Send R-help mailing list submissions to
r-help@r-project.org
To subscribe or unsubscribe via the World Wide Web, visit
https://stat.ethz.ch/mailman/listinfo/r-help
or, via email, send a message with subject or body 'help' to
r-help-requ...@r-project.org
You can reach the person managing the list at
r-help-ow...@r-project.org
When replying, please edit your Subject line so it is more specific
than "Re: Contents of R-help digest..."
Today's Topics:
1. Re: chippeakanno package: "getAllPeakSequence" problem (Nico902)
2. Re: How make a x,y dataset from a formula based entry
(Helios de Rosario)
3. Re: writing data from several matrices in R into one
excel-file with several sheets (Marion Wenty)
4. Significance test (setrofim)
5. Re: Subsetting a zooreg object using window / subset
(Wesley Roberts)
6. Re: R-help Digest, Vol 103, Issue 22 (mihalicza.pe...@emki.hu)
7. Clusplot axes (Chloe Strevens)
8. Re: Significance test (Yuta Tamberg)
9. Newbie question: Converting Table (Metronome123)
10. Odp: Newbie question: Converting Table (Petr PIKAL)
11. Re: Testing packages (Uwe Ligges)
12. Re: identifying cells in data frames with the same value
(Jean V Adams)
13. Re: How to do Multiple Comparisons for a Mixed Effects Model
(Ben Bolker)
14. Re: How make a x,y dataset from a formula based entry
(Jean-Christophe BOU?TT?)
15. Re: (sin asunto) (Terry Therneau)
16. Re: p values in coxph() (Terry Therneau)
17. 'save' saved object names instead of objects (Downey, Patrick)
18. Re: How make a x,y dataset from a formula based entry
(Gabor Grothendieck)
19. Re: 'save' saved object names instead of objects (Downey, Patrick)
20. Re: 'save' saved object names instead of objects
(Jean-Christophe BOU?TT?)
21. Re: Using method = "aic" with pspline& survreg (Terry Therneau)
22. Re: 'save' saved object names instead of objects (Sarah Goslee)
23. Re: 'save' saved object names instead of objects (Downey, Patrick)
24. Re: 'save' saved object names instead of objects (Duncan Murdoch)
25. How to fit a non-normal-dist.-GARCH() time series? (user84)
26. (Requested) caTools::runmean Patch (R. Michael Weylandt)
27. Re: Wrapper of linearHypothesis (car) for post-hoc of
repeated measures ANOVA (John Fox)
28. Re: Re-installing R (John C Frain)
29. comparing factor and value data (rather offtopic) (Petr PIKAL)
30. Re: Correlation of variables with repeated measures.
(Heverkuhn Heverkuhn)
31. Envfit, inconsistant result? (rodrock)
32. Re: Kolmogorov-Smirnov test (rommel)
33. Re: Newbie question: Converting Table (Metronome123)
34. Re: Significance test (setrofim)
35. Re: R functions (sujitha)
36. Error message when using 'optim' for numerical maximum
likelihood (Steven Craig)
37. Re: How to turn a LaTeX Sweave file (Rnw) into
.HTML/.odf/.docx? (under windows) (Frank Harrell)
38. spatstat => owin + image (tkdweber)
39. tikzDevice install problem (Helena Pe?a)
40. Homography with R (PtitBleu)
41. Re: identifying cells in data frames with the same value
(stevesp101)
42. [R-pkgs] new package 'SeleMix' for selective editing
(Teresa Buglielli)
43. Re: tikzDevice install problem (Uwe Ligges)
44. sorting multiple columns of a matrix (Maxim)
45. Re: sorting multiple columns of a matrix (William Dunlap)
46. LDA cutoff value (B Jessop)
47. Re: LDA cutoff value (Bert Gunter)
48. image function help required (Maxim)
49. converting object elements to variable names and making
subsequent assignments thereto (Jim Bouldin)
50. Re: LDA cutoff value (Prof Brian Ripley)
51. Re: converting object elements to variable names and making
subsequent assignments thereto (R. Michael Weylandt)
52. FW: ARIMA - Skipping intermediate lags (Bogaso Christofer)
53. Re: image function help required (Uwe Ligges)
54. Re: image function help required (Sarah Goslee)
55. Cross Spectrum : Conversion of 2-D spectrum into a single
complex array (Joseph Park)
56. vegan rda na adaptation (Sibylle St?ckli)
57. metaMDS (Lineth Contreras)
58. Re: tikzDevice install problem (helena)
59. Re: Homography with R (David Winsemius)
60. Re: converting object elements to variable names and making
subsequent assignments thereto (Jean V Adams)
61. Re: converting object elements to variable names and making
subsequent assignments thereto (Jim Bouldin)
62. Re: metaMDS (Jean V Adams)
63. Re: converting object elements to variable names and making
subsequent assignments thereto (R. Michael Weylandt)
64. Re: converting object elements to variable names and making
subsequent assignments thereto (Jim Bouldin)
65. Re: converting object elements to variable names and making
subsequent assignments thereto (R. Michael Weylandt)
66. Re: problem with function "Truncate" in package "distr"
(Peter Ruckdeschel)
67. Re: converting object elements to variable names and making
subsequent assignments thereto (Jim Bouldin)
68. Re: converting object elements to variable names and making
subsequent assignments thereto (R. Michael Weylandt)
69. Re: Newbie question: Converting Table (David Winsemius)
70. Re: randomForest - NaN in %IncMSE (Liaw, Andy)
71. Re: Small Area Estimate Using Structural Equation Models
(Peter Maclean)
72. Re: Kolmogorov-Smirnov test (Greg Snow)
73. Re: Adding weights to optim (Rolf Turner)
74. Re: Adding weights to optim (Ahnate Lim)
75. ncdf - install error (Muhammad Rahiz)
76. Re: ncdf - install error (Jeff Newmiller)
77. Re: spatstat => owin + image (Rolf Turner)
78. Re: Kolmogorov-Smirnov test (rommel)
79. ggplot2: expression() in legend labels? (Casper Ti. Vector)
----------------------------------------------------------------------
Message: 1
Date: Fri, 23 Sep 2011 03:31:01 -0700 (PDT)
From: Nico902<descos...@ciml.univ-mrs.fr>
To: r-help@r-project.org
Subject: Re: [R] chippeakanno package: "getAllPeakSequence" problem
Message-ID:<1316773861780-3836422.p...@n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
Thanks Martin, it worked.
I will post on BioC next time.
Cheers.
--
View this message in context:
http://r.789695.n4.nabble.com/chippeakanno-package-getAllPeakSequence-problem-tp3830284p3836422.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 2
Date: Fri, 23 Sep 2011 13:07:57 +0200
From: "Helios de Rosario"<helios.derosa...@ibv.upv.es>
To:<jcboue...@gmail.com>
Cc: r-help@r-project.org
Subject: Re: [R] How make a x,y dataset from a formula based entry
Message-ID:<4e7c84ad0200000c0000a...@mailhost.biomec.upv.es>
Content-Type: text/plain; charset=UTF-8
To separate the parts of a formula, use as.character
(check the examples in ?character)
Helios
22 Sep 2011 16:14:05 -0400
From: Jean-Christophe BOU?TT?<jcboue...@gmail.com>
Hello,
You can check ?model.frame.
I do not know however to extract only the right-hand of left-hand
part
of a formula.
JC
2011/9/22 trekvana<trekv...@aol.com>:
Hello all,
So I am using the (formula entry) method for randomForests:
randomForest(y~x1+x2+...+x39+x40,data=xxx,...) but the issue is that
some of
the items in that package dont take a formula entry - you have to
explicitly
state the y and x vector:
randomForest(x=xxx[,c('x1','x2',...,'x40')],y=xxx[,'y'],...)
Now my question is whether there is a function/way to tell R to take
a
formula and make the two corresponding datasets [x,y] (that way I
dont have
to create the x dataset manually with all 40 variables I have).
There must be a more elegant way to do this than
x=xxx[,c('x1','x2',...,'x40')]
Thanks!
George
INSTITUTO DE BIOMEC?NICA DE VALENCIA
Universidad Polit?cnica de Valencia ? Edificio 9C
Camino de Vera s/n ? 46022 VALENCIA (ESPA?A)
Tel. +34 96 387 91 60 ? Fax +34 96 387 91 69
www.ibv.org
Antes de imprimir este e-mail piense bien si es necesario hacerlo.
En cumplimiento de la Ley Org?nica 15/1999 reguladora de la Protecci?n
de Datos de Car?cter Personal, le informamos de que el presente mensaje
contiene informaci?n confidencial, siendo para uso exclusivo del
destinatario arriba indicado. En caso de no ser usted el destinatario
del mismo le informamos que su recepci?n no le autoriza a su divulgaci?n
o reproducci?n por cualquier medio, debiendo destruirlo de inmediato,
rog?ndole lo notifique al remitente.
------------------------------
Message: 3
Date: Fri, 23 Sep 2011 13:39:56 +0200
From: Marion Wenty<marion.we...@gmail.com>
To: Greg Snow<greg.s...@imail.org>
Cc: "r-help@r-project.org"<r-help@r-project.org>
Subject: Re: [R] writing data from several matrices in R into one
excel-file with several sheets
Message-ID:
<CA+=lhl0ubzyrsamrq2my4zxneoclmhxgp7hw-kmk7n8db5e...@mail.gmail.com>
Content-Type: text/plain
hello,
thank you for your help!
I was not successfull using the XLConnect-package. Anyway, I have to
postpone this problem for now as I have to sort out some other other
problems at the moment.
marion
2011/9/16 Greg Snow<greg.s...@imail.org>
Look at the XLConnect package.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-----Original Message-----
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of Marion Wenty
Sent: Friday, September 16, 2011 9:19 AM
To: r-help@r-project.org
Subject: [R] writing data from several matrices in R into one excel-
file with several sheets
hello,
does anyone know how I can write several matrices from R into one exel-
file
using different sheets for the different matrices?
thank you very much in advance for your help.
Marion
[[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, reproducible code.
[[alternative HTML version deleted]]
------------------------------
Message: 4
Date: Fri, 23 Sep 2011 01:25:04 -0700 (PDT)
From: setrofim<setro...@gmail.com>
To: r-help@r-project.org
Subject: [R] Significance test
Message-ID:<1316766304763-3836155.p...@n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
I have a bunch of benchmark measurements that look something like this:
sample.1 0.0000066660 0.0000062500 0.0000058330 0.0000058330
0.0000058330
sample.2 0.0000058330 0.0000058330 0.0000058330 0.0000058330
0.0000058330
sample.3 0.0000062500 0.0000062500 0.0000070830 0.0000062500
0.0000066660
i.e each measurement take on one of a set of values. The set values isn't
fixed, but they seem to go up increments; in this case, it appears to be
about 4.17e-07 (e.g. it would be impossible for a measurement to be
0.0000066440).
What is way to test for significant differences between two samples?
Sorry if this is a noob question, but I'm kinda new to this. The two tests
I'm aware of are the Student's t and Wilcoxon Rank Sum; neither seems to
apply here. I've tried Googling this, but haven't found anything useful
(maybe I'm not using the right terms...).
Any help would be greatly appreciated.
Regards,
setro
--
View this message in context:
http://r.789695.n4.nabble.com/Significance-test-tp3836155p3836155.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 5
Date: Fri, 23 Sep 2011 10:50:27 +0200
From: "Wesley Roberts"<wrobe...@csir.co.za>
To: "Gabor Grothendieck"<ggrothendi...@gmail.com>, "Achim Zeileis"
<achim.zeil...@uibk.ac.at>
Cc: r-help@r-project.org
Subject: Re: [R] Subsetting a zooreg object using window / subset
Message-ID:<4e7c64730200007300034...@pta-emo.csir.co.za>
Content-Type: text/plain; charset=US-ASCII
A nice alternative,
Many thanks Achim
Wesley
Achim Zeileis<achim.zeil...@uibk.ac.at> 22/09/2011 14:46>>>
On Thu, 22 Sep 2011, Gabor Grothendieck wrote:
On Thu, Sep 22, 2011 at 6:48 AM, Wesley Roberts<wrobe...@csir.co.za> wrote:
Dear R users,
I am currently working in subsetting a zooreg() object using either window or
subset. I have a solution but it may be a bit cumbersome when I start working
with actual data. Your inputs would be greatly appreciated.
Example: I have a zooreg() object that starts in 1997 and ends in 2001. This
object contains daily data for the 4 years
aa<-zooreg(1:1825,start=as.Date("1997-01-01"))
My aim is to subset the data according to seasons (Southern Hemisphere) for
continuous years: December - January - February (DJF-Summer: 1997-2001), March
- April - May (MAM-Autumn: 1997-2001), June - July - August (JJA-Winter:
1997-2001), September - October - November (SON-Spring: 1997-2001) thereby
analysing the seasons data only for all years. The example below is only for
DJF but I would like to replicate the analysis for each season.
My solution so far uses subset to select the monthly data for each year and
then rbind() the results.
bb<- subset(aa,
index(aa)>=as.Date("1998-12-01")&index(aa)<=as.Date("1999-02-28"))
cc<- subset(aa,
index(aa)>=as.Date("1999-12-01")&index(aa)<=as.Date("2000-02-28"))
dd<- subset(aa,
index(aa)>=as.Date("2000-12-01")&index(aa)<=as.Date("2001-02-28"))
ee<- rbind(bb,cc,dd)
The method above appears to do the job just fine except that I have around 30
locations (catchments) each with varying data availability and some with over
20 years worth of data. Ideally I would like to combine the second set of
commands into a single command where I specify the start and end year and the
months that I am interested in.
This gives the season (1 = djf, 2 = mam, 3 = jja, 5 = son):
seas<- as.numeric(format(as.yearqtr(as.yearmon(time(aa)) + 1/12), "%q"))
An alternative route might be to go via the "mon" component of POSIXlt,
e.g.,
as.POSIXlt(time(aa))$mon %in% c(11, 0, 1)
instead of
seas == 1
etc.
and this picks out djf:
aa[seas == 1]
--
Statistics& Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
______________________________________________
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, reproducible code.
