asics: ##.#. ##.#. Live Go...
Live: OO#.. Dead: OO#.. Playing
Research Engineer (Solar/BatteriesO.O#. #.O#. with
/Software/Embedded Controllers) .OO#. .OO#. rocks...1k
--
with
/Software/Embedded Controllers) .OO#. .OO#. rocks...1k
---
Sent from my phone. Please excuse my brevity.
Karl Brand wrote:
Esteemed UseRs,
I've got many biggish data frames which need a lot subs
; 1", C="> 0")
Hope this helps,
Rui Barradas
Em 06-12-2012 13:49, Karl Brand escreveu:
Esteemed UseRs,
I've got many biggish data frames which need a lot subsetting, like in
this example:
# example
eg <- data.frame(A = rnorm(10), B = rnorm(10), C = rnorm(10), D =
rn
quot; and "greater than" so google picks up this thread
Once again i find just how limited my grasp of R is...Is do.call() the
best way to call binary operators like < & > in a function? Is an ifelse
statement needed for each column to make filtering on it optional? etc
A
hway~variable, sum, fill=NA)
Jan
On 05/07/2012 12:30 PM, Karl Brand wrote:
Dimitris, Petra,
Thank you! aggregate() is my lesson for today, not melt() | cast()
Really appreciate the super fast help,
Karl
On 07/05/12 12:09, Dimitris Rizopoulos wrote:
you could try aggregate(), e.g.,
my.df
gregate(my.df[-1], my.df['pathway'], sum.)
I hope it helps.
Best,
Dimitris
On 5/7/2012 11:50 AM, Karl Brand wrote:
Esteemed UseRs,
This must be embarrassingly trivial to achieve with e.g., melt() and
cast(): deduplicating records ("pw.X" in example) for a given set of
resp
df
## The data fram i want:
wanted.df <- data.frame(pathway = c("pw.A", "pw.B", "pw.C"),
cond.one = c(0.5, 0.4, NA),
cond.two = c(0.6, 0.9, 0.2),
cond.three = c(NA, 0.1, NA))
wanted.df
--
Karl Brand
Dept of
he
couple simple steps you suggest. Also good to know that Java 1.7 can be
used with the latest R (which is all i intend to install).
Thanks again for the follow up,
Karl
On 02/20/2012 03:37 AM, Simon Urbanek wrote:
On Feb 19, 2012, at 4:31 PM, Karl Brand wrote:
Hi Hasan,
Success. For myself a
l r-cran-rjava
did NOT enable me to update my rJava. Unless i buggered up something
else along the way :/
On 02/18/2012 10:20 PM, Hasan Diwan wrote:
On 18 February 2012 13:13, Karl Brand wrote:
Thanks for yout fast response. Thing is - i managed to get Version 0.9-1
installed and fully
licit details for myself to be able use.
Thanks again, also for any further suggestions,
Karl
On 02/18/2012 07:45 PM, Simon Urbanek wrote:
On Feb 18, 2012, at 10:44 AM, Karl Brand wrote:
Esteemed useRs and Devs,
Attempts to update package:rJava to the latest version have failed. See my co
LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
--
Karl Brand
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
T +31 (0)10 704 3455 |F +31 (0)10 704 4743 |M
x, I use "su" not "sudo". Then I call R and install.packages.
Then I quit R and "su" and continue with what I want.
hope this helps.
Spencer
On 9/7/2011 5:11 AM, Karl Brand wrote:
Cheers Paul.
Its a very good point. Although i am curious how badly i can damage my
.ch
Karl
On 2011-09-07 11:02, Paul Hiemstra wrote:
On 09/07/2011 08:54 AM, Karl Brand wrote:
Esteemed UseRs and DevelopeRs,
Apologies if this question belongs else where, but it does concern R's
package installation/maintenance.
How does one start R within Emacs/ESS with root privileg
ers. If so i'd
really appreciate tips on efficient package installation/maintenance
using Emacs/ESS.
TIA,
karl
--
Karl Brand
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
P +31 (0)10 704 3455 | F +31 (0)10 704 4743 | M +31 (0)642 777 268
_
ead the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Karl Brand
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
P +31 (0)10 704 3455 | F +31 (0)10 704 4743 | M +31 (0)642 777 268
nted out to me that some times the best way to get
it just right is using more basic functions, which for heatmaps would be
image(). See:
https://www.stat.math.ethz.ch/pipermail/bioconductor/2010-August/034995.html
hth,
karl
On 04/18/2011 10:38 AM, chakri2...@yahoo.co.in wrote:
Dear Karl
-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Karl Brand
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
ficulties using them.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: Karl Brand [mailto:k.br...@erasmusmc.nl]
Sent: Thursday, December 02, 2010 2:22 AM
To: William Dunlap
Cc: r-help@r-project.org; Dimitris Rizopoulos
Subject: Re: [R] attempted merge() retur
On 12/2/2010 3:52 PM, David Winsemius wrote:
On Dec 2, 2010, at 5:58 AM, Karl Brand wrote:
On 12/2/2010 11:36 AM, David Winsemius wrote:
On Dec 2, 2010, at 5:22 AM, Karl Brand wrote:
Cheers Bill.
Inserting earlier debris:
I don't understand why i get this error message
On 12/2/2010 11:36 AM, David Winsemius wrote:
On Dec 2, 2010, at 5:22 AM, Karl Brand wrote:
Cheers Bill.
You got me halfway, since:
> temp <- merge(x=x, y=y[,17, drop=FALSE], by="rownames", sort=FALSE)
Error in fix.by(by.x, x) : 'by' must specify valid column
frames have, right? Although the output of merge()
is a data frame...
thanks again,
Karl
On 12/1/2010 6:08 PM, William Dunlap wrote:
Try
by="rownames"
instead of
by=rownames
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-he
the normal way here? I'm forced to
add the column using:
temp.b <- cbind(x, y[match(rownames(x), rownames(y)),17])
All insights appreciated for this leaRner,
cheers,
Karl
--
Karl Brand
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
P
in the hcl() call needed to produce a given palette?
ie., the 'h', 'c' and 'l' (and 'alpha' if appropriate) values for a
given color/shade??
Thanks again and in advance for any further pointers,
Karl
On 10/10/2010 10:41 PM, Paul Murrell wrote:
Hi
On
Karl
library(venneuler)
ve <- venneuler(c("A"=1, "B"=2, "C"=3, "A&C"=0.5, "A&B&C"=0.1))
class(ve)
[1] "VennDiagram"
ve$colors <- c("red", "green", "blue")
plot(ve)
Error in col * 360 :
Cheers Ista,
I thought 'labels' and 'colors' must have been accessible some how.
Thank you very much for showing how to access them,
Karl
On 10/7/2010 7:26 PM, Ista Zahn wrote:
Hi Kari,
On Thu, Oct 7, 2010 at 12:05 PM, Karl Brand wrote:
Esteemed UseRs and DevelopeRs,
locations within the circles?
and unions?
-specify circle colors?
-specify label font, size & color?
All thoughts and response's greatly appreciated, cheers,
Karl
--
Karl Brand
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
P +31 (0)10 704 3409 | F +31 (0)10 704
dnt return anything obvious for me...yet).
Sincere thanks for help thus far, and welcome any further pointers,
Karl
On 9/12/2010 4:50 PM, Duncan Murdoch wrote:
On 12/09/2010 10:12 AM, Karl Brand wrote:
Esteemed useRs and developeRs,
I need to create a '3D line plot' (proper name?) o
a where to start for an image like this.
I'd really appreciate suggestions & help on how might achieve this using R,
Karl
--
Karl Brand
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
T +31 (0)10 704 3457 |F +31 (0)10 704 4743 |M
Cheers Duncan, for your FAST answers and patience. (fast patience?!)
I was close. But closer reading of ?save would also have worked i see
now :$. LETTERS[] = :)
thanks again,
Karl
On 9/11/2010 2:10 PM, Duncan Murdoch wrote:
On 11/09/2010 8:00 AM, Karl Brand wrote:
Esteemed R users and
t;)
Both failed.
#** And while i've got your attention- is there a 'letter equivalent' to
seq() which would have worked nicely for prfxs? ie., letter.seq(A:F)
Thoughts and suggestions sincerely appreciated,
Karl
--
Karl Brand
Department of Genetics
Erasmus MC
Dr Molewaterpl
a for() loop the way I suggested.
Just a comment, of course.
Bill Venables.
-Original Message-
From: Karl Brand [mailto:k.br...@erasmusmc.nl]
Sent: Monday, 6 September 2010 6:46 PM
To: Venables, Bill (CMIS, Cleveland)
Cc: gaut...@yahoo.com; r-help@r-project.org
Subject: Re: [R] how do I
c(1, seq(5, 40, by = 5))
result_list = lapply(sseq, function(num) {
arima(data.ts[num:(num+200)], order=c(1,1,1))
})
cheers,
Paul
On 09/06/2010 10:46 AM, Karl Brand wrote:
Hi Bill,
I didn't make the original post, but its pretty similar to some thing
i would have queried the list about. B
rima(data.ts[30:230], order = c(1,1,1))
arima8<- arima(data.ts[35:235], order = c(1,1,1))
arima9<- arima(data.ts[40:240], order = c(1,1,1))
--
Karl Brand
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
P +31 (0)10 704 3409 | F +31 (0)10 704 4743 | M +31 (0)642 7
d ones?
rm(list=ls()) removes all R objects in the R work space.
Another question is that whether removing all R objects actually releases
the RAM? Thanks.
--
Karl Brand
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
P +31 (0)10 704 3409 | F +31 (0)10 704 4743 | M +31
evant functions? I think my PCA would
certainly appear a lot more '3d' with such a shaded box & axis.
tia,
Karl
*
http://tolstoy.newcastle.edu.au/R/e10/help/att-3419/vol_surface.png
--
Karl Brand
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
P +31 (0)10 704
am = "none",
density.info = "none",
margins=c(12, 8))
On 7/19/2010 12:42 PM, Karl Brand wrote:
Esteemed R-users,
heatmap.2() is yielding an inappropriate key based on my colors and
break-points.
In the reproducible example below, the key is inappr
race = "none",
dendrogram = "none",
density.info = "none",
margins=c(12, 8))
--
Karl Brand
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
P +31 (0)10 704 3409 | F +31 (0)10 704 4743 | M +31 (0)642 777 268
__
.wise from default)?
Any suggestions or pointers to helpful resources greatly appreciated,
Karl
--
Karl Brand
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
T +31 (0)10 704 3457 |F +31 (0)10 704 4743 |M +31 (0)642 777 268
__
R-
the
following error when attempting to open with Adobe acrobat:
"There was an error opening this document. This file cannot be opened
because it has no pages."
--
Karl Brand
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rott
2.1 grid_2.10.1
[4] gtools_2.6.1 lattice_0.17-26 preprocessCore_1.8.0
[7] svMisc_0.9-56tools_2.10.1
--
Karl Brand
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
P +31 (0)10 704 3409 | F +31 (0)10 704 4743 | M +31 (0)642 777 268
__
sults 1 (Int)", font=2, cex=1.5 )
plot.new()
text( .5, .5, "Results 2 (Int)", font=2, cex=1.5 )
plot.new()
text( .5, .5, "Results 3 (Int)", font=2, cex=1.5 )
--
Karl Brand
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
T +31 (0)10 704 3457
Jim,
What a great function: exactly as i needed.
I'm sure i'll be finding alot of use for the plotrix package.
Sincere thanks for your fast help, cheers,
Karl
On 6/27/2010 8:52 AM, Jim Lemon wrote:
On 06/26/2010 11:20 PM, Karl Brand wrote:
Dear List,
I'd really appreciat
orm(20), rnorm(20),
xlab = "Results 2 (Int)",
ylab = "Variable B")
#Graph 4:
plot(rnorm(20), rnorm(20),
xlab = "Results 2 (Int)",
ylab = "Variable B")
#Graph 5:
plot(rnorm(20), rnorm(20),
xlab = "Results 3 (Int)",
ot;
[59] "Time11:PperiodS" "Time12:PperiodS"
[61] "Time13:PperiodS" "Time14:PperiodS"
[63] "Time15:PperiodS" "Time16:PperiodS"
[65] "TissueC:PperiodL" "TissueC:PperiodS"
On 6/2/2010 8:26 PM, RICHARD M. HEIBERGER wr
he HH
package.
> Follow the example all the way to the end. It illustrates a problem and
> then the resolution
> of the problem.
> install.packages("HH") ## if you don't have it yet.
> library(HH)
> ?MMC
> Rich
--
Karl Brand
Department of Genetics
Erasmus MC
Dr Molewa
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
0, 0),
t1.E.RvsAll.E.R.Times =
c( 0, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
0, 0, 0, 0, 0, 0, 0, 0,
oose() function which does work
for your example.
-Peter Ehlers
On 2010-03-30 9:55, Charles C. Berry wrote:
On Tue, 30 Mar 2010, Karl Brand wrote:
Dear R Users,
I employed the phyper() function to estimate the likelihood that the
number of genes overlapping between 2 different lists of gene
ial' balls DRAWN
a <- choose(m,k)
b <- choose((N-m),(n-k))
z <- choose(N,n)
prK <- (a*b)/z #'the answer'
print(prK)
[1] NaN
> a
[1] 7.985852e+65
> b
[1] Inf
> z
[1] Inf
--
Karl Brand
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
T
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