[R] iplots Java
I run R 2.5.1 on a Mac, and use JGR as the front-end. When I performed an update.packages(), I believe it unpdated a component of JGR. I then quit and tried to relaunch JGR. It wouldn't launch. Instead it opened a panel that says: Cannot find iplot Java classes. Please make sure that the latest iplots R package is correctly installed. I would appreeciate hearing of strategies for solving the problem. _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Artifacts in pdf() of image() (w/o comments)
Dear Friends,
Thanks for your input.
FYI: Preview doesn't show PDF aliasing in the image I produced if I
uncheck the Anti-alias text and line art box under the PDF tab in
Preferences. So I'm not yet ready to drop Preview from my toolbox.
MK
On Aug 13, 2007, at 12:02 AM, Mark Wardle wrote:
It may be worth outputting postscript and converting to PDF from
there. Although Preview can do this, it may be worth looking at
Ghostscript which *may* not have simila problems.
I have also had PDFs which have displayed well in Preview and open
source tools and have been garbled in Adobe Acrobat, so the problems
aren't limited to Preview.
Best wishes,
Mark
On 13/08/07, Duncan Murdoch [EMAIL PROTECTED] wrote:
Michael Kubovy wrote:
On Aug 12, 2007, at 6:24 AM, Duncan Murdoch wrote:
Michael Kubovy wrote:
Dear r-helpers,
In my previous message there were comments in the code that may
have made cutting and pasting awkward. Here it is w/o them.
I have two questions:
(1) The following produces a pdf with artifacts. How do I prevent
them?
What artifacts do you see? It looks like a smoothly varying field
when produced by R 2.5.1 and viewed in Acrobat Reader 6.0 on
Windows.
Duncan Murdoch
require(grDevices)
imSize - 200
lambda - 10
theta - 15
sigma - 40
x - 1:imSize
x0 - x / imSize -.5
freq = imSize/lambda
xf = x0 * freq * 2 * pi
f - function(x, y){r - -((x^2 + y^2)/(sigma ^2)); exp(r)}
z - outer(xf, xf, f)
f1 - function(x, y){cos(.1 * x)}
z1 - outer(xf, xf, f1)
pdf('gabor.pdf')
image(xf, xf, z * z1, col = gray(250:1000/1000),
xlab = '', ylab = '', bty = 'n', axes = FALSE, asp = 1)
dev.off()
I'm working on a Mac. You're right, Acrobat 6.05 renders the figure
nicely, but when it's included in a LaTeX-produced pdf or viewed
with
the Mac Preview program, a grid of fine white lines is superimposed
on the figure. So I believe that it's a matter of aliasing, which I
might be able to prevent by adjusting the parameters of the figures.
I just don't know enough to figure this out, and would appreciate
guidance.
I see the artifacts in Preview on a Mac too. So it looks to me
like a
Mac bug.
Preview is actually pretty poor at graphics display; see
http://www.geuz.org/pipermail/gl2ps/2007/000223.html.
My only suggestion is not to use Preview.
Duncan Murdoch
--
Dr. Mark Wardle
Clinical research fellow and specialist registrar, Neurology
Cardiff, UK
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] Artifacts in pdf() of image() (w/o comments)
But is it a bug? Can a program anti-alias text and line drawings and not bitmaps? On Aug 13, 2007, at 9:30 AM, Duncan Murdoch wrote: On 8/13/2007 11:07 AM, Michael Kubovy wrote: Dear Friends, Thanks for your input. FYI: Preview doesn't show PDF aliasing in the image I produced if I uncheck the Anti-alias text and line art box under the PDF tab in Preferences. So I'm not yet ready to drop Preview from my toolbox. An alternative to dropping Preview is to report the bug in it to Apple. Apple has an online bug reporting web page somewhere; I haven't found them as helpful as R-help, but your mileage may vary. Duncan Murdoch _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Artifacts in pdf() of image() (w/o comments)
Hi Duncan, I was trying to learn to remove the artifacts by setting the parameters of the image so that anti-aliasing wouldn't produce them (analogous to making sure that the screens of two halftone screen process images are in register before combining them so as to avoid Moiré patterns). So, I wasn't complaining; I was looking for instruction. Since the image was computed with R, it's reasonable for me to ask R experts to help me out of what I thought was caused by my ineptitude. (Regarding your question, If it wasn't a bug, why did it bother you so much?---there are many things that bother me that are not bugs.) Moreover, I'm not opposed to complaining to Apple, once I have been assured that I'm not reporting a bug where there's none. On Aug 13, 2007, at 9:56 AM, Duncan Murdoch wrote: On 8/13/2007 11:43 AM, Michael Kubovy wrote: But is it a bug? Can a program anti-alias text and line drawings and not bitmaps? Anti-aliasing is the removal of artifacts caused by displaying an image on a low-resolution bitmapped display. Introducing artifacts is a bug. If it wasn't a bug, why did it bother you so much? And why do you think it's reasonable to complain about it on R-help, but not to complain about it to Apple, who are clearly responsible for it? Duncan Murdoch On Aug 13, 2007, at 9:30 AM, Duncan Murdoch wrote: On 8/13/2007 11:07 AM, Michael Kubovy wrote: Dear Friends, Thanks for your input. FYI: Preview doesn't show PDF aliasing in the image I produced if I uncheck the Anti-alias text and line art box under the PDF tab in Preferences. So I'm not yet ready to drop Preview from my toolbox. An alternative to dropping Preview is to report the bug in it to Apple. Apple has an online bug reporting web page somewhere; I haven't found them as helpful as R-help, but your mileage may vary. Duncan Murdoch _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Artifacts in pdf() of image() (w/o comments)
On Aug 12, 2007, at 6:24 AM, Duncan Murdoch wrote:
Michael Kubovy wrote:
Dear r-helpers,
In my previous message there were comments in the code that may
have made cutting and pasting awkward. Here it is w/o them.
I have two questions:
(1) The following produces a pdf with artifacts. How do I prevent
them?
What artifacts do you see? It looks like a smoothly varying field
when produced by R 2.5.1 and viewed in Acrobat Reader 6.0 on Windows.
Duncan Murdoch
require(grDevices)
imSize - 200
lambda - 10
theta - 15
sigma - 40
x - 1:imSize
x0 - x / imSize -.5
freq = imSize/lambda
xf = x0 * freq * 2 * pi
f - function(x, y){r - -((x^2 + y^2)/(sigma ^2)); exp(r)}
z - outer(xf, xf, f)
f1 - function(x, y){cos(.1 * x)}
z1 - outer(xf, xf, f1)
pdf('gabor.pdf')
image(xf, xf, z * z1, col = gray(250:1000/1000),
xlab = '', ylab = '', bty = 'n', axes = FALSE, asp = 1)
dev.off()
I'm working on a Mac. You're right, Acrobat 6.05 renders the figure
nicely, but when it's included in a LaTeX-produced pdf or viewed with
the Mac Preview program, a grid of fine white lines is superimposed
on the figure. So I believe that it's a matter of aliasing, which I
might be able to prevent by adjusting the parameters of the figures.
I just don't know enough to figure this out, and would appreciate
guidance.
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] Artifacts in pdf() of image()
Dear r-helpers,
I have two questions:
(1) The following produces a pdf with artifacts. How do I prevent them?
require(grDevices)
imSize - 200
lambda - 10
theta - 15
sigma - 40
x - 1:imSize
x0 - x / imSize -.5
freq = imSize/lambda# compute frequency from
wavelength
xf = x0 * freq * 2 * pi # convert X to radians: 0 -
( 2*pi * frequency)
f - function(x, y){r - -((x^2 + y^2)/(sigma ^2)); exp(r)}
z - outer(xf, xf, f)
f1 - function(x, y){cos(.1 * x)}
z1 - outer(xf, xf, f1)
pdf('gabor.pdf')
image(xf, xf, z * z1, col = gray(250:1000/1000), xlab = '', ylab =
'', bty = 'n',
axes = FALSE, asp = 1)
dev.off()
(2) I would like the output to be clipped to a circle, i.e., anything
outside the circle tangent to the sides of the square should be
transparent. How can I do that?
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] Artifacts in pdf() of image() (w/o comments)
Dear r-helpers,
In my previous message there were comments in the code that may have
made cutting and pasting awkward. Here it is w/o them.
I have two questions:
(1) The following produces a pdf with artifacts. How do I prevent them?
require(grDevices)
imSize - 200
lambda - 10
theta - 15
sigma - 40
x - 1:imSize
x0 - x / imSize -.5
freq = imSize/lambda
xf = x0 * freq * 2 * pi
f - function(x, y){r - -((x^2 + y^2)/(sigma ^2)); exp(r)}
z - outer(xf, xf, f)
f1 - function(x, y){cos(.1 * x)}
z1 - outer(xf, xf, f1)
pdf('gabor.pdf')
image(xf, xf, z * z1, col = gray(250:1000/1000),
xlab = '', ylab = '', bty = 'n', axes = FALSE, asp = 1)
dev.off()
(2) I would like the output to be clipped to a circle, i.e., anything
outside the circle tangent to the sides of the square should be
transparent. How can I do that?
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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] Standard errors of the predicted values from a lme (or lmer)-object
On Jun 1, 2007, at 6:08 AM, Dieter Menne wrote: Fränzi Korner fraenzi.korner at oikostat.ch writes: how do I obtain standard errors of the predicted values from a lme (or lmer)-object? Not totally clear what you mean. intervals(lmeresult) gives the confidence intervals for the coefficients. Otherwise, you can do some calculations with residuals(lmeresult). Most useful for diagnostic purposes is plot (lmeresult). Perhaps ?estimable in the gmodels package _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] title line
On May 21, 2007, at 8:21 AM, elyakhlifi mustapha wrote:
I know how to do to write down the columns in a data frame but I
also wanna write down the lines .
Do you know how could I do this?
I'm not sure what you mean by write down the lines. If you mean
that you want to know what the row names are, then an answer is:
df - data.frame(x1 = rnorm(3), x2 = rnorm(3))
names(df) # just to show that I gave the columns names while defining df
rownames(df)
If you mean that you want to assign names to the rows, then
df - data.frame(rnorm(3), rnorm(3))
names(df) - c('y1', 'y2') # not required
rownames(df) - c('a', 'b', 'c')
In one commandt:
df - data.frame(x1 = rnorm(3), x2 = rnorm(3), row.names = c('a',
'b', 'c'))
More detailed:
df - data.frame(x1 = rnorm(3), x2 = rnorm(3), row.names = c('a',
'b', 'c'), check.rows = TRUE, check.names = TRUE)
More importantly you could have found all this out by typing ?data.frame
I have seen several posts from you that seem to be rather elementary
questions, sometimes not using the correct terminology ('write down'
and 'lines of a data frame' are not standard). Have you taken the
time to go through any of the many introductions to R available on line?
Also, you're not asking your questions well (this comment is not
about knowing English well):
You would have been better off asking:
I have a data frame
df - data.frame(x1 = rnorm(3), x2 = rnorm(3))
How do I ?
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] Selecting complementary colours
Hi All, Complementary colors will not insure legibility. If the text and the background are equiluminant, visibility will be severely impaired. On May 21, 2007, at 8:22 PM, John Fox wrote: Dear Achim, As I mentioned in my response to Deepayan's suggestion, I didn't specify the original problem clearly: The object is to get contrasting colours, so that when one is plotted over the other, the two will be readily distinguishable. Your suggestions don't do this for neutral colours: x - #88 y_hcl - as(hex2RGB(x), polarLUV) [EMAIL PROTECTED], H] - [EMAIL PROTECTED], H] + 180 hex(y_hcl) [1] #88 y_hsv - as(hex2RGB(x), HSV) [EMAIL PROTECTED], H] - [EMAIL PROTECTED], H] + 180 hex(y_hsv) [1] #88 Thank you for trying to help. John John Fox, Professor Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox -Original Message- From: Achim Zeileis [mailto:[EMAIL PROTECTED] Sent: Monday, May 21, 2007 7:07 PM To: John Fox Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Selecting complementary colours On Mon, 21 May 2007, John Fox wrote: Dear r-helpers, I wonder whether, given the #rrggbb representation of a colour, there is a simple way to select the complementary colour, also expressed as a #rrggbb string. Is the complementary color uniquely defined? My understanding is that you can take opposite colors on a color wheel, but there are of course various color wheels available. With colorspace you can experiment with this, e.g.: x - #81A9D0 y_hcl - as(hex2RGB(x), polarLUV) [EMAIL PROTECTED], H] - [EMAIL PROTECTED], H] + 180 y_hcl - hex(y_hcl) which is a bit more balanced than y_hsv - as(hex2RGB(x), HSV) [EMAIL PROTECTED], H] - [EMAIL PROTECTED], H] + 180 y_hsv - hex(y_hsv) hth, Z __ R-help@stat.math.ethz.ch 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. _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Separate x-axis ticks for panels in xyplot()?
Dear r-helpers,
In an xyplot I have
xyplot(y ~ x | c, groups = g,
scales = list(
x = list(
at = v1,
labels = c('A', 'B', 'C', 'D'),
rot = 45
)
)
)
g consists of two groups. How do I define a different set of x ticks
and labels for the second panel? I'm looking for something like
xyplot(y ~ x | c, groups = g,
scales = list(
x = list(ifelse(g == g1, {
at = v1,
labels = c('A', 'B', 'C', 'D'),
rot = 45},
{at = v2,
labels = c('E', 'F' 'G),
rot = 45}
)
)
)
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] Example of mcmcsamp() failing with lmer() output
Hi,
I would appreciate help with the following model
1=
gunload - read.table(hh('datasets/gunload.dat'), header = T)
gunload$method - factor(gunload$method, labels = c('new', 'old'))
gunload$physique - factor(gunload$group, labels = c('slight',
'average', 'heavy'))
gunload$team9 - factor(rep(1:9, each = 2))
@
This is a split plot design with randomly selected teams for each
physique, which was crossed with two methods.
Following the Oats example in chap. 1 of MEMSS, and adapting to lmer:
2=
require(lme4)
gl.lmer - lmer(rounds ~ method * physique + (1 | physique/team),
data = gunload)
mcmcsamp(gl.lmer)
@
lmer runs as expected, but mcmcsamp() gives:
Error: Leading minor of order 1 in downdated X'X is not positive
definite
Error in t(.Call(mer_MCMCsamp, object, saveb, n, trans, verbose,
deviance)) :
error in evaluating the argument 'x' in selecting a method for
function 't'
I tried:
3=
require(nlme)
gl.lme - lme(rounds ~ method * physique, random = ~1 | physique/
team, data = gunload)
@
which gave all the expected output except that two p-values were NaN.
Which aspect of the data is making the simulation fail, and is there
anything to be done about it?
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] xyplot() and controlling panel.polygon()
Hi Deepayan,
Thanks for your advice. This is moving along, however:
The following is drawing the same polygons in each panel. I'm trying
to get a different polygon (confidence band) for each group in each
panel. That's why I thought I would need to pass groups and
subscripts to the panel.groups
est - c(1:4, 3:6, 7, 9, 11, 13, 12, 15, 18, 21)
cond - rep(c('a','b'), each = 8)
grp - rep(c('I', 'II'), each = 4, 2)
x - rep(c(.5, .7, .9, 1.1), 4)
upper - est + 1
lower = est - 1
data - data.frame(est = est, x = x, cond = cond, grp = grp, upper =
upper, lower = lower)
my.panel.polygon - function(..., font, fontface)
{
panel.polygon(...)
}
xyplot(est ~ x | cond, group = grp, data = data, type = 'b',
panel = function(x, y, ...){
panel.superpose(c(x, rev(x)), c(upper, rev(lower)),
panel.groups = 'my.panel.polygon', default.units =
'native', ...)
panel.xyplot(x, y, ...)
}
)
It's pretty clear that panel.superpose is not getting its x and y
values after they are split by group and panel.
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] xyplot() and controlling panel.polygon()
Hi Deepayan,
Your solution works, anf the polygon are drawn where I wanted them to
go. I thought that I could figure out how to gain control over the
colors of the four ensuing polygons (I'm trying to get two lighter
shades of the lines).
I've tried, for example, to see if I could control the color of the
polyon outline, by adding border = 'red' to panel.polygon. That
didn't work. Does it work only in lpolygon()?
I often can figure things out on my own, but obviously there's
something fundamental that I'm not getting about inheritance and
passing in these sorts of objects. I've been trying to get it from
the help pages and from Murrell's book, but neither offers enough of
a cookbook for me to figure these things out. Is there something I
should have read?
Thanks,
MIchael
On Apr 27, 2007, at 2:25 PM, Deepayan Sarkar wrote:
On 4/27/07, Michael Kubovy [EMAIL PROTECTED] wrote:
Hi Deepayan,
Thanks for your advice. This is moving along, however:
The following is drawing the same polygons in each panel. I'm trying
to get a different polygon (confidence band) for each group in each
panel. That's why I thought I would need to pass groups and
subscripts to the panel.groups
est - c(1:4, 3:6, 7, 9, 11, 13, 12, 15, 18, 21)
cond - rep(c('a','b'), each = 8)
grp - rep(c('I', 'II'), each = 4, 2)
x - rep(c(.5, .7, .9, 1.1), 4)
upper - est + 1
lower = est - 1
data - data.frame(est = est, x = x, cond = cond, grp = grp, upper =
upper, lower = lower)
my.panel.polygon - function(..., font, fontface)
{
panel.polygon(...)
}
xyplot(est ~ x | cond, group = grp, data = data, type = 'b',
panel = function(x, y, ...){
panel.superpose(c(x, rev(x)), c(upper, rev(lower)),
panel.groups = 'my.panel.polygon', default.units =
'native', ...)
panel.xyplot(x, y, ...)
}
)
It's pretty clear that panel.superpose is not getting its x and y
values after they are split by group and panel.
You are not even trying to do that; you have
panel.superpose(c(x, rev(x)), c(upper, rev(lower)), ...
so your x=c(x, rev(x)) is not the same length as x (and
subscripts), and your
y = c(upper, rev(lower)) is not the same length as anything. Also,
your upper and lower are being taken from the global env, not data
(they happen to be the same, but since your data has them, I assume
you want to use them).
Perhaps you are looking for something like this:
panel.bands -
function(x, y, upper, lower,
subscripts, ..., font, fontface)
{
upper - upper[subscripts]
lower - lower[subscripts]
panel.polygon(c(x, rev(x)), c(upper, rev(lower)), ...)
}
xyplot(est ~ x | cond, group = grp, data = data, type = 'b',
upper = data$upper,
lower = data$lower,
panel = function(x, y, ...){
panel.superpose(x, y, panel.groups = 'panel.bands', ...)
panel.xyplot(x, y, ...)
})
-Deepayan
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] xyplot() and controlling panel.polygon()
I can't thank you enough! (I am also grateful to Sundar Dorai-Raj and
Bert Gunter for their initial responses.)
On Apr 27, 2007, at 4:14 PM, Deepayan Sarkar wrote:
On 4/27/07, Michael Kubovy [EMAIL PROTECTED] wrote:
Hi Deepayan,
Your solution works, anf the polygon are drawn where I wanted them to
go. I thought that I could figure out how to gain control over the
colors of the four ensuing polygons (I'm trying to get two lighter
shades of the lines).
I've tried, for example, to see if I could control the color of the
polyon outline, by adding border = 'red' to panel.polygon. That
didn't work. Does it work only in lpolygon()?
No. This is a bug, and the border color can currently only be black or
transparent (but it's easy to find and fix the bug; lpolygon is very
short, so just write a replacement).
However, panel.superpose recognizes and splits certain graphical
parameters; border is not among them, but fill is. So you could do:
my.panel.bands -
function(x, y, upper, lower,
fill, col,
subscripts, ..., font, fontface)
{
upper - upper[subscripts]
lower - lower[subscripts]
panel.polygon(c(x, rev(x)), c(upper, rev(lower)),
col = fill, border = FALSE,
...)
}
xyplot(est ~ x | cond, group = grp, data = data, type = 'b',
col = c(#0080ff, #ff00ff),
fill = c(#bbddff, #ffbbff),
upper = data$upper,
lower = data$lower,
panel = function(x, y, ...){
panel.superpose(x, y, panel.groups = 'my.panel.bands', ...)
panel.xyplot(x, y, ...)
})
I often can figure things out on my own, but obviously there's
something fundamental that I'm not getting about inheritance and
passing in these sorts of objects. I've been trying to get it from
the help pages and from Murrell's book, but neither offers enough of
a cookbook for me to figure these things out. Is there something I
should have read?
The concepts are all there in the help page (but it's often difficult
to put them together). The main points are:
(1) unrecognized arguments get passed on to the panel function as is
(2) subscripts give indices of x, y, etc in the original data frame
(the implication being that if you have another column from the
original data frame, such as upper and lower in your example, indexing
by subscripts will give you the matching subset). Other than that, the
panel functions have to do their own work (and what they do should
ideally be documented); nothing is enforced, so nothing is guaranteed.
This sort of thing doesn't get used often enough for examples to be
easily found. The following demo in lattice might be helpful.
file.show(system.file(demo/intervals.R, package = lattice))
-Deepayan
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] xyplot() and controlling panel.polygon()
Dear R-helpers,
How do I tell panel.polygon what greoup and panel it applies to whithin
xyplot(y ~ x | c, groups = g
panel = function(x, y, groups, ...){
panel.polygon(x = xpol[c, g], y = ypol[c, g], default.units
= 'native')
panel.xYplot(x, y, groups, ...)
llines(x = c(1, 6), y = c(-24.28, 35.941667), lwd = 2, lty
=
3, col = 4)
}
x[c, g] and y[c, g] describe the polygon I want plotted for group g
in panel c.
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] xyplot() and controlling panel.polygon()
Hi Sundar,
Thanks for taking a look at this
On Apr 26, 2007, at 1:05 PM, Sundar Dorai-Raj wrote:
Michael Kubovy said the following on 4/26/2007 7:20 AM:
Dear R-helpers,
How do I tell panel.polygon what greoup and panel it applies to
whithin
xyplot(y ~ x | c, groups = g
panel = function(x, y, groups, ...){
panel.polygon(x = xpol[c, g], y = ypol[c, g],
default.units = 'native')
panel.xYplot(x, y, groups, ...)
llines(x = c(1, 6), y = c(-24.28, 35.941667), lwd = 2, lty
= 3, col = 4)
}
x[c, g] and y[c, g] describe the polygon I want plotted for group
g in panel c.
_
I believe you can just do:
panel = function(x, y, subscripts, groups, ...) {
## note addition of subscripts to arguments
panel.superpose(xpol, ypol, subscripts, groups,
panel.groups = panel.polygon,
default.units = native, ...)
panel.xYplot(x, y, subscripts, groups, ...)
llines(x = c(1, 6), y = c(-24.28, 35.941667),
lwd = 2, lty = 3, col = 4)
}
Also, it would be easier to provide tested answers if you gave a
reproducible example.
Here is a reproducible example in which I tried (unsuccesfully) to
apply your suggestion:
est - c(1:4, 3:6, 7, 9, 11, 13, 12, 15, 18, 21)
cond - rep(c('a','b'), each = 8)
grp - rep(c('I', 'II'), each = 4, 2)
x - rep(c(.5, .7, .9, 1.1), 4)
upper - est + 1
lower = est - 1
data - data.frame(est = est, x = x, cond = cond, grp = grp, upper =
upper, lower = lower)
xyplot(est ~ x | cond, group = grp, data = data, type = 'b',
panel = function(x, y, subscripts, groups, ...){
panel.superpose(c(x, rev(x)), c(upper, rev(lower)),
subscripts, groups,
panel.groups = 'panel.polygon', default.units =
'native', ...)
panel.xyplot(x, y, subscripts, groups, ...)
}
)
# returns: Error in validGP(list(...)) : Must specify only one of
'font' and 'fontface', which is incomprehensible to me.
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] xyplot() and controlling panel.polygon()
Hi Sundar,
On Apr 26, 2007, at 10:03 PM, Deepayan Sarkar wrote:
On 4/26/07, Michael Kubovy [EMAIL PROTECTED] wrote:
Hi Sundar,
Thanks for taking a look at this
On Apr 26, 2007, at 1:05 PM, Sundar Dorai-Raj wrote:
Michael Kubovy said the following on 4/26/2007 7:20 AM:
Dear R-helpers,
How do I tell panel.polygon what greoup and panel it applies to
whithin
xyplot(y ~ x | c, groups = g
panel = function(x, y, groups, ...){
panel.polygon(x = xpol[c, g], y = ypol[c, g],
default.units = 'native')
panel.xYplot(x, y, groups, ...)
llines(x = c(1, 6), y = c(-24.28, 35.941667),
lwd = 2, lty
= 3, col = 4)
}
x[c, g] and y[c, g] describe the polygon I want plotted for group
g in panel c.
_
I believe you can just do:
panel = function(x, y, subscripts, groups, ...) {
## note addition of subscripts to arguments
panel.superpose(xpol, ypol, subscripts, groups,
panel.groups = panel.polygon,
default.units = native, ...)
panel.xYplot(x, y, subscripts, groups, ...)
llines(x = c(1, 6), y = c(-24.28, 35.941667),
lwd = 2, lty = 3, col = 4)
}
Also, it would be easier to provide tested answers if you gave a
reproducible example.
Here is a reproducible example in which I tried (unsuccesfully) to
apply your suggestion:
est - c(1:4, 3:6, 7, 9, 11, 13, 12, 15, 18, 21)
cond - rep(c('a','b'), each = 8)
grp - rep(c('I', 'II'), each = 4, 2)
x - rep(c(.5, .7, .9, 1.1), 4)
upper - est + 1
lower = est - 1
data - data.frame(est = est, x = x, cond = cond, grp = grp, upper =
upper, lower = lower)
xyplot(est ~ x | cond, group = grp, data = data, type = 'b',
panel = function(x, y, subscripts, groups, ...){
panel.superpose(c(x, rev(x)), c(upper, rev(lower)),
subscripts, groups,
panel.groups = 'panel.polygon', default.units =
'native', ...)
panel.xyplot(x, y, subscripts, groups, ...)
}
)
# returns: Error in validGP(list(...)) : Must specify only one of
'font' and 'fontface', which is incomprehensible to me.
Yeah, it's happening because of this:
grid::gpar(font = 1, fontface = NULL)
Error in validGP(list(...)) : Must specify only one of 'font' and
'fontface'
panel.polygon needs a fix. Replace it by this:
my.panel.polygon - function(..., font, fontface)
{
panel.polygon(...)
}
xyplot(est ~ x | cond, group = grp, data = data, type = 'b',
panel = function(x, y, ...) {
panel.superpose(c(x, rev(x)), c(upper, rev(lower)),
panel.groups = my.panel.polygon,
...)
panel.xyplot(x, y, ...)
})
You are also better off not having arguments you are not using (your
code would have failed because of incorrect positional matching).
I'm not sure I understand.
I'm trying to add a filled band to show CIs around the data (which is
why I tried to use xYplot, where 'filled bands' have bug).
So with these data:
est - c(1:4, 3:6, 7, 9, 11, 13, 12, 15, 18, 21)
cond - rep(c('a','b'), each = 8)
grp - rep(c('I', 'II'), each = 4, 2)
x - rep(c(.5, .7, .9, 1.1), 4)
upper - est + 1
lower = est - 1
data - data.frame(est = est, x = x, cond = cond, grp = grp, upper =
upper, lower = lower)
I'm trying to decorate this with bands:
xyplot(est ~ x | cond, group = grp, data = data, type = 'b')
So I'm not sure why your proposal is failing:
my.panel.polygon - function(..., font, fontface)
{
panel.polygon(...)
}
xYplot(est ~ x | cond, group = grp, data = data, type = 'b',
panel = function(x, y, subscripts, groups, ...){
panel.superpose(c(x, rev(x)), c(upper, rev(lower)),
subscripts, groups,
panel.groups = 'my.panel.polygon', default.units =
'native', ...)
panel.xYplot(x, y,,...)
}
)
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] Bug in xYplot() with method = 'filled bands'
Dear r-helpers,
I have been bitten by a cryptic comment in the help page for xYplot().
Here is some code from Madeline Bauer, one of the authors, which is
essentailly the code on the help page for xYplot():
# This example uses the summarize function in Hmisc to
# compute the median and outer quartiles. The outer quartiles are
# displayed using filled bands
set.seed(111)
dfr - expand.grid(month=1:12, year=c(1997,1998), reps=1:100)
month - dfr$month; year - dfr$year
y - abs(month-6.5) + 2*runif(length(month)) + year-1997
s - summarize(y, llist(month,year), smedian.hilow, conf.int=.5)
# filled bands: default fill = pastel colors matching solid colors
# in superpose.line (this works differently in R)
xYplot ( Cbind ( y, Lower, Upper ) ~ month, groups=year,
method=filled bands , data=s, type=l)
The comment this works differently in R should be ammended to a
more explicit danger sign (otherwise users like myself might find
themselves wasting a great deal of time). There appear to be two
differences between S+ and R here: (1) the default colors of the
bands are not as expected (but they can be changed at will, so that's
not a serious problem); (2) I have not been able get rid of the
outline around the filled bands or change their colors to match the
fill.
I would have thought that ...
xYplot ( Cbind ( y, Lower, Upper ) ~ month, groups=year,
method=filled bands , data=s, type=l, lwd.bands = 0,
lty.bands = 0, col.bands = 'white')
... would do the trick.
I even tried to fix the problem in the code of xYplot:
panel.XYplot
function (x, y, subscripts, groups = NULL, type = if (is.function
(method) ||
...
if (method == filled bands) {
if (.R.)
grid.polygon(x = c(x, rev(x)), y = c(lower, rev(upper)),
gp = gpar(fill = col.fill, col = col.bands,
lty = lty.bands, lwd = lwd.bands),
default.units = native)
else polygon(x = c(x, rev(x)), y = c(lower, rev(upper)),
col = col.fill)
}
...
}
Obviously I don't know grid well enough to fix the problem. Help
would be much appreciated, as well as a more explicit warning on the
xYplot() help page.
There is, of course, the possibility that there's something wrong
with my version of R or my OS or my machine. In that case a
replication or non-replication of this problem on a different OS
might alert me to this.
R version 2.5.0 RC (2007-04-21 r41269)
i386-apple-darwin8.9.1
locale:
C
attached base packages:
[1] grDevices datasets grid graphics stats utils
[7] methods base
other attached packages:
coda lme4 Matrix car
cacheSweave stashR
0.10-7 0.9975-13 0.9975-11 1.2-1
0.3 0.2-1
filehash digest circular boot gmodels
multcompView
0.9-4 0.2.3 0.3-6 1.2-27
2.13.2 0.1-0
reshape vcd colorspace effects
Hmisc acepack
0.7.2 1.0-3 0.95 1.0-10 3.3-1
1.3-2.2
HH multcomp mvtnorm JGR
iplots JavaGD
1.18-30.991-9 0.7-5 1.4-15
1.0-7 0.3-6
MASS gridBase lattice latticeExtra
rJava xtable
7.2-33 0.4-3 0.15-4 0.1-6
0.4-15 1.4-3
Thanks,
Michael Kubovy
__
R-help@stat.math.ethz.ch 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] Positioning in xyplot
Hi Deepayan,
There appears to be a small problem in the code you created to
reposition one panel in xyplot: it plots the panels but not the
contents. Putting together everything that you did on this problem, I
have the following:
require(lattice)
require(grid)
## this is a safer version of current.panel.limits()
current.limits -
function ()
{
xlim - convertX(unit(c(0, 1), npc), native, valueOnly = TRUE)
ylim - convertY(unit(c(0, 1), npc), native, valueOnly = TRUE)
if (any(!is.finite(xlim))) xlim - c(0, 1)
if (any(!is.finite(ylim))) ylim - c(0, 1)
list(xlim = xlim, ylim = ylim)
}
## this calls 'fun' after moving its viewport if panel.number() == 5
callAfterMoving -
function(fun, border = TRUE, move.x = 1, ...)
{
if (panel.number() != 5) { ## was == 5
fun(...)
if (border) grid.rect()
}
else {
cpl - current.limits()
pushViewport(viewport(x = move.x,
width = unit(1, npc),
xscale = cpl$xlim,
yscale = cpl$ylim,
clip = off))
fun(...)
if (border) grid.rect()
upViewport()
}
}
## panel function with axes on the left:
panel.leftaxes - function(...)
{
if (panel.number() == 5)
panel.axis(left, outside = TRUE,
line.col = black)
panel.xyplot(...)
}
z - expand.grid(x = 1:10, p = 1:5, r = 1:10)
z$y - rnorm(nrow(z))
z$p - factor(z$p, levels = c(1, 5, 2, 4, 3))
xyplot(y ~ x | p, z, groups = r,
layout = c(2, 3), type = l,
par.settings =
list(axis.line = list(col = transparent),
strip.border = list(col = transparent)),
panel = function(...) {
callAfterMoving(panel.leftaxes, ...)
},
strip = function(...) {
callAfterMoving(strip.default, ...)
},
axis = function(..., line.col, side) {
if (side != left || panel.number() != 5) {
callAfterMoving(axis.default,
border = FALSE,
line.col = 'black',
side = side,
...)
}
})
I also wonder why one doesn't need to call panel.xyplot().
Thanks,
MK
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] Changing appearance of band edges in xYplot()
Dear R-helpers, I would like the bands in an xYplot() to be gray without dark edges. I've tried playing around with col.bands, but that seems not to affect the edges, although changin col.fill does change the fill as I would expect. I would appreciate pointers. _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Changing appearance of band edges in xYplot()
On Apr 21, 2007, at 11:08 AM, Michael Kubovy wrote: Dear R-helpers, I would like the bands in an xYplot() to be gray without dark edges. I've tried playing around with col.bands, but that seems not to affect the edges, although changin col.fill does change the fill as I would expect. I would appreciate pointers. I forgot to give: R version 2.5.0 RC (2007-04-19 r41248) i386-apple-darwin8.9.1 locale: C attached base packages: [1] grDevices datasets grid graphics stats utils [7] methods base other attached packages: coda gmodelsHmisc acepack lme4 Matrix 0.10-7 2.13.2 3.3-11.3-2.2 0.9975-13 0.9975-11 cacheSweave stashR filehash digest JGR iplots 0.3 0.2-1 0.9-4 0.2.3 1.4-15 1.0-7 JavaGD MASS gridBase lattice latticeExtrarJava 0.3-6 7.2-33 0.4-3 0.15-4 0.1-6 0.4-15 xtable 1.4-3 _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Positioning in xyplot
Wow! Thanks to Sundar and to Deepayan for this selfless effort.(I
rather suspect they had a good time figuring this out.) The outcome
is that I will be able to publish just the right figure for the job.
I will be sure to aknowledge your contribtution.
Michael
On Apr 12, 2007, at 12:48 AM, Deepayan Sarkar wrote:
On 4/11/07, Sundar Dorai-Raj [EMAIL PROTECTED] wrote:
Hi, Deepayan,
See the attached image for what your code produced. Not sure if
this is
what you intended.
Here's the correct version of callAfterMoving (I thought I had fixed
it, but I guess I pasted the wrong thing):
## this calls 'fun' after moving its viewport if panel.number() == 5
callAfterMoving -
function(fun, border = TRUE, move.x = 1, ...)
{
if (panel.number() != 5) { ## was == 5
fun(...)
if (border) grid.rect()
}
else {
cpl - current.limits()
pushViewport(viewport(x = move.x,
width = unit(1, npc),
xscale = cpl$xlim,
yscale = cpl$ylim,
clip = off))
fun(...)
if (border) grid.rect()
upViewport()
}
}
-Deepayan
__
[EMAIL PROTECTED] 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] Positioning in xyplot
Dear R-helpers,
I have an xyplot
of the following kind:
xYplot(y ~ x | p, groups = factor(gg, levels = c('1', '5', '2', '4',
'3')),
strip = strip.custom(var.name = 'g', factor.levels = c(1', '5', '2',
'4', '3'),
strip.levels = T, strip.names = T, sep = ' = ',
shingle.intervals =
NULL),
data = df, type = 'b', label.curves = F, layout = c(2, 3),
)
Currently this puts the panels as follows
3
2 4
1 5
I need:
3
2 4
1 5
How can I do this? Any help will be much appreciated.
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] Positioning in xyplot
On Apr 10, 2007, at 7:07 PM, Deepayan Sarkar wrote:
On 4/10/07, Michael Kubovy [EMAIL PROTECTED] wrote:
Dear R-helpers,
I have an xyplot
of the following kind:
xYplot(y ~ x | p, groups = factor(gg, levels = c('1', '5', '2', '4',
'3')),
strip = strip.custom(var.name = 'g', factor.levels = c(1',
'5', '2',
'4', '3'),
strip.levels = T, strip.names = T, sep = ' = ',
shingle.intervals =
NULL),
data = df, type = 'b', label.curves = F, layout = c(2, 3),
)
Currently this puts the panels as follows
3
2 4
1 5
I need:
3
2 4
1 5
How can I do this? Any help will be much appreciated.
I don't understand what you mean. If you meant this:
+---+
| |
+---+---+
| | |
+---+---+
| | |
+---+---+
then see Sundar's answer. If you meant this:
+---+
| |
+-+---+-+
| | |
+---+---+
| | |
+---+---+
then you are out of luck (unless you are willing to do some low
level coding).
I guess I'm out of luck (I understood your two figures after turning
them into fixed width font). At least you put me out of *this*
misery. Thanks so much,
Michael
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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] Failure of mcsamp() but not mcmcsamp()
Daer r-helpers, Can anyone help with the following: I get: mcmcsamp(txt.lmer3f) Markov Chain Monte Carlo (MCMC) output: Start = 1 End = 1 Thinning interval = 1 But: mcsamp(txt.lmer3f) Error in as.bugs.array(sims, program = lmer, n.iter = n.iter, n.burnin = n.burnin, : error in parameter sigma.s in parameters.to.save I had attached the arm package: library(arm) Loading required package: R2WinBUGS arm (Version 1.0-15, built: 2007-3-17) Working directory is /Users/mk/Documents/projects/Mike/prediss/Exp-Text Loading required package: foreign sessionInfo() R version 2.4.1 (2006-12-18) i386-apple-darwin8.8.1 locale: C attached base packages: [1] tools grid datasets stats graphics grDevices utils methods [9] base other attached packages: foreign armR2WinBUGS coda Hmisc gmodels effects lme4 0.8-18 1.0-15 2.0-4 0.10-7 3.2-1 2.13.2 1.0-9 0.9975-13 Matrix car weavercodetools digest xtable latticeExtra lattice 0.9975-11 1.2-1 1.0.1 0.0-3 0.2.3 1.4-3 0.1-40.14-17 gridBase MASS JGR iplots JavaGDrJava 0.4-3 7.2-33 1.4-15 1.0-5 0.3-6 0.4-14 Thanks, MK _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Why does lmList() fail when lm() doesn't?
Dear r-helpers, Can anyone suggest why lm() doesn't complain here: summary(osss.lm1 - lm(logOdds ~ c.setSize %in% task, data = osss)) whereas in package:nlme (and in package:lme4) osss.lmL - lmList(logOdds ~ c.setSize %in% task | subj, data = osss) # Error in `contrasts-`(`*tmp*`, value = contr.treatment) : # contrasts can be applied only to factors with 2 or more levels If it were because for each subj I have only 1 datum per cell: with(subset(osss, osss$subj == '42'), table(setSize, task)) # task # setSize os ss # 2 1 1 # 3 1 1 # 4 1 1 # 5 1 1 # 6 1 0 # 7 1 0 then osss.lm1 - lm(logOdds ~ c.setSize %in% task, data = subset(osss, osss $subj == '42')) should fail as well, but I get anova(osss.lm1) # Analysis of Variance Table # # Response: logOdds #Df Sum Sq Mean Sq F value Pr(F) # c.setSize:task 2 6.8269 3.4134 1.9976 0.2059 # Residuals 7 11.9612 1.7087 _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] partial R
On Apr 2, 2007, at 5:49 AM, Pedram Rowhani wrote:
i am wondering if there is a command in R that will give me the
partial regression coefficients
To answer your question, you could have started with
RSiteSearch('partial regression')
It's then likely that you would figured out that one way to proceed is
install.packages('car')
?cr.plots
(You may have to restart R to get the help on a newly-installed
package.)
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] Doing partial-f test for stepwise regression
On Apr 1, 2007, at 1:54 AM, [EMAIL PROTECTED] wrote:
Hello all,
I am trying to figure out an optimal linear model by using stepwise
regression which requires partial f-test, I did some Googling on the
Internet and realised that someone seemed to ask the question before:
Jim Milks [EMAIL PROTECTED] writes:
Dear all:
I have a regression model that has collinearity problems (between
three regressor variables). I need a F-test that will allow me to
compare between full (with all variables) and partial models (minus
1= variables). The general F-test formula I'm using is:
F = {[SS(full model) - SS(reduced model)] / (#variables taken out)} /
MSS(full model)
Unfortunately, the ANOVA table parses the SS and MSS between the
variables and does not give the statistics for the regression
model as
a whole, otherwise I'd do this by hand.
So, really, I have two questions: 1) Can I just add up all the SS and
MSS for all the variables to get the model SS and MSS and 2) Are
there any functions or packages I can use to calculate the F-
statistic?
Just use anova(model1, model2).
(One potential catch: Make sure that both models are fitted to the
same
data set. Missing values in predictors may interfere.)
However, in the answer provided by Mr. Peter Dalgaard,(use
anova(model1,model2) I could not understand what model1 and model2 are
supposed to referring to, which one is supposedly to be the full
model and
which one is to be the partial model? Or it does not matter?
You can tell which is which by looking at the degrees of freedom.
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] Newbie: Combn and scripting
x - matrix(c('a', 'b', 'c', 'd', 1:4, 'g', 3, 6, 't'), nrow = 3,
byrow = T)
comb - vector('list', 3)
for(i in 1:3) comb[[i]] - combn(x[i,], 3)
On Mar 27, 2007, at 1:55 AM, [EMAIL PROTECTED] wrote:
I have just installed my R 2.4 (windows) as a test trying to load a
data
frame and run combn() for each line into another file. How do I do
this?
data.csv:
a,b,c,d
1,2,3.4
g,3,6,t
etc
x=data.csv, m=3
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] distribution graph
?violinplot (You need to install the UsingR package first.) On Mar 23, 2007, at 4:06 AM, Plessen, Christian von wrote: I am looking for a way to produce a distribution graph as in the example: (http://cecsweb.dartmouth.edu/release1.1/datatools/dgraph.php? year=2003geotype=STD_HRRevent=A01_DISeventtype=UTIL Anybody who can help? __ R-help@stat.math.ethz.ch 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] package:AlgDesign and .Random.seed
On Mar 21, 2007, at 4:16 AM, Uwe Ligges wrote: Michael Kubovy wrote: Dear r-helpers, Could you please help me solve the following problem: When I run require(AlgDesign) trt - LETTERS[1:5] blk - 10 trtblk - 3 BIB - optBlock(~., withinData = trt, blocksizes = rep(trtblk, blk)) In response to the last command, R complains: Error in optBlock(~., withinData = trt, blocksizes = rep(trtblk, blk)) : object .Random.seed not found The documentation of optBlock() in AlgDesign doesn't say that I needed to set .Random.seed. I thought it was initiated automatically at the beginning of a session. What am I missing? The first line in that function is seed - .Random.seed but .Random.seed is generated at the first use of R's RNG, hence maybe later. This means the function contains a bug which you should report to the package maintainer, please. Best, Uwe Ligges Bob Wheeler's response: From: Bob Wheeler [EMAIL PROTECTED] Date: March 21, 2007 9:19:29 AM EDT To: Michael Kubovy [EMAIL PROTECTED] Subject: Re: Each workspace in R requires you to set a random seed to start. You have not done this. It is an R artifact, and has nothing to do with AlgDesign. -- Bob Wheeler --- http://www.bobwheeler.com/ ECHIP, Inc. --- Randomness comes in bunches. __ R-help@stat.math.ethz.ch 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] package:AlgDesign and .Random.seed
Dear r-helpers, Could you please help me solve the following problem: When I run require(AlgDesign) trt - LETTERS[1:5] blk - 10 trtblk - 3 BIB - optBlock(~., withinData = trt, blocksizes = rep(trtblk, blk)) In response to the last command, R complains: Error in optBlock(~., withinData = trt, blocksizes = rep(trtblk, blk)) : object .Random.seed not found The documentation of optBlock() in AlgDesign doesn't say that I needed to set .Random.seed. I thought it was initiated automatically at the beginning of a session. What am I missing? sessionInfo() R version 2.4.1 (2006-12-18) i386-apple-darwin8.8.1 locale: C attached base packages: [1] grid datasets stats graphics grDevices utils methods base other attached packages: AlgDesign xtable latticeExtra lattice gridBase MASS JGR iplots 1.0-7 1.4-3 0.1-40.14-16 0.4-3 7.2-32 1.4-15 1.0-5 JavaGDrJava 0.3-6 0.4-14 _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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 with xYplot() in package Hmisc
Dear r-helpers, I would like to add three fitted lines to this plot. I don't know how to include three panel.abline() to the call to xYplot. I would like the colors of the lines correspond to the color of the dots and CI bars. x - c(1:4, 1:4, 3:6) y - c(4:1, 6:3, 5:2) e - runif(12) - .5 y - y + e ll - y - 1 ul - y + 1 g - c(rep(1, 4), rep(2, 4), rep(3, 4)) df - data.frame(x, y, ll, ul, g) xYplot(Cbind(y, ll, ul) ~ x, groups = g, type = 'p', data = df) _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] logging mouse clicks
Hi Seth, On Mar 10, 2007, at 11:55 PM, Seth Roberts wrote: How can I use R to record the time of a mouse click? Perhaps ievent.wait() in iplots? (I haven't used this.) I found all sorts of functions (most of which I couldn't understand) by ?event. _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Problem with ci.lmer() in package:gmodels
Dear Friends, Please note that in the following CI lower CI higher: require(lmer) require(gmodels) fm2 - lmer(Reaction ~ Days + (1|Subject) + (0+Days|Subject), sleepstudy) ci(fm2) Estimate CI lower CI upper Std. Error p-value (Intercept) 251.66693 266.06895 238.630280 7.056447 0 Days 10.52773 13.63372 7.389946 1.646900 0 _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Is the gmodels package being maintained?
Dear r-helpers, I sent a cc of a recent message about a problem with ci.lmer() in the gmodels package to the author (Gregory R Warnes), and the message bounced. If the author or someone else is maintaining this package or this function, would you kindly supplement the author's name and/or address with a current maintainer and/or provide a current email address? _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Is the gmodels package being maintained?
Hi, Finding his email address was not immediate, but I finally did, and did bring the problem to Greg's attention @ rochester, and the message didn't bounce this time. On Mar 9, 2007, at 7:43 AM, Peter Dalgaard wrote: Michael Kubovy wrote: Dear r-helpers, I sent a cc of a recent message about a problem with ci.lmer() in the gmodels package to the author (Gregory R Warnes), and the message bounced. If the author or someone else is maintaining this package or this function, would you kindly supplement the author's name and/or address with a current maintainer and/or provide a current email address? Haven't heard that Greg should be out of circulation. You might try the address from his homepage: [EMAIL PROTECTED] _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Extracting the p of F statistics from lm
On Mar 9, 2007, at 11:18 AM, Cressoni, Massimo ((NIH/NHLBI)) [F] wrote: I need to extract the p value from a ANOVA done with lm model fitting - lm(var ~ group) Sfitting - summary(fitting) Sfitting[10][1] gives the F value and the degrees of freedom but I am not able to get the p value. try Sfitting[4]$coefficients[,4] I'm not sure that this is the best way, but it works with the example for lm() summary(lm.D9)[4]$coefficients[,4] # (Intercept) groupTrt # 9.547128e-15 2.490232e-01 _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Table Construction from calculations
On Mar 9, 2007, at 9:23 PM, Seth Imhoff wrote:
I am trying to create a table of values by adding pairs of
vectors, but
am running into some problems. The problem is best expressed by a
simple example.
Starting with a data table basis:
atom x y z
1 Cu 0.0 0.0 0.0
2 Cu 0.5 0.5 0.5
I want to add 0.5 0.5 0.5 (and also the 0 0 0 but it wouldn't change
the values below so I won't refer to it in the rest of the example)
to a
list of vectors in the form of:
latpoints
V1 V2 V3
1 0 0 0
2 0 0 1
3 0 0 2
4 0 0 3
5 0 1 1
so that I end up with a table such as:
V1 V2 V3
0.5 0.5 0.5
0.5 0.5 1.5
0.5 0.5 2.5
0.5 0.5 3.5
0.5 1.5 1.5
I've tried many variations on the following: (not just cat, but
most of
the data/data.table options)
test = for(i in 1:5) {cat(basis[1,2:4] + latticemultipliers[i,],
append=TRUE)}
However, I either end up with an error telling me that cat doesn't
handle type 'list' or with a table with length of 1 such as:
xyz
2 0.5 1.5 1.5
Is this what you want?
(latpoints - data.frame(matrix(c(0,0,0,0,0,1,0,0,2,0,0,3,0,1,1),
nrow = 5, byrow = T)))
X1 X2 X3
1 0 0 0
2 0 0 1
3 0 0 2
4 0 0 3
5 0 1 1
(latpoints - latpoints + c(0.5, 0.5, 0.5))
X1 X2 X3
1 0.5 0.5 0.5
2 0.5 0.5 1.5
3 0.5 0.5 2.5
4 0.5 0.5 3.5
5 0.5 1.5 1.5
This is an important feature of R called vectorization (see, .e.g,
cran.r-project.org/doc/contrib/Paradis-rdebuts_en.pdf or
www.ms.washington.edu/stat390/winter07/R_primer.pdf) which allows you
do avoid writing loops.
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] Failure to run mcsamp() in package arm
Dear r-helpers, I can run the examples on the mcsamp help page. For example: M1 - lmer (y1 ~ x + (1|group)) (M1.sim - mcsamp (M1)) fit using lmer, 3 chains, each with 1000 iterations (first 500 discarded) n.sims = 1500 iterations saved mean sd 2.5% 25% 50% 75% 97.5% Rhat n.eff beta.(Intercept) 0.1 0.7 -1.2 -0.3 0.1 0.5 1.4 1.0 1500 beta.x 2.5 0.4 1.7 2.2 2.5 2.7 3.2 1.0 1500 sigma.y3.8 0.3 3.3 3.6 3.7 3.9 4.3 1.061 sigma.grop.(In)1.5 0.8 0.0 1.0 1.4 1.9 3.3 1.412 eta.group.(Intercept)[1] 0.0 1.0 -2.1 -0.5 0.0 0.6 2.0 1.0 1500 eta.group.(Intercept)[2] 1.0 1.1 -0.9 0.2 0.9 1.7 3.4 1.059 eta.group.(Intercept)[3] -1.3 1.2 -4.0 -2.0 -1.3 -0.4 0.5 1.066 eta.group.(Intercept)[4] 1.3 1.1 -0.6 0.4 1.1 2.0 3.7 1.143 eta.group.(Intercept)[5] -0.7 1.0 -3.0 -1.4 -0.6 0.0 1.2 1.0 120 eta.group.(Intercept)[6] 1.5 1.2 -0.3 0.6 1.4 2.2 4.0 1.049 eta.group.(Intercept)[7] 0.3 1.0 -1.7 -0.3 0.1 0.8 2.5 1.0 440 eta.group.(Intercept)[8] -1.6 1.2 -4.0 -2.4 -1.5 -0.6 0.3 1.141 eta.group.(Intercept)[9] 0.4 1.0 -1.6 -0.2 0.2 0.9 2.7 1.0 180 eta.group.(Intercept)[10] -1.0 1.1 -3.3 -1.6 -0.9 -0.2 0.8 1.086 For each parameter, n.eff is a crude measure of effective sample size, and Rhat is the potential scale reduction factor (at convergence, Rhat=1). But when I try to do this with my own data I get an error: display(e7.lmer2) lmer(formula = baLO ~ I(baRatio - 0.985) + delta + (1 + I(baRatio - 0.985) + delta | subject), data = e7) coef.est coef.se (Intercept)-0.19 0.06 I(baRatio - 0.985) -4.95 0.74 delta 0.41 0.06 Error terms: Groups Name Std.Dev. Corr subject (Intercept)0.13 I(baRatio - 0.985) 2.57 0.45 delta 0.22 -0.12 -0.94 Residual0.39 number of obs: 494, groups: subject, 13 deviance = 551.4 e7.sim - mcsamp(e7.lmer2) Error in as.bugs.array(sims, program = lmer, n.iter = n.iter, n.burnin = n.burnin, : error in parameter sigma. in parameters.to.save I would appreciate a pointer to what the problem might be. _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Failure to run mcsamp() in package arm
More problems. If I run sim(fm1 - lmer(Reaction ~ Days + (Days|Subject), sleepstudy)) from the lmer() help page. I get the error Error in mvrnorm(n.sims, bhat[j, ], V.beta) : 'Sigma' is not positive definite On Mar 7, 2007, at 1:30 PM, Michael Kubovy wrote: Dear r-helpers, I can run the examples on the mcsamp help page. For example: M1 - lmer (y1 ~ x + (1|group)) (M1.sim - mcsamp (M1)) fit using lmer, 3 chains, each with 1000 iterations (first 500 discarded) n.sims = 1500 iterations saved mean sd 2.5% 25% 50% 75% 97.5% Rhat n.eff beta.(Intercept) 0.1 0.7 -1.2 -0.3 0.1 0.5 1.4 1.0 1500 beta.x 2.5 0.4 1.7 2.2 2.5 2.7 3.2 1.0 1500 sigma.y3.8 0.3 3.3 3.6 3.7 3.9 4.3 1.061 sigma.grop.(In)1.5 0.8 0.0 1.0 1.4 1.9 3.3 1.412 eta.group.(Intercept)[1] 0.0 1.0 -2.1 -0.5 0.0 0.6 2.0 1.0 1500 eta.group.(Intercept)[2] 1.0 1.1 -0.9 0.2 0.9 1.7 3.4 1.059 eta.group.(Intercept)[3] -1.3 1.2 -4.0 -2.0 -1.3 -0.4 0.5 1.066 eta.group.(Intercept)[4] 1.3 1.1 -0.6 0.4 1.1 2.0 3.7 1.143 eta.group.(Intercept)[5] -0.7 1.0 -3.0 -1.4 -0.6 0.0 1.2 1.0 120 eta.group.(Intercept)[6] 1.5 1.2 -0.3 0.6 1.4 2.2 4.0 1.049 eta.group.(Intercept)[7] 0.3 1.0 -1.7 -0.3 0.1 0.8 2.5 1.0 440 eta.group.(Intercept)[8] -1.6 1.2 -4.0 -2.4 -1.5 -0.6 0.3 1.141 eta.group.(Intercept)[9] 0.4 1.0 -1.6 -0.2 0.2 0.9 2.7 1.0 180 eta.group.(Intercept)[10] -1.0 1.1 -3.3 -1.6 -0.9 -0.2 0.8 1.086 For each parameter, n.eff is a crude measure of effective sample size, and Rhat is the potential scale reduction factor (at convergence, Rhat=1). But when I try to do this with my own data I get an error: display(e7.lmer2) lmer(formula = baLO ~ I(baRatio - 0.985) + delta + (1 + I(baRatio - 0.985) + delta | subject), data = e7) coef.est coef.se (Intercept)-0.19 0.06 I(baRatio - 0.985) -4.95 0.74 delta 0.41 0.06 Error terms: Groups Name Std.Dev. Corr subject (Intercept)0.13 I(baRatio - 0.985) 2.57 0.45 delta 0.22 -0.12 -0.94 Residual0.39 number of obs: 494, groups: subject, 13 deviance = 551.4 e7.sim - mcsamp(e7.lmer2) Error in as.bugs.array(sims, program = lmer, n.iter = n.iter, n.burnin = n.burnin, : error in parameter sigma. in parameters.to.save I would appreciate a pointer to what the problem might be. _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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] Failure to run mcsamp() in package arm
Andrew Robinson has gently chided me for not including more information. So here goes: R version 2.4.1 (2006-12-18) powerpc-apple-darwin8.8.0 locale: C attached base packages: [1] stats graphics grDevices utils methods base other attached packages: foreign car arm R2WinBUGSlme4 Matrix lattice 0.8-18 1.2-11.0-13 2.0-4 0.9975-13 0.9975-11 0.14-16 MASS JGR iplots JavaGD rJava 7.2-321.4-15 1.0-5 0.3-50.4-14 On Mar 7, 2007, at 4:30 PM, Michael Kubovy wrote: More problems. If I run sim(fm1 - lmer(Reaction ~ Days + (Days|Subject), sleepstudy)) from the lmer() help page. I get the error Error in mvrnorm(n.sims, bhat[j, ], V.beta) : 'Sigma' is not positive definite On Mar 7, 2007, at 1:30 PM, Michael Kubovy wrote: Dear r-helpers, I can run the examples on the mcsamp help page. For example: M1 - lmer (y1 ~ x + (1|group)) (M1.sim - mcsamp (M1)) fit using lmer, 3 chains, each with 1000 iterations (first 500 discarded) n.sims = 1500 iterations saved mean sd 2.5% 25% 50% 75% 97.5% Rhat n.eff beta.(Intercept) 0.1 0.7 -1.2 -0.3 0.1 0.5 1.4 1.0 1500 beta.x 2.5 0.4 1.7 2.2 2.5 2.7 3.2 1.0 1500 sigma.y3.8 0.3 3.3 3.6 3.7 3.9 4.3 1.061 sigma.grop.(In)1.5 0.8 0.0 1.0 1.4 1.9 3.3 1.412 eta.group.(Intercept)[1] 0.0 1.0 -2.1 -0.5 0.0 0.6 2.0 1.0 1500 eta.group.(Intercept)[2] 1.0 1.1 -0.9 0.2 0.9 1.7 3.4 1.059 eta.group.(Intercept)[3] -1.3 1.2 -4.0 -2.0 -1.3 -0.4 0.5 1.066 eta.group.(Intercept)[4] 1.3 1.1 -0.6 0.4 1.1 2.0 3.7 1.143 eta.group.(Intercept)[5] -0.7 1.0 -3.0 -1.4 -0.6 0.0 1.2 1.0 120 eta.group.(Intercept)[6] 1.5 1.2 -0.3 0.6 1.4 2.2 4.0 1.049 eta.group.(Intercept)[7] 0.3 1.0 -1.7 -0.3 0.1 0.8 2.5 1.0 440 eta.group.(Intercept)[8] -1.6 1.2 -4.0 -2.4 -1.5 -0.6 0.3 1.141 eta.group.(Intercept)[9] 0.4 1.0 -1.6 -0.2 0.2 0.9 2.7 1.0 180 eta.group.(Intercept)[10] -1.0 1.1 -3.3 -1.6 -0.9 -0.2 0.8 1.086 For each parameter, n.eff is a crude measure of effective sample size, and Rhat is the potential scale reduction factor (at convergence, Rhat=1). But when I try to do this with my own data I get an error: display(e7.lmer2) lmer(formula = baLO ~ I(baRatio - 0.985) + delta + (1 + I(baRatio - 0.985) + delta | subject), data = e7) coef.est coef.se (Intercept)-0.19 0.06 I(baRatio - 0.985) -4.95 0.74 delta 0.41 0.06 Error terms: Groups Name Std.Dev. Corr subject (Intercept)0.13 I(baRatio - 0.985) 2.57 0.45 delta 0.22 -0.12 -0.94 Residual0.39 number of obs: 494, groups: subject, 13 deviance = 551.4 e7.sim - mcsamp(e7.lmer2) Error in as.bugs.array(sims, program = lmer, n.iter = n.iter, n.burnin = n.burnin, : error in parameter sigma. in parameters.to.save I would appreciate a pointer to what the problem might be. _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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@stat.math.ethz.ch 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
How can I evaluate two or more expressions to return two or more columns? eval(expression(with(bd,Var1*100),with(bd,Var2*200))) The execution is always for the last expression. I can't execute the two expressions at the same time. It is possible? How about something like this with(bd, c(Var1 * 100, Var2 * 200)) _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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 override ordering of panels in xyplot()
On Mar 3, 2007, at 3:19 PM, Deepayan Sarkar wrote: On 3/3/07, Michael Kubovy [EMAIL PROTECTED] wrote: Dear r-helpers, I'm conditioning an xyplot on a variable whose levels are'low', 'med', 'high'. How do I override the alphabetical ordering for the panels of the plot? This has less to do with xyplot and more to do with the default of the 'levels' argument in the factor() function. Just make sure the levels are in the right order in your data when xyplot is called. Unless one makes the factor ordered, reordering the levels of a factor does not seem to be a trivial matter. The only R function I've found that makes it easy is reorder_factor() (package:reshape). Or am I missing something? _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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 with paste()
Dear r-helpers,
Could you please tell me what's missing:
rbind(paste('txt.est',1:24, sep = ''))
txt.est1, ... txt.est24 are vectors that I wish to rbind.
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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 override ordering of panels in xyplot()
Dear r-helpers, I'm conditioning an xyplot on a variable whose levels are'low', 'med', 'high'. How do I override the alphabetical ordering for the panels of the plot? _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] mtext bold font problem
On Feb 24, 2007, at 6:12 PM, Joseph Retzer wrote: I'd like to create an mtext title which has certain words bold, the rest not bold. x - 1:10 y - x^2 plot(x, y, main = expression(paste( Overall Satisfaction Call, bold( Difference ), vs. Overall Satisfaction Rep., bold( Difference))) ) _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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 boxplot
On Feb 22, 2007, at 2:56 PM, Smith, Phil ((CDC/CCID/NCIRD)) wrote: boxplot( p.prop ~ R + bins ) This command makes nice boxplot for the factor R crossed with the factor bins. I am having alot of trouble getting control of the labels on the X axis. I want to control it more by specifying what the labels are, controling the 'size' of those labels (by using cex), and then control the rotation of the character strings of those labels (by using srt or crt). There is a names argument to boxplot, but I haven't had much luck controlling what it prints, the size of the font, and the character rotation. Would you consider an easy way out---an alternative with reasonable defaults? data(ToothGrowth) bwplot(dose ~ len | supp, ToothGrowth) _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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 with xlab and ylab distance from axes
Dear r-helpers, In basic graphics, I have a figure with x and y axes suppresed. I would like to move the xlab and the ylab closer to the axes. Do I have to use mtext()? _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Suppressing \newcolumntype{} declaration in latex.default() in Hmisc
Dear r-helpers,
When use latex() on a matrix, I set the option dcolumn = T. As a
result, in front of each tabular I get
\newcolumntype{.}{D{.}{.}{-1}}
The LaTeX compiler complains about these multiple redeclarations.
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] Suppressing \newcolumntype{} declaration in latex.default() in Hmisc
Dear r-helpers,
I didn't include a clear question in my previous posting. Here is a
better version:
When I use latex() on a matrix, I set the option dcolumn = T. As a
result, in the *.tex file before each tabular I get
\newcolumntype{.}{D{.}{.}{-1}}
The LaTeX compiler complains about these multiple redeclarations. Is
there a way to suppress this?
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] Suppresing default text in pairs.lmList() in package = nlme
Thanks Ken and Dieter,
I added xlab = '' and the text 'Scatter Plot Matrix' produced by pairs
() applied to an lmList object (in nlme) went away. Skip the rest ---
which is mainly autobiographical --- unless you're curious.
On Feb 11, 2007, at 4:25 AM, Dieter Menne wrote:
Michael Kubovy kubovy at virginia.edu writes:
I would like to suppress the text 'Scatter Plot Matrix' that appears
under the plot. Could someone please suggest how?
Must be as special Virginia Brand of lmList. That Test does not
turn up in my
output, and the only place I found it in the sources was as a comment
## scatter plot matrix plots, generally based on coef or ranef
Overnight I flew to New York (a slightly more left-leaning state),
bought a new computer, installed R and all the packages, and then
flew back with the new machine; the symptom remained ;)
On Feb 11, 2007, at 5:20 AM, Ken Knoblauch wrote:
It looks like you get this default xlab with splom so the title is
misleading,
though pairs.lmList calls splom in some cases, see near the end of the
function
where plotfun is assigned a value of either xyplot or splom. I
was able
to get the xlab to change by providing an explicit xlab = machin
argument
to override the xlab argument in the call to splom and which is passed
along by
the ... argument.
Is it documented somewhere how to figure this out? It just didn't
occur to me that the problem was as simple as changing the xlab and I
don't yet have the habit of looking at code. Nevertheless I had done
the following:
pairs
function (x, ...)
UseMethod(pairs)
environment: namespace:graphics
... which did not make me happy. So then I tried:
pairs.lmList
Error: object pairs.lmList not found
... which did not make me happy. So then I tried:
apropos('pairs')
[1] pairs pairs.default panel.pairs
pairs.default
function (x, labels, panel = points, ..., lower.panel = panel,
...
... and then my eyes glazed over because nothing I saw seemed relevant.
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] OT: question about transformation
If x is a r.v. 1/log(x) ~ N (approximately) what does that tell me about the distribution of x (i.e., is it a standard distribution?) Can you point me to a list where I would have appropriately posted this? _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Suppresing default text in pairs.lmList() in package = nlme
I would like to suppress the text 'Scatter Plot Matrix' that appears under the plot. Could someone please suggest how? _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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 count the number of NAs in each column of a df?
Dear Jim (25 minutes!), Richard (27 minutes!), and Chuck, Thanks to your hints, I have come up with what I hope is a pithy idiom that drops columns of a dataframe (df) in which the number of NAs is (e.g.) 30. tmp - df tmp - tmp[, which(as.numeric(colSums(is.na(tmp))) 30)] df - tmp I wonder if we have a place to keep R programming idioms (which probably get unnecessarily reinvented). Is the R-Wiki suitable? _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Replace individual values in a data frame with NA
On Feb 9, 2007, at 11:10 AM, Jason Horn wrote: I'd like to replace a value in a data frame with an NA, but can't figure out how. For example, say you have a-c(1,2,3,4) b-c(5,6,7,8) data-data.frame(a,b) Now, how would you set the third row of the second column ( data [[3,2]] ) to NA? a-c(1,2,3,4) b-c(5,6,7,8) data-data.frame(a,b) data[3, 2] - NA ?Extract _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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 add the variable name to a qqplot or densityplot in the diagonal of an splom?
splom() doesn't complain here, but writes no names in the diagonal
boxes. What am I missing?
I believe that I need to add something like grid.text(x, ...) to the
diagonal panel, but I don't know how to get it cycle through the
column labels. And should
varname.col = 'blue', varname.cex = 1
be inside the diag.panel() function?
splom(szw[, n], pscales = 0,
diag.panel = function(x, ...){
panel.qqmathline(x, ...)
panel.qqmath(x, ...)
},
lower.panel = function(x, y, ...){
panel.xyplot(x, y, ..., col = 'lightblue')
panel.loess(x, y, ..., col = 'red')
},
upper.panel = function(x, y, ...){
panel.abline(lm(y~x),...)
grid.text(round(cor(x, y, use = 'pairwise.complete.obs'), 2),
x = unit(1, 'mm'),
y = unit(1, 'npc') - unit(1, 'mm'),
just = c('left', 'top'),
gp = gpar(fontsize = 10))
},
varname.col = 'blue', varname.cex = 1
)
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] smartpred depends on fitted() in flexmix?
Hi, I was going through the examples in smartpred. It seems there's an unstated dependency on the fitted() function in package flexmix. n = 20 set.seed(86) x = sort(runif(n)) y = sort(runif(n)) library(splines) fit = lm(y ~ ns(x, df=5)) plot(x, y) lines(x, fitted(fit)) # won't work w/o prior loading of the flexmix package. newx = seq(0, 1, len=n) points(newx, predict(fit, data.frame(x=newx)), type=b, col=2, err=-1) _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Strange behavior of abc.ci() in boot
require(boot) # [1] TRUE set.seed(1) summary(rn - rnorm(30)) # Min. 1st Qu. Median Mean 3rd Qu. Max. # -2.21500 -0.43500 0.25660 0.08246 0.70870 1.59500 abc.ci(rnorm(30), mean) # [1] 0.9500 0.08245817 0.08245817 * sessionInfo() R version 2.4.1 (2006-12-18) i386-apple-darwin8.8.1 locale: C attached base packages: [1] grid datasets stats graphics grDevices utils methods base other attached packages: boot xtable latticeExtra lattice gridBase MASS JGR iplots JavaGD 1.2-27 1.4-3 0.1-40.14-16 0.4-3 7.2-31 1.4-15 1.0-5 0.3-5 rJava 0.4-13 _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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 count the number of NAs in each column of a df?
I would like to remove columns of a df which have too many NAs. I think that summary() should give me the information, I just don't know how to access it. Advice? _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] lmer2 error under Mac OS X on PowerPC G5 but not on Dual-Core Intel Xeon
On Jan 28, 2007, at 9:39 PM, Benilton Carvalho wrote: This seems to be due to the fact that you didn't have enough memory when running lmer2. I might be wrong, but I think Calloc tries to get contiguous memory, so this might the problem. If you are positive that you have enough memory, a gc() might help. I have 2 GB memory on this machine. Should be enough, no? gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 1008175 27.01476915 39.5 1368491 36.6 Vcells 540055 4.21031040 7.9 1031026 7.9 (fm1 - lmer2(Reaction ~ Days + (Days|Subject), sleepstudy)) Error in as.double(start) : Calloc could not allocate (903190944 of 4) memory On Jan 28, 2007, at 8:35 PM, Michael Kubovy wrote: (fm1 - lmer2(Reaction ~ Days + (Days|Subject), sleepstudy)) Error in as.double(start) : Calloc could not allocate (888475968 of 4) memory * sessionInfo() R version 2.4.1 (2006-12-18) powerpc-apple-darwin8.8.0 locale: C attached base packages: [1] grid datasets stats graphics grDevices utils methods [8] base other attached packages: lme4 Matrix xtable latticeExtra lattice gridBase MASS 0.9975-11 0.9975-8 1.4-3 0.1-40.14-16 0.4-3 7.2-31 JGR iplots JavaGDrJava 1.4-15 1.0-5 0.3-5 0.4-13 * lmer runs the example w/o a problem I just tried to run it on on Intel-based MacPro, and lmer2 ran without a hitch. _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] lmer2 error under Mac OS X on PowerPC G5 but not on Dual-Core Intel Xeon
(fm1 - lmer2(Reaction ~ Days + (Days|Subject), sleepstudy)) Error in as.double(start) : Calloc could not allocate (888475968 of 4) memory * sessionInfo() R version 2.4.1 (2006-12-18) powerpc-apple-darwin8.8.0 locale: C attached base packages: [1] grid datasets stats graphics grDevices utils methods [8] base other attached packages: lme4 Matrix xtable latticeExtra lattice gridBase MASS 0.9975-11 0.9975-8 1.4-3 0.1-40.14-16 0.4-3 7.2-31 JGR iplots JavaGDrJava 1.4-15 1.0-5 0.3-5 0.4-13 * lmer runs the example w/o a problem I just tried to run it on on Intel-based MacPro, and lmer2 ran without a hitch. _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Unbalanced design help
Dear r-helpers, I am looking at a designed experiment in which one predictor variable has 5 levels (0, ..., 4) and the other has 6 levels (1.1, ..., 1.6), with 33 observations per cell. This design was given to 13 subjects. 0 1 2 3 4 1.1 32 33 0 0 0 1.2 33 33 33 0 0 1.3 33 33 33 33 0 1.4 0 0 33 33 33 1.5 0 0 0 33 33 1.6 0 0 0 0 33 The reason for this design is that low values of one predictor combined with high values of the other produce floor or ceiling effects at any reasonable sample size. Can anyone point me to a theoretical discussion of the analysis of such data, and tools in R to use? _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Adding lines to xYplot
I am using xYplot to plot data and CIs. How do I add several lines to the figure? _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Finding the effect of Box-Cox transformation using vis.boxcoxu
?box.cox ?boxcox On Jan 22, 2007, at 2:25 AM, Arun Kumar Saha wrote: I have a dataset 'data' and I want to see the effect of Box-Cox transformation on it Interactively for different lambda values. I already got a look on function vis.boxcoxu in package TeachingDemos. But I didn't find any option to put user's own dataset. Can anyone tell me how to put my own dataset here i.e. data? _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Newbie question: Statistical functions (e.g., mean, sd) in a transform statement?
On Jan 19, 2007, at 12:54 PM, Ben Fairbank wrote: Given a data frame such as times time1time2 time3time4 1 70.408543 48.92378 7.399605 95.93050 2 17.231940 27.48530 82.962916 10.20619 3 20.279220 10.33575 66.209290 30.71846 4 NA 53.31993 12.398237 35.65782 5 9.295965 NA 48.929201 NA 6 63.966518 42.16304 1.777342 NA I cannot, however, find a way, other than for looping, to use statistical functions, such as mean or sd, to compute the new column. times - data.frame(time1 = rnorm(6, 50, 20), time2 = rnorm(6, 40, 15), time3 = rnorm(6, 60, 25), time4 = rnorm(6, 55, 23)) times[4,1] - NA times[5, c(2, 4)] - NA times[6, 4] - NA times$totaltime - apply(times, 1, sum, na.rm = T) times$meantime - apply(times, 1, mean, na.rm = T) times$sdtime - apply(times, 1, sd, na.rm = T) time1time2time3time4 totaltime meantime sdtime 1 28.84859 29.94037 92.11518 71.80472 222.70886 89.08354 71.11911 2 50.72260 39.02439 61.18364 31.63962 182.57024 73.02810 55.68944 3 11.75829 28.61262 72.37066 79.23817 191.97974 76.79189 62.99902 4 NA 27.23659 75.69952 38.19262 141.12872 70.56436 44.52787 5 31.05109 NA 52.41755 NA 83.46864 55.64576 21.52078 6 54.01291 52.48922 53.97689 NA 160.47902 80.23951 46.33038 _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] ANCOVA
On Jan 6, 2007, at 8:34 AM, John Cardinale wrote:
Are there any R function which can do analysis of covariance?
?lm
RSiteSearch('ancova')
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] Help with filled.contour()
To Jeff: a tip of the hat.
I have another question after Jeff's solution:
On Jan 3, 2007, at 5:09 PM, Jeffrey Horner wrote:
Michael Kubovy kubovy at virginia.edu writes:
I tried and it gave a strange result. See
http://people.virginia.edu/~mk9y/mySite/twoGaussian.R
and
http://people.virginia.edu/~mk9y/mySite/twoGaussian.pdf
Try the image function. The smoothness of the plot will be
proportional to the length of x and y. For instance 200 isn't bad:
mu1 - 0
mu2 - 5
s - 1
x - seq(-2.5, 7.5, length = 200)
y - seq(-2.5, 2.5, length = 200)
f - function(x,y){
term1 - 1/(2*pi*sqrt(s*s))
term2 - -1/2
term3 - (x - mu1)^2/s
term4 - (y - mu1)^2/s
term5 - (x - mu2)^2/s
term1*(.5 * exp(term2*(term3 + term4)) + .5 * exp(term2*(term5
+ term4)))
} # setting up the function of the multivariate normal density
z - outer(x, y, f)
# persp(x, y, z)
require(grDevices)
#pdf('twoGaussian.pdf')
#filled.contour(x, y, z, axes = F, frame.plot = F, asp = 1,
# col = gray(seq(0, 0.9, len = 25)), nlevels = 25)
image(x,y,z,col=gray(seq(0,0.9,len=200)))
Is there a simpler way to get rid of axes, frame, and axis labels than
image(x, y, z, col = gray(seq(0, 0.9, len = 200)), asp = 1, xaxt =
'n', yaxt = 'n', bty = 'n', ann = F)
?
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] New to R
On Dec 31, 2006, at 10:15 PM, Obinna Duru wrote:
I have installed acepack but efforts to get started has been
unsuccessful. I can't seem to be able to load my data files because I
am yet to figure the syntax to use. Is there a work directory in R
where I can put my files and call them anytime, like in Matlab? My
files are on my C drive and I just can't figure the syntax to get
them into R.
Start by looking at
?getwd
?read.table
intall.packages('foreign') # if not installed
?read.spss
?read.ssd
etc.
and then
http://www.bioconductor.org/developers/progRef/fileHandling.pdf
followed by the more general
http://cran.r-project.org/doc/manuals/R-intro.pdf
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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 with filled.contour()
The following plot is a first approximation to what I need:
***
mu1 - 0
mu2 - 5
s - 1
x - seq(-2.5, 7.5, length = 41)
y - seq(-2.5, 2.5, length = 41)
f - function(x,y){
term1 - 1/(2*pi*sqrt(s*s))
term2 - -1/2
term3 - (x - mu1)^2/s
term4 - (y - mu1)^2/s
term5 - (x - mu2)^2/s
term1*(.5 * exp(term2*(term3 + term4)) + .5 * exp(term2*(term5 +
term4)))
}
z - outer(x, y, f)
persp(x, y, z)
require(grDevices)
filled.contour(x, y, z, axes = F, frame.plot = F, asp = 1,
col = palette(gray(seq(0, 0.9, len = 25))), nlevels = 25)
***
It has four drawbacks. I would like:
(1) to remove the white grid;
(2) to remove the white contours;
(3) its appearance to be smooth;
(4) to remove the key.
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] Help with filled.contour()
On Jan 1, 2007, at 2:13 PM, Dieter Menne wrote:
Michael Kubovy kubovy at virginia.edu writes:
The following plot is a first approximation to what I need:
.. see below
***
It has four drawbacks. I would like:
(1) to remove the white grid;
(2) to remove the white contours;
(3) its appearance to be smooth;
(4) to remove the key.
In partial fulfillment of your requirements, increasing the levels
gives a nice
smooth plot.
mu1 - 0
mu2 - 5
s - 1
x - seq(-2.5, 7.5, length = 41)
y - seq(-2.5, 2.5, length = 41)
f - function(x,y){
term1 - 1/(2*pi*sqrt(s*s))
term2 - -1/2
term3 - (x - mu1)^2/s
term4 - (y - mu1)^2/s
term5 - (x - mu2)^2/s
term1*(.5 * exp(term2*(term3 + term4)) + .5 * exp(term2*(term5 +
term4)))
}
z - outer(x, y, f)
persp(x, y, z)
require(grDevices)
filled.contour(x, y, z, axes = F, frame.plot = F, asp = 1,
col = palette(gray(seq(0, 0.9, len = 500))), nlevels = 500)
Thanks, Dieter.
I tried and it gave a strange result. See
http://people.virginia.edu/~mk9y/mySite/twoGaussian.R
and
http://people.virginia.edu/~mk9y/mySite/twoGaussian.pdf
*
Session Info
*
sessionInfo()
R version 2.4.1 (2006-12-18)
powerpc-apple-darwin8.8.0
locale:
C
attached base packages:
[1] datasets grid graphics grDevices stats
utils methods
[8] base
other attached packages:
JGR iplots JavaGD MASS
gridBase lattice
1.4-14 1.0-5 0.3-5 7.2-30 0.4-3
0.14-16
latticeExtrarJava xtable
0.1-4 0.4-12 1.4-2
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] slightly extended lm class
On Jan 1, 2007, at 9:00 PM, ivo welch wrote: I have written a short lme.R function, which adds normalized coefficients and White heteroskedasticity-adjusted statistics to the standard output. Otherwise, it behaves like lm. Is it a good idea to call it lme, since there's a widely used lme() in the nlme package? _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Difference of array and vector
On Dec 29, 2006, at 2:16 PM, Geoffrey Zhu wrote: Does anyone know what is the real difference of vector and array? # Here's a vector: letv - letters is.vector(letv) # Here's an array: leta - as.array(letters) is.array(leta) attributes(letv) attributes(leta) To understand the importance of attributes: http://www.burns-stat.com/pages/Spoetry/essentials.pdf There Burns writes (p. 3): An S array is merely a vector that has a dim attribute, and optionally a dimnames attribute. _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] sequential row selection in dataframe
On Dec 26, 2006, at 12:07 AM, Pedro Mardones wrote: I'm wondering if there is any 'efficient' approach for selecting a sample of 'every nth rows' from a dataframe. For example, let's use the dataframe GAGurine in MASS library: length(GAGurine[,1]) [1] 314 # select an 75% of the dataset, i.e. = 236 rows, every 2 rows starting from row 1 test-GAGurine[seq(1,314,2),] length(test[,1]) [1] 157 # so, I still need another 79 rows, one way could be: test2-GAGurine[-seq(1,314,2),] length(test2[,1]) [1] 157 test3-test2[seq(1,157,2),] # and then final-rbind(test2,test3) length(final[,1]) [1] 236 Does anyone have a better idea to get the same results but without creating different datasets like test2 and test3? A probabilistic approach: len - length(GAGurine[,1]) GAGu - GAGurine[sample(1:len, round(.75 * len)), ] # 236 rows A deterministic one: nr - 1 #or 2 GAGu2 - GAGurine[-seq(nr, len, 4),] # drop every 4th, giving 235 rows nr - 3 # or 4 will give 236 rows. _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Rating competitors
I would start with elimination-by-aspects models: ?eba I would read the Tversky 1972 paper (cited on the help page for the eba() function), which is brilliant. Jeff Newmiller wrote: I am looking for hints on how to estimate ratings for competitors in an ongoing pairwise competition using R... my particular area of interest being the game of Go, but the idea of identifying ratings (on a continuous scale) rather than relative rankings seems easily generalized to other competitions so I thought someone might be studying something related already. I presume the rating of a competitor would be best modeled as a random variate on the rating scale, and an encounter between two competitors would be represented by a binary result. Logistic regression seems promising, but I am at a loss how to represent the model since the pairings are arbitrary and not necessarily repeated often. _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] complex barplot enquiry
On Dec 23, 2006, at 12:07 AM, Bob Green wrote: snip The data consists of a series of pre and post variables, in a dataframe called 'offend'. I am interested in graphically depicting the pre post values for a factor variable called 'decision' which has 4 values : nusm, fit, unsound unfit. An example of a pre and post variable is: pre.damage and post.damage (data below). I wanted to exclude all values = 0, and collapse the remaining values into 3 categories .e.g 1, 2-5, 6 plus. For each 'decision' group the final graph would contain the alternating pre and post values for 'damage'. For example, for 'fit' the first bar would have a pre value = 18 a post value = 4, the second pre bar would = 17 and the post bar = 2, and the third pre bar would = 2 the post = 1. snip table(decision,pre.damage) pre.damage decision0 1 2 3 4 5 6 7 8 9 10 11 13 14 20 fit 89 189 4 2 2 1 0 0 1 0 0 0 0 0 nusm 158 44 15 5 5 6 6 3 1 1 2 0 0 0 0 unfit 272 2 0 0 1 0 0 0 0 0 0 0 0 0 unsound 333 68 36 8 5 4 1 0 0 0 0 1 1 1 1 table(decision,post.damage) post.damage decision0 12 3 4 5 6 7 10 12 13 fit 11941 1 0 0 0 0 1 0 0 nusm 212 16 11 2 0 2 1 1 0 1 0 unfit 3110 0 0 0 0 0 0 0 0 unsound 44185 3 1 0 0 0 0 0 1 Could you please post commands to define the df 'offend'? _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Newbie data organisation/structures question...
On Dec 20, 2006, at 11:05 AM, Gav Wood wrote: So my data is in this sort of format: P T I 1 1 (1, 2, 3) 2 1 (2, 4) 1 2 (1, 3, 6, 7) 2 2 (6) Not knowing why you organized the data as you did, let me suggest another approach: iv - c(1, 2, 3, 2, 4, 1, 3, 6, 7, 6) p - c(1, 1, 1, 2, 2, 1, 1, 1, 1, 2) t - rep(1:2, each = 5) dat - data.frame(iv, p, t) And I want to be able to quickly get: The I when both P and T are given. e.g.: P = 2, T = 2; I = (6) subset(dat, p == 2 t ==2)$iv The concatenated vector of Is when P and a subset of T is given, e.g.: P = 1, T = 1:2; Is = (1, 2, 3, 1, 3, 6, 7) (iv1 - subset(dat, p == 1)$iv) The length of that vector. length(iv1) A list of Is when either P or T is given. e.g.: P = 2: I = (2, 4), (6) T = 1: I = (1, 2, 3), (1, 3, 6, 7) list(p2t1 = subset(dat, p == 2 t ==1)$iv, p2t2 = subset(dat, p == 2 t ==2)$iv) list(p1t1 = subset(dat, p == 1 t ==1)$iv, p1t2 = subset(dat, p == 1 t ==2)$iv) # correcting your requirement to get your result There are many other ways of getting the results you need as Marc Schwartz pointed out in his reply. _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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 replace some objects?
On Dec 19, 2006, at 3:05 AM, Zhang Jian wrote:
I want to replace some objects in one row or column.For example,
One colume: a,b,a,c,b,b,a,a,c.
I want to replace a with 1, b with 2, and c with 3.
Like this: 1,2,1,3,2,2,1,1,3.
let - c('a', 'b', 'a', 'c', 'b', 'b', 'a', 'a', 'c')
library(car)
num - recode(let, 'a' = 1; 'b' = 2; else = 3 )
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] Problem with glmmADMB
library(glmmADMB) #Example for glmm.admb data(epil2) glmm.admb(y~Base*trt+Age +Visit,random=~Visit,group=subject,data=epil2,family=nbinom) Gives: Error in glmm.admb(y ~ Base * trt + Age + Visit, random = ~Visit, group = subject, : The function maximizer failed ** R version 2.4.1 RC (2006-12-14 r40181) powerpc-apple-darwin8.8.0 locale: C attached base packages: [1] utils stats graphics grDevices datasets methods base other attached packages: glmmADMB JGRiplotsJavaGD rJava MASS lattice 0.3 1.4-14 1.0-5 0.3-5 0.4-12 7.2-30 0.14-16 _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] digital length
?Round On Dec 14, 2006, at 2:52 AM, XinMeng wrote: How can I control the digital length of data? e.g: 0.1234 is the output of an algorithm. What I want is 0.12 instead. _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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 smal fitting problem...
On Dec 8, 2006, at 7:42 AM, David Barron wrote: b = mean(y) On 08/12/06, Kåre Edvardsen [EMAIL PROTECTED] wrote: Dear R-helpers, I'm for sure not familiar with R, but it seem like a nice sofware tool, so I've decided to try using it. Here is my problem I just can't figure out: I'd like to do least square fit of a straight horizontal (a = 0) line y = ax + b through some data points x = (3,4,5,6,7,8) y = (0.62, 0.99, 0.83, 0.69, 0.76, 0.82) How would i find b? And in the context of linear models: x - 3:8 y - c(0.62, 0.99, 0.83, 0.69, 0.76, 0.82) lm(y ~ 1) _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Sweave and warning messages
How does one tell Sweave() to include analysis warning messages in the verbatim output? _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] stat question - not R question so ignore if not interested
On Dec 5, 2006, at 3:42 PM, Leeds, Mark ((IED)) wrote: If do a scattrplot of data ( x and y ) and there are two clouds of points. One cloud is in the left bottom corner of the plot and the other cloud is in the upper right. If I fit a regression line to this data ( or equivalently , calculate a correlation ), then obviously, it is going to seem like x and y are related because a line has to be connected between the 2 clouds. But, there must be a regression assumption that is violated here because if the regressions are done separately on each cloud, then there really isn't a relationship between x and y. I was just wondering 1) what assumption in regression is being violated in the first case or 2) possibly if the regression is valid and the results just have some different interpreation ? One needs only to look at diagnostic plots: Suppose set.seed(2) xy - data.frame(y = c(rnorm(300), rnorm(300, 5)), x = c(rnorm(300), rnorm(300, 5))) op - par(mfrow = c(2,2)) plot(lm(y ~ x, xy)) par(op) The model does not fit well because the residuals aren't flat as a function of fit and because homoscedasticity is violated. When this happens we might try a different approach: require(sm) xy.sm - sm.regression(xy$x, xy$y) Whenever there's a big discrepancy between an OLS fit and a robust one, we should not pursue the OLS one w/o reinterpretation, which others have discussed in their replies. _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Help with response CIs for lme
Thanks, Spencer, for spending time on my question.
On Dec 5, 2006, at 1:48 AM, Spencer Graves wrote:
No, your example computation does NOT produce the desired lme
prediction intervals. I ran your script and got exactly the same
numbers for upper and lower limits. Even without any consideration
of statistical theory, this suggests either shockingly precise
statistical estimation or a problem with your algorithm.
There may have been a typo in what I sent to the list.
The following script produces prediction intervals that are not
nearly as shocking as intervals with 0 width:
library(mlmRev)
library(nlme)
hsb.lme - lme(mAch ~ minrty * sector, random = ~ 1 | cses, Hsb82)
(hsb.int - intervals(hsb.lme))
hsb.new - data.frame(
minrty = rep(c('No', 'Yes'), 2),
sector = rep(c('Public', 'Catholic'), each = 2))
cbind(hsb.new, predict(hsb.lme, hsb.new, level = 0))
cbind(hsb.new, rbind(
hsb.int[[1]][1,],
hsb.int[[1]][1,] + hsb.int[[1]][2,],
hsb.int[[1]][1,] + hsb.int[[1]][3,],
hsb.int[[1]][1,] + hsb.int[[1]][2,] + hsb.int[[1]][3,] + hsb.int
[[1]][4,]
))
The latter produces:
minrty sector lower est.upper
1 No Public 12.467015 12.712155 12.95730
2Yes Public 6.657422 7.387386 8.11735
3 No Catholic 14.54 15.123113 15.72400
4Yes Catholic 10.062856 11.821924 13.58099
snip
To briefly outline some of the difficulties, we first should
ask if you want confidence intervals for the MEAN of future values
or for the future values themselves?
I want the former, and that's what I think I computed.
And how do you want to handle the random effects? If you want the
mean of the fixed effects, averaging over random effects, that
should be fairly easy.
Exactly. And my question is --- if the CIs I obtained were correct
--- is there a less laborious way to obtain them?
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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] overplot() examples fail (package:gplots)
require(gplots) data(rtPCR) overplot( RQ ~ Conc..ug.ml. | Test.Substance, data=rtPCR, subset=Detector==ProbeType 7 Conc..ug.ml. 0, same.scale=TRUE, log=xy, f=3/4, main=Detector=ProbeType 7, xlab=Concentration (ug/ml), ylab=Relative Gene Quantification ) # Error in lowess.default(mf[[-response]], mf[[response]], f = f, iter = iter, : # 'x' is empty # In addition: Warning messages: # 1: no non-missing arguments to min; returning Inf # 2: no non-missing arguments to max; returning -Inf ** # The second example fails as well, but with: # Error in plot.window(xlim, ylim, log, asp, ...) : # need finite 'ylim' values # In addition: Warning messages: # 1: no non-missing arguments to min; returning Inf # 2: no non-missing arguments to max; returning -Inf ** R version 2.4.0 (2006-10-03) powerpc-apple-darwin8.7.0 locale: C attached base packages: [1] splines grid methods utils stats graphics grDevices datasets [9] base other attached packages: gplots gdata gtools lme4gam effects Hmisc codagmodels 2.3.22.3.12.3.0 0.9975-9 0.971.0-9 3.1-2 0.10-7 2.13.1 MatrixreshapeJGR iplots JavaGD rJava MASSlattice 0.9975-60.7.1 1.4-131.0-50.3-5 0.4-12 7.2-30 0.14-15 _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Problem with pairs() in nlme
Dear r-helpers, After successfully running require(nlme) vfr.lmL - lmList( estimate ~ (slant + respType + visField + hand)^2 | subject, vfr ) pairs(vfr.lmL, id = 0.01, adj = -0.5) # Pinheiro Bates (p. 141) produces the following error: Error in sprintf(gettext(fmt, domain = domain), ...) : object form not found Any guesses as to what I may have done wrong? vfr is not a grouped object because: vfrg - groupedData(estimate ~ slant | subject, data = vfr) vfrg.lmL - lmList( estimate ~ (slant + respType + visField + hand)^2 | subject, vfrg) Error in function (classes, fdef, mtable) : unable to find an inherited method for function lmList, for signature formula, nfnGroupedData The data are at http://www.people.virginia.edu/~mk9y/LongFormat.csv To get the working data.frame: vf - read.table(http://www.people.virginia.edu/~mk9y/ LongFormat.csv, header = TRUE, sep=',') names(vf) - c( 'slant', 'estimate', 'respType', 'visField', 'hand', 'order', 'sex', 'subject', 'handPref' ) require(reshape) vf - sort_df(vf, vars = 'slant') vf$subject - factor(vf$subject) summary(vf) vfr - subset(vf, handPref == 'R', select = -handPref) vfr - subset(vfr, slant %in% c(10, 20, 30)) _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Slight discrepancy between predict.lm() and all.effects()
In the course of exploring response prediction, I stumbled upon a
small discrepancy between the CIs produced by predict.lm() and
all.effects()
require(mlmRev)
require(effects)
hsb.lm - lm(mAch ~ minrty * sector, Hsb82)
hsb.new - data.frame(
minrty = rep(c('No', 'Yes'), 2),
sector = rep(c('Public', 'Catholic'), each = 2))
hsb.eff - all.effects(hsb.lm)
cbind(
hsb.new,
predict(hsb.lm, hsb.new, interval = 'confidence', type =
'response')
)
# the following lower and upper bounds differ starting with the
fourth decimal place
data.frame(
hsb.new,
fit = hsb.eff[[1]]$fit,
lwr = hsb.eff[[1]]$lower,
upr = hsb.eff[[1]]$upper
)
Is this due to rounding or algorithm?
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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 with response CIs for lme
Hi,
Can someone please offer a procedure for going from CIs produced by
intervals.lme() to fixed-effects response CIs.
Here's a simple example:
library(mlmRev)
library(nlme)
hsb.lme - lme(mAch ~ minrty * sector, random = ~ 1 | cses, Hsb82)
(intervals(hsb.lme))
(hsb.new - data.frame
minrty = rep(c('No', 'Yes'), 2),
sector = rep(c('Public', 'Catholic'), each = 2)))
cbind(hsb.new, predict(hsb.lme, hsb.new, level = 0))
Is the following correct (I know from the previous command that the
estimate is correct)?
cbind(hsb.new, rbind(hsb.int[[1]][1,], hsb.int[[1]][1,]+hsb.int[[1]]
[2,], hsb.int[[1]][1,]+hsb.int[[1]][3,], hsb.int[[1]][1,]+hsb.int[[1]]
[2,] + hsb.int[[1]][3,] + hsb.int[[1]][4,]))
If so, is there an easier way to write it?
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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 with plot(augPred()) plot(comparePred()) in nlme
Dear r-helpers, When I issue the commands plot(augPred(mcc.lme, primary = ~ mcc$age, length.out = 2, level = c (0, 1))) or plot(comparePred(mcc1.lis, mcc.lme, primary = ~ mcc$age, length.out = 2), layout = c(4, 3))) no lines are drawn. But fm1 - lme(Orthodont) plot(augPred(fm1, level = 0:1, length.out = 2)) does plot lines. augPred() and comparePredict() seem to be working correctly, as shown below augPred(mcc.lme, primary = ~ mcc$age, length.out = 2, level = c(0, 1)) mcc$age .groups score.type 1 30 1 108 original 2 30 2 103 original 3 30 396 original 4 30 484 original 5 30 5 118 original 6 30 6 110 original ... 91 30 10 101 predict.subject 92 48 10 101 predict.subject 93 30 11 109 predict.subject 94 48 11 109 predict.subject 95 30 12 122 predict.subject 96 48 12 122 predict.subject comparePred(mcc1.lis, mcc.lme, primary = ~ mcc$age, length.out = 2)) mcc$age subject score.type 1 30 1 108 original 2 30 296 original 3 30 3 110 original 4 30 4 122 original 5 30 5 103 original 6 30 6 117 original ... 671 30 10 101 mcc.lme 681 48 10 101 mcc.lme 691 30 11 109 mcc.lme 701 48 11 109 mcc.lme 711 30 12 122 mcc.lme 721 48 12 122 mcc.lme _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] have I an actual matrix?
On Nov 7, 2006, at 6:25 PM, Ricardo Rodríguez - Your EPEC ICT Team wrote: library(RMySQL) con - dbConnect(dbDriver (MySQL),host='localhost',username='root',dbname='ibdona') rs - dbGetQuery (con,select n,year from ibdona.library_location) dbDisconnect(con) Graph - barplot(rs) And here the error I get... Error in barplot.default(rs) : 'height' must be a vector or a matrix paste(rs) gives me... [1] c(307, 65, 2, 28, 3, 229, 81, 5, 7, 558, 134, 53, 9) [2] c(2002, 2002, 2002, 2002, 2002, 2003, 2003, 2003, 2003, 2004, 2004, 2004, 2004) nums - c(307, 65, 2, 28, 3, 229, 81, 5, 7, 558, 134, 53, 9) names(nums) - c(2002, 2002, 2002, 2002, 2002, 2003, 2003, 2003, 2003, 2004, 2004, 2004, 2004) barplot(nums) or require(gplots) barplot2(nums, plot.grid = TRUE, las = 1) # offers many nice options _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Equivalent to Stata command
On Nov 4, 2006, at 10:57 AM, Jon Minton wrote: Do any of you know if there's an equivalent function to the Stata command: Use v1 v3 v5 v2 v7 using file.dat In R? (i.e. something that just selectively loads certain variables from a file and not others)? How about (assuming that columns in 'file.dat' are separated by white space) data - read.table(file.dat, header = T, sep = ) # reads in the whole file data - data[, c(1, 3, 5, 2, 7)] # keeps the columns you need For more, see http://finzi.psych.upenn.edu/R/doc/manual/R-data.html _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] CI -- fixed effects -- response -- mixed models
Dear Friends,
I have been following the discussions of mixed-effects models with
some confusion, and I realize that much of this is work in progress,
and that much of the discussion is beyond my knowledge of statistics.
My question is simple, though: Is there a set of commands that will
produce an output equivalent to the exceedingly useful
predict(bl.lm, newdata = bl.new, type = 'response', interval =
'confidence')
for (at least) gaussian mixed-effects model (but preferably for glmm
models)? I have looked at
predict.glmmPQL {MASS}
predict.lme {nlme}
and neither of them offer exactly what I need, and I just don't know
enough to go from what they do offer to what I need. I have Pinheiro
Bates as well as MASS, and both come tantalizingly close to what I
need, but I can't figure out the next step.
AFAIK, there's nothing of the sort for aov(. ~ ., Error(...) ...)
either.
In order to publish results of designed psychological experiments
(most of which are of the classic anova variety, with all the
predictors being factors), we need to plot error bars on our
interaction plots. I suspect (from the discussion on this list) that
my colleagues are using SPSS or SAS, and reporting incorrect CIs.
Not being a statistician I have hit a wall here. I'm not sure if the
transition to the results I need is staring me in the face, and I
don't know enough to take the next step, or if the tools aren't yet
available. In any event, I would be very grateful to you for guidance
on how to proceed.
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] no possible to load a package correctly dowloaded by the R prompt
Hi,
On Oct 30, 2006, at 11:43 AM, Tancredi Caruso wrote:
install.packages(c(untb))
library(untb)
Carico il pacchetto richiesto: partitions (I'm loading requested
package:partitions)
Errore: pacchetto 'partitions' non caricato (Error: package
partitions not loadad)
Warning messages:
1: the package 'untb' has been created with R version 2.3.1
2: non c'è alcun pacchetto chiamato 'partitions' in: library(pkg,
character.only = TRUE, logical = TRUE, lib.loc = lib.loc) (there's
not a package named partitions in..)
This means that you need to also
install.packages('partitions')
You could have said
install.packages('untb', dependencies = TRUE),
and this would have done the job for you.
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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 with unlist
Dear r-helpers, I have a list whose elements are str(durCut[[1]]) Ord.factor w/ 5 levels vLowlowmed..: 3 2 5 2 2 2 4 4 3 5 ... How do I unlist durCut into an ordered factor? str(unlist(durCut)) int [1:3024] 3 2 5 2 2 2 4 4 3 5 ... _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] plot(all.effects)
Dear r-helpers,
plot(all.effects()) uses trellis for its output, and often produces
several effect plots in a layout. Can anyone tell me how to set the
arguments to plot.effect which default to
row=1, col=1, nrow=1, ncol=1, more=FALSE
so that I can plot multiple effect plots on one layout?
I was hoping that a call like
last - rep(c(TRUE, FALSE), c(3, 1))
lay -matrix(c(1:4,), 2, 2, byrow = T)
for(i in 1:4) {
tmp.lm - lm(y ~ a + b, data)
spl - which(lay == i, arr.ind = TRUE)
rowN = spl[1]
colN = spl[2]
plot(all.effects(tmp.lm), row = rowN, col = colN, nrow = 2, ncol =
2, more = last[i])
}
would work (my data are complicated, and have not had the time to set
up a replicable example).
Here is what I ran, and what R told me:
for(i in 1:4) {
tmp.lm - lm(duration ~ (pitch + vis + aud + display)^2 -
aud:display - vis:aud -
pitch:vis, data = subset(txt, subj == unique(txt$subj)[i]))
spl - which(lay == i, arr.ind = TRUE)
rowN = spl[1]
colN = spl[2]
plot(all.effects(tmp.lm), rug = F, ask = F,
main = paste('Subject = ',sep = '', i),
row = rown, col = coln, nrow = 2, ncol = 2, more = last[i])
}
Error in plot.effect(x[[(i - 1) * cols + j]], row = i, col = j, nrow
= rows, :
formal argument row matched by multiple actual arguments
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
R-help@stat.math.ethz.ch 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] Constructing predictions from HPDinterval() after lmer()
Dear r-helpers, Following up on http://finzi.psych.upenn.edu/R/Rhelp02a/archive/ 81159.html where Douglas Bates gives a helpful application of lmer() to data(sleepstudy, package = 'lme4'), I need a bit more help in order to plot the correct confidence intervals of a designed experiment such as: data(ratdrink, package = 'faraway') I follow the steps Douglas took in his example: summary( rd.er - lmer(wt ~ weeks*treat + (1 | subject), data = ratdrink) ) Linear mixed-effects model fit by REML Formula: wt ~ weeks * treat + (1 | subject) Data: ratdrink AIC BIC logLik MLdeviance REMLdeviance 962.4 982.8 -474.2 964.3948.4 Random effects: Groups NameVariance Std.Dev. subject (Intercept) 71.206 8.4384 Residual 51.222 7.1570 number of obs: 135, groups: subject, 27 Fixed effects: Estimate Std. Error t value (Intercept)52.8800 3.1928 16.56 weeks 26.4800 0.7157 37.00 treatthiouracil 4.7800 4.51531.06 treatthyroxine -0.7943 4.9756 -0.16 weeks:treatthiouracil -9.3700 1.0121 -9.26 weeks:treatthyroxine0.6629 1.11530.59 Correlation of Fixed Effects: (Intr) weeks trtthr trtthy wks:trtthr weeks -0.448 treatthircl -0.707 0.317 treatthyrxn -0.642 0.288 0.454 wks:trtthrc 0.317 -0.707 -0.448 -0.203 wks:trtthyr 0.288 -0.642 -0.203 -0.448 0.454 rd.mc - mcmcsamp(rd.er, 5) library(coda) HPDinterval(rd.mc) lower upper (Intercept)46.420404 59.406398 weeks 25.070131 27.930363 treatthiouracil-4.420942 14.009291 treatthyroxine-10.758369 9.435761 weeks:treatthiouracil -11.404620 -7.337025 weeks:treatthyroxine -1.603858 2.842704 log(sigma^2)3.683085 4.226153 log(sbjc.(In)) 3.633853 4.955867 deviance 965.750351 980.825613 attr(,Probability) [1] 0.95 ***To make sure my request is clear*** What I need is the analog of what is produced by all.effects() in the effects package: summary(rd - lm(wt ~ weeks*treat, data = ratdrink)) Call: lm(formula = wt ~ weeks * treat, data = ratdrink) Residuals: Min 1Q Median 3Q Max -23.514 -6.660 0.230 6.914 28.343 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept)52.8800 2.6547 19.919 2e-16 *** weeks 26.4800 1.0838 24.433 2e-16 *** treatthiouracil 4.7800 3.7544 1.2730.205 treatthyroxine -0.7943 4.1371 -0.1920.848 weeks:treatthiouracil -9.3700 1.5327 -6.113 1.08e-08 *** weeks:treatthyroxine0.6629 1.6890 0.3920.695 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Residual standard error: 10.84 on 129 degrees of freedom Multiple R-Squared: 0.9121, Adjusted R-squared: 0.9087 F-statistic: 267.8 on 5 and 129 DF, p-value: 2.2e-16 rd.eff - all.effects(rd) rd.ci - data.frame(y = rd.eff[[1]]$fit, Lower = rd.eff[[1]] $lower, Upper = rd.eff[[1]]$upper) _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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 95% confidence bands on a simple linear regression model from lm()
On Oct 20, 2006, at 2:46 PM, Jason Horn wrote: What's the best / simplest way to create 95% confidence bands for a model created with lm() that can be plotted around teh regression line? I've looked everywhere for this - I guess I must be missing something. - Jason library(effects) ?summary.effect _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Hide line ends behind unfilled circles?
Dear r-helpers, xx - c(0.000, 0.210, 0.714, 0.514, 1.000, 0.190, 0.590, 0.152) yy - c(0.000, 0.265, 0.256, 0.521, 0.538, 0.761, 0.821, 1.000) aa - c(19, 19, 19, 21, 19, 21, 21, 21) x0 - xx[c(1, 1, 2, 2, 2, 3, 3, 4, 4, 4, 5, 6, 6, 7)] y0 - yy[c(1, 1, 2, 2, 2, 3, 3, 4, 4, 4, 5, 6, 6, 7)] x1 - xx[c(2, 3, 3, 4, 6, 4, 5, 5, 6, 7, 7, 7, 8, 8)] y1 - yy[c(2, 3, 3, 4, 6, 4, 5, 5, 6, 7, 7, 7, 8, 8)] plot(yy ~ xx, pch = aa, cex = 3) segments(x0, y0, x1, y1) Can anyone suggest a way of insuring that the lines are hidden behind the unfilled circles? _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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] Compact presentation of multiple figures
Dear r-helpers, I have six panels: op(par(mfrow = c(2, 3), xaxt = 'n', yaxt = 'n', pty = 's'). Each of them has a variable main = 'i', and xlab = '', ylab = '' I would like to achieve two things: (1) a common x-axis label under panel 5, and one label to the left of panels 1 and 4 (2) minimal space between the panels. I have looked for examples, and even the thorough Les paramètres graphiques didn't help me: I haven't been able to reduce the space between the rows of panels nearly enough. My best attempt: par(pty = 's', xaxt = 'n', yaxt = 'n', mfrow = c(2, 3), mgp = c(1, 0, 0), mar = c(1.1, 2.1, 1.1, 0.1)) _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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.
