Re: [R] a rounding option for \Sexpr{}?
Yihui Xie-2 wrote:
Currently Sweave does not format the (especially numeric) value in
\Sexpr{}, and I often have to round() the numbers explicitly,
otherwise I will get more than 10 digits, which is not necessary for
me in most cases. Is there a way to specify the number of digits to be
kept for values in \Sexpr{}? e.g. can we make \Sexpr{} respect
getOption('digits')?
Currently, Sweave does an eval on Sexpr, and that can be anything other than
a number (is mostly is, though). And you cannot define a new version of
Sexpr in latex, because Sexpr only looks like latex, but is processed before
texing.
My solution is to always do the rounding and formating in the R chunk (e.g.
with latexSN of Hmisc) to unclutter the Sexpr.
Dieter
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Re: [R] latex tables with quantreg
Frank Black-2 wrote: I'm using the quantreg package to run some regressions. I'm trying to save the output as latex tables using the helpful latex command, which works fine. However, I've been unable to modify its behavior in some ways I'm insterested in. For instance, I'd like a table in which I had the asterisks corresponding to the significance levels of each variable, but I have been unable to find how to do it. For some other models (lm, glm, lme), I have made some customizations (using well-formatted p-values, asterisks are a bit outdated and not loved by most journals). You can download the source from http://www.menne-biomed.de/download/Dmisc_1.2.1.tar.gz Check, for example, latex.lm.R Dieter -- View this message in context: http://r.789695.n4.nabble.com/latex-tables-with-quantreg-tp3049844p3050027.html Sent from the R help mailing list archive at Nabble.com. __ 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] conditional mean between two data frames with different levels
Thank you so much Josh, that's exactly what i needed! Cheers alb -- View this message in context: http://r.789695.n4.nabble.com/conditional-mean-between-two-data-frames-with-different-levels-tp3049010p3049980.html Sent from the R help mailing list archive at Nabble.com. __ 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] Plotting number of patients at risk below survival curve
Thorsten Raff wrote: does anyone know of a R-package that has implemented the increasingly popular inclusion of the number of patients at risk below Kaplan-Meier curves like in http://bloodjournal.hematologylibrary.org/content/vol116/issue19/images/large/zh89991058760001.jpeg survplot in Frank Harrell's package Design (looks like the example was created with it). Dieter -- View this message in context: http://r.789695.n4.nabble.com/Plotting-number-of-patients-at-risk-below-survival-curve-tp3048900p3050032.html Sent from the R help mailing list archive at Nabble.com. __ 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] profile in lme4 and lme4a/lme4b
Dear R-users, from Douglas Bates lme4 book I'm trying to run profile() on a quite large dataset, in order to have some confidence intervals on random effects parameter in mixed models. When I run it in lme4 however I'm faced with the following error: Errore in UseMethod(profile) : no applicable method for 'profile' applied to an object of class mer Surfing on R-help mailing lists I understood that this has to do with some compatibility problems which are undergoing development for next version of the lme4 package, right? Also, I found that this function is active in the development packages lme4a and lme4b, available from R-forge... I was trying to install these packages, at least to have profile() running. I've tried different ways for doing this but I'm stuck in a blind alley...I've tried the following (all suggestions from R users found on the Internet): - install.packages(lme4a, repos=http://R-Forge.R-project.org;) returning Warning message: In getDependencies(pkgs, dependencies, available, lib) : package lme4a is not available - installing binary file directly in the .libpaths directory, but: lme4a binary for MAC can not be retrieved on the web (page not found), and lme4b gives similar problem. Now only installing package from source files remain, but this does not seem so easy...at least not for me! I have a Macbook Pro (running Mac OS/X 10.6.4 with Leopard)... Any help is appreciated, since previous talks on R mailing list kind of confused me much!! thanx in advance niccolò [[alternative HTML version deleted]] __ 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] R: how do I build panel data/longitudinal data models with AR terms using the plm package or any other package
Hello Jude. Please find my remarks below, with '##' Da: Jude Ryan [mailto:jr...@marketsharepartners.com] Inviato: giovedì 18 novembre 2010 23:52 A: R-help@r-project.org Cc: yves.croiss...@univ-reunion.fr; Millo Giovanni Oggetto: how do I build panel data/longitudinal data models with AR terms using the plm package or any other package Hi All, I am doing econometric modeling of panel data (fixed effects). We currently use Eviews to do this, but I have discovered a bug in Eviews 7 and am exploring the use of R to build panel data models / longitudinal data models. I looked at the plm package but do not see how I can incorporate AR terms in the model using the plm package. ## Two possible meanings here: either you want autoregressive y or autoregressive errors 1) y = rho1*y(-1) + rho2*y(-2) + Xb + e or 2) y = Xb + u, u = rho1*u(-1) + rho2*u(-2) 1) is easy: just use lags, like fm - y ~ lag(y) + lag(y,2) + x but be aware of the Nickell bias: your estimator needs T-asymptotics. I have an Eviews model with two AR terms, AR(1) and AR(2), ## ...then, chances are you want 2) ! all my other remarks below apply to this second case (while 1) would fail for lack of strict endogeneity) and I am trying to replicate that model using R (and SAS too, if possible) as the fitted values in Eviews for panel data (fixed effects) appear to be wrong. In Eviews I tried a second approach and explicitly coded the fixed effects as dummy variables but the standard errors I get are very different from using the panel data options in Eviews, and thus the final model selected could be very different based on these two approaches. Can I incorporate AR terms in a panel data model using the plm package, and if so, how? ## As of now, no. We plan to add feasible AR(1) à la Baltagi, but it won't be tomorrow. This is also because --- Also, are there any other packages like nlme, lme4, .. that will let me build panel data models / longitudinal data models with AR terms? ## Yes. You can try 'nlme' and its newer sibling 'lme4'. I'm sure it can do random effects + AR(1), and sure you can put in the FEs as dummies; there are probably more elegant solutions but I'm not that familiar with it myself. For an introduction from the econometrician's viewpoint, see here http://www.jstatsoft.org/v27/i02 Ch. 7 Do any of these packages let you build panel data models / longitudinal data models specifying both AR and MA terms? Looking at the ACF and PCAF it seems that some of the error processes are best/more compactly represented by a combination of AR and MA terms, but unfortunately Eviews only lets you use AR terms for panel data and getting rid of the cross-sections in the panel data and building ARIMA models, which let you specify both AR and MA terms for the error process, will mean building separate models for each cross-section. Besides, we do not have that much data to build time series models and panel data methods let us circumvent the limited data issue. ## The issue here is, of course, cross-sectional poolability. The ARMA process in the errors should be the same for each individual. I am confident that you may find something in 'nlme''s rich error covariance structures. If you do, another possibility to get rid of the FEs and use standard methods is using first-difference data (but of course this modifies the errors' covariance specification, and you should reparameterize it). It is my understanding (but I could be wrong) that some of the SAS procs, like HPMIXED, let you specify only one AR term for panel data so I am hoping there is some R package that will let me replicate what I can do in Eviews, and possibly even go beyond what Eviews can do by specifying both AR and MA terms. ## If you're comfortable with ML, you could as well try to write down the likelihood and optimize it. There are facilities in package 'maxLik'. Thanks in advance for your time, Jude Ryan MarketShare Partners 1270 Avenue of the Americas, Suite # 2702 New York, NY 10020 http://www.marketsharepartners.com Work: (646)-745-9916 ext: 222 Cell: (973)-943-2029 ## No ready solutions, sorry. HTH, Giovanni Giovanni Millo Research Dept., Assicurazioni Generali SpA Via Machiavelli 4, 34132 Trieste (Italy) tel. +39 040 671184 fax +39 040 671160 [[alternative HTML version deleted]] __ 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] latex tables with quantreg
Ok, thank you very much, I'll try it. Kind regards, Emili 2010/11/19 Dieter Menne dieter.me...@menne-biomed.de Frank Black-2 wrote: I'm using the quantreg package to run some regressions. I'm trying to save the output as latex tables using the helpful latex command, which works fine. However, I've been unable to modify its behavior in some ways I'm insterested in. For instance, I'd like a table in which I had the asterisks corresponding to the significance levels of each variable, but I have been unable to find how to do it. For some other models (lm, glm, lme), I have made some customizations (using well-formatted p-values, asterisks are a bit outdated and not loved by most journals). You can download the source from http://www.menne-biomed.de/download/Dmisc_1.2.1.tar.gz Check, for example, latex.lm.R Dieter -- View this message in context: http://r.789695.n4.nabble.com/latex-tables-with-quantreg-tp3049844p3050027.html Sent from the R help mailing list archive at Nabble.com. __ 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. [[alternative HTML version deleted]] __ 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] Question on overdispersion
Dear Nameless,
The quasi distribution can no longer be used in lme4 because a) the
results were not very reliable b) there is an alternative to model
overdispersion.
The alternative is to expand your dataset to bernoulli trials. Then add
a random effect with one level per observation. This random effect will
model additive overdisperion. The quasi distributions model
overdisperion multiplicative.
In the example below, the random effect of RowID has 0 variance. Hence
no overdispersion.
dataset - data.frame(
male_chick_no = c(2,4,1,0,3,5,2),
female_chick_no=c(1,0,3,3,1,0,2),
FemaleID=c(A,A,B,B,C,D,E))
longFormat - do.call(rbind, lapply(seq_len(nrow(dataset)), function(i){
with(dataset, data.frame(Sex = c(rep(M, male_chick_no[i]),
rep(F, female_chick_no[i])), FemaleID = FemaleID[i]))
}))
longFormat$FemaleID - factor(longFormat$FemaleID)
longFormat$RowID - factor(seq_len(nrow(longFormat)))
longFormat$Male - longFormat$Sex == M
library(lme4)
fit1 - glmer(Male ~ (1|FemaleID), data = longFormat, family = binomial)
fit2 - glmer(Male ~ (1|FemaleID) + (1|RowID), data = longFormat, family
= binomial)
anova(fit1, fit2)
Best regards,
Thierry
PS sig-mixed-models is a better mailinglist for this kind of questions.
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek
team Biometrie Kwaliteitszorg
Gaverstraat 4
9500 Geraardsbergen
Belgium
Research Institute for Nature and Forest
team Biometrics Quality Assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
thierry.onkel...@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-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] Namens cct663
Verzonden: vrijdag 19 november 2010 5:39
Aan: r-help@r-project.org
Onderwerp: [R] Question on overdispersion
I have a few questions relating to overdispersion in a sex
ratio data set that I am working with (note that I already
have an analysis with GLMMs for fixed effects, this is just
to estimate dispersion). The response variable is binomial
because nestlings can only be male or female. I have samples of
1-5 nestlings from each nest (individuals within a nest are
not independent, so the response variable is the ratio of
sons to daughters) and some females have multiple nests in
the data set (so I need to include female identity as a
random effect).
Here is an example of what the three vectors used in the
model look like (the real data set is much bigger, just to
illustrate what I'm talking
about):
male_chick_no=c(2,4,1,0,3,5,2)
female_chick_no=c(1,0,3,3,1,0,2)
FemaleID=c(A,A,B,B,C,D,E)
My first question relates to coding the test in R. I received
this suggested R syntax from a reviewer:
SexRatio = cbind(male_chick_no, female_chick_no)
Model - lmer(SexRatio ~ 1 +(1|FemaleID), family = quasibinomial)
But when I try to use this in R I get the error: Error in
glmer(formula = ratio ~ 1 + (1 | femid), family =
quasibinomial) : quasi families cannot be used in glmer.
I've tried playing around with some other mixed model
functions but can't seem to find one that will provide an
estimate of dispersion and allow me to include my random effect.
Is there some other function I should be using? Or is there a
different syntax that I should use for lmer?
My second question is more general: I understand that with
binomial data overdispersion suggests that the observed data
have a greater variance than expected given binomial errors
(in my case this means that more nests would be all male/all
female than expected if sex is random). So with binomial
errors the expected estimate of dispersion is 1, if I find
that dispersion is 1 it suggests that my data are
overdispersed. My question is, how much greater than 1 should
that number be to conclude that the data are overdispersed?
Is there a rule of thumb or does it just depend on the dataset?
I was thinking of doing a randomization test with the same
structure (nest size and female id) as my real data set but
with sex ratio of each nest randomized with a 50:50 chance of
individuals being sons or daughters and comparing my observed
dispersion to the distribution of dispersions from the
randomization test. Would this be a valid way to ask whether
my data are overdispersed? Is it even necessary?
Any help/advice that you can provide would be greatly
appreciated. I am relatively new to R so explicit
[R] Calculating distance between longitude,latitude of 2 points
Hi all, I would like to know a way of calculating the distance between 2 points when I already have the longitude and latitude of the points. For example : Point 1 : 52° 9'54.00N 4°25'8.40E Point 2 : 52°27'46.80N 4°33'18.00E Distance between point 1 and point in km Is there any functions already available for this ? Any help will be much appreciated! -- View this message in context: http://r.789695.n4.nabble.com/Calculating-distance-between-longitude-latitude-of-2-points-tp3050123p3050123.html Sent from the R help mailing list archive at Nabble.com. __ 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] [R-sig-ME] Question on overdispersion
Hi Thierry + nameless,
It is not necessary to expand the binomial into Bernoulli trials (nor
advisable if n and/or the binomial size are large). You can just fit
observation-level random effects:
dataset$resid-as.factor(1:dim(dataset)[1])
fit3 - glmer(cbind(male_chick_no, female_chick_no) ~ 1+(1|FemaleID)+
(1|resid), data = dataset, family = binomial)
gives the same answer as fit2
Cheers,
Jarrod
Quoting ONKELINX, Thierry thierry.onkel...@inbo.be:
Dear Nameless,
The quasi distribution can no longer be used in lme4 because a) the
results were not very reliable b) there is an alternative to model
overdispersion.
The alternative is to expand your dataset to bernoulli trials. Then add
a random effect with one level per observation. This random effect will
model additive overdisperion. The quasi distributions model
overdisperion multiplicative.
In the example below, the random effect of RowID has 0 variance. Hence
no overdispersion.
dataset - data.frame(
male_chick_no = c(2,4,1,0,3,5,2),
female_chick_no=c(1,0,3,3,1,0,2),
FemaleID=c(A,A,B,B,C,D,E))
longFormat - do.call(rbind, lapply(seq_len(nrow(dataset)), function(i){
with(dataset, data.frame(Sex = c(rep(M, male_chick_no[i]),
rep(F, female_chick_no[i])), FemaleID = FemaleID[i]))
}))
longFormat$FemaleID - factor(longFormat$FemaleID)
longFormat$RowID - factor(seq_len(nrow(longFormat)))
longFormat$Male - longFormat$Sex == M
library(lme4)
fit1 - glmer(Male ~ (1|FemaleID), data = longFormat, family = binomial)
fit2 - glmer(Male ~ (1|FemaleID) + (1|RowID), data = longFormat, family
= binomial)
anova(fit1, fit2)
Best regards,
Thierry
PS sig-mixed-models is a better mailinglist for this kind of questions.
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek
team Biometrie Kwaliteitszorg
Gaverstraat 4
9500 Geraardsbergen
Belgium
Research Institute for Nature and Forest
team Biometrics Quality Assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
thierry.onkel...@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-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] Namens cct663
Verzonden: vrijdag 19 november 2010 5:39
Aan: r-help@r-project.org
Onderwerp: [R] Question on overdispersion
I have a few questions relating to overdispersion in a sex
ratio data set that I am working with (note that I already
have an analysis with GLMMs for fixed effects, this is just
to estimate dispersion). The response variable is binomial
because nestlings can only be male or female. I have samples of
1-5 nestlings from each nest (individuals within a nest are
not independent, so the response variable is the ratio of
sons to daughters) and some females have multiple nests in
the data set (so I need to include female identity as a
random effect).
Here is an example of what the three vectors used in the
model look like (the real data set is much bigger, just to
illustrate what I'm talking
about):
male_chick_no=c(2,4,1,0,3,5,2)
female_chick_no=c(1,0,3,3,1,0,2)
FemaleID=c(A,A,B,B,C,D,E)
My first question relates to coding the test in R. I received
this suggested R syntax from a reviewer:
SexRatio = cbind(male_chick_no, female_chick_no)
Model - lmer(SexRatio ~ 1 +(1|FemaleID), family = quasibinomial)
But when I try to use this in R I get the error: Error in
glmer(formula = ratio ~ 1 + (1 | femid), family =
quasibinomial) : quasi families cannot be used in glmer.
I've tried playing around with some other mixed model
functions but can't seem to find one that will provide an
estimate of dispersion and allow me to include my random effect.
Is there some other function I should be using? Or is there a
different syntax that I should use for lmer?
My second question is more general: I understand that with
binomial data overdispersion suggests that the observed data
have a greater variance than expected given binomial errors
(in my case this means that more nests would be all male/all
female than expected if sex is random). So with binomial
errors the expected estimate of dispersion is 1, if I find
that dispersion is 1 it suggests that my data are
overdispersed. My question is, how much greater than 1 should
that number be to conclude that the data are overdispersed?
Is there a rule of thumb or does it just depend on the dataset?
I was thinking of doing a randomization test with the same
structure (nest size and female id) as my real data set but
with sex ratio of each nest randomized
Re: [R] Playwith-problem with loading
At the end it seems to be that the failure of R is not connected with instaling GTK+, because it occures after loading playwith library no matter if I confirm the GTK+ installation or not. In fact it does not fail imediatelly you can even continue to input commands to the comand line but it fails after scolling left e.g. to see some longer expression. The error message looks like this: R for Windowa GUI front-end has encountered a problem and needs to close The details of error are specified like this: AppName: rgui.exe AppVer: 2.120.53317.0 ModName: msvcrt.dll ModVer: 7.0.2600.5512 Offset: 00037fd4 If I confirm the instalation of GTK+ after calling the library playwith it the instalation proceed (the GTK2-Runtime with banch of dll files occures on disk) but I cannot say if it is really completed succesfuly. After running the R again and calling the playwith library the same problem occurs no matter if there is GTK+ installed or not. Thanks, Martin From: Michael Lawrence [lawrence.mich...@gene.com] Sent: 18 November 2010 23:26 To: Fencl, Martin Cc: r-help@r-project.org Subject: Re: [R] Playwith-problem with loading On Tue, Nov 16, 2010 at 10:59 AM, Fencl, Martin martin.fe...@eawag.chmailto:martin.fe...@eawag.ch wrote: Helllo, I am having trouble with running the library Playwith in the R-2.12.0. running under 32bit Windows XP. After calling the library the error message The procedure entry point gdk_cairo_reset_clip could not be located in the dynamic library libgdk-win32-2.0-0.dll. occurs and the R asks for instaling the GTK+ package. However the instalation of GTK+ thorugh the R fails. I have installed GTK+ by installing GIMP 2.0 version 2.6.10 and set the path of environment variables. But it still does not work. It seems to be that the problem is in gtk2 (which I also installed). Thank you for any hints! The GIMP binary of GTK+ has been known not to work well with R, and probably simply is not new enough in this case. What do you mean the GTK+ installer fails? Some details on that would be helpful. Thanks, Michael library(playwith) Loading required package: lattice Loading required package: cairoDevice Loading required package: gWidgetsRGtk2 Loading required package: gWidgets Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared object 'C:/PROGRA~1/R/R-212~1.0/library/RGtk2/libs/i386/RGtk2.dll': LoadLibrary failure: The specified procedure could not be found. Failed to load RGtk2 dynamic library, attempting to install it. trying URL 'http://downloads.sourceforge.net/gtk-win/gtk2-runtime-2.22.0-2010-10-21-ash.exe?download' Content type 'application/x-msdos-program' length 7820679 bytes (7.5 Mb) opened URL downloaded 7.5 Mb Learn more about GTK+ at http://www.gtk.org If the package still does not load, please ensure that GTK+ is installed and that it is on your PATH environment variable IN ANY CASE, RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN Error : .onAttach failed in attachNamespace() for 'gWidgetsRGtk2', details: call: .Call(name, ..., PACKAGE = PACKAGE) error: C symbol name S_gtk_icon_factory_new not in DLL for package RGtk2 Error: package 'gWidgetsRGtk2' could not be loaded __ R-help@r-project.orgmailto: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.
[R] assigment
Hello R Users, I have vectors x - c(a2,b7,c8) y1 - c(1,2,3,2) y2 - c(4,2,7,5,4,3,8) y3 - c(1:10) and I want to assign values form vector y1 to a new variable which name comes from the 1st value of the vector x etc. How to do it using only vector x. As a result I should have: a2 - y1 b7 - y2 c8 - y3 More general problem: I have 2 txt files. First is a one column C4 C6 F D D1 D2 D5 D6 Second is (non-define number of columns): 44, 60, 65, 139, 138 47 48 49, 46 . is it possible to automatically assign: C4 - c(44, 60, 65, 139, 138) C6 - c(47) ... I would appreciate for any help. Robert __ 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] profile in lme4 and lme4a/lme4b
Hi: 2010/11/19 Niccolò Bassani biostatist...@gmail.com Dear R-users, from Douglas Bates lme4 book I'm trying to run profile() on a quite large dataset, in order to have some confidence intervals on random effects parameter in mixed models. When I run it in lme4 however I'm faced with the following error: Errore in UseMethod(profile) : no applicable method for 'profile' applied to an object of class mer Surfing on R-help mailing lists I understood that this has to do with some compatibility problems which are undergoing development for next version of the lme4 package, right? Also, I found that this function is active in the development packages lme4a and lme4b, available from R-forge... If you were surfing on R-mixed-models, you should have discovered somewhere along the way that the release version of lme4 on CRAN does not have (m?)any of the experimental functions in the first draft of Prof. Bates' book. The code/functions corresponding to the book in progress reside in package lme4a on R-forge and much, if not all, of it is in active development and subject to change (both in the book and the code). lme4b is not intended for general use, if I've read Prof. Bates' meaning from past posts correctly. I don't know what you infer by 'compatibility problems', but my understanding is that the eventual goal is to have an integrated computational platform that provides a unified way of modeling [non]linear [generalized] mixed effects problems. Considering that the theory itself is in quite active development, this project is very ambitious in scope. Because it's bleeding edge methodology, I understand why Prof. Bates is loath to add new features to the release version lme4 until they meet his performance standards on the computational side and whatever issues exist on the methodological side are more or less resolved, since his name is on it. I trust his judgment in these matters. Moreover, Prof. Bates does his development work in Linux, so binaries for Windows and Macs are not always completely up to date. He has also mentioned several times this term that his teaching schedule gives him little opportunity to make substantial progress re development and maintenance of lme4(a). Such is life on the bleeding edge. The operative word here is patience. I'm certain that when he has the time to do so, the binaries for non-Linux platforms will be updated and reported here and/or R-mixed-models. With thanks to Prof. Bates for all the great work he's done on this project and many others, Dennis I was trying to install these packages, at least to have profile() running. I've tried different ways for doing this but I'm stuck in a blind alley...I've tried the following (all suggestions from R users found on the Internet): - install.packages(lme4a, repos=http://R-Forge.R-project.org;) returning Warning message: In getDependencies(pkgs, dependencies, available, lib) : package lme4a is not available - installing binary file directly in the .libpaths directory, but: lme4a binary for MAC can not be retrieved on the web (page not found), and lme4b gives similar problem. Now only installing package from source files remain, but this does not seem so easy...at least not for me! I have a Macbook Pro (running Mac OS/X 10.6.4 with Leopard)... Any help is appreciated, since previous talks on R mailing list kind of confused me much!! thanx in advance niccolò [[alternative HTML version deleted]] __ 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. [[alternative HTML version deleted]] __ 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] Plotting number of patients at risk below survival curve
Dear Dieter, thanks a lot, that was exactly what I was looking for. Best regards Thorsten From: Dieter Menne dieter.menne_at_menne-biomed.de Date: Fri, 19 Nov 2010 00:36:58 -0800 (PST) Thorsten Raff wrote: does anyone know of a R-package that has implemented the increasingly popular inclusion of the number of patients at risk below Kaplan-Meier curves like in http://bloodjournal.hematologylibrary.org/content/vol116/issue19/images/large/zh89991058760001.jpeg survplot in Frank Harrell's package Design (looks like the example was created with it). Dieter -- Thorsten Raff 2nd Medical Department, University Hospital Schleswig-Holstein, Campus Kiel Chemnitzstraße 33 24116 Kiel GERMANY phone: +49 431 1697-5234 fax: +49 431 1697-1264 email: t.raffatmed2.uni-kiel.de web: www.uk-sh.de -- Thorsten Raff 2nd Medical Department, University Hospital Schleswig-Holstein, Campus Kiel Chemnitzstraße 33 24116 Kiel GERMANY phone: +49 431 1697-5234 fax: +49 431 1697-1264 email: t.raffatmed2.uni-kiel.de web: www.uk-sh.de __ 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] assigment
Hi Robert, What about a named list? This will generalize to your two text files one with data, the other with names. x - c(a2,b7,c8) y1 - c(1,2,3,2) y2 - c(4,2,7,5,4,3,8) y3 - c(1:10) dat - list(c(1,2,3,2), c(4,2,7,5,4,3,8), c(1:10)) names(dat) - c(a2,b7,c8) dat # example dat$a2 dat[[a2]] ## or using your variables dat2 - list(y1, y2, y3) names(dat2) - x Cheers, Josh On Fri, Nov 19, 2010 at 2:57 AM, Robert Ruser robert.ru...@gmail.com wrote: Hello R Users, I have vectors x - c(a2,b7,c8) y1 - c(1,2,3,2) y2 - c(4,2,7,5,4,3,8) y3 - c(1:10) and I want to assign values form vector y1 to a new variable which name comes from the 1st value of the vector x etc. How to do it using only vector x. As a result I should have: a2 - y1 b7 - y2 c8 - y3 More general problem: I have 2 txt files. First is a one column C4 C6 F D D1 D2 D5 D6 Second is (non-define number of columns): 44, 60, 65, 139, 138 47 48 49, 46 . is it possible to automatically assign: C4 - c(44, 60, 65, 139, 138) C6 - c(47) ... I would appreciate for any help. Robert __ 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. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ __ 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] Converting matrix data to a list
Hi, I've looked through the posts but couldn't find a solution to this. I'd be really grateful if someone could help, I'd like to convert a data file of mutual information that is formatted as a matrix: TF1 TF2 TF3 TF200... Gene1 0.0 0.2 0.2 Gene2 1.4 0.0 2.8 Gene3 0.3 0.6 1.7 Gene6000 To a list: Gene1 TF1 0.0 Gene1 TF2 0.2 Gene1 TF3 0.2 Gene2 TF1 1.4 Gene2 TF2 0.0 Gene2 TF3 2.8 Gene3 TF1 0.3 Gene3 TF2 0.6 Gene3 TF3 1.7 Gene6000...TF200...etc The matrix is ~6000X200 in size, Adam [[alternative HTML version deleted]] __ 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] assigment
Thank you, but unfortunately it's not resolve my problem. After writing in R console e.g. a2 a should get the values. Do you know how to read file 2 into R? 2010/11/19 Joshua Wiley jwiley.ps...@gmail.com: Hi Robert, What about a named list? This will generalize to your two text files one with data, the other with names. x - c(a2,b7,c8) y1 - c(1,2,3,2) y2 - c(4,2,7,5,4,3,8) y3 - c(1:10) dat - list(c(1,2,3,2), c(4,2,7,5,4,3,8), c(1:10)) names(dat) - c(a2,b7,c8) dat # example dat$a2 dat[[a2]] ## or using your variables dat2 - list(y1, y2, y3) names(dat2) - x Cheers, Josh On Fri, Nov 19, 2010 at 2:57 AM, Robert Ruser robert.ru...@gmail.com wrote: Hello R Users, I have vectors x - c(a2,b7,c8) y1 - c(1,2,3,2) y2 - c(4,2,7,5,4,3,8) y3 - c(1:10) and I want to assign values form vector y1 to a new variable which name comes from the 1st value of the vector x etc. How to do it using only vector x. As a result I should have: a2 - y1 b7 - y2 c8 - y3 More general problem: I have 2 txt files. First is a one column C4 C6 F D D1 D2 D5 D6 Second is (non-define number of columns): 44, 60, 65, 139, 138 47 48 49, 46 . is it possible to automatically assign: C4 - c(44, 60, 65, 139, 138) C6 - c(47) ... I would appreciate for any help. Robert __ 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. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ __ 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] assigment
Hi: On Fri, Nov 19, 2010 at 2:57 AM, Robert Ruser robert.ru...@gmail.comwrote: Hello R Users, I have vectors x - c(a2,b7,c8) y1 - c(1,2,3,2) y2 - c(4,2,7,5,4,3,8) y3 - c(1:10) and I want to assign values form vector y1 to a new variable which name comes from the 1st value of the vector x etc. How to do it using only vector x. As a result I should have: a2 - y1 b7 - y2 c8 - y3 l - list(y1, y2, y3) for(i in seq_along(x)) assign(x[i], l[[i]]) More general problem: I have 2 txt files. First is a one column C4 C6 F D D1 D2 D5 D6 Second is (non-define number of columns): 44, 60, 65, 139, 138 47 48 49, 46 . is it possible to automatically assign: C4 - c(44, 60, 65, 139, 138) C6 - c(47) ... Same concept as above. HTH, Dennis I would appreciate for any help. Robert __ 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. [[alternative HTML version deleted]] __ 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] Ggplot and irregular timeseries
Hello there,
Could anybody please help on how to correctly use ggplot when
printing irregural time series, by irregural here I mean for example
the absence of some dates in the whole timespan of a dataset. To be
more precise in the following example I generated some random data
which spans the whole November up to now and dropped weekend days but
for some reasons ggplot continues to plot the days I just dropped. The
ggplot generated outputs for comparison purposes can be found here
(http://img269.imageshack.us/img269/121/ggplotweekends.png) where the
upper image is for the regular timeseries and the bottom one is for
the irregular one. Datasets for both the charts are
(http://img521.imageshack.us/img521/6729/regularts.png) and
(http://img517.imageshack.us/img517/8651/irregularts.png)
correspondingly. The R code used to generate them is
dates-seq(ISOdate(2010,11,1), by = day, length.out = 19)
rets-xts(rlnorm(19),order.by=dates)
# the following line drops weekends from the timeseries
rets-rets[!weekdays(index(rets))%in%c('Saturday','Sunday'),]
rets.m-data.frame(index(rets),rets,check.names=F)
colnames(rets.m)-c('Date','Rets')
rets.m-melt(rets.m,id.vars=c('Date','Rets'))
ggplot(data=rets.m,aes(Date,Rets))+geom_bar(stat=identity)+scale_x_datetime(major
= freqprint, format='%m/%d')
Thanks in advance for your help/patience and my bad English.
Kind regards,
Alex
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Re: [R] Converting matrix data to a list
Hi, Not sure how since I never use it, but I think melt() and then cast() from the reshape (or reshape2?) package are designed for this kind of transformations Ivan Le 11/19/2010 12:08, Adam Streline a écrit : Hi, I've looked through the posts but couldn't find a solution to this. I'd be really grateful if someone could help, I'd like to convert a data file of mutual information that is formatted as a matrix: TF1TF2TF3TF200... Gene10.00.20.2 Gene21.40.02.8 Gene30.30.61.7 Gene6000 To a list: Gene1TF10.0 Gene1TF20.2 Gene1TF30.2 Gene2TF11.4 Gene2TF20.0 Gene2TF32.8 Gene3TF10.3 Gene3TF20.6 Gene3TF31.7 Gene6000...TF200...etc The matrix is ~6000X200 in size, Adam [[alternative HTML version deleted]] __ 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. -- Ivan CALANDRA PhD Student University of Hamburg Biozentrum Grindel und Zoologisches Museum Abt. Säugetiere Martin-Luther-King-Platz 3 D-20146 Hamburg, GERMANY +49(0)40 42838 6231 ivan.calan...@uni-hamburg.de ** http://www.for771.uni-bonn.de http://webapp5.rrz.uni-hamburg.de/mammals/eng/1525_8_1.php __ 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] Converting matrix data to a list
Hi:
Look into melt() from package reshape2. Assuming m is your matrix,
library(reshape2)
meltm - melt(m, id = rownames(m))
str(meltm)
head(meltm)
## Toy example:
m - matrix(1:30, nrow = 3)
rownames(m) - paste('Gene', 1:nrow(m), sep = '')
colnames(m) - paste('T', 1:ncol(m), sep = '')
m
T1 T2 T3 T4 T5 T6 T7 T8 T9 T10
Gene1 1 4 7 10 13 16 19 22 25 28
Gene2 2 5 8 11 14 17 20 23 26 29
Gene3 3 6 9 12 15 18 21 24 27 30
mm - melt(m, id = rownames(m))
mm
X1 X2 value
1 Gene1 T1 1
2 Gene2 T1 2
3 Gene3 T1 3
4 Gene1 T2 4
5 Gene2 T2 5
6 Gene3 T2 6
...
str(mm)
'data.frame': 30 obs. of 3 variables:
$ X1 : Factor w/ 3 levels Gene1,Gene2,..: 1 2 3 1 2 3 1 2 3 1 ...
$ X2 : Factor w/ 10 levels T1,T10,T2,..: 1 1 1 3 3 3 4 4 4 5 ...
$ value: int 1 2 3 4 5 6 7 8 9 10 ...
HTH,
Dennis
On Fri, Nov 19, 2010 at 3:08 AM, Adam Streline astrel...@yahoo.com wrote:
Hi, I've looked through the posts but couldn't find a solution to this. I'd
be
really grateful if someone could help,
I'd like to convert a data file of mutual information that is formatted as
a matrix:
TF1TF2TF3TF200...
Gene10.00.20.2
Gene21.40.0 2.8
Gene30.30.61.7
Gene6000
To a list:
Gene1TF10.0
Gene1TF20.2
Gene1TF30.2
Gene2TF11.4
Gene2TF20.0
Gene2TF32.8
Gene3TF10.3
Gene3TF20.6
Gene3TF31.7
Gene6000...TF200...etc
The matrix is ~6000X200 in size,
Adam
[[alternative HTML version deleted]]
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[[alternative HTML version deleted]]
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Re: [R] Converting matrix data to a list
Try this: x TF1 TF2 TF3 Gene1 0.0 0.2 0.2 Gene2 1.4 0.0 2.8 Gene3 0.3 0.6 1.7 as.data.frame.table(as.matrix(x)) On Fri, Nov 19, 2010 at 9:08 AM, Adam Streline astrel...@yahoo.com wrote: Hi, I've looked through the posts but couldn't find a solution to this. I'd be really grateful if someone could help, I'd like to convert a data file of mutual information that is formatted as a matrix: TF1TF2TF3TF200... Gene10.00.20.2 Gene21.40.02.8 Gene30.30.61.7 Gene6000 To a list: Gene1TF10.0 Gene1TF20.2 Gene1TF30.2 Gene2TF11.4 Gene2TF20.0 Gene2TF32.8 Gene3TF10.3 Gene3TF20.6 Gene3TF31.7 Gene6000...TF200...etc The matrix is ~6000X200 in size, Adam [[alternative HTML version deleted]] __ 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ 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] assigment
On Fri, Nov 19, 2010 at 3:20 AM, Robert Ruser robert.ru...@gmail.com wrote: a2 a should get the values. Lists are a nice way to allow variable data (e.g., vectors, data frames, matrices, etc. all of different sizes) but still group related things (such as data from a single file) together, kind of like putting all your vegetables on one shelf of your fridge and all your drinks on another. If you really just want everything tossed in the fridge (as it were), Dennis provided an option. Do you know how to read file 2 into R? Hmm, it is difficult to say precisely without the actual file, but it sounds like you should look at: ?readLines You may need to do some additional processing if you get the data in with readLines (I think it pulls everything in as character data, so you might need to split each row and convert to numeric or integer. See ?strsplit for one way to split data, ?as.numeric, ?as.integer for potential conversions). Usually for reading in data I try (in this order because read.table() is generally much easier to use than readLines or scan): read.table(), readLines(), and if all else fails, scan() HTH, Josh [snip] -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ __ 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] assigment
Try this: mapply(assign, x, list(y1, y2, y3), MoreArgs = list(envir = globalenv())) On Fri, Nov 19, 2010 at 8:57 AM, Robert Ruser robert.ru...@gmail.comwrote: Hello R Users, I have vectors x - c(a2,b7,c8) y1 - c(1,2,3,2) y2 - c(4,2,7,5,4,3,8) y3 - c(1:10) and I want to assign values form vector y1 to a new variable which name comes from the 1st value of the vector x etc. How to do it using only vector x. As a result I should have: a2 - y1 b7 - y2 c8 - y3 More general problem: I have 2 txt files. First is a one column C4 C6 F D D1 D2 D5 D6 Second is (non-define number of columns): 44, 60, 65, 139, 138 47 48 49, 46 . is it possible to automatically assign: C4 - c(44, 60, 65, 139, 138) C6 - c(47) ... I would appreciate for any help. Robert __ 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ 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] expand comma separated field vertically in data.frame
Hello,
I have a data.frame like this:
a 1,2,3,4 b1
b 6,7 b3
And I would like to transform it to this:
a 1 b1
a 2 b1
a 3 b1
a 4 b1
b 6 b3
b 7 b3
I have been looking at ddply but can't seem to work it out. ANy help
would be gratefully received.
Dan
--
**
Daniel Brewer, Ph.D.
Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.bre...@icr.ac.uk
**
The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company
Limited by Guarantee, Registered in England under Company No. 534147 with its
Registered Office at 123 Old Brompton Road, London SW7 3RP.
This e-mail message is confidential and for use by the a...{{dropped:2}}
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Re: [R] expand comma separated field vertically in data.frame
Try this:
transform(x[rep(seq(nrow(x)), sapply(v.s - strsplit(as.character(x$V2),
,), length)),], V2 = unlist(v.s))
On Fri, Nov 19, 2010 at 10:04 AM, Daniel Brewer daniel.bre...@icr.ac.ukwrote:
Hello,
I have a data.frame like this:
a 1,2,3,4 b1
b 6,7 b3
And I would like to transform it to this:
a 1 b1
a 2 b1
a 3 b1
a 4 b1
b 6 b3
b 7 b3
I have been looking at ddply but can't seem to work it out. ANy help
would be gratefully received.
Dan
--
**
Daniel Brewer, Ph.D.
Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.bre...@icr.ac.uk
**
The Institute of Cancer Research: Royal Cancer Hospital, a charitable
Company Limited by Guarantee, Registered in England under Company No. 534147
with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
This e-mail message is confidential and for use by the...{{dropped:20}}
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Re: [R] negative axis values in image() and scalebar in cor.plot() {psych}
2010/11/19 Lara Poplarski larapoplar...@gmail.com In order to make the output more readable You can just copy the style of the cor.plot. mat-matrix(rnorm(256e4),16e2,16e2) image(cor(mat),axes=F,col= grey((dim(mat)[1]:0)/dim(mat)[1]),main=Like this) -- Mi³ego dnia [[alternative HTML version deleted]] __ 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] Question on overdispersion
cct663 cct663 at gmail.com writes: I have a few questions relating to overdispersion in a sex ratio data set that I am working with (note that I already have an analysis with GLMMs for fixed effects, this is just to estimate dispersion). The response variable is binomial because nestlings can only be male or female. I have samples of 1-5 nestlings from each nest (individuals within a nest are not independent, so the response variable is the ratio of sons to daughters) and some females have multiple nests in the data set (so I need to include female identity as a random effect). Here is an example of what the three vectors used in the model look like (the real data set is much bigger, just to illustrate what I’m talking about): male_chick_no=c(2,4,1,0,3,5,2) female_chick_no=c(1,0,3,3,1,0,2) FemaleID=c(A,A,B,B,C,D,E) My first question relates to coding the test in R. I received this suggested R syntax from a reviewer: SexRatio = cbind(male_chick_no, female_chick_no) Model - lmer(SexRatio ~ 1 +(1|FemaleID), family = quasibinomial) But when I try to use this in R I get the error: “Error in glmer(formula = ratio ~ 1 + (1 | femid), family = quasibinomial) : quasi families cannot be used in glmer”. After many discussions of the unreliability of quasi-likelihood estimation in lme4, Doug Bates added this error/warning in a fairly recent version. The recommended approach now is to use individual-level random effects: to continue your example above, indiv - 1:length(FemaleID) Model - lmer(SexRatio ~ 1 + (1|indiv) + (1|FemaleID), family=binomial) By the way, it is generally better practice to put all of your data into a dataframe and use the data= argument to lmer. My second question is more general: I understand that with binomial data overdispersion suggests that the observed data have a greater variance than expected given binomial errors (in my case this means that more nests would be all male/all female than expected if sex is random). So with binomial errors the expected estimate of dispersion is 1, if I find that dispersion is 1 it suggests that my data are overdispersed. My question is, how much greater than 1 should that number be to conclude that the data are overdispersed? Is there a rule of thumb or does it just depend on the dataset? Very generally/crudely, the (squared) Pearson residuals are expected to be chi-square distributed. Specifically, if you know the residual degrees of freedom (which can be a bit tricky/poorly defined for mixed models, but is approximately (# data points)-(# estimated parameters), then sum(residuals^2) should be chi-squared distributed with df equal to the residual degrees of freedom. Venables and Ripley have a useful discussion. I was thinking of doing a randomization test with the same structure (nest size and female id) as my real data set but with sex ratio of each nest randomized with a 50:50 chance of individuals being sons or daughters and comparing my observed dispersion to the distribution of dispersions from the randomization test. Would this be a valid way to ask whether my data are overdispersed? Is it even necessary? It seems reasonable. You could go even farther and simulate data from your estimated model with binomial errors (i.e. use the estimated sex ratios rather than assuming a 50/50 sex ratio). Followups should probably be sent to the r-sig-mixed-models list. __ 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] Calculating distance between longitude, latitude of 2 points
On Nov 19, 2010, at 4:50 AM, Lily_stats wrote:
Hi all,
I would like to know a way of calculating the distance between 2
points when
I already have the longitude and latitude of the points.
For example :
Point 1 : 52° 9'54.00N 4°25'8.40E
Point 2 : 52°27'46.80N 4°33'18.00E
Distance between point 1 and point in km
Is there any functions already available for this ?
Searching on: distance points longitude latitude
gdist {Imap} Geodesic distance (great circle distance) between points
Ellipsoidal.Distance {GEOmap} Ellipsoidal Distance
deg.dist {fossil} Haversine Distance Formula
distaz {RSEIS} Distance and Azimuth from two points
distaz {GEOmap} Distance and Azimuth from two points (# one probably
borrowed from the other)
AlongGreat {RFOC} Get Points Along Great Circle
distAB {clim.pact} Distance between two points on Earth
Any help will be much appreciated!
Suggest you learn to search.
--
David Winsemius, MD
West Hartford, CT
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Re: [R] Plotting number of patients at risk below survival curve
Use the rms package, a replacement for of Design Frank - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Plotting-number-of-patients-at-risk-below-survival-curve-tp3048900p3050315.html Sent from the R help mailing list archive at Nabble.com. __ 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] Error: could not find function.
Dear all, I use TinnR to write commands for R. Why sometimes I can't call some basic functions, such as anova, var ? Following is my command and reponse. anova(addative,saturated,test='Chisq') Error: could not find function anova Thanks:) Regards, Lei [[alternative HTML version deleted]] __ 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] how to save object created by assign()
Hi there,
When I run the following code, I could get correct objects (with correct
values):
for(i in 1:6) { #-- Create objects 'r.1', 'r.2', ... 'r.6' --
nam - paste(r,i, sep=.)
assign(nam, 1:i)
# save(nam, file = paste(nam, RData, sep = .))
}
I hope to save the object 'r.1', 'r.2', ..., 'r.6' using the above
commented line, however, I just got 'r.1.RData' with a object 'nam' in
it, which had the value, e.g., 'r.6', not the value of 'r.6', i.e., 1:6.
Any suggestions? Thanks in advance.
Jinsong
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[R] Still confused with lapply
Hello,
I would like to replace a for loop with lapply in order to speed up the
treatment of my data (I've read lapply can help to do it).
At the end of the message, you will find a simple example (function is more
complex and data frames is more than 1 million of rows) of what I would like
to do, that is applying the same calculation to all the rows of the data
frame (knowing that I cannot change the structure of the function).
I hope you understand my french explainations ...
Thanks in advance for your help,
Have a nice week-end,
Ptit Bleu.
df1-data.frame(c(1,2,3,4), c(9,6,5,8), c(5,4,8,6))
names(df1)-c(C1, C2, C3)
fcttest-function(a1,a2,a3) {
v-a1*a2
w-a2+a3
return(c(v,w))
}
# The following for loop works
result-data.frame()
for (i in 1:length(df1[,1])) {
result-rbind(result,fcttest(df1[i,1],df1[i,2],df1[i,3]))
}
# But the command
lapply(df1, fcttest)
# gives (in french, sorry)
# Erreur dans FUN(X[[1L]], ...) : l'élément 2 est vide ;
# la partie de la liste d'arguments de '*' en cours d'évaluation était :
# (a1, a2)
--
View this message in context:
http://r.789695.n4.nabble.com/Still-confused-with-lapply-tp3050414p3050414.html
Sent from the R help mailing list archive at Nabble.com.
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Re: [R] assigment
Joshua, Dennis ans Henrique I'm immensely indebted to you. Thanks to
you I resolved my problem - a code works perfectly. I put the code,
maybe someone finds it's helpful.
f1 - readLines(file(file1.txt))
f2 - readLines(file(file2.txt))
for ( i in seq_along(f1)){
assign(f1[i],as.numeric(unlist(strsplit(f2[i],,)) ))
}
file 1 (names of the variables; just copy and paste to see how it works)
A
A2
A3
A4
A7
B
B4
B5
B7
C
C1
C3
C4
C6
F
D
file 2 (values of the variables; just copy and paste to see how it
works as well)
1
3, 6, 7
4, 13, 9
5, 2
8,10, 11,12,15
17
21, 29, 18, 32, 145
22, 34, 19, 27, 20
24, 23, 33, 28, 25, 26
35
36, 40
38, 37
39
41
92
42
Robert
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Re: [R] Still confused with lapply
PtitBleu ptit_bleu at yahoo.fr writes:
Hello,
I would like to replace a for loop with lapply in order to speed up the
treatment of my data (I've read lapply can help to do it).
At the end of the message, you will find a simple example (function is more
complex and data frames is more than 1 million of rows) of what I would like
to do, that is applying the same calculation to all the rows of the data
frame (knowing that I cannot change the structure of the function).
I hope you understand my french explainations ...
Thanks in advance for your help,
Have a nice week-end,
Ptit Bleu.
df1-data.frame(c(1,2,3,4), c(9,6,5,8), c(5,4,8,6))
names(df1)-c(C1, C2, C3)
fcttest-function(a1,a2,a3) {
v-a1*a2
w-a2+a3
return(c(v,w))
}
# The following for loop works
result-data.frame()
for (i in 1:length(df1[,1])) {
result-rbind(result,fcttest(df1[i,1],df1[i,2],df1[i,3]))
why bother with lapply when you can just do this
with(df1, cbind(df1[[1]] * df1[[2]], df1[[2]] + df1[[3]]))
HTH
Ken
--
Ken Knoblauch
Inserm U846
Stem-cell and Brain Research Institute
Department of Integrative Neurosciences
18 avenue du Doyen Lépine
69500 Bron
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
portable: +33 (0)6 84 10 64 10
http://www.sbri.fr/members/kenneth-knoblauch.html
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[R] Option to Print with numbers formatted
Hello group, I have a data frame called test.df with a bunch of columns. When I do a print(test.df), I want the numbers to appear a pre-defined setting. I believe this can be achieved by sprintf but this needs to be done individually for the data. However, is there an option that I can set so that all numerical values default to comma separated, 2 decimal places when they appear? Thanks, S __ 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] Still confused with lapply
Thanks for your answer but do you have a solution using the function ? I need to you use the data frame with a function (not the one given). Thanks in advance again. Ptit Bleu. -- View this message in context: http://r.789695.n4.nabble.com/Still-confused-with-lapply-tp3050414p3050455.html Sent from the R help mailing list archive at Nabble.com. __ 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] RGoogleDocs stopped working
Any new thoughts on this? I really want to get this working again! Is there
someone else that can help or somewhere else I should be asking?
Thanks!
-Harlan
On Wed, Nov 17, 2010 at 10:16 AM, Harlan Harris har...@harris.name wrote:
Following up again. I found on the forums for the Google Apps API this
thread that seems to be about a similar issue:
http://www.google.com/support/forum/p/apps-apis/thread?tid=1c22cb44eb5cbba6hl=ensearch_impression_id=ab161b010ecf8803%3A12c5a65ce83search_source=related_question
It's using Java and is rather over my head, but it seems to suggest that
something related to the content type might be wrong? Does this offer any
suggestions on how to fix my use of RGoogleDocs?
Thanks,
-Harlan
On Mon, Nov 15, 2010 at 12:16 PM, Harlan Harris har...@harris.namewrote:
Thanks, Duncan. Finally getting a chance to follow up on this...
I tried again, changing and resetting my password, and trying to specify
my login and password manually in the getGoogleDocsConnection argument list.
I also tried removing either or both of the service and error options. No
luck in any case. I also tried a different Google account, also with no
luck.
I've also tried tweaking the URL being generated by the code, and in all
cases, I get a 403: Forbidden error with content Error=BadAuthentication.
I don't really know enough about how authentication is supposed to work to
get much farther. Can you help? Should I try the Google API forum instead?
-Harlan
From: Duncan Temple Lang dun...@wald.ucdavis.edu
To: r-help@r-project.org
Date: Wed, 10 Nov 2010 10:33:47 -0800
Subject: Re: [R] RGoogleDocs stopped working
Hi Harlan
I just tried to connect to Google Docs and I had ostensibly the same
problem.
However, the password was actually different from what I had specified.
After resetting it with GoogleDocs, the getGoogleDocsConnection() worked
fine. So I don't doubt that the login and password are correct, but
you might just try it again to ensure there are no typos.
The other thing to look at is the values for Email and Passwd
sent in the URL, i.e. the string in url in your debugging
below. (Thanks for that by the way). If either has special characters,
e.g. , it is imperative that they are escaped correctly, i.e. converted
to %24. This should happen and nothing should have changed, but it is
worth verifying.
So things still seem to work for me. It is a data point, but not one
that gives you much of a clue as to what is wrong on your machine.
D.
On Wed, Nov 10, 2010 at 10:36 AM, Harlan Harris har...@harris.namewrote:
Hello,
Some code using RGoogleDocs, which had been working smoothly since the
summer, just stopped working. I know that it worked on November 3rd, but it
doesn't work today. I've confirmed that the login and password still work
when I log in manually. I've confirmed that the URL gives the same error
when I paste it into Firefox. I don't know enough about this web service to
figure out the problem myself, alas...
Here's the error and other info (login/password omitted):
ss.con - getGoogleDocsConnection(login=gd.login, password=gd.password,
service='wise', error=FALSE)
Error: Forbidden
Enter a frame number, or 0 to exit
1: getGoogleDocsConnection(login = gd.login, password = gd.password,
service = wise, error = FALSE)
2: getGoogleAuth(..., error = error)
3: getForm(https://www.google.com/accounts/ClientLogin;, accountType =
HOSTED_OR_GOOGLE, Email = login, Passw
4: getURLContent(uri, .opts = .opts, .encoding = .encoding, binary =
binary, curl = curl)
5: stop.if.HTTP.error(http.header)
Selection: 4
Called from: eval(expr, envir, enclos)
Browse[1] http.header
Content-Type
Cache-control Pragma
text/plainno-cache,
no-store no-cache
ExpiresDate
X-Content-Type-Options
Mon, 01-Jan-1990 00:00:00 GMT Wed, 10 Nov 2010 15:24:39
GMT nosniff
X-XSS-Protection
Content-Length Server
1; mode=block
24 GSE
status statusMessage
403 Forbidden\r\n
Browse[1] url
[1]
https://www.google.com/accounts/ClientLogin?accountType=HOSTED%5FOR%5FGOOGLEEmail=***Passwd=***service=wisesource=R%2DGoogleDocs%2D0%2E1
Browse[1] .opts
$ssl.verifypeer
[1] FALSE
R.Version()
$platform
[1] i386-apple-darwin9.8.0
$arch
[1] i386
$os
[1] darwin9.8.0
$system
[1] i386, darwin9.8.0
$status
[1]
$major
[1] 2
$minor
[1] 10.1
$year
[1] 2009
$month
[1] 12
$day
[1] 14
$`svn rev`
[1] 50720
$language
[1] R
$version.string
[1] R version 2.10.1 (2009-12-14)
installed.packages()[c('RCurl', 'RGoogleDocs'), ]
Package
LibPath
[R] Job scheduling in R
Hi All, Can anyone point to any package/resouce to schedule a job in R which runs a .R file at a specified time ? I couldn't find anything useful in R Reference manual or RSiteSearch. I am sure its there but i am unable to locate. Thanks for your help. Puneet __ 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] a rounding option for \Sexpr{}?
Maybe this should go to R-devel as a wishlist:
Can we change as.character() to format() in this line in
src/library/utils/R/Sweave.R?
val - as.character(eval(parse(text=cmd), envir=.GlobalEnv))
i.e.
val - format(eval(parse(text=cmd), envir=.GlobalEnv))
I guess this would not affect Sweave users, unless they really want 12
digits in the output (e.g. the standard error is 0.123456789012).
Since format() can respect getOption('digits'), it will be much easier
to control the number of digits globally.
Regards,
Yihui
--
Yihui Xie xieyi...@gmail.com
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA
On Fri, Nov 19, 2010 at 2:02 AM, Dieter Menne
dieter.me...@menne-biomed.de wrote:
Yihui Xie-2 wrote:
Currently Sweave does not format the (especially numeric) value in
\Sexpr{}, and I often have to round() the numbers explicitly,
otherwise I will get more than 10 digits, which is not necessary for
me in most cases. Is there a way to specify the number of digits to be
kept for values in \Sexpr{}? e.g. can we make \Sexpr{} respect
getOption('digits')?
Currently, Sweave does an eval on Sexpr, and that can be anything other than
a number (is mostly is, though). And you cannot define a new version of
Sexpr in latex, because Sexpr only looks like latex, but is processed before
texing.
My solution is to always do the rounding and formating in the R chunk (e.g.
with latexSN of Hmisc) to unclutter the Sexpr.
Dieter
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Re: [R] Option to Print with numbers formatted
On 19/11/2010 9:59 AM, Santosh Srinivas wrote:
Hello group,
I have a data frame called test.df with a bunch of columns.
When I do a print(test.df), I want the numbers to appear a pre-defined
setting.
I believe this can be achieved by sprintf but this needs to be done
individually for the data.
However, is there an option that I can set so that all numerical values
default to comma separated, 2 decimal places when they appear?
No, there's no global option with that level of flexibility. You can
set options(digits), but you won't get the commas.
You should probably write your own function to do this. For example,
myformat - function(x, big.mark=,, scientific = FALSE, nsmall=2, ...) {
format.data.frame(x, big.mark=big.mark, scientific=scientific,
nsmall=2, ...)
}
and then print(myformat(df)) should give what you want. It is possible
to replace the print.data.frame and format.data.frame functions with new
ones, but that's probably not advisable.
Duncan Murdoch
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[R] Function call on every prompt
Someone on stackoverflow.com was wondering how to display the current time in the R prompt. I could have swore there was a mechanism for hooking a function into R such that it is was called before the prompt was given, but no amount of searching in R's docs, R's source, or RSiteSearch can find it. I've searched for 'hook', 'event', 'signal', and various combinations of those with 'console', 'prompt', 'after' and 'before' with no joy. I'm sure other people have asked this on R-help before, but I can't find those messages either. Have I been hallucinating or is my search-fu week this Friday? Barry __ 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] Still confused with lapply
On Nov 19, 2010, at 10:00 AM, PtitBleu wrote: Thanks for your answer but do you have a solution using the function ? I need to you use the data frame with a function (not the one given). I do not think lapply is the *apply you want. since it will individually access the columns and you appear to want row operations. See if apply(..., 1, fctest) works better. (Since you Nabble users often don't include context, I can't check spelling in this post, but ISTR your function's name is something like that.) Thanks in advance again. Ptit Bleu. -- View this message in context: http://r.789695.n4.nabble.com/Still-confused-with-lapply-tp3050414p3050455.html David Winsemius, MD West Hartford, CT __ 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] library(datasets)
## i have one question anouth this package.. library(datasets) eurodist ## if i type this i get max distance between european cities max(eurodist) [1] 4532 ## but i would like get something like this: 4532 Gilbratar - Anthens ## and another one.. ## if a live in barcelona and i would like travel in all cities ## how can i get sum of all distance to other cities... i try sapply(eurodist[Barcelona], sum) ## and rowSums(eurodist[Barcelona,]) and it doesn't working.. tnx for helping ;) -- View this message in context: http://r.789695.n4.nabble.com/library-datasets-tp3050497p3050497.html Sent from the R help mailing list archive at Nabble.com. __ 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] a rounding option for \Sexpr{}?
On 19/11/2010 10:12 AM, Yihui Xie wrote:
Maybe this should go to R-devel as a wishlist:
Can we change as.character() to format() in this line in
src/library/utils/R/Sweave.R?
val- as.character(eval(parse(text=cmd), envir=.GlobalEnv))
i.e.
val- format(eval(parse(text=cmd), envir=.GlobalEnv))
I guess this would not affect Sweave users, unless they really want 12
digits in the output (e.g. the standard error is 0.123456789012).
Since format() can respect getOption('digits'), it will be much easier
to control the number of digits globally.
I don't like the current behaviour, but that change could break a lot of
existing documents. Since you can easily wrap your Sexpr arguments in a
call to whatever formatting function you want, why force all of those
users to change their documents?
Duncan Murdoch
Regards,
Yihui
--
Yihui Xiexieyi...@gmail.com
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA
On Fri, Nov 19, 2010 at 2:02 AM, Dieter Menne
dieter.me...@menne-biomed.de wrote:
Yihui Xie-2 wrote:
Currently Sweave does not format the (especially numeric) value in
\Sexpr{}, and I often have to round() the numbers explicitly,
otherwise I will get more than 10 digits, which is not necessary for
me in most cases. Is there a way to specify the number of digits to be
kept for values in \Sexpr{}? e.g. can we make \Sexpr{} respect
getOption('digits')?
Currently, Sweave does an eval on Sexpr, and that can be anything other than
a number (is mostly is, though). And you cannot define a new version of
Sexpr in latex, because Sexpr only looks like latex, but is processed before
texing.
My solution is to always do the rounding and formating in the R chunk (e.g.
with latexSN of Hmisc) to unclutter the Sexpr.
Dieter
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Function call on every prompt
On Nov 19, 2010, at 9:23 AM, Barry Rowlingson wrote: Someone on stackoverflow.com was wondering how to display the current time in the R prompt. I could have swore there was a mechanism for hooking a function into R such that it is was called before the prompt was given, but no amount of searching in R's docs, R's source, or RSiteSearch can find it. I've searched for 'hook', 'event', 'signal', and various combinations of those with 'console', 'prompt', 'after' and 'before' with no joy. I'm sure other people have asked this on R-help before, but I can't find those messages either. Have I been hallucinating or is my search-fu week this Friday? Barry Baz, What's wrong with: options(prompt = paste(format(Sys.time(), %a %b %d %X %Y %Z), )) Fri Nov 19 09:30:53 2010 CST Fri Nov 19 09:30:53 2010 CST Fri Nov 19 09:30:53 2010 CST ? HTH, Marc Schwartz __ 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] how to improve this inefficient R code for imputing missing values
Hello all,
I have a big data.frame multiple studies, subjects and timepoints per
subject, i.e.
STUDY[,1] SUBJECT[,2] .. WT[,16] HT[,17] TEMP[,18] BSA[,19]
1 150 170 37
1.90
1 1NA NA NA
NA
1 152 170 38
1.94
In this dataset, three types of missing (demographic) values exist:
1) first value for a subject is missing:
ie. study 1, subject 1: mis X1 X2 X3.
Here I want to carry the first non-missing value backwards to the missing value.
2) last values for a subject is missing:
ie. study 1, subject 1: X1 X2 X3 mis.
Here I want to carry the last non-missing value forwards to the missing value
3) some intermediate value for a subject is missing (like example
data.frame above)
i.e. study 1, subject 1: X1 mis X2 X3.
Here I want to impute the missing value with the mean value between X1 and X2
The missing value is actually a subset of columns in the data frame,
ie. always the columns WT HT TEMP BSA (m[,16:19]) are missing
altogether.
I have written some R code that tries to do this, but it is incredibly
slow due to the many for-loops and the big dataset I have (and might
not even be completely correct yet).
QUESTION:
I would greatly appreciate it if somebody can be give me some
guidance/hints on what direction I should roughly think for coding the
above a little more efficient then the horribly inefficient code
pasted below.
Thank you in advance and best regards,
Coen
for(s in unique(m$Study)){ # for each study
for(i in unique(m$Subject[m$Study==s is.na(m$Wt)])){ # for each
subject with a missing value (if $Wt is missing, all 4 columns 16:19
are missing)
vals-which(m$Study==s m$Subject==i !is.na(m$Wt)) # values
with NO missing values
for(w in which(m$Study==s m$Subject==i is.na(m$Wt))){ # for
each value that is missing for subject i and study s
if(w min(vals) ){ # FIRST VALUES MISSING ? #
carry the backwards
m[w,][16:19]-m[min(vals),][16:19]
} else if(w max(vals) ) { # LAST VALUES MISSING#
carry forwards
m[w,][16:19]-m[max(vals),][16:19]
} else { # INTERMEDIATE VALUES MISSING #
impute missing with mean
maxV-min(vals[valsw])
minV-max(vals[valsw])
m[w,][16:19]- mean(m[c(maxV,minV),][16:19],na.rm=T)
}
}
}
}
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and provide commented, minimal, self-contained, reproducible code.
[R] problems with rJava
Hello, using r-2.12.0 on a Toshiba laptop with Win7 I am trying to install JGR, iut installs OK but when loading, complains about rJava so I did: install.packages(rJava) Installing package(s) into ‘I:\R\cran’ (as ‘lib’ is unspecified) trying URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.12/rJava_0.8-8.zip' Content type 'application/zip' length 636680 bytes (621 Kb) opened URL downloaded 621 Kb The downloaded packages are in C:\Users\Heberto\AppData\Local\Temp\Rtmpyd0JHa\downloaded_packages library(rJava) Error : .onLoad failed in loadNamespace() for 'rJava', details: call: inDL(x, as.logical(local), as.logical(now), ...) error: unable to load shared object 'I:/R/cran/rJava/libs/i386/rJava.dll': LoadLibrary failure: The device is not ready. Error: package/namespace load failed for 'rJava' rJava.dll is in that place. Is it a problem witm Win7? Thanks R.Heberto Ghezzo Ph.D. Montreal - Canada __ 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] Function call on every prompt
On 19/11/2010 10:31 AM, Marc Schwartz wrote: On Nov 19, 2010, at 9:23 AM, Barry Rowlingson wrote: Someone on stackoverflow.com was wondering how to display the current time in the R prompt. I could have swore there was a mechanism for hooking a function into R such that it is was called before the prompt was given, but no amount of searching in R's docs, R's source, or RSiteSearch can find it. I've searched for 'hook', 'event', 'signal', and various combinations of those with 'console', 'prompt', 'after' and 'before' with no joy. I'm sure other people have asked this on R-help before, but I can't find those messages either. Have I been hallucinating or is my search-fu week this Friday? Barry was probably remembering SweaveHook. Barry Baz, What's wrong with: options(prompt = paste(format(Sys.time(), %a %b %d %X %Y %Z), )) Fri Nov 19 09:30:53 2010 CST Fri Nov 19 09:30:53 2010 CST Fri Nov 19 09:30:53 2010 CST That one doesn't get updated with every prompt. Duncan Murdoch __ 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] Function call on every prompt
On Nov 19, 2010, at 9:36 AM, Duncan Murdoch wrote: On 19/11/2010 10:31 AM, Marc Schwartz wrote: On Nov 19, 2010, at 9:23 AM, Barry Rowlingson wrote: Someone on stackoverflow.com was wondering how to display the current time in the R prompt. I could have swore there was a mechanism for hooking a function into R such that it is was called before the prompt was given, but no amount of searching in R's docs, R's source, or RSiteSearch can find it. I've searched for 'hook', 'event', 'signal', and various combinations of those with 'console', 'prompt', 'after' and 'before' with no joy. I'm sure other people have asked this on R-help before, but I can't find those messages either. Have I been hallucinating or is my search-fu week this Friday? Barry was probably remembering SweaveHook. Barry Baz, What's wrong with: options(prompt = paste(format(Sys.time(), %a %b %d %X %Y %Z), )) Fri Nov 19 09:30:53 2010 CST Fri Nov 19 09:30:53 2010 CST Fri Nov 19 09:30:53 2010 CST That one doesn't get updated with every prompt. Duncan Murdoch D'ohyou are right. Thanks Duncan Time for more coffee... Marc __ 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] a rounding option for \Sexpr{}?
Duncan Murdoch-2 wrote: On 19/11/2010 10:12 AM, Yihui Xie wrote: Maybe this should go to R-devel as a wishlist: val- format(eval(parse(text=cmd), envir=.GlobalEnv)) I don't like the current behaviour, but that change could break a lot of existing documents. Not necessarily. Add an Sweave option useFormat=FALSE to keep the old behavior. Dieter -- View this message in context: http://r.789695.n4.nabble.com/a-rounding-option-for-Sexpr-tp3049872p3050529.html Sent from the R help mailing list archive at Nabble.com. __ 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] Function call on every prompt
On Fri, Nov 19, 2010 at 3:36 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: Barry was probably remembering SweaveHook. The key is the taskCallbackManager. Does exactly what it says on the tin. Doesn't come up with any of my search strings! Hopefully now this is in R-help it'll come up when people search for do something before every prompt. Barry __ 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] Odp: Still confused with lapply
Hi
r-help-boun...@r-project.org napsal dne 19.11.2010 15:41:08:
Hello,
I would like to replace a for loop with lapply in order to speed up the
treatment of my data (I've read lapply can help to do it).
Not exactly. For loop if correctly written can be as quick as lapply. See
P.Burns' R inferno.
At the end of the message, you will find a simple example (function is
more
complex and data frames is more than 1 million of rows) of what I would
like
to do, that is applying the same calculation to all the rows of the data
frame (knowing that I cannot change the structure of the function).
Why? You do not have access to the code of a function?
I hope you understand my french explainations ...
Thanks in advance for your help,
Have a nice week-end,
Ptit Bleu.
df1-data.frame(c(1,2,3,4), c(9,6,5,8), c(5,4,8,6))
names(df1)-c(C1, C2, C3)
fcttest-function(a1,a2,a3) {
v-a1*a2
w-a2+a3
return(c(v,w))
}
# The following for loop works
result-data.frame()
for (i in 1:length(df1[,1])) {
result-rbind(result,fcttest(df1[i,1],df1[i,2],df1[i,3]))
}
Let assume you want to use some function for first two columns and some
for the columns 2 and 3. Than why not just do it?
matrix(fcttest(df1[,1],df1[,2],df1[,3]),ncol=2)
[,1] [,2]
[1,]9 14
[2,] 12 10
[3,] 15 13
[4,] 32 14
Regards
Petr
# But the command
lapply(df1, fcttest)
# gives (in french, sorry)
# Erreur dans FUN(X[[1L]], ...) : l'élément 2 est vide ;
# la partie de la liste d'arguments de '*' en cours d'évaluation était :
# (a1, a2)
--
View this message in context:
http://r.789695.n4.nabble.com/Still-confused-
with-lapply-tp3050414p3050414.html
Sent from the R help mailing list archive at Nabble.com.
__
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
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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.
Re: [R] Function call on every prompt
On Nov 19, 2010, at 10:23 AM, Barry Rowlingson wrote: Someone on stackoverflow.com was wondering how to display the current time in the R prompt. I could have swore there was a mechanism for hooking a function into R such that it is was called before the prompt was given, but no amount of searching in R's docs, R's source, or RSiteSearch can find it. I've searched for 'hook', 'event', 'signal', and various combinations of those with 'console', 'prompt', 'after' and 'before' with no joy. I'm sure other people have asked this on R-help before, but I can't find those messages either. Have I been hallucinating or is my search-fu week this Friday? The question on SO as I understood it was how to get the time on the prompt to keep changing without hitting the enter key. The questioner had already figured out how to use: options(prompt=paste(format(Sys.time(), %H:%M:%S), )) -- David Winsemius, MD West Hartford, CT __ 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] printCoefmat() for a data.frame with factors
I want to use something like printCoefmat() in a print.summary method to print a more nicely formatted version of the result from a summary method, but where the estimates may be cross-classified by one or more factors. However, printCoefmat() assumes that the labels for the parameters are the rownames of the object, and prints factors as integers. With one factor, I could just assign that as the rownames, but with 1, I would be forced to paste() them together, giving a less readable display. Perhaps printCoefmat() needs another argument for this case (factor.ind= indices of column numbers which are factors, or stringsAsFactors=TRUE), or maybe there is some other method I could use. Here is an example: summary(lor.Emp) EmploymentLength LayoffCause Log Odds Ratio Std. Error z value Pr(|z|) 1 1Mo:1-3Mo Closure -0.04082199 0.5143769 -0.07936203 0.468372334 2 1-3Mo:3-12Mo Closure 0.02353050 0.2782868 0.08455486 0.466307643 3 3-12Mo:1-2Yr Closure 0.04904020 0.2327390 0.21070895 0.416557193 4 1-2Yr:2-5Yr Closure -0.07555132 0.2468528 -0.30605823 0.379780157 5 2-5Yr:5Yr Closure -0.26157903 0.2943756 -0.88858949 0.187111872 6 1Mo:1-3Mo Replaced -0.19415601 0.3173846 -0.61173729 0.270355791 7 1-3Mo:3-12Mo Replaced -0.77994333 0.2546200 -3.06316597 0.001095043 8 3-12Mo:1-2Yr Replaced -0.18513757 0.3192303 -0.57994984 0.280974223 9 1-2Yr:2-5Yr Replaced 0.19521478 0.3422052 0.57046111 0.284182498 10 2-5Yr:5Yr Replaced -0.24791884 0.3971645 -0.62422200 0.266240900 str(summary(lor.Emp)) 'data.frame': 10 obs. of 6 variables: $ EmploymentLength: Factor w/ 5 levels 1Mo:1-3Mo,1-3Mo:3-12Mo,..: 1 2 3 4 5 1 2 3 4 5 $ LayoffCause : Factor w/ 2 levels Closure,Replaced: 1 1 1 1 1 2 2 2 2 2 $ Log Odds Ratio : num -0.0408 0.0235 0.049 -0.0756 -0.2616 ... $ Std. Error : num 0.514 0.278 0.233 0.247 0.294 ... $ z value : num -0.0794 0.0846 0.2107 -0.3061 -0.8886 ... $ Pr(|z|) : num 0.468 0.466 0.417 0.38 0.187 ... Result from printCoefmat() is considerably worse: printCoefmat(summary(lor.Emp)) EmploymentLength LayoffCause Log Odds Ratio Std. Error z value Pr(|z|) [1,] 1.00 1.00 -0.040822 0.514377 -0.0794 0.468372 [2,] 2.00 1.00 0.023530 0.278287 0.0846 0.466308 [3,] 3.00 1.00 0.049040 0.232739 0.2107 0.416557 [4,] 4.00 1.00 -0.075551 0.246853 -0.3061 0.379780 [5,] 5.00 1.00 -0.261579 0.294376 -0.8886 0.187112 [6,] 1.00 2.00 -0.194156 0.317385 -0.6117 0.270356 [7,] 2.00 2.00 -0.779943 0.254620 -3.0632 0.001095 ** [8,] 3.00 2.00 -0.185138 0.319230 -0.5799 0.280974 [9,] 4.00 2.00 0.195215 0.342205 0.5705 0.284182 [10,] 5.00 2.00 -0.247919 0.397165 -0.6242 0.266241 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ 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] a rounding option for \Sexpr{}?
On 19/11/2010 10:38 AM, Dieter Menne wrote: Duncan Murdoch-2 wrote: On 19/11/2010 10:12 AM, Yihui Xie wrote: Maybe this should go to R-devel as a wishlist: val- format(eval(parse(text=cmd), envir=.GlobalEnv)) I don't like the current behaviour, but that change could break a lot of existing documents. Not necessarily. Add an Sweave option useFormat=FALSE to keep the old behavior. I think the default would have to be FALSE, so that old documents didn't suddenly change. But is it really so hard to define your own formatting? Duncan Murdoch __ 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] Odp: Still confused with lapply
Hello Petr, Your solution works well with my example. But with the function I want to use (which calls another functions), I still have errors. I have to work on it again (but only on monday). Again thank you, Ptit Bleu. PS : I have access to all the functions but I don't want to modify all of them because I just need to correct an error I discovered in already-treated data (not sure I'm clear ...). -- View this message in context: http://r.789695.n4.nabble.com/Still-confused-with-lapply-tp3050414p3050573.html Sent from the R help mailing list archive at Nabble.com. __ 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] Function call on every prompt
On Nov 19, 2010, at 10:38 AM, Marc Schwartz wrote: What's wrong with: options(prompt = paste(format(Sys.time(), %a %b %d %X %Y %Z), )) Fri Nov 19 09:30:53 2010 CST Fri Nov 19 09:30:53 2010 CST Fri Nov 19 09:30:53 2010 CST That one doesn't get updated with every prompt. Duncan Murdoch D'ohyou are right. Thanks Duncan Time for more coffee... Me too, but I think there is a descending limb on the coffee x efficiency curve and I may have already reached it. -- David Winsemius, MD West Hartford, CT __ 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] all extended ASCII characters exist for R console output?
Hi, can the R console print all extended ASCII characters? I am especially interested in characters 176-178 from http://www.asciitable.com/ bottom table. As far as I know the character mapping in R is somewhat different (octal). So as I am not familiar with these things I am not sure if it exists. TIA Mark Mark Heckmann Dipl. Wirt.-Ing. cand. Psych. Celler Straße 27 28205 Bremen Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com [[alternative HTML version deleted]] __ 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] Job scheduling in R
On Nov 19, 2010, at 10:09 AM, amit jain wrote: Hi All, Can anyone point to any package/resouce to schedule a job in R which runs a .R file at a specified time ? That wouldn't be an R function but rather a system function, wouldn't it? I couldn't find anything useful in R Reference manual or RSiteSearch. I am sure its there but i am unable to locate. Search with: R CMD BATCH (that pulled up about twenty R documents including the fullrefman just looking on my harddrive) RSiteSearch terms = BATCH chron terms = batch scheduling terms = schedule batch (all of them worked to varying extents) Thanks for your help. Puneet __ 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, MD West Hartford, CT __ 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] Odp: how to improve this inefficient R code for imputing missing values
Hi
r-help-boun...@r-project.org napsal dne 19.11.2010 16:34:04:
Without going too deeply to your code, try to check na.locf function from
zoo package.
I would split your data to list according to study and subject, use
na.locf with respect to your miising value types
x-c(NA, 1:5)
y-rev(x)
x
[1] NA 1 2 3 4 5
y
[1] 5 4 3 2 1 NA
z-c(y,x)
z
[1] 5 4 3 2 1 NA NA 1 2 3 4 5
lll-list(x,y,z)
lll
[[1]]
[1] NA 1 2 3 4 5
[[2]]
[1] 5 4 3 2 1 NA
[[3]]
[1] 5 4 3 2 1 NA NA 1 2 3 4 5
library(zoo)
lapply(lll[unlist(lapply(lll, function(x) all(which(is.na(x))==1)))],
na.locf, fromLast=TRUE)
lapply(lll[unlist(lapply(lll, function(x)
all(which(is.na(x))==length(x], na.locf)
The third you shall probably do without na.locf, but I do not have clear
idea how exactly.
After that you will get three lists and you can put them together again.
However I am not sure if it is the best way how to do what you want.
Regards
Peetr
[R] how to improve this inefficient R code for imputing missing values
Hello all,
I have a big data.frame multiple studies, subjects and timepoints per
subject, i.e.
STUDY[,1] SUBJECT[,2] .. WT[,16] HT[,17] TEMP[,18] BSA[,19]
1 150 170 37
1.90
1 1NA NA NA
NA
1 152 170 38
1.94
In this dataset, three types of missing (demographic) values exist:
1) first value for a subject is missing:
ie. study 1, subject 1: mis X1 X2 X3.
Here I want to carry the first non-missing value backwards to the
missing value.
2) last values for a subject is missing:
ie. study 1, subject 1: X1 X2 X3 mis.
Here I want to carry the last non-missing value forwards to the missing
value
3) some intermediate value for a subject is missing (like example
data.frame above)
i.e. study 1, subject 1: X1 mis X2 X3.
Here I want to impute the missing value with the mean value between X1
and X2
The missing value is actually a subset of columns in the data frame,
ie. always the columns WT HT TEMP BSA (m[,16:19]) are missing
altogether.
I have written some R code that tries to do this, but it is incredibly
slow due to the many for-loops and the big dataset I have (and might
not even be completely correct yet).
QUESTION:
I would greatly appreciate it if somebody can be give me some
guidance/hints on what direction I should roughly think for coding the
above a little more efficient then the horribly inefficient code
pasted below.
Thank you in advance and best regards,
Coen
for(s in unique(m$Study)){ # for each study
for(i in unique(m$Subject[m$Study==s is.na(m$Wt)])){ # for each
subject with a missing value (if $Wt is missing, all 4 columns 16:19
are missing)
vals-which(m$Study==s m$Subject==i !is.na(m$Wt)) # values
with NO missing values
for(w in which(m$Study==s m$Subject==i is.na(m$Wt))){ # for
each value that is missing for subject i and study s
if(w min(vals) ){ # FIRST VALUES MISSING ? #
carry the backwards
m[w,][16:19]-m[min(vals),][16:19]
} else if(w max(vals) ) { # LAST VALUES MISSING#
carry forwards
m[w,][16:19]-m[max(vals),][16:19]
} else { # INTERMEDIATE VALUES MISSING #
impute missing with mean
maxV-min(vals[valsw])
minV-max(vals[valsw])
m[w,][16:19]- mean(m[c(maxV,minV),][16:19],na.rm=T)
}
}
}
}
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PLEASE do read the posting guide
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__
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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.
Re: [R] Odp: Still confused with lapply
Hi r-help-boun...@r-project.org napsal dne 19.11.2010 16:58:01: PtitBleu ptit_b...@yahoo.fr Hello Petr, Your solution works well with my example. But with the function I want to use (which calls another functions), I still have errors. I have to work on it again (but only on monday). Again thank you, Ptit Bleu. PS : I have access to all the functions but I don't want to modify all of them because I just need to correct an error I discovered in already-treated data (not sure I'm clear ...). In that case probably only person who can help you are yourself. Regards Petr -- View this message in context: http://r.789695.n4.nabble.com/Still-confused- with-lapply-tp3050414p3050573.html Sent from the R help mailing list archive at Nabble.com. __ 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] all extended ASCII characters exist for R console output?
In the plot window: plot(1, main = \u2591\u2592\u2593) On Fri, Nov 19, 2010 at 2:02 PM, Mark Heckmann mark.heckm...@gmx.de wrote: Hi, can the R console print all extended ASCII characters? I am especially interested in characters 176-178 from http://www.asciitable.com/ bottom table. As far as I know the character mapping in R is somewhat different (octal). So as I am not familiar with these things I am not sure if it exists. TIA Mark Mark Heckmann Dipl. Wirt.-Ing. cand. Psych. Celler Straße 27 28205 Bremen Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com [[alternative HTML version deleted]] __ 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ 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] Job scheduling in R
http://hudson-ci.org/ give hudson a try. It's incredibly easy to set up, and handles job dependencies and notifications for job failures. Its suggested use case is for automated software builds, but it fits the role of scheduled jobs (and interjob dependencies) very well. -Whit On Fri, Nov 19, 2010 at 10:09 AM, amit jain budd...@indiatimes.com wrote: Hi All, Can anyone point to any package/resouce to schedule a job in R which runs a .R file at a specified time ? I couldn't find anything useful in R Reference manual or RSiteSearch. I am sure its there but i am unable to locate. Thanks for your help. Puneet __ 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.
[R] Set colour in tcl variable
Hello all,
using package tcltk this is my problem:
I want to set a colour of a tclVar().
I have a tklabel (fixed in position) which should display two variables
occasionally.
If a constraint is fulfilled, the tklabel should display
correct-tclVar('correct') in green, otherwise it should display
wrong-tclVar('wrong') in red!
To display the variables is no problem, but getting colour into them.
Up to now for me it was only possible to set the colour of the whole label.
Any advice?
Thanks!
Immanuel Seeger
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Re: [R] all extended ASCII characters exist for R console output?
is it also possible on the console? that is what i am actually interested in? Thanks in advance! Mark Am 19.11.2010 um 17:24 schrieb Henrique Dallazuanna: In the plot window: plot(1, main = \u2591\u2592\u2593) On Fri, Nov 19, 2010 at 2:02 PM, Mark Heckmann mark.heckm...@gmx.de wrote: Hi, can the R console print all extended ASCII characters? I am especially interested in characters 176-178 from http://www.asciitable.com/ bottom table. As far as I know the character mapping in R is somewhat different (octal). So as I am not familiar with these things I am not sure if it exists. TIA Mark Mark Heckmann Dipl. Wirt.-Ing. cand. Psych. Celler Straße 27 28205 Bremen Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com [[alternative HTML version deleted]] __ 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O Mark Heckmann Dipl. Wirt.-Ing. cand. Psych. Celler Straße 27 28205 Bremen Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com [[alternative HTML version deleted]] __ 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] all extended ASCII characters exist for R console output?
just found it out. to get an overview: for (i in 2590:3000) cat(eval(parse(text=paste(\\\u, i, \, sep= Thanks, Mark Am 19.11.2010 um 17:24 schrieb Henrique Dallazuanna: In the plot window: plot(1, main = \u2591\u2592\u2593) On Fri, Nov 19, 2010 at 2:02 PM, Mark Heckmann mark.heckm...@gmx.de wrote: Hi, can the R console print all extended ASCII characters? I am especially interested in characters 176-178 from http://www.asciitable.com/ bottom table. As far as I know the character mapping in R is somewhat different (octal). So as I am not familiar with these things I am not sure if it exists. TIA Mark Mark Heckmann Dipl. Wirt.-Ing. cand. Psych. Celler Straße 27 28205 Bremen Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com [[alternative HTML version deleted]] __ 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O Mark Heckmann Dipl. Wirt.-Ing. cand. Psych. Celler Straße 27 28205 Bremen Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com [[alternative HTML version deleted]] __ 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] all extended ASCII characters exist for R console output?
The glyphs displayed depend on the terminal you are using, which may be operating-system dependent. Beware of assuming that other people will see the same things you do in their consoles. Mark Heckmann mark.heckm...@gmx.de wrote: just found it out. to get an overview: for (i in 2590:3000) cat(eval(parse(text=paste(\\\u, i, \, sep= Thanks, Mark Am 19.11.2010 um 17:24 schrieb Henrique Dallazuanna: In the plot window: plot(1, main = \u2591\u2592\u2593) On Fri, Nov 19, 2010 at 2:02 PM, Mark Heckmann mark.heckm...@gmx.de wrote: Hi, can the R console print all extended ASCII characters? I am especially interested in characters 176-178 from http://www.asciitable.com/ bottom table. As far as I know the character mapping in R is somewhat different (octal). So as I am not familiar with these things I am not sure if it exists. TIA Mark ��� Mark Heckmann Dipl. Wirt.-Ing. cand. Psych. Celler Stra�e 27 28205 Bremen Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com [[alternative HTML version deleted]] __ 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. -- Henrique Dallazuanna Curitiba-Paran�-Brasil 25� 25' 40 S 49� 16' 22 O ��� Mark Heckmann Dipl. Wirt.-Ing. cand. Psych. Celler Stra�e 27 28205 Bremen Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com [[alternative HTML version deleted]] __ 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. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. __ 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] predict() an rpart() model: how to ignore missing levels in a factor
many thanks - that's perfect, excluding records on a rep-by-rep basis is what I was just hoping for but I probably didn't explain myself that well! James -- View this message in context: http://r.789695.n4.nabble.com/predict-an-rpart-model-how-to-ignore-missing-levels-in-a-factor-tp3049218p3050670.html Sent from the R help mailing list archive at Nabble.com. __ 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] all extended ASCII characters exist for R console output?
On Nov 19, 2010, at 11:45 AM, Jeff Newmiller wrote: The glyphs displayed depend on the terminal you are using, which may be operating-system dependent. Beware of assuming that other people will see the same things you do in their consoles. On a Mac this: cat(\u2591,\u2592,\u2593) ░ ▒ ▓ Prints three rectangles of varying size and density. This appears somewhat similar to what I see im my browser except for the noticeable variation in size. -- David Mark Heckmann mark.heckm...@gmx.de wrote: just found it out. to get an overview: for (i in 2590:3000) cat(eval(parse(text=paste(\\\u, i, \, sep= Thanks, Mark Am 19.11.2010 um 17:24 schrieb Henrique Dallazuanna: In the plot window: plot(1, main = \u2591\u2592\u2593) On Fri, Nov 19, 2010 at 2:02 PM, Mark Heckmann mark.heckm...@gmx.de wrote: Hi, can the R console print all extended ASCII characters? I am especially interested in characters 176-178 from http://www.asciitable.com/ bottom table. As far as I know the character mapping in R is somewhat different (octal). So as I am not familiar with these things I am not sure if it exists. TIA Mark � � � � � � � � � � � � � � � � � �� Mark Heckmann Dipl. Wirt.-Ing. cand. Psych. Celler Stra�e 27 28205 Bremen Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com [[alternative HTML version deleted]] __ 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. -- Henrique Dallazuanna Curitiba-Paran�-Brasil 25� 25' 40 S 49� 16' 22 O � � � � � � � � � � � � � � � � ��� Mark Heckmann Dipl. Wirt.-Ing. cand. Psych. Celler Stra�e 27 28205 Bremen Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com [[alternative HTML version deleted]] __ 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. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. __ 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, MD West Hartford, CT __ 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] calculating martingale residual on new data using predict.coxph
Hi list, I was trying to use predict.coxph to calculate martingale residuals on a test data, however, as pointed out before http://tolstoy.newcastle.edu.au/R/e4/help/08/06/13508.html predict(mycox1, newdata, type=expected) is not implemented yet. Dieter suggested to use 'cph' and 'predict.Design', but from my reading so far, I'm not sure they can do that. Do you other ways to calculate martingale residuals on a new data? Thank you very much! ...Tao __ 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] how do I build panel data/longitudinal data models with AR terms using the plm package or any other package
Hi Giovanni, Thanks a lot for your input. I will explore using 'nlme' and 'lme4'. I had read your paper early on and was hoping, for reasons outlined in your paper regarding the differences in approaches and jargon between statisticians and econometricians ..., I could do what I needed with the 'plm' package. When you do get around to adding this capability to your package, let me know if there is any way I can help, such as testing the functionality out with data I work with, QA'ing, ... Regards, Jude Ryan MarketShare Partners 1270 Avenue of the Americas, Suite # 2702 New York, NY 10020 http://www.marketsharepartners.com Work: (646)-745-9916 ext: 222 Cell: (973)-943-2029 From: Millo Giovanni [mailto:giovanni_mi...@generali.com] Sent: Friday, November 19, 2010 1:22 AM To: Jude Ryan; R-help@r-project.org Cc: yves.croiss...@univ-reunion.fr Subject: R: how do I build panel data/longitudinal data models with AR terms using the plm package or any other package Hello Jude. Please find my remarks below, with '##' Da: Jude Ryan [mailto:jr...@marketsharepartners.com] Inviato: giovedì 18 novembre 2010 23:52 A: R-help@r-project.org Cc: yves.croiss...@univ-reunion.fr; Millo Giovanni Oggetto: how do I build panel data/longitudinal data models with AR terms using the plm package or any other package Hi All, I am doing econometric modeling of panel data (fixed effects). We currently use Eviews to do this, but I have discovered a bug in Eviews 7 and am exploring the use of R to build panel data models / longitudinal data models. I looked at the plm package but do not see how I can incorporate AR terms in the model using the plm package. ## Two possible meanings here: either you want autoregressive y or autoregressive errors 1) y = rho1*y(-1) + rho2*y(-2) + Xb + e or 2) y = Xb + u, u = rho1*u(-1) + rho2*u(-2) 1) is easy: just use lags, like fm - y ~ lag(y) + lag(y,2) + x but be aware of the Nickell bias: your estimator needs T-asymptotics. I have an Eviews model with two AR terms, AR(1) and AR(2), ## ...then, chances are you want 2) ! all my other remarks below apply to this second case (while 1) would fail for lack of strict endogeneity) and I am trying to replicate that model using R (and SAS too, if possible) as the fitted values in Eviews for panel data (fixed effects) appear to be wrong. In Eviews I tried a second approach and explicitly coded the fixed effects as dummy variables but the standard errors I get are very different from using the panel data options in Eviews, and thus the final model selected could be very different based on these two approaches. Can I incorporate AR terms in a panel data model using the plm package, and if so, how? ## As of now, no. We plan to add feasible AR(1) à la Baltagi, but it won't be tomorrow. This is also because --- Also, are there any other packages like nlme, lme4, .. that will let me build panel data models / longitudinal data models with AR terms? ## Yes. You can try 'nlme' and its newer sibling 'lme4'. I'm sure it can do random effects + AR(1), and sure you can put in the FEs as dummies; there are probably more elegant solutions but I'm not that familiar with it myself. For an introduction from the econometrician's viewpoint, see here http://www.jstatsoft.org/v27/i02 Ch. 7 Do any of these packages let you build panel data models / longitudinal data models specifying both AR and MA terms? Looking at the ACF and PCAF it seems that some of the error processes are best/more compactly represented by a combination of AR and MA terms, but unfortunately Eviews only lets you use AR terms for panel data and getting rid of the cross-sections in the panel data and building ARIMA models, which let you specify both AR and MA terms for the error process, will mean building separate models for each cross-section. Besides, we do not have that much data to build time series models and panel data methods let us circumvent the limited data issue. ## The issue here is, of course, cross-sectional poolability. The ARMA process in the errors should be the same for each individual. I am confident that you may find something in 'nlme''s rich error covariance structures. If you do, another possibility to get rid of the FEs and use standard methods is using first-difference data (but of course this modifies the errors' covariance specification, and you should reparameterize it). It is my understanding (but I could be wrong) that some of the SAS procs, like HPMIXED, let you specify only one AR term for panel data so I am hoping there is some R package that will let me replicate what I can do in Eviews, and possibly even go beyond what Eviews can do by specifying both AR and MA terms. ## If you're comfortable with ML, you could as well try to write down the likelihood and optimize it. There are facilities in package 'maxLik'. Thanks in advance for your time, Jude Ryan MarketShare Partners 1270
Re: [R] calculating martingale residual on new data using predict.coxph
On Nov 19, 2010, at 12:32 PM, Shi, Tao wrote: Hi list, I was trying to use predict.coxph to calculate martingale residuals on a test data, however, as pointed out before What about resid(fit) ? It's my reading of Therneau Gramsch [and of help(coxph.object) ] that they consider those martingale residuals. http://tolstoy.newcastle.edu.au/R/e4/help/08/06/13508.html predict(mycox1, newdata, type=expected) is not implemented yet. Dieter suggested to use 'cph' and 'predict.Design', but from my reading so far, I'm not sure they can do that. Do you other ways to calculate martingale residuals on a new data? Thank you very much! ...Tao David Winsemius, MD West Hartford, CT __ 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] all extended ASCII characters exist for R console output?
Just to get the message through that some already tried, e.g. on Windows 7 with R (Rterm) you get: cat(\u2591,\u2592,\u2593) ¦ ¦ ¦ See it didn't even cut'n'paste the same visual symbols as I see in Rterm but I guess you cannot see that. Make sense? No? Point is, expect issues if you're running this outside your own system/on different setup. (This has nothing to do with R). /H On Fri, Nov 19, 2010 at 9:16 AM, David Winsemius dwinsem...@comcast.net wrote: On Nov 19, 2010, at 11:45 AM, Jeff Newmiller wrote: The glyphs displayed depend on the terminal you are using, which may be operating-system dependent. Beware of assuming that other people will see the same things you do in their consoles. On a Mac this: cat(\u2591,\u2592,\u2593) ░ ▒ ▓ Prints three rectangles of varying size and density. This appears somewhat similar to what I see im my browser except for the noticeable variation in size. -- David Mark Heckmann mark.heckm...@gmx.de wrote: just found it out. to get an overview: for (i in 2590:3000) cat(eval(parse(text=paste(\\\u, i, \, sep= Thanks, Mark Am 19.11.2010 um 17:24 schrieb Henrique Dallazuanna: In the plot window: plot(1, main = \u2591\u2592\u2593) On Fri, Nov 19, 2010 at 2:02 PM, Mark Heckmann mark.heckm...@gmx.de wrote: Hi, can the R console print all extended ASCII characters? I am especially interested in characters 176-178 from http://www.asciitable.com/ bottom table. As far as I know the character mapping in R is somewhat different (octal). So as I am not familiar with these things I am not sure if it exists. TIA Mark ��� Mark Heckmann Dipl. Wirt.-Ing. cand. Psych. Celler Stra�e 27 28205 Bremen Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com [[alternative HTML version deleted]] __ 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. -- Henrique Dallazuanna Curitiba-Paran�-Brasil 25� 25' 40 S 49� 16' 22 O ��� Mark Heckmann Dipl. Wirt.-Ing. cand. Psych. Celler Stra�e 27 28205 Bremen Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com [[alternative HTML version deleted]] __ 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. --- Jeff Newmiller The . . Go Live... DCN:jdnew...@dcn.davis.ca.us Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries O.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. __ 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, MD West Hartford, CT __ 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] Set colour in tcl variable
Immanuel -
I don't believe you can associate a color with a TclVar,
but you can use tkconfigure to change the color of a label.
Does this little program help?
library(tcltk)
base = tktoplevel()
lab = tklabel(base,text='correct',foreground='green')
tkpack(lab)
red = function(...)tkconfigure(lab,foreground='red',text='wrong')
green = function(...)tkconfigure(lab,foreground='green',text='correct')
tkpack(tkbutton(base,text='Red',command=red))
tkpack(tkbutton(base,text='Green',command=green))
- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
spec...@stat.berkeley.edu
On Fri, 19 Nov 2010, Immanuel Seeger wrote:
Hello all,
using package tcltk this is my problem:
I want to set a colour of a tclVar().
I have a tklabel (fixed in position) which should display two variables
occasionally.
If a constraint is fulfilled, the tklabel should display
correct-tclVar('correct') in green, otherwise it should display
wrong-tclVar('wrong') in red!
To display the variables is no problem, but getting colour into them.
Up to now for me it was only possible to set the colour of the whole label.
Any advice?
Thanks!
Immanuel Seeger
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Re: [R] a rounding option for \Sexpr{}?
Dear all,
I don't like the current behaviour, but that change could break a lot of
existing documents. Since you can easily wrap your Sexpr arguments in a call to
whatever formatting function you want, why force all of those users to change
their documents?
I'm someone who would change a whole lot of \Sexpr{}s: I could get rid of all
those round() and format()s...
Currently almost don't use \Sexpr as I find the advantage of just having a tiny
little R expression in the text is lost if half a line of formatting code is
required. Particularly, as one has to be careful not to have a line break in the
\Sexpr{} as Sweave doesn't recognize those.
At the moment, I tend to use chunks with result=latex instead – which is not the
nicest thing to read in the source as it breaks the flow of a sentence quite
badly. But currently, it is much faster to type for me. On the other hand, maybe
it's just about time to write a template/snippet for \Sexpr{format (, digits =
3)}...
An alternative of course would be introducing a new kind of those commands. If
that's going to happen, I'd vote for something really short like the brew
syntax. But maybe I just didn't understand the advantage of \Sexpr{} and
\VignetteXXX{} looking like Latex commands although they aren't (particularly as
Latex source code highlighting without taking into account Sweave syntax is
anyways messed up by $ in the \Sexpr{}.
Also, very subjectively, I'd find a syntax with angle brackets more consistent
as the code chunks start with angle brackets anyways.
My 2 ct,
Claudia
--
Claudia Beleites
Dipartimento dei Materiali e delle Risorse Naturali
Università degli Studi di Trieste
Via Alfonso Valerio 6/a
I-34127 Trieste
phone: +39 0 40 5 58-37 68
email: cbelei...@units.it
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] RGoogleDocs stopped working
I second Harlan's call. Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Fri, Nov 19, 2010 at 5:00 PM, Harlan Harris har...@harris.name wrote: Any new thoughts on this? I really want to get this working again! Is there someone else that can help or somewhere else I should be asking? Thanks! -Harlan On Wed, Nov 17, 2010 at 10:16 AM, Harlan Harris har...@harris.name wrote: Following up again. I found on the forums for the Google Apps API this thread that seems to be about a similar issue: http://www.google.com/support/forum/p/apps-apis/thread?tid=1c22cb44eb5cbba6hl=ensearch_impression_id=ab161b010ecf8803%3A12c5a65ce83search_source=related_question It's using Java and is rather over my head, but it seems to suggest that something related to the content type might be wrong? Does this offer any suggestions on how to fix my use of RGoogleDocs? Thanks, -Harlan On Mon, Nov 15, 2010 at 12:16 PM, Harlan Harris har...@harris.name wrote: Thanks, Duncan. Finally getting a chance to follow up on this... I tried again, changing and resetting my password, and trying to specify my login and password manually in the getGoogleDocsConnection argument list. I also tried removing either or both of the service and error options. No luck in any case. I also tried a different Google account, also with no luck. I've also tried tweaking the URL being generated by the code, and in all cases, I get a 403: Forbidden error with content Error=BadAuthentication. I don't really know enough about how authentication is supposed to work to get much farther. Can you help? Should I try the Google API forum instead? -Harlan From: Duncan Temple Lang dun...@wald.ucdavis.edu To: r-help@r-project.org Date: Wed, 10 Nov 2010 10:33:47 -0800 Subject: Re: [R] RGoogleDocs stopped working Hi Harlan I just tried to connect to Google Docs and I had ostensibly the same problem. However, the password was actually different from what I had specified. After resetting it with GoogleDocs, the getGoogleDocsConnection() worked fine. So I don't doubt that the login and password are correct, but you might just try it again to ensure there are no typos. The other thing to look at is the values for Email and Passwd sent in the URL, i.e. the string in url in your debugging below. (Thanks for that by the way). If either has special characters, e.g. , it is imperative that they are escaped correctly, i.e. converted to %24. This should happen and nothing should have changed, but it is worth verifying. So things still seem to work for me. It is a data point, but not one that gives you much of a clue as to what is wrong on your machine. D. On Wed, Nov 10, 2010 at 10:36 AM, Harlan Harris har...@harris.name wrote: Hello, Some code using RGoogleDocs, which had been working smoothly since the summer, just stopped working. I know that it worked on November 3rd, but it doesn't work today. I've confirmed that the login and password still work when I log in manually. I've confirmed that the URL gives the same error when I paste it into Firefox. I don't know enough about this web service to figure out the problem myself, alas... Here's the error and other info (login/password omitted): ss.con - getGoogleDocsConnection(login=gd.login, password=gd.password, service='wise', error=FALSE) Error: Forbidden Enter a frame number, or 0 to exit 1: getGoogleDocsConnection(login = gd.login, password = gd.password, service = wise, error = FALSE) 2: getGoogleAuth(..., error = error) 3: getForm(https://www.google.com/accounts/ClientLogin;, accountType = HOSTED_OR_GOOGLE, Email = login, Passw 4: getURLContent(uri, .opts = .opts, .encoding = .encoding, binary = binary, curl = curl) 5: stop.if.HTTP.error(http.header) Selection: 4 Called from: eval(expr, envir, enclos) Browse[1] http.header Content-Type Cache-control Pragma text/plainno-cache, no-store no-cache ExpiresDate X-Content-Type-Options Mon, 01-Jan-1990 00:00:00 GMT Wed, 10 Nov 2010 15:24:39 GMT nosniff X-XSS-Protection Content-Length Server 1; mode=block 24 GSE status statusMessage 403 Forbidden\r\n Browse[1] url [1]
Re: [R] calculating martingale residual on new data using predict.coxph
Hi David, Thank you for the quick reply! resid(fit) only gives the residuals on the training data not on test data. ...Tao - Original Message From: David Winsemius dwinsem...@comcast.net To: Shi, Tao shida...@yahoo.com Cc: r-help@r-project.org; dieter.me...@menne-biomed.de; r_ting...@hotmail.com Sent: Fri, November 19, 2010 9:50:06 AM Subject: Re: [R] calculating martingale residual on new data using predict.coxph On Nov 19, 2010, at 12:32 PM, Shi, Tao wrote: Hi list, I was trying to use predict.coxph to calculate martingale residuals on a test data, however, as pointed out before What about resid(fit) ? It's my reading of Therneau Gramsch [and of help(coxph.object) ] that they consider those martingale residuals. http://tolstoy.newcastle.edu.au/R/e4/help/08/06/13508.html predict(mycox1, newdata, type=expected) is not implemented yet. Dieter suggested to use 'cph' and 'predict.Design', but from my reading so far, I'm not sure they can do that. Do you other ways to calculate martingale residuals on a new data? Thank you very much! ...Tao David Winsemius, MD West Hartford, CT __ 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] calculating martingale residual on new data using predict.coxph
On Nov 19, 2010, at 12:50 PM, David Winsemius wrote: On Nov 19, 2010, at 12:32 PM, Shi, Tao wrote: Hi list, I was trying to use predict.coxph to calculate martingale residuals on a test data, however, as pointed out before What about resid(fit) ? It's my reading of Therneau Gramsch [and of help(coxph.object) ] that they consider those martingale residuals. The manner in which I _thought_ this would work was to insert some dummy cases into the original data and then to get residuals by weighting the cases appropriately. That doesn't seem to be as successful as I imagined: test1 - list(time=c(4,3,1,1,2,2,3,3), weights=c(rep(1,7), 0), + status=c(1,1,1,0,1,1,0,1), + x=c(0,2,1,1,1,0,0,1), + sex=c(0,0,0,0,1,1,1,1)) coxph(Surv(time, status) ~ x , test1, weights=weights)$weights Error in fitter(X, Y, strats, offset, init, control, weights = weights, : Invalid weights, must be 0 # OK then make it a small number test1 - list(time=c(4,3,1,1,2,2,3,3), weights=c(rep(1,7), 0.01), + status=c(1,1,1,0,1,1,0,1), + x=c(0,2,1,1,1,0,0,1), + sex=c(0,0,0,0,1,1,1,1)) print(resid( coxph(Surv(time, status) ~ x , test1,weights=weights) ) ,digits=3) 1 2 3 4 5 6 7 8 -0.6410 -0.5889 0.8456 -0.1544 0.4862 0.6931 -0.6410 0.0509 Now take out constructed case and weights test1 - list(time=c(4,3,1,1,2,2,3), + status=c(1,1,1,0,1,1,0), + x=c(0,2,1,1,1,0,0), + sex=c(0,0,0,0,1,1,1)) print(resid( coxph(Surv(time, status) ~ x , test1) ) ,digits=3) 1 2 3 4 5 6 7 -0.632 -0.589 0.846 -0.154 0.486 0.676 -0.632 Expecting approximately the same residuals for first 7 cases but not really getting it. There must be something about weights in coxph that I don't understand, unless a one-hundreth of a case gets up indexed inside the machinery of coxph? Still think that inserting a single constructed case into a real dataset of sufficient size ought to be able to yield some sort of estimate, and only be a minor perturbation, although I must admit I'm having trouble figuring out ... why are we attempting such a maneuver? The notion of residuals around constructed cases makes me statistically suspicious, although I suppose that is just some sort of cumulative excess/deficit death fraction. http://tolstoy.newcastle.edu.au/R/e4/help/08/06/13508.html predict(mycox1, newdata, type=expected) is not implemented yet. Dieter suggested to use 'cph' and 'predict.Design', but from my reading so far, I'm not sure they can do that. Do you other ways to calculate martingale residuals on a new data? Thank you very much! ...Tao -- David Winsemius, MD West Hartford, CT __ 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] Calculating distance between longitude, latitude of 2 points
Also
spDists
spDistsN1 Euclidean or Great Circle distance between points
In the sp package.
(and in my personal opinion, the sp package would be a good place to start,
since its part of a group of packages I view as Rs core packages for working
with spatial data)
-Don
On 11/19/10 5:17 AM, David Winsemius dwinsem...@comcast.net wrote:
On Nov 19, 2010, at 4:50 AM, Lily_stats wrote:
Hi all,
I would like to know a way of calculating the distance between 2
points when
I already have the longitude and latitude of the points.
For example :
Point 1 : 52° 9'54.00N 4°25'8.40E
Point 2 : 52°27'46.80N 4°33'18.00E
Distance between point 1 and point in km
Is there any functions already available for this ?
Searching on: distance points longitude latitude
gdist {Imap} Geodesic distance (great circle distance) between points
Ellipsoidal.Distance {GEOmap} Ellipsoidal Distance
deg.dist {fossil} Haversine Distance Formula
distaz {RSEIS} Distance and Azimuth from two points
distaz {GEOmap} Distance and Azimuth from two points (# one probably
borrowed from the other)
AlongGreat {RFOC} Get Points Along Great Circle
distAB {clim.pact} Distance between two points on Earth
Any help will be much appreciated!
Suggest you learn to search.
--
Don MacQueen
Environmental Protection Department
Lawrence Livermore National Laboratory
925 423-1062
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[R] Color Alaska in USA map
Hello: I have a problem when I tried to color the USA map with different colors. The following is my data (I only used the second column of data): alaska,1, 2 Hawaii, 0, 0 USA,5, 5 And here is my code: library(latticeExtra) library(mapproj) state-read.table(C:\\usaclass.txt,sep=,) state range-with(state,range(state[1:3,3])) range nbreaks=6 breaks-do.breaks(range,nbreaks) StateName-state[1:3,1] StateName mapplot(StateName~state[1:3,3],data=state,breaks=breaks, map=map(world, c(USA, Hawaii), fill=TRUE) ,scales=list(draw=FALSE), colramp = colorRampPalette(c(white, black)),xlab=NULL) After I run this code, the continental USA could be colored, but alaska is not colored. I have tried to write alaska as Alaska and USA:alaska. However, it does not work. Do you have any suggestion? Thanks! Sun __ 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] simple loop problemo (Geo brownian motion)
I would like to plot multiple random walks onto the same graph. My p
variable dictates how may random walks there will be.
par(mfrow=c(1,1))
p - 100
N - 1000
S0 - 10
mu - 0.03
sigma - 0.2
nu - mu-sigma^2/2
x - matrix(rep(0,(N+1)*p),nrow=(N+1))
y - matrix(rep(0,(N+1)*p),nrow=(N+1))
t- (c(0:N))/N
for (j in 1:p)
{
z - rnorm(N,0,1)
x[1,j] - 0
y[1,j] - S0
for (i in 1:N)
{
x[i+1,j] - (1/sqrt(N))*sum(z[1:i])
y[i+1,j] - y[1,j]*exp(nu*t[i+1]+sigma*x[i+1,j])
}
plot(t,y,type=l,xlab=time, ylab=Geometric Brownian motion)
}
Any help would be appreciated, thanks.
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[R] how to apply sample function to each row of a data frame?
this is a simple question, but I wasn't able to figure it out myself. here is the data frame: M P Q 1 2 3 4 5 6 7 8 9 M, P, Q each represent a variable I want to draw 2 random sample from each row separately to create a new data frame. how can I do it? thanks!! -- View this message in context: http://r.789695.n4.nabble.com/how-to-apply-sample-function-to-each-row-of-a-data-frame-tp3050787p3050787.html Sent from the R help mailing list archive at Nabble.com. __ 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] simple loop problemo (Geo brownian motion)
On 19/11/2010 1:09 PM, newbster wrote:
I would like to plot multiple random walks onto the same graph. My p
variable dictates how may random walks there will be.
par(mfrow=c(1,1))
p- 100
N- 1000
S0- 10
mu- 0.03
sigma- 0.2
nu- mu-sigma^2/2
x- matrix(rep(0,(N+1)*p),nrow=(N+1))
y- matrix(rep(0,(N+1)*p),nrow=(N+1))
t- (c(0:N))/N
for (j in 1:p)
{
z- rnorm(N,0,1)
x[1,j]- 0
y[1,j]- S0
for (i in 1:N)
{
x[i+1,j]- (1/sqrt(N))*sum(z[1:i])
y[i+1,j]- y[1,j]*exp(nu*t[i+1]+sigma*x[i+1,j])
}
plot(t,y,type=l,xlab=time, ylab=Geometric Brownian motion)
}
Any help would be appreciated, thanks.
You can use the matplot function to plot multiple columns of a matrix at
once. So with your code as above, leave out the call to plot(), then
matplot(t, y) would give you approximately what you're looking for
(though the colour and symbol choices need some work).
You can get rid of the inner loop by using cumsum() and vectorized
calculations; then it will be reasonably fast.
Another way to do this is to create the plot before the loop, then use
lines() to add lines to it within the loop. Then you need to guess the
scale ahead of time, or do a little experimentation.
Duncan Murdoch
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[R] question about constraint minimization
Hi, I am a beginner of R. There is a question about constraint minimization. A function, y=f(x1,x2,x3x12), needs to be minimized. There are 3 requirements for the minimization: (1) x2+x3+...+x12=1.5 (x1 is excluded); (2) x1=x3=x4; (3) x1, x3 and x5 are in the range of -1~0, respectively. The rest variables (x2, x4, x6, x7, , x12) are in the range of 0~1, respectively. The optim function is used. And part of my input is as follow, where xx1r represents the x12: xx1r=1.5-x[2]-x[1]-x[1]-x[3]-x[4]-x[5]-x[6]-x[7]-x[8]-x[9] start=rnorm(9) up=1:9/1:9*1 lo=1:9/1:9*-1 out=optim(start,f,lower=lo,upper=up,method=L-BFGS-B,hessian=TRUE, control=list(trace=6,maxit=1000)) There are two problems in this input. the up and lo only define a range of -1~1 for x1 to x11, which can not meet the requirement (3). In addition, there is not any constraint imposed on x12. I have no idea how to specify a matrix that can impose different constraints on individual variables in a function. Any suggestion is highly appreciated. Best, Hao -- View this message in context: http://r.789695.n4.nabble.com/question-about-constraint-minimization-tp3050880p3050880.html Sent from the R help mailing list archive at Nabble.com. __ 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] question about constraint minimization
Does ?constrOptim look as though it will handle your needs? -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 11/19/2010 02:51:46 PM: [image removed] [R] question about constraint minimization dhacade...@gmail.com to: r-help 11/19/2010 03:15 PM Sent by: r-help-boun...@r-project.org Hi, I am a beginner of R. There is a question about constraint minimization. A function, y=f(x1,x2,x3x12), needs to be minimized. There are 3 requirements for the minimization: (1) x2+x3+...+x12=1.5 (x1 is excluded); (2) x1=x3=x4; (3) x1, x3 and x5 are in the range of -1~0, respectively. The rest variables (x2, x4, x6, x7, , x12) are in the range of 0~1, respectively. The optim function is used. And part of my input is as follow, where xx1r represents the x12: xx1r=1.5-x[2]-x[1]-x[1]-x[3]-x[4]-x[5]-x[6]-x[7]-x[8]-x[9] start=rnorm(9) up=1:9/1:9*1 lo=1:9/1:9*-1 out=optim(start,f,lower=lo,upper=up,method=L-BFGS-B,hessian=TRUE, control=list(trace=6,maxit=1000)) There are two problems in this input. the up and lo only define a range of -1~1 for x1 to x11, which can not meet the requirement (3). In addition, there is not any constraint imposed on x12. I have no idea how to specify a matrix that can impose different constraints on individual variables in a function. Any suggestion is highly appreciated. Best, Hao -- View this message in context: http://r.789695.n4.nabble.com/ question-about-constraint-minimization-tp3050880p3050880.html Sent from the R help mailing list archive at Nabble.com. __ 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] how to apply sample function to each row of a data frame?
Hi wangwallace,
Here are two ways of doing it. Could you please be more specific?
# data set
X - matrix(1:9, ncol = 3, byrow = TRUE)
colnames(X) - c('M', 'P', 'Q')
X
# option 1 -- two samples per row
replicate(2, {
out - t(apply(X, 1, sample))
colnames(out) - colnames(X)
list(out)
})
# option 2 -- two samples of the whole data
replicate(2,{
X - X[sample(3),]
list(X)
})
HTH,
Jorge
On Fri, Nov 19, 2010 at 1:34 PM, wangwallace wrote:
this is a simple question, but I wasn't able to figure it out myself.
here is the data frame:
M P Q
1 2 3
4 5 6
7 8 9
M, P, Q each represent a variable
I want to draw 2 random sample from each row separately to create a new
data
frame. how can I do it?
thanks!!
--
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[R] RGoogleDocs stopped working
Harlan and Tal have had problems. I had lots too. I spent hours getting it to work. Terrible process to go through but RGoogleDocs is so useful that the time was worth it - I think! My problems were overcome when 1. I used the latest zip file by Duncan Temple Lang see below 2. I inserted an options line that loosened the ssl security - do not know if that was a good thing or not but it got it to work Duncan said: I have put an updated version of the source of the package with these changes. It is available from http://www.omegahat.org/RGoogleDocs/RGoogleDocs_0.4-1.tar.gz There is a binary for Windows in http://www.omegahat.org/RGoogleDocs/RGoogleDocs_0.4-1.zip Here is my script that works. Does yours look like this? library(RGoogleDocs) packageDescription(RGoogleDocs) ps -readline(prompt=get the password in ) options(RCurlOptions = list(capath = system.file(CurlSSL, cacert.pem, package = RCurl), ssl.verifypeer = FALSE)) sheets.con = getGoogleDocsConnection(getGoogleAuth(fjb...@gmail.com, ps, service =wise)) ts2=getWorksheets(OnCall,sheets.con) #OnCall is just the name of a spreadsheet names(ts2) y2005-sheetAsMatrix(ts2$y2005,header=TRUE, as.data.frame=TRUE, trim=TRUE) Finally, I am willing to offer you a TeamViewer session where we can take control of one another's computers and see if the problem is code or the installation. I warn you that I am neither a programmer nor a developer, just a very enthusiastic RGoogleDocs user who probably perseveres more than is good for him. Farrel Buchinsky [[alternative HTML version deleted]] __ 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] Integrating functions / vector arithmetic
Some remarks:
Why are you using assignments to indicate the return values of functions?
This is R idiom:
f-function(u){
f-0
for (j in 1:4){
f-f+coeff[j]*(zeta(j)(u))
}
f
}
If you only want the inner product of 2 vector, outer probably is an overkill.
g - function(u){
sum(coeff * zeta(1:4)(u))
}
should be enough.
And plot(g) does not work because g is not vectorized.
plot(Vectorize(g))
will work
On Nov 16, 2010, at 1:18 AM, Eduardo de Oliveira Horta wrote:
Hello,
I was trying to build some functions which I would like to integrate over an
interval using the function 'integrate' from the 'stats' package. As an
example, please consider the function
h(u)=sin(pi*u) + sqrt(2)*sin(pi*2*u) + sqrt(3)*sin(pi*3*u) + 2*sin(pi*4*u)
Two alternative ways to 'build' this function are as in f and g below:
coeff-sqrt(1:4)
zeta-function(i) {force(i); function(u){
zeta-sqrt(2)+sin(pi*i*u)
}}
f-function(u){
f-0
for (j in 1:4){
f-f+coeff[j]*(zeta(j)(u))
}
f-f
}
g-function(u){
g-crossprod(coeff,zeta(1:4)(u))
}
Obviously, f and g are equivalent, but in the actual code I am writing, g is
much faster. However, I can't seem to integrate (neither to plot) g. In
fact, these are the error messages I get:
print(f(.1))
[1] 4.443642
print(g(.1))
[,1]
[1,] 4.443642
Everything ok until here... but...
When using plot(), I get this:
plot(f) #plots, as expected.
plot(g)
Error in crossprod(coeff,zeta(1:4)(u)) : arguments not compatible
Besides that: Warning message:
In pi * i * u :
longer object length is not a multiple of shorter object length
When using integrate(), I get this:
integrate(f,0,1)
1.004172 with absolute error 2.5e-13
integrate(g,0,1)
Error in crossprod(coeff,zeta(1:4)(u)) : arguments not compatible
Besides that: Warning message:
In pi * i * u :
longer object length is not a multiple of shorter object length
I have already tried some simple 'solutions', for example to set
g-function(u){
vec1-drop(coeff)
vec2-drop(zeta(1:4)(u))
g-drop(crossprod(coeff,zeta(1:4)(u)))
}
as well as using the %*% operation, but these won't solve my problem.
Any suggestions would be welcome. Thanks in advance,
Eduardo Horta
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and provide commented, minimal, self-contained, reproducible code.
[R] ?summaryRprof running at 100% cpu for one hour ...
This is very strange. (Debian squeeze, R 2.12.0 compiled from source) I did some moderately large computation (including svd of a 560x50 matrix), running a few minutes, and R memory increasing to about 900MB on this 2 GB ram laptop. I had done Rprof(memory.profiling=TRUE) first. Then doing summaryRprof(). Then doing ?summaryRprof and then the computer running with one of two cores at 100% for more than an hour! Whats happening? (running R from within emacs-ess) Kjetil __ 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] memory profiling
I'm trying to configure Version 2.12.0 or R to do memory profiling. I've reconfigured the code: % ./compile --enable-memory-profiling=YES and verified that it's configured correctly by examining the output. I then rebuild R: % make Then I fire up R and run a script, using Rprof with the memory-profiling switch set to TRUE: Rprof(output, memory.profiling=TRUE); # a bunch of R code Rprof(NULL); When I examine the output, however, using either R CMD Rprof from the shell, or summaryRprof from within R, the output I see is identical to the output I got when I ran R BEFORE I recompiled with memory profiling enabled. Anyone see something that I'm missing? Thanks, Patrick [[alternative HTML version deleted]] __ 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] a rounding option for \Sexpr{}?
I will appreciate a lot if you do not mind add a new option like 'useFormat'. I suggested format() because I'm allergic to too many options. I must say it is not hard to define the formatting, but it is just tedious to do it for every single number because by default we have too many digits especially for decimals. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Fri, Nov 19, 2010 at 9:55 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 19/11/2010 10:38 AM, Dieter Menne wrote: Duncan Murdoch-2 wrote: On 19/11/2010 10:12 AM, Yihui Xie wrote: Maybe this should go to R-devel as a wishlist: val- format(eval(parse(text=cmd), envir=.GlobalEnv)) I don't like the current behaviour, but that change could break a lot of existing documents. Not necessarily. Add an Sweave option useFormat=FALSE to keep the old behavior. I think the default would have to be FALSE, so that old documents didn't suddenly change. But is it really so hard to define your own formatting? Duncan Murdoch __ 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.
[R] How to print graph1.png graph2.png graph3.png ... ?
Dear All, I want to print out graph1.png graph2.png graph3.png ... How can I print it out? Thank you, __ 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] how to apply sample function to each row of a data frame?
On Fri, Nov 19, 2010 at 10:34:26AM -0800, wangwallace wrote:
this is a simple question, but I wasn't able to figure it out myself.
here is the data frame:
M P Q
1 2 3
4 5 6
7 8 9
M, P, Q each represent a variable
I want to draw 2 random sample from each row separately to create a new data
frame. how can I do it?
I am not sure, what you exactly mean. Can you provide an example of
the expected output?
If you consider each row as a sample of size 3 and want to use the
function sample() or sample(, replace=TRUE) to create a new sample
of the same size as a row of a new table, then in addition to the
already posted solutions you can use
X - matrix(1:9, ncol = 3, byrow = TRUE)
j - rep(seq(nrow(X)), each=2)
Y - matrix(, ncol=ncol(X), nrow=length(j))
for (i in seq(nrow(Y))) {
Y[i, ] - sample(X[j[i], ]) # or add replace=TRUE
}
colnames(Y) - c(M, P, Q)
data.frame(Y)
M P Q
1 2 3 1
2 1 3 2
3 5 4 6
4 6 4 5
5 7 9 8
6 8 9 7
PS.
__
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[R] autocorrelation in count data
hello, I try to model traffic accidents with the following model: glm.nb(y~j+w+m+sf+b+ft,data=fr[]). the problem is that there exist autocorrelation in the data. one possibility is to model traffic accidents with inar(1)-models. has anyone an idea how to change this model in order to abtain an integer valued time series model? thanks nazli __ 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] How to print graph1.png graph2.png graph3.png ... ?
Perhaps this?
paste('graph', 1:10, '.png', sep = )
Please give us more context/details on what you are trying to do. I
will undoubtedly help us to help you. In this case, the posting guide is
your friend.
HTH,
Jorge
On Fri, Nov 19, 2010 at 3:57 PM, Soyeon Kim wrote:
Dear All,
I want to print out graph1.png graph2.png graph3.png ... How
can I print it out?
Thank you,
__
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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]]
__
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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.
Re: [R] How to print graph1.png graph2.png graph3.png ... ?
Yes. This is what I want to do. Thanks!
I've tried to paste function but I didn't know how to use
appropriately in this case.
Have a nice weekend.
On Fri, Nov 19, 2010 at 3:05 PM, Jorge Ivan Velez
jorgeivanve...@gmail.com wrote:
Perhaps this?
paste('graph', 1:10, '.png', sep = )
Please give us more context/details on what you are trying to do. I
will undoubtedly help us to help you. In this case, the posting guide is
your friend.
HTH,
Jorge
On Fri, Nov 19, 2010 at 3:57 PM, Soyeon Kim wrote:
Dear All,
I want to print out graph1.png graph2.png graph3.png ... How
can I print it out?
Thank you,
__
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] autocorrelation in count data
see http://onlinelibrary.wiley.com/doi/10./j.1467-9892.2010.00684.x/abstract kjetil On Fri, Nov 19, 2010 at 6:02 PM, sa...@hsu-hh.de wrote: hello, I try to model traffic accidents with the following model: glm.nb(y~j+w+m+sf+b+ft,data=fr[]). the problem is that there exist autocorrelation in the data. one possibility is to model traffic accidents with inar(1)-models. has anyone an idea how to change this model in order to abtain an integer valued time series model? thanks nazli __ 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.
[R] TukeyHSD error
All - I think I'm being dense, but for the life of me, I can't figure out why I get error message with the code below. I have data that looks like param level perc.surv asin.tran DO 3 0.6864407 0.9764544 DO 3 0.125 0.3613671 DO 3 0.8738739 1.2077299 DO 4 0.4615385 0.7468986 DO 4 0.5691057 0.8547258 DO 4 0.8504673 1.1737517 DO 6 0.5494505 0.8349297 DO 6 0.4938272 0.7792252 DO 6 0.1230769 0.3584500 DO 6 0.7209302 1.0142339 DO 6 0.2297297 0.4998584 DO 6 0.930 1.3030330 DO 6 0.4482759 0.7335813 DO 6 0.000 0.000 DO 6 0.6018519 0.8879679 and code aov.DO - aov(asin.tran~level) summary(aov.DO) TukeyHSD(aov.DO) When I run the final line, I get the following error message Error in TukeyHSD.aov(aov.DO) : no factors in the fitted model In addition: Warning message: In replications(paste(~, xx), data = mf) : non-factors ignored: level What am I missing? Thanks for your help - Steven Ranney steven.ran...@montana.edu __ 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] TukeyHSD error
Rescinded. Problem solved. I discovered that TukeyHSD doesn't like numeric factors; changing the level to a factor solved my problem. SR Steven H. Ranney steven.ran...@montana.edu __ 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.
