_1.6.1 > ?[9] lmtest_0.9-23 ? ? ?zoo_1.5-5 ? ? ? ? ?psychometric_2.1 > multilevel_2.3 > [13] MASS_7.2-46 ? ? ? ?nlme_3.1-92 ? ? ? ?languageR_0.953 > lme4_0.999375-31 > [17] Matrix_0.999375-26 zipfR_0.6-5 ? ? ? ?lattice_0.17-22 > gplots_2.7.0 > [21] caTools_1.9 ? ? ? ?bitops_1.0-4.1 ? ? gdata_2.4.2 > gtools_2.5.0-1 > [25] gmodels_2.14.1 ? ? ggplot2_0.8.3 ? ? ?reshape_0.8.3 > plyr_0.1.8 > [29] proto_0.3-8 ? ? ? ?doBy_3.9 ? ? ? ? ? foreign_0.8-34 > car_1.2-14 > [33] Design_2.1-2 ? ? ? survival_2.35-4 ? ?Hmisc_3.6-0 > > loaded via a namespace (and not attached): > [1] cluster_1.12.0 ? Formula_0.1-3 ? ?kinship_1.1.0-22 > plm_1.1-2 ? ? ? ?sandwich_2.2-1 > [6] tools_2.9.0 > > ______________________________________________ > R-h... at r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
ONKELINX, Thierry
2009-Jun-01 22:32 UTC
[R] Sweave:Figures from plot (LME output) not getting generated(pdf or eps)
Dear Girish,
As they are lattice plots, you need to print() them explicitly. It is
FAQ 7.22:
http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-do-lattice_002ftrellis-
graphics-not-work_003f
<<fig=TRUE>>print(plot(fm1, distance ~ fitted(.) | Subject, abline =
c(0,1)))
@
------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be
www.inbo.be
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey
-----Oorspronkelijk bericht-----
Van: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
Namens Girish A.R.
Verzonden: maandag 1 juni 2009 7:46
Aan: r-help at r-project.org
Onderwerp: [R] Sweave:Figures from plot (LME output) not getting
generated(pdf or eps)
Hi,
I seem to be facing a strange problem when I use Sweave for creating a
LaTeX document of the R lme() output --- The EPS and PDF figure files
get created, but are empty. I have attached a reproducible example below
(taken from the R lme() help example).
------------------------------------------------------------------------
------------
\documentclass[a4paper,10pt]{article}
\usepackage{Sweave}
\SweaveOpts{keep.source=TRUE}
\begin{document}
<<>>fm1 <- lme(distance ~ age, Orthodont, random = ~ age |
Subject) @
<<fig=TRUE>>plot(fm1, distance ~ fitted(.) | Subject, abline =
c(0,1)) @
\end{document}
------------------------------------------------------------------------
------------
I don't seem to face this problem while plotting other objects. Any help
is appreciated.
Thanks,
-Girish
==========================> sessionInfo()
R version 2.9.0 (2009-04-17)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.
1252;LC_MONETARY=English_United States.
1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] grid splines stats graphics grDevices utils
datasets methods
[9] base
other attached packages:
[1] RWinEdt_1.8-1 coda_0.13-4 verification_1.29
CircStats_0.2-3
[5] boot_1.2-36 fields_5.02 spam_0.15-4
waveslim_1.6.1
[9] lmtest_0.9-23 zoo_1.5-5 psychometric_2.1
multilevel_2.3
[13] MASS_7.2-46 nlme_3.1-92 languageR_0.953
lme4_0.999375-31
[17] Matrix_0.999375-26 zipfR_0.6-5 lattice_0.17-22
gplots_2.7.0
[21] caTools_1.9 bitops_1.0-4.1 gdata_2.4.2
gtools_2.5.0-1
[25] gmodels_2.14.1 ggplot2_0.8.3 reshape_0.8.3
plyr_0.1.8
[29] proto_0.3-8 doBy_3.9 foreign_0.8-34
car_1.2-14
[33] Design_2.1-2 survival_2.35-4 Hmisc_3.6-0
loaded via a namespace (and not attached):
[1] cluster_1.12.0 Formula_0.1-3 kinship_1.1.0-22
plm_1.1-2 sandwich_2.2-1
[6] tools_2.9.0
______________________________________________
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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