' on port 80.
2: In getDependencies(pkgs, dependencies, available, lib) :
package ‘Matching’ is not available (for R version 2.13.1)
Thanks.
JP
--
View this message in context:
http://r.789695.n4.nabble.com/trouble-in-installing-package-matching-tp3858594p3858594.html
Sent from the R help mailing
On 4 May 2011 15:32, peter dalgaard pda...@gmail.com wrote:
On May 4, 2011, at 15:11 , JP wrote:
Peter thanks for the fantastically simple and understandable explanation...
To sum it up... to find the z values of a number of pairwise wilcox
tests do the following:
# pairwise tests
- statistic(t) # signed and everything
# correct for multiple testing if you are doing a number of the above...
I would never have got here without your guidance - so kudos to you.
JP
On 5 May 2011 14:52, peter dalgaard pda...@gmail.com wrote:
On May 5, 2011, at 10:58 , JP wrote:
On 4 May 2011 15:32
On 3 May 2011 20:50, peter dalgaard pda...@gmail.com wrote:
On Apr 28, 2011, at 15:18 , JP wrote:
I have found that when doing a wilcoxon signed ranked test you should report:
- The median value (and not the mean or sd, presumably because of the
underlying potential non normal
, paired=T)
# what is the data structure we got back
is.matrix(x$p.value)
# p vals
x$p.value
# z.scores for each
z.score - qnorm(x$p.value / 2)
On 4 May 2011 13:25, peter dalgaard pda...@gmail.com wrote:
On May 4, 2011, at 11:03 , JP wrote:
On 3 May 2011 20:50, peter dalgaard pda...@gmail.com
Thanks Uwe,
How do I calculate the Z score and r value - please (once I have the p values)?
Many Thanks
JP
2011/5/2 Uwe Ligges lig...@statistik.tu-dortmund.de:
To get the statsitics, you will have to run each wilcox.test manually. the
pairwise... version just extracts the p-values
(some places even
quote W and df) ? What else would you suggest?
- How do I calculate the Z score and r for the above example?
- How do I get each statistic from the pairwise.wilcox.test call?
Many Thanks
JP
__
R-help@r-project.org mailing list
https
to change the above ggplot2 code to do just that? I have been
playing with facet_grid all day... Also the values on the axis are
incorrect ... they should be in the range 1:5 (as r above) and a plot
should show the probability density of that value...
Any help? I am going mad...
Many Thanks
JP
Sorry for the cross post - but I will post your answer in the other place
too for completeness
And thanks for your answer... that is brilliant especially the second
transparent plot
Fantastic
On 30 March 2011 12:21, ONKELINX, Thierry thierry.onkel...@inbo.be wrote:
Dear JP,
Please do
these are working properly
box.umbrella = list(col = black))
)
On 24 March 2011 21:59, David Winsemius dwinsem...@comcast.net wrote:
On Mar 24, 2011, at 1:37 PM, JP wrote:
Using Trellis, am successfully setting up a number of panels (25) in which
I
have two box and violin plots.
I would like
))
)
--
David.
On Mar 25, 2011, at 12:06 PM, David Winsemius wrote:
OK, I did it , but it required a minor hack to panel.violin, since in its
native state panel.violin only passes a single vector the the grid plotting
functions.
On Mar 25, 2011, at 6:29 AM, JP wrote:
Hi there David
Using Trellis, am successfully setting up a number of panels (25) in which I
have two box and violin plots.
I would like to colour - one plot as RED and the other as BLUE (in each
panel). I can do that with the box plots, but the violin density areas just
take on one colour.
My basic call is as
JP
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained
0
[2,]0 0
[3,]0 0
[4,]0 1
I'll greatly appreciate it if you may help!
JP Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
UNC at Chapel Hill
Chapel Hill, NC
US
[[alternative HTML version deleted
.Treatment vs. Measurement.T2.M6.placebo (I did not include
Treatment as a factor in the query below yet).
Thanks for your help (data was attached)!
Jp Jin
summary(glm(data$Lesion.Size~Time+Measurement+Time*Measurement, data=data))
Call:
glm(formula = data$Lesion.Size ~ Time + Measurement + Time
Hi Jim,
Thanks for the answer.
What I actually want is a session sequence 1,2,... per patient. This would
be very useful to look at trends of HPV infections from the first to the
second sample etc. It would also allow me to extract the HPV data of the
first sample (session 1).
Thx
JP
On Sat
of the session to a session id (1-9). This would be necessary to obtain
information and do some analysis on the first occurence of a specific
patient or to look for trends.
Thanks
JP Bogers
University of Antwerp
[[alternative HTML version deleted
I wonder if the right approach is to convert temp.ts into a matrix, add the
column at the end, and then call xtable()... ...anyone have any
suggestions?
TIA.
- Ken
Ken-JP wrote:
Hi,
I saw this example for 2.10 Time series in the xtable gallery
documentation.
http://cran.r
(as.data.frame(temp.table)),
2), digits = 0)
On Sun, Sep 27, 2009 at 2:24 PM, Ken-JP kfmf...@gmail.com wrote:
Hi,
I saw this example for 2.10 Time series in the xtable gallery
documentation.
http://cran.r-project.org/web/packages/xtable/vignettes/xtableGallery.pdf
How would I add a column at the end
Hi,
I saw this example for 2.10 Time series in the xtable gallery documentation.
http://cran.r-project.org/web/packages/xtable/vignettes/xtableGallery.pdf
How would I add a column at the end Total which sums the row, with minimal
changes to the code below?
Thanks in advance.
- Ken
2.10
I've been experimenting recently with the fantastic Sweave/xtable combination
for generating latex. In the xtable vignette, I found this great example of
printing a ts object by months.
Is there a way to modify this code to generate RED numbers inside xtable for
negative results in x.ts?
For instance, I am trying to run Roxygen on:
require( zoo ) # needed for time series
setClass( zoo ) # lets S4 know about S3 class so we can use as an
argument
setClass( myClass, representation( .zoo=zoo ), prototype( 0,
as.Date(1970-01-01) ))
When I run this code through
Any way to tell Roxygen to ignore a block of code? It is generating an
unwanted .Rd file.
I've been searching for hours for an example, scouring documentation, but no
luck...
Thanks.
- Ken
--
View this message in context:
Hi,
I have been using R for a while. Recently, I have begun converting my
package into S4 classes. I was previously using Rdoc for documentation.
Now, I am looking to use the best tool for S4 documentation. It seems that
the best choices for me are Roxygen and Sweave (I am fine with tex).
Thanks, Uwe, Peter, and Ray, for taking the time to look into this.
Just to wrap up this thread, and so that others may benefit,
I tried writing both a R code version and an inline C version.
Tested on a 8GB Ubuntu 64amd box, R 2.81, the speed difference was:
104secs vs 0.534secs, or the C
The code below shows what I'm trying to get rid of.
If there is no way to get rid of the loop, I will try to use package( inline
).
I'm just curious as to whether there is a vector way of doing this
algorithm.
#
set.seed(1)
x - runif(100)
# I want to calculate y such that:
#
# 1. if x0.75, y - 1
# 2. else if x0.25, y - -1
# 3. else if y_prev==1 x0.5, y - 0
# 4. else if y_prev==-1 x0.5, y - 0
# 5. else y - y_prev
#
# 1. and 2. are directly doable without looping.
#
# How do I do 3.-5. without looping?
Is your CSV file really that big? Have you passed the correct parameters to
read.table()?
For example, specified the correct sep=, parameter?
If you've done everything correctly and are still running out of memory,
maybe you need to go to 64-bit. R works great under 64-bit Ubuntu (8GB on
my
Let's start with a concrete case of n=3 dimensions.
Along dimension x, I have a matrix of 5 vectors (each with ten rows)
Along dimension y, I have a matrix of 3 vectors (each with ten rows)
Along dimension z, I have a matrix of 2 vectors (each with ten rows)
I am trying to write a:
Peter,
Thank you for your array() hint for multi-dimensional matrices.
Actually, my final answer should be of dimension 5,3,2 because my
funcp(a,b,c) will be reduced to one number when I set a to a column of x, b
to a column of y, and c to a column of z.
I did make some useful observations,
Hi,
I used Tinn-R for a long time, but had real headaches on Vista (commands not
being sent, etc...) that were not resolved since R 2.8 or so.
Since then, I have switched to Eclipse/StatET. The setup requires more
effort, but it is much easier to manage your own packages. With the Eclipse
IDE
This is what I'm trying to do:
HasPersistence - an Interface class which implements things like
WriteToDisk(), ReadFromDisk()
B isA A
C isA A, but also implements HasPersistence
My solution in R.oo is to have a root class called A which implements
IsPersistent() by returning FALSE, but is
yearly 8% drift, 25% sd
why are x and y so different (x and z look ok)?
Does this have something to do with biases due to the relationship between
population and sample-estimates as a function of n samples and sd? Or am I
doing something wrong?
Hi Karl,
Your comment is very interesting.
Do you mean I should favor:
rnorm(n, 0, 1) * b + a
over
rnorm(n, a, b)
? What is the proper/safe way to use rnorm()?
FWIW,
set.seed( 1 );
yy - mean( rnorm( 10 ) *
Hi Duncan,
I tried
\encoding{latin1}
and it gave me the same result as
\encoding{UTF-8}
In other words, no errors, but I plenty of warnings from
Warning in grep(^[[:blank:]]*\n?$, x, perl = TRUE) :
perl = TRUE is only fully implemented in UTF-8 locales
Hi,
I posted this message on the StatET-user board last week, but it looks like
a ghost-town...
I have a bad feeling that there is some code in the plug-in which doesn't
work well with my environment, but if I am lucky, maybe other users have
worked around this problem somehow - I am hoping
UPDATE on StatET and Ubuntu 8.10 amd64:
StatET also works perfectly on Ubuntu 8.10 amd64, but the installation
procedure takes a lot more effort than on XP Pro 32-bit or Vista 32-bit (at
least from my experience).
But I am very happy to have more RAM and having StatET working definitely
helps
working on a 64-bit Windoze system, do please let
us know.
Thank you.
- Ken
John Fox-6 wrote:
Dear Ken-JP,
I'm not sure that this is relevant, but I posted a question recently to
the
StatET list about using StatET with 64 bit Vista (I don't yet have the
machine), and was told that it would
Is there a specific place where we can place code to run once only in a
package?
I have code that switches based on Sys.info()[[nodename]] - but since this
just about never changes, I would like to run it only once when someone
runs:
require( mypackage ) or library( vte )
I'm tempted to have
Thanks to pointers from Uwe, I first tried zzz.R and .First.lib(), which
does what I needed (initialize once).
Then under Martin's suggestion, I converted the package to use NAMESPACE and
.onLoad().
Using NAMESPACE, I was able to hide my globals behind a . (eg .myGlobal
- 72) and use
Hi,
I need some help with 2.9.0 parse_Rd() Version 2 changes. I read the .pdf
file and some posts on r-help, but after playing with this for several
hours, I can't seem to get around this UTF-8 problem.
- I'm trying to get rid of some warnings during R CMD Check for R 2.9.0Alpha
on Japanese
Rolf Turner-3 wrote:
On 7/04/2009, at 3:34 PM, Ken-JP wrote:
snip
Using NAMESPACE, I was able to hide my globals behind a
. (eg .myGlobal
- 72) and use exportPattern(^[^\\.]*) to prevent users from
seeing my
globals, yet I was able to access their values inside my package
Peter Dalgaard wrote:
Hum.. Fedora 9 doesn't have it either.
It does have /usr/share/X11/rgb.txt though, so please check whether it
has moved. I'm curious as to why (only) R/tcltk would be confused by
this sort of thing.
If you check here:
On the boards for Ubuntu 8.10 64-bit, there were comments along the lines
that:
/etc/X11/rgb.txt
was missing.
However, even after I replace this file, and logged back out in, this
problem went away.
It's shocking that a file as old/basic as /etc/X11/rgb.txt can be removed -
I'm sure a lot
An update: after several days of struggling, I got StatET to work on Ubuntu
8.10 amd64, R 2.8.1.
Here are some tips:
1. You may run into an X11 issue with tktcl in R as someone decided to omit
/etc/X11/rgb.txt If you get weird issues with your R installation with
window colors like red or
Yes, I have x11-common installed, and dpkg -S /etc/X11/rgb.txt shows not
found for me.
This is on Ubuntu 8.10 amd64.
http://ubuntuforums.org/archive/index.php/t-59024.html
Thanks for the detailed explanation on how R decides on where to install
packages!
I think I ran into problems when I
I am running on 64-bit Ubuntu, R version 2.8.1
If I do anything Tcl/Tk related like:
library( Rcmdr )
or
available.packages()
I get the error:
Error in structure(.External(dotTclObjv, objv, PACKAGE=tcltk), class =
tclObj) :
[tcl] unknown color name red
with very good examples of statistical visualization.
Talks Hans Rosling: Debunking third-world myths with the best stats you've
ever seen
http://www.ted.com/index.php/talks/hans_rosling_shows_the_best_stats_you_ve_ever_seen.html
--
View this message in context:
I recently got a RFC on Eclipse and StatET setup from a R-help user, so here
it is.
Note: there may be slight errors of omission in my directions as I am making
these notes after I had a successful install. If you have questions post
here.
Setup tested with Eclipse 3.4.0 on XP 32-bit and
I had all these headaches with Tinn-R on Vista - tried reading all the
message boards, reconfiguring .Rprofile, etc... ...no luck.
I finally gave up and started using Eclipse with StatET. Now, it's actually
easier to run RCMDs to check and release a package, and with SVN integration
in
Say I have:
set.seed( 1 )
m - matrix( runif(5^2), nrow=5, dimnames = list( c(A,B,C,D,E),
c(O,P,Q,R,S) ) )
m
O P Q R S
A 0.2655087 0.89838968 0.2059746 0.4976992 0.9347052
B 0.3721239 0.94467527 0.1765568 0.7176185 0.2121425
C 0.5728534 0.66079779
Okay, this one is hard to put into words:
x - 1:9; names(x) - x
y - x %o% x
y
1 2 3 4 5 6 7 8 9
1 1 2 3 4 5 6 7 8 9
2 2 4 6 8 10 12 14 16 18
3 3 6 9 12 15 18 21 24 27
4 4 8 12 16 20 24 28 32 36
5 5 10 15 20 25 30 35 40 45
6 6 12 18 24 30 36 42 48 54
7 7 14 21 28 35 42
CORRECTION:
my.foo - function( a, b ) { c - a - b; } #really more complex, but just
to illustrate
--
View this message in context:
http://www.nabble.com/Doing--o--that-operates-on-columns-instead-of-atomics-tp22701363p22701400.html
Sent from the R help mailing list archive at Nabble.com.
zoo's rollapply() function appears to be extremely useful for plugging in a
function on-the-fly to run over a window. With inline, there is a lot more
coding and room for error, and the code is less portable because the user
has to have R compiling set up or it won't work.
However, rollapply()
I agree with Duncan. I used to do exactly what you did - source()ing data
files inside a wrapper not unlike C #define wrappers, but it became a
headache with more files and the files began looking more cluttered.
It has taken me several days to learn about how create a package properly,
along
Hi,
I need some help improving this ugly code I wrote. I would like to shift
forward a zoo object, matrix, ts, or list by shift items (default 1) and
fill the holes with 0's.
The code below works, but it looks ugly. I could write a function
lag.zerofill() which calls the two functions below
require( zoo )
inp - c( 5, 9, 4, 2, 1 );
m - zoo( cbind( inp ), as.Date(2003-02-01) + (0:(length(inp)-1)));
dim( m ) # [1] 5 1
dim( m[1,,drop=FALSE] ) # [1] 1 1 - ok
dim( lag( m, -1 )) # [1] 4 1 - ok
dim( rbind( m[1,,drop=FALSE], lag(m,-1) )) # NULL - converted from zoo
matrix to zoo
Thank you for your reply, but I am still confused.
Let me clarify... ...my problem isn't with zoo-ness per se.
With zoo objects, there appears to be zoo-matrices and zoo-vectors.
My problem is this - I start with a zoo-matrix:
x - m[1,,drop=FALSE]
x
inp
2003-02-01 5
is.matrix(
Hi Achim,
That was a very quick reply/fix that got posted in between my reading and my
response.
I have downloaded your fix from:
svn checkout svn://r-forge.r-project.org/svnroot/zoo
for the HEAD revision and confirmed that it works as expected - I tested
using the code I posted in the first
hi,
I am sure this is an obvious question,
I have a optimized model with coefficients from
stepAIC. I can't figure out how to find the
max value of a function with those coefficients.
Its part of a dynamic web page or else i would
have done it by hand. The code works fine, so you probably
don't
60 matches
Mail list logo
