e to connect to 'cran.r-project.org' on port 80.
2: In getDependencies(pkgs, dependencies, available, lib) :
package ‘Matching’ is not available (for R version 2.13.1)
Thanks.
JP
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(t)
sweet.zscore <- 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 wrote:
>
> On May 5, 2011, at 10:58 , JP wrote:
>
&
On 4 May 2011 15:32, peter dalgaard 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 follo
nferroni", exact=F, 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 wrote:
>
> On May 4, 2011, at 11:03 , JP wrote:
>
>> On 3 May 2011 20:50,
On 3 May 2011 20:50, peter dalgaard 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
>>
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 :
> To get the statsitics, you will have to run each wilcox.test manually. the
> pairwise... version just extracts the p-values and adjusts them.
>
>
score (or value)
- r
- p value
My questions are:
- Are the above enough/correct values to report (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?
Ma
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 wrote:
> Dear JP,
>
> Please do not cross pos
as r above) and a plot
should show the probability density of that value...
Any help? I am going mad...
Many Thanks
JP
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
= "black"),
>box.umbrella = list(col = "black"))
>)
>
> --
> 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
>> na
o)
panel.bwplot(..., box.ratio = .1)
},
par.settings = list(plot.symbol = list(pch = 21, col = "gray"),
box.rectangle = list(col = "black"), # not sure these are working properly
box.umbrella = list(col = "black"))
)
On 24 March 2011 21:59, David Winsemius wrote:
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
here is no direct
relationship between the values of a single row, or is there?)
I am using R 1.12.1 for Linux,
Many Thanks
JP
[[alternative HTML version deleted]]
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1
## between Male and Female
Male Female
[1,] -1 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
.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 + T
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
te 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 de
table(addmargins(as.matrix(as.data.frame(temp.table)),
> 2), digits = 0)
>
> On Sun, Sep 27, 2009 at 2:24 PM, Ken-JP wrote:
>>
>> Hi,
>>
>> I saw this example for 2.10 Time series in the xtable gallery
>> documentation.
>>
>> http://cran.r-project.org/w
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.
>
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 Ti
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?
Thank
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
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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).
Ar
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 versi
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.
#
-
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
set.seed(1)
x <- runif(100)
# I want to calculate y such that:
#
# 1. if x>0.75, y <- 1
# 2. else if x<0.25, y <- -1
# 3. else if y_prev==1 && x<0.5, y <- 0
# 4. else if y_prev==-1 && x>0.5, y <- 0
# 5. else y <- y_prev
#
# 1. and 2. are directly doable without looping.
#
# How do I do 3.-5. with
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, tho
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:
function(..
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 overri
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
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 ) * (0.25/sqrt(252
I think I got it...
I assumed that n=10 would be big enough to give me a sample mean which
converges on the population mean, but this was a bad assumption.
Using sigma / sqrt(n) for the standard error of the sample mean, I get...
-
se.x.m
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 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
-exported code. Thx!
- Ken
Rolf Turner-3 wrote:
>
>
> On 7/04/2009, at 3:34 PM, Ken-JP wrote:
>
>
>
>> Using NAMESPACE, I was able to hide my globals behind a
>> "." (eg .myGlobal
>> <<- 72) and use exportPattern("^[^\\.]*"
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 Vis
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 export
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
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
>
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
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 that
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:
https://bugs.launchpad.net/ubuntu/+
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 ha
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 "bla
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 of
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"
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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
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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 Eclips
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 Eclipse
CORRECTION:
> my.foo <- function( a, b ) { c <- a - b; } #really more complex, but just
> to illustrate
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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
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
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() s
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 wi
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 m
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.matr
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 vector
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 belo
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 nee
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