Dear list members,
In sem, std.coef() will give me standardized coefficients from a sem model.
But is there a trick so that path.diagram can use these coefficients rather
than unstandardized ones?
Thanks
Steve Powell
From: John Fox
Date: Wed 28 Feb 2007 - 14:37:22 GMT
Dear Tim,
See ?standardi
Dear all, I try to consider overdispersion in a lmer model. But using
family=quasibinomial rather than family=binomial seems to change the fit but
not the result of an anova test. In addition if we specify test="F" as it is
recomanded for glm using quasibinomial, the test remains a Chisq test. Are
The following link is an excellent reference which gives R code for making
different plots in R.
http://addictedtor.free.fr/graphiques/thumbs.php
Is it something like this you want:
http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=52
The code can be found to do this on the webp
In ltm (version 0.8-1) you may also check the following functions:
descript(), cronbach.alpha(), mult.choice()
I hope it helps.
Best,
Dimitris
ps, you may find more information about `ltm' as well as sample
analysis files at the Rwiki page:
http://wiki.r-project.org/rwiki/doku.php?id=packages
Hi!
I want to create a plot of a predicted term similar to the function term.plot()
in the gamlss package. I have tried several options, but I could not work it
out so far...
Thank you for your help!
Nikolaus
here is my example:
library(gamlss)
data(rent)
attach(rent)
# Estimating some model
Hello R users,
before asking my question I'd like to stress that I'm an (absolute)
beginner in using R, but enthused about the incredible possibilities of
it.
So I hope my questions are not too stupid.
Here's my problem:
I have a dataset with skewed distributions. In order to obtain approx
multi
Hello R users,
before asking my question I'd like to stress that I'm an (absolute)
beginner in using R, but enthused about the incredible possibilities of
it.
So I hope my questions are not too stupid.
Here's my problem:
I have a dataset with skewed distributions. In order to obtain approx
multi
Handling multiple files automatically is easy in R and has been answered
several times on this list: please pok up the archives as suggested in
the posting guide to this list which also asks you to use a sensible
subject line.
Additionally, there is a FAQ entry called "How can I save the result
Hi,
I am using glampath package for L1 regularized logistic regression. I got
the following error messege.
> model.fit <- glmpath(train.data[,1:20], train.data$RES, family=binomial)
Error in one %*% x : requires numeric matrix/vector arguments
where train.data is a 700X21 matrix and 21st colum
Tirthadeep wrote:
> Hi,
>
> I am using glampath package for L1 regularized logistic regression. I got
> the following error messege.
>
>
>> model.fit <- glmpath(train.data[,1:20], train.data$RES, family=binomial)
>>
> Error in one %*% x : requires numeric matrix/vector arguments
>
> where t
Dear all
I try to print 9 plots on a page, arranged as the code shows below.
nf <- layout(matrix(c(1,0,2,0,0,3,0,4,0,5,0,6,0,0,0,0,7,0,8,9), 10,2))
layout.show(nf)
but when I try to plot, an error message
Fehler in plot.new() : Grafikränder zu groß
appears
to verify p.e. with
plot(runif(10:1
Then what is the solution?
Duncan Murdoch-2 wrote:
>
> Tirthadeep wrote:
>> Hi,
>>
>> I am using glampath package for L1 regularized logistic regression. I got
>> the following error messege.
>>
>>
>>> model.fit <- glmpath(train.data[,1:20], train.data$RES, family=binomial)
>>>
>> Err
Dear All,
Folks at the West Bengal University of Technology has set up a mirror to
distribute R and associated packages. Here is the URL:
http://mirror.wbut.ac.in/CRAN
This will be helpful for R users in South Asia and the adjoining countries.
I have yet to see the site featured in the CRAN list
Dear Steve,
My intention was to provide this flexibility via the parameters argument to
path.diagram.sem(), but it isn't implemented. Here's a version that should
do what you want:
- snip
path.diagram.sem <- function (model, out.file, min.rank = NULL, max.rank =
Hi,
I am trying to run some simple tktcl code
## in a file called test.R
require(tcltk)
tt <- tktoplevel()
OK.but <- tkbutton(tt,text="OK",command=function()tkdestroy(tt))
tkgrid(OK.but)
tkfocus(tt)
Using a batch file with the command
Rterm < test.R > testOutput.Rout --slave
The GUI pops u
http://cran.r-project.org/mirror-howto.html
Arin Basu-3 wrote:
>
> Dear All,
>
> Folks at the West Bengal University of Technology has set up a mirror to
> distribute R and associated packages. Here is the URL:
>
> http://mirror.wbut.ac.in/CRAN
>
> This will be helpful for R users in South A
On 9/19/07, Karin Lagesen <[EMAIL PROTECTED]> wrote:
> "Gustaf Rydevik" <[EMAIL PROTECTED]> writes:
>
>
> > The second warning message tells you that:
> > 2: the condition has length > 1 and only the first element will be
> > used in: if (terminus > origin)
> >
> > You are comparing two vectors,
Hello,
I have a list of filenames extracted from a data-frame thus:
files <- main$file
e.g. file[[1]] returns
[1] Ca00Mn48_0.gout
4702 Levels: Ca00Mn48_0.gout Ca01Mn47_0.gout Ca01Mn47_1.gout
... Ca48Mn00_0.gout
I want to extract the substring that contains the two digits after
"Ca". This wor
Hi Samuel,
An easy solution is the following. Let the R script wait until a certain
variable (ok_to_quit) got changed.
Hope it helps,
Jonne.
## in a file called test.R
quit <- function() {
.Tcl("set ok_to_quit 1")
tkdestroy(tt)
}
require(tcltk)
tt <<- tktoplevel()
OK.but <- tkbutton(tt,text
it also works with vectors, e.g.
x <- c("Ca00Mn48_0.gout", "Ca01Mn47_0.gout", "Ca01Mn47_1.gout",
"Ca48Mn00_0.gout")
substr(x, 3, 4)
I hope it helps.
Best,
Dimitris
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapu
Jonne Zutt wrote:
> Hi Samuel,
>
> An easy solution is the following. Let the R script wait until a certain
> variable (ok_to_quit) got changed.
>
> Hope it helps,
> Jonne.
>
> ## in a file called test.R
> quit <- function() {
> .Tcl("set ok_to_quit 1")
> tkdestroy(tt)
> }
>
> require(tcltk)
>
Dear all
I try to print 9 plots on a page, arranged as the code shows below.
nf <- layout(matrix(c(1,0,2,0,0,3,0,4,0,5,0,6,0,0,0,0,7,0,8,9), 10,2))
layout.show(nf)
but when I try to plot, an error message
Fehler in plot.new() : Grafikränder zu groß
appears
to verify p.e. with
plot(runif(10:1
Fisher's "exact" test is for comparing two proportions, which is a completely
different problem than Cox regression, and so the test has no relevance to this
problem. It has, however, sparked a large literature of debate; already
alluded
to by many of the responses.
The tests in the coxph
Dear R-Users:
I am trying to find the robust (or sandwich) estimates of the standard error of
fixed effects parameter estimates using the package "lmer2". In model-1, I used
"robust=TRUE" on the other, in model-2, I used "robust=FALSE". Both models
giving me the same estimates. So my question i
Hi,
I'm new to R and there is something I'm missing about how it uses
memory. I'm doing a simple query (using RODBC package) and immediately
set the data.frame to null close the connection/channel and explicitly
call to the garbage collector (gc()) however when I look in the task
monitor I see bo
On 9/19/2007 7:46 AM, Tirthadeep wrote:
> Then what is the solution?
The same method you used for the other columns:
train.data[,21]
Duncan Murdoch
>
>
>
>
> Duncan Murdoch-2 wrote:
>>
>> Tirthadeep wrote:
>>> Hi,
>>>
>>> I am using glampath package for L1 regularized logistic regression.
Is train.data a *numeric* matrix?
Peter Ehlers
Tirthadeep wrote:
> Then what is the solution?
>
>
>
>
> Duncan Murdoch-2 wrote:
>> Tirthadeep wrote:
>>> Hi,
>>>
>>> I am using glampath package for L1 regularized logistic regression. I got
>>> the following error messege.
>>>
>>>
model
Sorry about this one being long, and I apologise beforehand if there
is something obvious here that I have missed. I am new to creating my
own functions in R, and I am uncertain of how they work.
I have a data set that I have read into a data frame:
> gctable[1:5,]
refseq geometry X60_origi
Hello all you helpful people out there!
I am stil R Beginner using R 2.5.1 on a Apple Power Book G4 with Mac
OS X 10.4.10 .
I have two tabels like this:
MalTabChi
X1 X4 X6 X8 X10 X14 X21 X24 X29 X38 X43 X50
X67 X76 X78 X80 X82 X84
Anth_cap 1 1 1 165
On Wed, 19 Sep 2007, Duncan Murdoch wrote:
> On 9/19/2007 7:46 AM, Tirthadeep wrote:
>> Then what is the solution?
>
> The same method you used for the other columns:
>
> train.data[,21]
However, the error message is about the first argument (x) and not NULL
for the second argument (and applying
I have a data set where I want the correlations between 2 variables
conditional on a students grade level.
This code works just fine.
by(tmp[,c('mtsc07', 'DCBASmathscoreSPRING')], tmp$Grade, cor,
use='complete', method='pearson')
However, this generates an error
by(tmp[,c('mtsc07', 'DCBASmathsc
Hi!
When I apply the lars (least-angle-regression) method to my data
(3655 features, only 355 data points, no I did not mistype), I
observe a strange behaviour:
1) The beta values tend to grow into real high values quite fast up
to a point where they overflow and get negative. The overflow
Doran, Harold wrote:
> I have a data set where I want the correlations between 2 variables
> conditional on a students grade level.
>
> This code works just fine.
>
> by(tmp[,c('mtsc07', 'DCBASmathscoreSPRING')], tmp$Grade, cor,
> use='complete', method='pearson')
>
> However, this generates an
I can't read what your error message, but on mine I get the error:
"Error in plot.new(): margins too large", which is happening because
the default margins do not have enough space. You can reduce the
margins with using par
par(mar=c(0,0,0,0))
Which will let plot.new() work. I hope this helps.
Abdus Sattar said the following on 9/19/2007 7:03 AM:
> Dear R-Users:
>
> I am trying to find the robust (or sandwich) estimates of the standard error
> of fixed effects parameter estimates using the package "lmer2". In model-1, I
> used "robust=TRUE" on the other, in model-2, I used "robust=FAL
Thanks, Chuck. Seems odd though, doesn't it? There must be something
with my data set. But, I don't have any clue what it might be since I
can compute pearson using by() and I can subset and actually compute
spearman using just cor()
> -Original Message-
> From: Chuck Cleland [mailto:[EMA
I still get an error
> tmp$Grade <- factor(tmp$Grade)
> lapply(split(tmp, f = tmp$Grade),
function(x){cor(x[,c("mtsc07","DCBASmathscoreSPRING")], use='complete',
+ method='spearman')})
Error in cor(x[, c("mtsc07", "DCBASmathscoreSPRING")], use = "complete",
:
'x' is empty
I noticed tmp
Folks,
I have a 3000 x 4 matrix (y), which I need to regress row-by-row against a
4-vector (x) to create a
matrix lm.y of intercepts and slopes. To illustrate:
y <- matrix(rnorm(12000), ncol = 4)
x <- c(1/12, 3/12, 6/12, 1)
system.time(lm.y <- t(apply(y, 1, function(z) lm(z ~ x)$coefficient)))
This has come up before and I'll again ask the question "why would you
want robust standard errors in lmer"? Traditional econometric thinking
suggests that there is model mispecification if OLS is used and there is
a violation to the assumption of independence. So, one may still get the
point estim
Hello
It seems like method="pearson" accept missing values, that is, none
complete cases, and only generate correlation coefficients of NA, while
using method="spearman" gives and error message. try e.g.
testdata <- cbind.data.frame(gr=rep(letters[1:4], each=5), aa=rnorm(20),
bb=rnorm(20))
te
Hi, Harold,
In cases like this I usually add some print info to the function. E.g.
tmp$Grade <- factor(tmp$Grade)
lapply(split(tmp, f = tmp$Grade),
function(x) {
z <- x[,c("mtsc07","DCBASmathscoreSPRING")]
print(levels(factor(z$Grade)))
print(summary(z))
Hi,
as I read, maximum likelihood is the better method for
estimating selection-biased models. But I also want to
predict from that model. Is there any predict method
for the selection function when using maximum
likelihood estimation in micEcon? I couldn't find any.
Many thanks,
Werner
__
[EMAIL PROTECTED] said the following on 9/19/2007 9:50 AM:
> Folks,
>
> I have a 3000 x 4 matrix (y), which I need to regress row-by-row against a
> 4-vector (x) to create a
> matrix lm.y of intercepts and slopes. To illustrate:
>
> y <- matrix(rnorm(12000), ncol = 4)
> x <- c(1/12, 3/12, 6/12,
[EMAIL PROTECTED] wrote:
> Folks,
>
> I have a 3000 x 4 matrix (y), which I need to regress row-by-row against a
> 4-vector (x) to create a
> matrix lm.y of intercepts and slopes. To illustrate:
>
> y <- matrix(rnorm(12000), ncol = 4)
> x <- c(1/12, 3/12, 6/12, 1)
>
> system.time(lm.y <- t(appl
On Wed, 19 Sep 2007, Doran, Harold wrote:
> This has come up before and I'll again ask the question "why would you
> want robust standard errors in lmer"?
And I'll again answer: using lmer() does not automatically guarantee correct
model specification, either for the correlation structure or for
> system.time( lm( t(y) ~ x ) )
user system elapsed
0.008 0.000 0.010
On Wed, 19 Sep 2007,
[EMAIL PROTECTED] wrote:
> Folks,
>
> I have a 3000 x 4 matrix (y), which I need to regress row-by-row against a
> 4-vector (x) to create a
> matrix lm.y of intercepts and slopes. To illust
I want to pass a predefined string ww ("fa*fb+fc") to function lme so
that I can run
> lme(y ~ fa*fb+fc, random = ~1|subj, model)
I've tried something like
> lme(y ~ paste(ww), random = ~1|subj, model)
and
> lme(y ~ sprintf(ww), random = ~1|subj, model)
but both give me the following
Hi Doran,
My interests to estimate fixed effects parameters in a mixed model (not the
random effects parameters) and, in addition, in the model there are some
nuisace parameters. For this estimation I am using pseudo-maximum likelihood
methods. First I am estimating nuisance parameters then us
lme(as.formula(paste("y~",ww)),random=~1|subj,model)
Gang Chen-3 wrote:
>
> I want to pass a predefined string ww ("fa*fb+fc") to function lme so
> that I can run
>
> > lme(y ~ fa*fb+fc, random = ~1|subj, model)
>
> There must be a simple way to do this. Any help?
>
> Thanks,
> Gang
>
Yes, as.formula is the magic tool! Thanks a lot...
Gang
On Sep 19, 2007, at 2:00 PM, Vladimir Eremeev wrote:
>
> lme(as.formula(paste("y~",ww)),random=~1|subj,model)
>
>
> Gang Chen-3 wrote:
>>
>> I want to pass a predefined string ww ("fa*fb+fc") to function lme so
>> that I can run
>>
>>> lme(
Using ann=F just tells R not to put anything in the margins, it does not reduce
the size of the margins. You need to reduce the margin size using par(mar=
...) with appropriate values. You can then shrink what goes in the margins
rather than not plotting it at all (though that is a good first
On 9/19/07, Gustaf Rydevik <[EMAIL PROTECTED]> wrote:
> On 9/19/07, Karin Lagesen <[EMAIL PROTECTED]> wrote:
> > "Gustaf Rydevik" <[EMAIL PROTECTED]> writes:
> >
> >
> > > The second warning message tells you that:
> > > 2: the condition has length > 1 and only the first element will be
> > > used
Hi,
I’m trying to get smooth curves connecting points in a plot using
"spline" but I don’t get what I whant.
Eg.:
x<-1:5
y <- c(0.31, 0.45, 0.84, 0.43, 0.25)
plot(x,y)
lines(spline(x,y))
Creates a valley between the first and second points, then peaks at 3rd,
and another valley between 4th and
On Wed, 19 Sep 2007, Greg Snow wrote:
> Using ann=F just tells R not to put anything in the margins, it does not
> reduce the size of the margins. You need to reduce the margin size
> using par(mar= ...) with appropriate values. You can then shrink what
> goes in the margins rather than not p
how about:
require(splines)
x<-1:5
y <- c(0.31, 0.45, 0.84, 0.43, 0.25)
yy <-predict(interpSpline(x, y))
plot(x, y)
lines(yy)
Katharine Mullen
mail: Department of Physics and Astronomy, Faculty of Sciences
Vrije Universiteit Amsterdam, de Boelelaan 1081
1081 HV Amsterdam, The Netherlands
ro
Gavin Simpson wrote:
> On Fri, 2007-09-14 at 11:24 +0100, Robin Hankin wrote:
>> Hi Gavin
>>
>> thanks for that. . . it does 99% of what I wanted.
>> I'd forgotten about the na.print argument.
>>
>> It's considerably nicer than my other solution
>> which converted to character, then jj[is.na(jj)] <
Try:
> lines(spline(x,y, method='n', n=250))
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Nestor Fernandez
> Sent: Wednesday,
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of
> [EMAIL PROTECTED]
> Sent: Wednesday, 19 September 2007 2:04 p.m.
> To: [EMAIL PROTECTED]
> Subject: [R] fontsize in mosaic plot lables
>
> Hi List,
>
> I am trying unsucessfully to modify the fontsize of lables in mosaic:
>
>
is there a straigthforward way to get the holidays for Toronto ?
like the function for NYSE e.g.
the timeDate class says that setting a finCenter will give the right
holidays, but how?
thank you very much.
stephen
__
R-help@r-project.org mailing list
I have been trying, unsuccessfully, to use identify() to (simply)
return a list of
the indices of points clicked on and overplot (with say a solid dot)
each clicked-on
point so that I can see where I've been. I.e. I don't want to see
the indices printed
on the screen; I just want the points
Steve Powell wrote:
> Thanks again Frank for quick reply.
> True,
>
> someobject=2
> Test=function(obj,labe)
>{
>label(obj)=labe
>#at this point add the line:
>obj
>}
> Test(someobject,"somelabel")
> #returns a label. But if you retype
> someobject
> #the label has gone. Th
Hi everyone
I need help with subseting a data set. In my dataset there is a
specific row that will either have a value or be blank. I would like to
subset (or split) the dataset into one dataset with the row that has the
value and another dataset that has just the blanks. Now the thing is
that t
I think the function you need is 'help.search'; try:
help.search("binomial")
and look for something obvious in the 'stats' package. A good deal quicker
and easier than posting to an internet forum!
Cheers, Mike.
cathelf wrote:
>
> Dear all,
>
> I am trying a find the value "p" in binomial.
On 19-Sep-07 23:04:57, Mike Meredith wrote:
>
>
> I think the function you need is 'help.search'; try:
>
> help.search("binomial")
>
> and look for something obvious in the 'stats' package.
> A good deal quicker and easier than posting to an internet forum!
>
> Cheers, Mike.
Well ...
help.
Thanks Patric,
mosaic{vdc} takes gpar parameters. So cex.axis does not work for
mosaic(Titanic, pop=FALSE,
labeling_args=list(rot_labels=c(bottom=90,top=90),cex.axis=0.5))
or
mosaic(Titanic, pop=FALSE,
labeling_args=list(rot_labels=c(bottom=90,top=90)),cex.axis=0.5)
However,
mosaic(Titanic, po
On 20/09/2007, at 11:04 AM, Mike Meredith wrote:
>
> I think the function you need is 'help.search'; try:
>
> help.search("binomial")
>
> and look for something obvious in the 'stats' package. A good deal
> quicker
> and easier than posting to an internet forum!
>
I don't think so. I
On 9/19/07, Karin Lagesen <[EMAIL PROTECTED]> wrote:
>
> Sorry about this one being long, and I apologise beforehand if there
> is something obvious here that I have missed. I am new to creating my
> own functions in R, and I am uncertain of how they work.
>
> I have a data set that I have read int
You can use 'split' to create a list of dataframes and then operate on them:
Day Month Year Time Hits Misses F.type
1 0101 1999 0600 120 80 0600
2 0101 1999 1015 300 10
3 0101 1999 1216 250 50 1216
4 0101 1999 1649 380 0
5 0101 1999 2132 1100
Sub uses POSIX-extended regular expressions. It searches for the
first argument, the pattern, and replaces it with the second argument
in the variable defined by the third argument. [[:digit:]] is a
match-any-digit operator; it matches the characters 0-9. The {#} is
the interval operator
Hi Gabor,
I am coming back to you about the method you described to me a month ago
to define the level order during a read.table call. I initially thought
that I would need to apply the 'unique' function on a single column of
my dataset, so I only used it after the read.table step (to make my l
What is the preferred method to view a pdf (not generated by Sweave so not a
vignette) in a package /doc ? Some options are openPDF(Biobase), and the
README and Help files.
Bill Morphet
ATK, Space Launch Systems
Postflight Evaluation Eng
[[alternative HTML version deleted]]
__
On Thu, 20 Sep 2007, Rolf Turner wrote:
>
> On 20/09/2007, at 11:04 AM, Mike Meredith wrote:
>
>>
>> I think the function you need is 'help.search'; try:
>>
>> help.search("binomial")
>>
>> and look for something obvious in the 'stats' package. A good deal
>> quicker
>> and easier than posting to
If you don't know ahead of time how many columns you have and
only that they are a mix of numeric and character (to be converted to
factor) then you can do this:
DF <- read.table(textConnection(Input), header = TRUE, as.is = TRUE)
f <- function(x) if (is.character(x)) factor(x, levels = unique(x))
This is a configuration/OS problem, but it's affecting my use of R ...
Whenever I try to open _any_ vignette (as far as I can tell)
from within R, I get "Could not get a file descriptor referring to the
console",
coming from /usr/bin/openvt, which is pointed to by /usr/bin/open,
which is cal
If you are interested in regular expressions you may also be
interested in a solution using the gsubfn package. Here x
is the input character string, re is Jeffrey's regular expression
and strapply applies the regular expression to x calling the function
which is represented in formula notation us
Rolf turner wrote:
>I have been trying, unsuccessfully, to use identify() to (simply)
>return a list of the indices of points clicked on and overplot (with
>say a solid dot) each clicked-on point so that I can see where I've
>been. I.e. I don't want to see the indices printed on the screen; I
Hi all,
I'd like to distribute an R package that compiles some (small) C functions
every time it's sourced. The relevant code in the top level R script is as
follows:
system("R CMD SHLIB Selma_extensions.c")
if (.Platform$OS.type=="windows") {
slash = '\\'
dyn.load("Selma_extensions.dll"
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> Sent: Thursday, 20 September 2007 11:38 a.m.
> To: Patrick Connolly; [EMAIL PROTECTED]
> Subject: RE: [R] fontsize in mosaic plot lables
>
> Thanks Patric,
>
> mosaic{vdc} takes gpar parameters. So cex.axis does not work for
OK, my mistake.
Or maybe:
> while(length(ind <- identify(x,y,n = 1, plot = F)))
> points(x[ind], y[ind], pch = 19)
(highlights each point as you select it, until you click _stop_)
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Crombie, Joe
Sent: Thursday, 20 Septembe
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