[R] help
Mathew Brown
mathew.brown at forst.uni-goettingen.de
Sat Sep 24 13:56:59 CEST 2011
Mathew Brown
Institute of Bioclimatology
University of Göttingen
Büsgenweg 2
37077 Göttingen, Germany
t: +49 551 39 9359
mathew.brown at forst.uni-goettingen.de
On 9/24/2011 6:00 PM, r-help-request at r-project.org wrote:
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> 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.peter at 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<descostes at ciml.univ-mrs.fr>
> To: r-help at r-project.org
> Subject: Re: [R] chippeakanno package: "getAllPeakSequence" problem
> Message-ID:<1316773861780-3836422.post at 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.derosario at ibv.upv.es>
> To:<jcbouette at gmail.com>
> Cc: r-help at r-project.org
> Subject: Re: [R] How make a x,y dataset from a formula based entry
> Message-ID:<4E7C84AD0200000C0000A9F8 at 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?<jcbouette at 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<trekvana at 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
>
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>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 23 Sep 2011 13:39:56 +0200
> From: Marion Wenty<marion.wenty at gmail.com>
> To: Greg Snow<Greg.Snow at imail.org>
> Cc: "r-help at r-project.org"<r-help at r-project.org>
> Subject: Re: [R] writing data from several matrices in R into one
> excel-file with several sheets
> Message-ID:
> <CA+=LhL0uBZyrSamRq2MY4ZXnEOCLMHxGp7hw-kmk7N8DB5Ecxg at 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.Snow at imail.org>
>
>> Look at the XLConnect package.
>>
>> --
>> Gregory (Greg) L. Snow Ph.D.
>> Statistical Data Center
>> Intermountain Healthcare
>> greg.snow at imail.org
>> 801.408.8111
>>
>>
>>> -----Original Message-----
>>> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
>>> project.org] On Behalf Of Marion Wenty
>>> Sent: Friday, September 16, 2011 9:19 AM
>>> To: r-help at 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 at 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<setrofim at gmail.com>
> To: r-help at r-project.org
> Subject: [R] Significance test
> Message-ID:<1316766304763-3836155.post at 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"<wroberts at csir.co.za>
> To: "Gabor Grothendieck"<ggrothendieck at gmail.com>, "Achim Zeileis"
> <Achim.Zeileis at uibk.ac.at>
> Cc: r-help at r-project.org
> Subject: Re: [R] Subsetting a zooreg object using window / subset
> Message-ID:<4E7C64730200007300034FB0 at pta-emo.csir.co.za>
> Content-Type: text/plain; charset=US-ASCII
>
> A nice alternative,
>
> Many thanks Achim
>
> Wesley
>
>>>> Achim Zeileis<Achim.Zeileis at 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<wroberts at 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 at 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.
>>
>
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