Re: [R] metafor package
At 22:11 11/02/2014, Nathan Pace wrote: Hi, I have a random effects meta analysis of a proportion (logit transformation) using rma.glmm. I have created a forest plot of the proportion (inverse logic transformation) using forest.rma. I have added the credibility interval. The forest plot is saved as a pdf. The dotted line and whiskers of the credibility interval are too faint. I need help on the argument(s) to widen the credibility interval dots and whiskers. I have looked at the forest.default function, but don't see anything obvious to me. Dear Nathan I think you need to look at forest.rma. There is a fairly obvious section (search for addcred). If worst comes to worst you can always hack it and save as nathansforest.rma. Nathan -- Nathan Pace, MD, MStat Department of Anesthesiology University of Utah 801.581.6393 n.l.p...@utah.edu [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ 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.
Re: [R] metafor package
Like most plotting routines in R, forest has a ... argument that passes names
arguments through to other routines.
In forest's case, ... passes (at least) to abline, axis and segments, so all
the lines and axes in the plot are affected by any argument that is valid for
those.
In your case, specifying lwd=2 in your forest call will give all the lines
width 2 instead of the default.
S Ellison
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Nathan Pace
Sent: 11 February 2014 22:11
To: r-help@R-project.org
Subject: [R] metafor package
Hi,
I have a random effects meta analysis of a proportion (logit transformation)
using rma.glmm.
I have created a forest plot of the proportion (inverse logic transformation)
using forest.rma.
I have added the credibility interval.
The forest plot is saved as a pdf.
The dotted line and whiskers of the credibility interval are too faint.
I need help on the argument(s) to widen the credibility interval dots and
whiskers.
I have looked at the forest.default function, but don't see anything obvious
to me.
Nathan
--
Nathan Pace, MD, MStat
Department of Anesthesiology
University of Utah
801.581.6393
n.l.p...@utah.edu
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Re: [R] r hepl
Hi I do not understand what do you want? You have continuous variable, from which you made 2 interval variables. If you want that in those variables intervals to be named in particular way, make them factor and name them as you wish. factor(bins_age, labels=letters[1:7]) [1] e e c f c b g a f d c b g c b f f e e b c f e b d a d a b f g a g a e b f a [39] c f d d a a g d d d f b Levels: a b c d e f g Regards Petr -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Amaleswara Rao Sent: Wednesday, February 12, 2014 7:06 AM To: r-help@r-project.org Subject: [R] r hepl Hi guye's if u don't mind solve this problem please Data- data.frame(Age=sample(10:75,50),Income=sample(6000:5,50),Profit=sa mple(2000:4,50),stringsAsFactors=F) uniq1-unique(quantile(Data[[1]],seq(0,1,0.01))) Interval_age-findInterval(Data[[1]],uniq1) bins_age-cut(Data$Age,seq(9,80,by=10),labels=F) uniq2-unique(quantile(Data[[2]],seq(0,1,0.01))) Interval_income-findInterval(Data[[2]],uniq2) bins_income-cut(Data$Income,seq(6000,54000,by=4000),labels=F) uniq3-unique(quantile(Data[[3]],seq(0,1,0.01))) Interval_profit-findInterval(Data[[3]],uniq3) bins_profit-cut(Data$Profit,seq(1999,43000,by=5000),labels=F) l-cbind(Data,Interval_age) m-cbind(Data,Interval_income) n-cbind(Data,Interval_profit) ll-l[,c(-2,-3)] mm-m[,c(-1,-3)] nn-n[,c(-1,-2)] AG-cbind(ll,bins_age) IN-cbind(mm,bins_income) PF-cbind(nn,bins_profit) Final-cbind(AG,IN,PF) Final result in this program coming intervals and bin's corresponding variables But I Want Interval Columns Arranging = or = or , for exp:-0=10 10=20 20=30 this type [[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. Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny pouze jeho adresátům. Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze svého systému. Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat. Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či zpožděním přenosu e-mailu. V případě, že je tento e-mail součástí obchodního jednání: - vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, a to z jakéhokoliv důvodu i bez uvedení důvodu. - a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany příjemce s dodatkem či odchylkou. - trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným dosažením shody na všech jejích náležitostech. - odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu případně osobě, kterou adresát zastupuje, předloženy nebo jejich existence je adresátovi či osobě jím zastoupené známá. This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients. If you received this e-mail by mistake, please immediately inform its sender. Delete the contents of this e-mail with all attachments and its copies from your system. If you are not the intended recipient of this e-mail, you are not authorized to use, disseminate, copy or disclose this e-mail in any manner. The sender of this e-mail shall not be liable for any possible damage caused by modifications of the e-mail or by delay with transfer of the email. In case that this e-mail forms part of business dealings: - the sender reserves the right to end negotiations about entering into a contract in any time, for any reason, and without stating any reasoning. - if the e-mail contains an offer, the recipient is entitled to immediately accept such offer; The sender of this e-mail (offer) excludes any acceptance of the offer on the part of the recipient containing any amendment or variation. - the sender insists on that the respective contract is concluded only upon an express mutual agreement on all its aspects. - the sender of this e-mail informs that he/she is not authorized to enter into any contracts on behalf of the company except for cases in which he/she is expressly authorized to do so in writing, and such authorization or power of attorney is submitted to the recipient or the person represented by the recipient, or the existence of such authorization is known to the recipient of the person represented by
Re: [R] metafor package
Good advice already from Michael and S Ellison. I must apologize for the 'hack-job of a function' called forest() in metafor. I realized a while ago that people would prefer more fine-grained control over the various elements of the plot (this has come up a few times before). I think Paul Murrell described the issue best in his R Journal article: http://journal.r-project.org/archive/2012-2/RJournal_2012-2_Murrell.pdf But it is what it is at this point. I noticed the problem with the dotted line of the credibility interval myself a while back. In an updated version of the metafor package (to be released at some point in the near future), there will at least be the possibility to control the color of that line. Maybe also the line type (a dotted line is indeed often too faint). You can try changing efac=2 (or something larger than 1) to at least make the whiskers longer. Best, Wolfgang -- Wolfgang Viechtbauer, Ph.D., Statistician Department of Psychiatry and Psychology School for Mental Health and Neuroscience Faculty of Health, Medicine, and Life Sciences Maastricht University, P.O. Box 616 (VIJV1) 6200 MD Maastricht, The Netherlands +31 (43) 388-4170 | http://www.wvbauer.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Michael Dewey Sent: Wednesday, February 12, 2014 12:50 To: Nathan Pace; r-help@R-project.org Subject: Re: [R] metafor package At 22:11 11/02/2014, Nathan Pace wrote: Hi, I have a random effects meta analysis of a proportion (logit transformation) using rma.glmm. I have created a forest plot of the proportion (inverse logic transformation) using forest.rma. I have added the credibility interval. The forest plot is saved as a pdf. The dotted line and whiskers of the credibility interval are too faint. I need help on the argument(s) to widen the credibility interval dots and whiskers. I have looked at the forest.default function, but don't see anything obvious to me. Dear Nathan I think you need to look at forest.rma. There is a fairly obvious section (search for addcred). If worst comes to worst you can always hack it and save as nathansforest.rma. Nathan -- Nathan Pace, MD, MStat Department of Anesthesiology University of Utah 801.581.6393 n.l.p...@utah.edu [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ 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.
[R] creating a figure with different shades in R?
Hello, everyone, I have following csv-file(simplified) as instance: 0.29,2,50 0.32,3,10 0.28,4,71 0.27,1,62 0.53,1,33 0.83,5,100 with the first column for x-axis (proportion shared), the second for y-axis (number of shared segments), the shades for 'number of pairs'. I wonder how to realize that the number of pairs are denoted by different shades as shown in the attachment ? So far, I can plot a histogram by these codes, but have no idea how to correctly add information of shades to it. df-read.csv(file=c-all-prop-test.csv,head=F,sep=,) require(ggplot2) qplot(x=df[,1],weight=df[,2],geom=histogram,xlab=proportion shared,ylab=number of shared segments,colour = I(darkgreen), fill = I(blue)) It seems that d + stat_bin2d() may help. Or maybe heatmap? Could you give me some suggestions? Best regards attachment: R.png__ 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.
Re: [R] metafor package
-Original Message-
I must apologize for the 'hack-job of a function' called forest() in metafor.
Well, certainly no apology needed there!
I realized a while ago that people would prefer more fine-grained control over
the various elements of the plot (this has come up a few times before).
Ploting functions should ideally never have hard-coded defaults.
Having said that, it's an absolute pain to do anything else.
I've tinkered a fair bit with the problem in my own package, which for at least
some plots tries to match graphical arguments in ... with those applicable to
specific plotting functions so as to avoid the frequent 'duplicate parameters'
or 'xxx is not a recognised parameter in some_plotting_function'
Another useful approach I've toyed with is to allow a list like
this.special.line.pars=list(lwd=2, col=3, lty=2) to be provided, and then use
do.call with functions like line, axis etc. That avoids a plot function full of
things like like this.special.line.lwd, like this.special.line.col, like
this.special.line.lty
But there's no really simple answer; at some point we have to give up and point
out that if saomeone really wants that much control, they can always hack the
code!
S Ellison
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[R] metafor package
If your command looks something like this: forest(x,xlim=c(-6,7),cex=.8,order=prec, xlab=Effect Size, alim=c(-.5,4),mlab=RE Average for All Studies) In alim=c(-.5,4), increase the numbers. Make them higher than your highest confidence interval upper bound and lower than your lowest confidence interval lower bound. The bars may run into the text, but that may be fixed by stretching the output window in R. Will Shadish ** Date: Tue, 11 Feb 2014 22:11:20 + From: Nathan Pace n.l.p...@utah.edu To: r-help@R-project.org r-help@r-project.org Subject: [R] metafor package Message-ID: cf1fef68.2490a%n.l.p...@utah.edu Content-Type: text/plain Hi, I have a random effects meta analysis of a proportion (logit transformation) using rma.glmm. I have created a forest plot of the proportion (inverse logic transformation) using forest.rma. I have added the credibility interval. The forest plot is saved as a pdf. The dotted line and whiskers of the credibility interval are too faint. I need help on the argument(s) to widen the credibility interval dots and whiskers. I have looked at the forest.default function, but don?t see anything obvious to me. Nathan -- Nathan Pace, MD, MStat Department of Anesthesiology University of Utah 801.581.6393 n.l.p...@utah.edu -- William R. Shadish Distinguished Professor Founding Faculty Mailing Address: William R. Shadish University of California School of Social Sciences, Humanities and Arts 5200 North Lake Rd Merced CA 95343 Physical/Delivery Address: University of California Merced ATTN: William Shadish School of Social Sciences, Humanities and Arts Facilities Services Building A 5200 North Lake Rd. Merced, CA 95343 209-228-4372 voice 209-228-4007 fax (communal fax: be sure to include cover sheet) wshad...@ucmerced.edu http://faculty.ucmerced.edu/wshadish/index.htm http://psychology.ucmerced.edu __ 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.
[R] Actual code for LDA
Hi All, I've been trying to write my own code for LDA (linear discrim) so I can modify it to be weighted LDA since some of my groups are outliers. However, the code I write for standard LDA gives me slightly different results to those from R (slightly different LDAs.and not just scalar differences. Does R simply invert the pooled within groups scatter matrix e.g. solve(Sw) and multiply it by the between groups scatter Sb, then take the eigen vectors? This is the approach that I use, yet get slightly different results..does R by default use a slightly more robust inverse or estimate of Sw?? I've looked at the source code, and I find it very hard to follow. If anyone has any ideas that would be great!! Thanks, Ben -- View this message in context: http://r.789695.n4.nabble.com/Actual-code-for-LDA-tp4685194.html Sent from the R help mailing list archive at Nabble.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.
[R] plot with 3 axes and different shades
Hello, everyone, I have following csv-file(simplified) as instance: Greetings, I have following csv-file: 0.29,2,50 0.32,3,10 0.28,4,71 0.27,1,62 0.53,1,33 0.83,5,100 with the first column for x-axis (proportion shared), the second for y-axis (number of shared segments), the shades for 'number of pairs'. In the attachment, you can find the figure. I wonder how to realize that the number of pairs are denoted by different shades as shown in the attachment ? So far, I can plot a histogram by these codes, but have no idea how to correctly add information of shades to it. df-read.csv(file=c-all-prop-test.csv,head=F,sep=,) require(ggplot2) qplot(x=df[,1],weight=df[,2],geom=histogram,xlab=proportion shared,ylab=number of shared segments,colour = I(darkgreen), fill = I(blue)) It seems that d + stat_bin2d() may help. Or maybe heatmap? Could you give me some suggestions? Best regards attachment: R.png__ 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.
Re: [R] SDM using BIOMOD2 error message
I think it is a problem with your directory setting changing your directory. When you make your enviro stack you set your directory to: setwd(V:/BIOCLIM) Then when you import your species coordinates and presence/absence status you change your directory to: setwd(C:/Users/Lindsie/Documents/R) Then you try to run your model R says 'pred' is missing ~ because it cannot find your raster stacks. CHANGE YOUR R DIRECTORY BACK TO WHERE YOU STORED YOUR ENVIRONMENTAL LAYERS PRIOR TO RUNNING THE MODEL! myBiomodModelOut - BIOMOD_Modeling(myBiomodDa... __ 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.
Re: [R] Biomod model access
I have been struggling with this same problem. I always have to re-run. PLEASE HELP!! I have however figured out the whole data-format issue am now able to save grid files for use in other GIS programs after they are re-exported. On Thursday, August 15, 2013 1:32:31 AM UTC-7, Jenny Williams wrote: I am still trying to get my head around biomod2. I have run through the tutorial a few times, which works really well in a linear format. But, I want to see the models and assess them at every part of the process. So, I need to: 1: be able to re-access all the files from /.BIOMOD_DATA/ once R is closed and all the file links are lost. e.g myBiomodModelOut 2: call the summary parameters for the models e.g GLM, I can see the files but not sure how to access them. e.g myGLMs - BIOMOD_LoadModels(myBiomodModelOut, models='GLM') #just produces a list summary(myGLMs[1]) Length Class Mode 1 character character #summary(GLM) doesn't work, but is the output that I am looking to find. 3. find the split datasets used for each of the iterations BIOMOD_Modeling options; NbRunEval for DataSplit Any help or pointers in the right direction would be greatly appreciated. FYI the vignette does not seem to work: http://127.0.0.1:15505/library/biomod2/doc/index.html ** Jenny Williams Spatial Information Scientist, GIS Unit Herbarium, Library, Art Archives Directorate Royal Botanic Gardens, Kew Richmond, TW9 3AB, UK Tel: +44 (0)208 332 5277 email: jenny.w...@kew.org javascript:mailto:jenny.willi...@kew.orgjavascript: ** Film: The Forgotten Home of Coffee - Beyond the Gardens http://www.youtube.com/watch?v=-uDtytKMKpAsns=tw Stories: Coffee Expedition - Ethiopia http://storify.com/KewGIS/coffee-expedition-ethiopia Kew in Harapan Rainforest Sumatra http://storify.com/KewGIS/kew-in-harapan-rainforest Articles: Seeing the wood for the trees http://www.kew.org/ucm/groups/public/documents/document/kppcont_060602.pdf How Kew's GIS team and South East Asia botanists are working to help conserve and restore a rainforest in Sumatra. Download a pdf of this article here. http://www.kew.org/ucm/groups/public/documents/document/kppcont_060602.pdf The Royal Botanic Gardens, Kew is a non-departmental public body with exempt charitable status, whose principal place of business is at Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom. The information contained in this email and any attachments is intended solely for the addressee(s) and may contain confidential or legally privileged information. If you have received this message in error, please return it immediately and permanently delete it. Do not use, copy or disclose the information contained in this email or in any attachment. Any views expressed in this email do not necessarily reflect the opinions of RBG Kew. Any files attached to this email have been inspected with virus detection software by RBG Kew before transmission, however you should carry out your own virus checks before opening any attachments. RBG Kew accepts no liability for any loss or damage which may be caused by software viruses. [[alternative HTML version deleted]] __ r-h...@r-project.org javascript: 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. __ 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.
[R] mean help?
Hey everyone, I need help getting the mean, standard deviation, median, etc. I'm just not sure how to write those codes in r and if someone could also help me out with the table command that would be great too. same issue just not really sure how to write it out. thanks for your time everyone! -- View this message in context: http://r.789695.n4.nabble.com/mean-help-tp4685212.html Sent from the R help mailing list archive at Nabble.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.
[R] simple linear regression
okay so how do you run a simple linear regression, obtain the summary of that, and then put it in an object? -- View this message in context: http://r.789695.n4.nabble.com/simple-linear-regression-tp4685213.html Sent from the R help mailing list archive at Nabble.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.
Re: [R] simple linear regression
On Wed, Feb 12, 2014 at 2:22 PM, frankreynolds mz1...@txstate.edu wrote: okay so how do you run a simple linear regression, obtain the summary of that, and then put it in an object? You start by reading the Introduction to R that came with your installation, and then using some common sense and basic statistical knowledge. PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. This bit is also a good idea. Sarah -- Sarah Goslee http://www.functionaldiversity.org __ 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.
Re: [R] plot with 3 axes and different shades
On 02/13/2014 02:49 AM, Wei Ding wrote: Hello, everyone, I have following csv-file(simplified) as instance: Greetings, I have following csv-file: 0.29,2,50 0.32,3,10 0.28,4,71 0.27,1,62 0.53,1,33 0.83,5,100 with the first column for x-axis (proportion shared), the second for y-axis (number of shared segments), the shades for 'number of pairs'. In the attachment, you can find the figure. I wonder how to realize that the number of pairs are denoted by different shades as shown in the attachment ? So far, I can plot a histogram by these codes, but have no idea how to correctly add information of shades to it. df-read.csv(file=c-all-prop-test.csv,head=F,sep=,) require(ggplot2) qplot(x=df[,1],weight=df[,2],geom=histogram,xlab=proportion shared,ylab=number of shared segments,colour = I(darkgreen), fill = I(blue)) It seems that d + stat_bin2d() may help. Or maybe heatmap? Could you give me some suggestions? Best regards Hi Wei, You can do something like this with color2D.matplot (plotrix). x-matrix(sample(1:100,100),nrow=10) x[sample(1:10,20,TRUE),sample(1:10,20,TRUE)]-NA library(plotrix) color2D.matplot(x, cellcolors=color.scale(x,extremes=c(lightgray,blue))) Jim __ 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.
Re: [R] mean help?
Frank — you need to read the R tutorial that came with your installation. If you don’t have the answers to your VERY BASIC questions after that, let us know. On Feb 12, 2014, at 10:20 AM, frankreynolds mz1...@txstate.edu wrote: Hey everyone, I need help getting the mean, standard deviation, median, etc. I'm just not sure how to write those codes in r and if someone could also help me out with the table command that would be great too. same issue just not really sure how to write it out. thanks for your time everyone! -- View this message in context: http://r.789695.n4.nabble.com/mean-help-tp4685212.html Sent from the R help mailing list archive at Nabble.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. Don McKenzie Research Ecologist Pacific Wildland Fire Sciences Lab US Forest Service Affiliate Professor School of Environmental and Forest Sciences University of Washington d...@uw.edu __ 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.
Re: [R] mean help?
Hello, At an R prompt type ?mean ?sd ?median And read the file R-intro.pdf that comes with your installation of R. Hope this helps, Rui Barradas Em 12-02-2014 18:20, frankreynolds escreveu: Hey everyone, I need help getting the mean, standard deviation, median, etc. I'm just not sure how to write those codes in r and if someone could also help me out with the table command that would be great too. same issue just not really sure how to write it out. thanks for your time everyone! -- View this message in context: http://r.789695.n4.nabble.com/mean-help-tp4685212.html Sent from the R help mailing list archive at Nabble.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. __ 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.
Re: [R] Biomod model access
Accessing BIOMOD2 model output is possible, but a bit convoluted.
Here's a whole chunk of code that creates a reproducible example; the
most important part is at the end.
I hope this is enough to let you get going.
Sarah
### First use a slightly modified version of the example from the help file
# species occurrences
DataSpecies -
read.csv(system.file(external/species/mammals_table.csv,
package=biomod2))
# the name of studied species
myRespName - 'GuloGulo'
# the presence/absences data for our species
myResp - as.numeric(DataSpecies[,myRespName])
# the XY coordinates of species data
myRespXY - DataSpecies[,c(X_WGS84,Y_WGS84)]
# Environmental variables extracted from BIOCLIM (bio_3, bio_4,
bio_7, bio_11 bio_12)
myExpl = stack( system.file( external/bioclim/current/bio3.grd,
package=biomod2),
system.file( external/bioclim/current/bio4.grd,
package=biomod2),
system.file( external/bioclim/current/bio7.grd,
package=biomod2),
system.file(
external/bioclim/current/bio11.grd, package=biomod2),
system.file(
external/bioclim/current/bio12.grd, package=biomod2))
# 1. Formatting Data
myBiomodData - BIOMOD_FormatingData(resp.var = myResp,
expl.var = myExpl,
resp.xy = myRespXY,
resp.name = myRespName)
# 2. Defining Models Options using default options.
myBiomodOption - BIOMOD_ModelingOptions()
# 3. Doing Modelisation
myBiomodModelOut - BIOMOD_Modeling( myBiomodData,
models = c('SRE','RF', 'GAM'),
models.options = myBiomodOption,
NbRunEval=2,
DataSplit=80,
VarImport=0,
models.eval.meth = c('ROC'),
do.full.models=FALSE,
modeling.id=test)
### assume we quit without saving the workspace, since everything is
on disk anyway
### q(no) ## commented out for your protection
### here's the access code
### come back later
### everything is stored in GuloGulo, and all thing are R objects
R
library(biomod2)
# R objects can be imported with load()
R load(GuloGulo/models/test/GuloGulo_AllData_RUN1_GAM)
R ls()
[1] GuloGulo_AllData_RUN1_GAM
R GuloGulo_AllData_RUN1_GAM
# various outputs deleted
## here's how to get the GAM itself
R get_formal_model(GuloGulo_AllData_RUN1_GAM)
Family: binomial
Link function: logit
Formula:
GuloGulo ~ 1 + s(bio3, k = -1) + s(bio4, k = -1) + s(bio7, k = -1) +
s(bio11, k = -1) + s(bio12, k = -1)
environment: 0x9a5e918
Estimated degrees of freedom:
3.04 6.51 6.07 5.78 5.08 total = 27.47
UBRE score: -0.6562
## and it can be summarized
R summary(get_formal_model(GuloGulo_AllData_RUN1_GAM))
Family: binomial
Link function: logit
Formula:
GuloGulo ~ 1 + s(bio3, k = -1) + s(bio4, k = -1) + s(bio7, k = -1) +
s(bio11, k = -1) + s(bio12, k = -1)
environment: 0x9a5e918
Parametric coefficients:
Estimate Std. Error z value Pr(|z|)
(Intercept) -11.14 4.23 -2.63 0.0085
Approximate significance of smooth terms:
edf Ref.df Chi.sq p-value
s(bio3) 3.04 3.74 15.9 0.0027
s(bio4) 6.51 6.98 151.1 2e-16
s(bio7) 6.07 6.77 107.6 2e-16
s(bio11) 5.78 6.46 130.5 2e-16
s(bio12) 5.08 6.06 59.2 7.3e-11
R-sq.(adj) = 0.738 Deviance explained = 72.2%
UBRE score = -0.65625 Scale est. = 1 n = 2488
On Wed, Feb 12, 2014 at 12:22 PM, Matthew Bayly matt.j.ba...@gmail.com wrote:
I have been struggling with this same problem. I always have to re-run.
PLEASE HELP!!
I have however figured out the whole data-format issue am now able to
save grid files for use in other GIS programs after they are re-exported.
On Thursday, August 15, 2013 1:32:31 AM UTC-7, Jenny Williams wrote:
I am still trying to get my head around biomod2. I have run through the
tutorial a few times, which works really well in a linear format.
But, I want to see the models and assess them at every part of the
process. So, I need to:
1: be able to re-access all the files from /.BIOMOD_DATA/ once R is closed
and all the file links are lost.
e.g myBiomodModelOut
2: call the summary parameters for the models e.g GLM, I can see the files
but not sure how to access them.
e.g
myGLMs - BIOMOD_LoadModels(myBiomodModelOut, models='GLM')
#just produces a list
summary(myGLMs[1])
Length Class Mode
1 character character
#summary(GLM) doesn't work, but is the output that I am looking to find.
3. find the split datasets used for each of the iterations BIOMOD_Modeling
options; NbRunEval for DataSplit
Any help or pointers
Re: [R] Urgent Inquiry
You might consider reading
http://cran.r-project.org/doc/contrib/Hiebeler-matlabR.pdf. I strongly
recommend reading the Introduction to R document that comes with the R software.
As to where to ask questions, this mailing list is fine as long as you follow
the Posting Guide recommendations (see the bottom of this email) and stay on
topic (Matlab is off topic, R is on-topic). Note that most attachments are
stripped by the mailing list.. you are expected to communicate in plain text.
Some people prefer the website experience... you might try
http://stackoverflow.com/questions/tagged/r for that.
---
Jeff NewmillerThe . . Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go...
Live: OO#.. Dead: OO#.. Playing
Research Engineer (Solar/BatteriesO.O#. #.O#. with
/Software/Embedded Controllers) .OO#. .OO#. rocks...1k
---
Sent from my phone. Please excuse my brevity.
On February 12, 2014 1:09:33 PM PST, Woo Young Kang eric...@hotmail.com wrote:
Hi, my name is Woo Young Kang and I am a current user of R-programming.
I am looking for an R-programming online questioning community and was
having difficulty finding it.
I wonder what webaddress I can use to ask question regarding the
R-programming.
Before that, I do have one critical question that I would like to ask
regarding the R-programming.
I am trying to make about 10 lines of MATLAB code into the equivalent
R-programming code.
The backgroud for this is to produce initial parameters for the
Cox-Ross-Ingersoll short rate model using the
OLS method.
I found out the MATLAB code for OLS initial parameter estimation for
the CIR interest rate model from
one of the literature but have a bit difficulty in understanding 100%
of the code since I was trying to convert
this code in terms of R-programming code.
The code itself is as follows:
% Initial parameters using OLS
Nobs = length(Model.Data);
x = Model.Data(1:end-1);
dx = diff(Model.Data);
dx = dx./x.^0.5;
regressors = [Model.TimeStep./x.^0.5, Model.TimeStep*x.^0.5];
drift = regressors\dx;
res = regressors*drift - dx;
alpha = -drift(2);
mu = -drift(1)/drift(2);
sigma = sqrt(var(res, 1)/Model.TimeStep);
InitialParams = [alpha mu sigma];
if ~isfield(Model, 'Disp'), Model.Disp = 'y'; end;
if strcmp(Model.Disp, 'y')
fprintf('\n initial alpha = %+3.6f\n initial mu= %+3.6f\n initial
sigma = %+3.6f\n', alpha, mu, sigma);
end
% where
%Model.Data = Time series of interest rates observations
% Model.TimeStep = Delta t; recommended: 1/250 for daily data, 1/12
for monthly data
I am attaching also the source of this code to this email as well which
is one of the literature that I found recently.
The relavent source in the literature for your reference is in the
section 2.2. initial estimates.
Since my main purpose of this is to convert this into the R-programming
code,
it would be great if I could know the equivalent R-programming code for
this MATLAB code,
and also the online R-programming questioning website address as well.
Thank you very much!
Sincerely,
Woo Young Kang
__
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.
__
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.
Re: [R] Urgent Inquiry
You may find http://stackoverflow.com/ to be a useful website to ask R
questions.
Kevin
On Wed, Feb 12, 2014 at 3:09 PM, Woo Young Kang eric...@hotmail.com wrote:
Hi, my name is Woo Young Kang and I am a current user of R-programming.
I am looking for an R-programming online questioning community and was
having difficulty finding it.
I wonder what webaddress I can use to ask question regarding the
R-programming.
Before that, I do have one critical question that I would like to ask
regarding the R-programming.
I am trying to make about 10 lines of MATLAB code into the equivalent
R-programming code.
The backgroud for this is to produce initial parameters for the
Cox-Ross-Ingersoll short rate model using the
OLS method.
I found out the MATLAB code for OLS initial parameter estimation for the
CIR interest rate model from
one of the literature but have a bit difficulty in understanding 100% of
the code since I was trying to convert
this code in terms of R-programming code.
The code itself is as follows:
% Initial parameters using OLS
Nobs = length(Model.Data);
x = Model.Data(1:end-1);
dx = diff(Model.Data);
dx = dx./x.^0.5;
regressors = [Model.TimeStep./x.^0.5, Model.TimeStep*x.^0.5];
drift = regressors\dx;
res = regressors*drift - dx;
alpha = -drift(2);
mu = -drift(1)/drift(2);
sigma = sqrt(var(res, 1)/Model.TimeStep);
InitialParams = [alpha mu sigma];
if ~isfield(Model, 'Disp'), Model.Disp = 'y'; end;
if strcmp(Model.Disp, 'y')
fprintf('\n initial alpha = %+3.6f\n initial mu= %+3.6f\n
initial sigma = %+3.6f\n', alpha, mu, sigma);
end
% where
%Model.Data = Time series of interest rates observations
% Model.TimeStep = Delta t; recommended: 1/250 for daily data, 1/12 for
monthly data
I am attaching also the source of this code to this email as well which is
one of the literature that I found recently.
The relavent source in the literature for your reference is in the section
2.2. initial estimates.
Since my main purpose of this is to convert this into the R-programming
code,
it would be great if I could know the equivalent R-programming code for
this MATLAB code,
and also the online R-programming questioning website address as well.
Thank you very much!
Sincerely,
Woo Young Kang
__
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.
--
Kevin Wright
[[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.
Re: [R] Regression of complex-valued functions
Dear Rolf, Thank you for your suggestion. Based on your remarks I solved my problem using nlm(). Actually there are two quite straightforward ways to split the complex-valued problem into two “linked” real-valued problems. ### 1. Real part and Imaginary part # Experimental data E1_data - Re(E) E2_data - Im(E) # Model function (same of my previous post only different notations) E_2S2P1D - function(f,logaT,logEg,logEe,k,h,delta,logbeta,logtau) 10^logEe+(10^logEg-10^logEe)*( 1+delta*(2i*pi*10^(logtau)*f*10^logaT)^-k + (2i*pi*10^(logtau)*f*10^logaT)^-h + (2i*pi*10^(logtau)*f*10^logaT*10^(logbeta))^-1 )^-1 # Distance function dist - function(p) sum( ( (E1_data - Re(E_2S2P1D(f_data,c(rep(p[1],5),rep(p[2],5),rep(p[3],5),rep(0,5),rep(p[4],5)), p[5],p[6],p[7],p[8],p[9],p[10],p[11])) ) / E1_data )^2 ) + sum( ( (E2_data - Im(E_2S2P1D(f_data,c(rep(p[1],5),rep(p[2],5),rep(p[3],5),rep(0,5),rep(p[4],5)), p[5],p[6],p[7],p[8],p[9],p[10],p[11])) ) / E2_data )^2 ) # fitting fit - nlm(dist, p = c(-3.76,-2.63,-1.39,1.68,log10(27000),log10(200),0.16,0.47,1.97,2.2,0.02)) ### 2. Modulus and argument # Experimental data Emod_data - Mod(E) Earg_data - Arg(E) # Model function: same as above # Distance function dist - function(p) sum(((Emod_data - log10(Mod(E_2S2P1D(f_data,c(rep(p[1],5),rep(p[2],5),rep(p[3],5),rep(0,5),rep(p[4],5)), p[5],p[6],p[7],p[8],p[9],p[10],p[11])) ) / Emod_data )^2 ) + sum( ( (Earg_data - Arg(E_2S2P1D(f_data,c(rep(p[1],5),rep(p[2],5),rep(p[3],5),rep(0,5),rep(p[4],5)), p[5],p[6],p[7],p[8],p[9],p[10],p[11])) ) / Earg_data )^2 ) # fitting: same as above Using the same starting values, the two approaches bring to slightly different solutions: ### 1. Real part and Imaginary part fit$estimate [1] -3.8519181 -2.7342861 -1.4823740 1.7173982 4.4529298 1.4383334 0.1564904 0.4856774 2.2789567 3.9011926 0.1227758 ### 2. Modulus and argument fit$estimate [1] -3.8674680 -2.7250640 -1.4574350 1.6447868 4.4355748 1.2400092 0.1574215 0.4731295 2.0624878 3.7526197 0.1161640 Do you believe this is due only to “numerical reasons linked to how the nls() function works? Anyway...Thanks again! Andrea Il giorno 11/feb/2014, alle ore 09:42, Rolf Turner r.tur...@auckland.ac.nz ha scritto: I have not the mental energy to go through your somewhat complicated example, but I suspect that your problem is simply the following: The function nls() is trying to minimize a sum of squares, and that does not make sense in the context of complex observations. That is, nls() is trying to minimize a sum of terms of the form (f(x_i,theta) - z_i)^2 where f(x_i,theta) and z_i are complex quantities (and theta is the vector of parameters with respect to which minimization is trying to be done. But as I said, this makes no sense. Not that (f(x_i,theta) - z_i)^2 is a complex quantity and *not* a positive real quantity. You need to minimize a sum of terms of the form |f(x_i,theta) - z_i|^2 where |w|^2 equal to w times the complex conjugate of w. You get this in R via the Mod() function, i.e. |w|^2 is (Mod(w))^2. Thus it seems to me that nls() cannot handle what you want handled. You need to code up the function to be minimized yourself, using Mod() and then use optim() or nlm() to minimize it that function with respect to theta. HTH cheers, Rolf Turner On 10/02/14 11:45, Andrea Graziani wrote: Hi everyone, I previously posted this question but my message was not well written and did not contain any code so I will try to do a better job this time. The goal is to perform a non-linear regression on complex-valued data. I will first give a short description of the data and then describe the complex-valued non-linear function. ***The Data Obtained from mechanical tests performed at 5 loading frequencies 0.1, 0.25, 1, 0.4 and 12 Hz, and at 5 temeperatures. The independent variable used in the regression is: f_data - rep(c(0.1,0.25,1,4,12),5) The measured values of the response variable are: E - c(289.7411+ 225.0708i , 386.4417+ 303.5021i , 671.5132+ 521.1253i , 1210.8638+ 846.6253i , 1860.9623+1155.4139i , 862.8984+ 636.2637i , 1159.0436+ 814.5609i , 1919.0369+1186.5679i , 3060.7207+1573.6088i , 4318.1781+1868.4761i , 2760.7782+1418.5450i , 3306.3013+1612.2712i , 4746.6958+1923.8662i , 6468.5769+2148.9502i , 8072.2642+2198.5344i , 6757.7680+2061.3110i , 7591.9787+2123.9168i , 9522.9471+2261.8489i , 11255.0952+2166.6411i , 12601.3970+2120.7178i , 11913.6543+2016.0828i , 12906.8294+2030.0610i , 14343.7693+1893.4877i , 15942.7703+1788.0910i , 16943.2261+1665.9847i) To visualize the data: plot(f_data,Re(E),log=xy) plot(f_data,Im(E),log=xy) plot(E) ***Non-linear regression function: Obtained from an analytical model
Re: [R] Regression of complex-valued functions
Hi Frede, Thank you for your accurate answer! If I understand well, your way to use nls() solves the problem using too many physical parameters. I solved the problem following the other way that you and Rolf Turner suggested (i.e. splitting the complex-valued problem into two real-valued problems and using nlm() ). If you are interested in more details, please see my answer to Rolf’s mail. Why are loga40, loga30, loga20, 0 (zero value), and loga0 not independent variables that you control? If so you don't want to estimate those. If the logaT parameters are not under your control do you still really want to estimate the same set of values of the parameters of the model for each set of your data? And not separate estimates for each curve? You noticed a key point of the mechanical problem! However I’m looking for a “single curve”, so-called “master curve”, to fit all experimental data! However (putting my head under my shoulder) you can do something like this (Having just noticed Rolf Turner's answer you should absolutely explore that solutions. That would probably the best way to go). ;) Thanks again! Andrea ## this seems to run fit.re - nls(Re(E) ~ Re(E_2S2P1D(f,c(rep(loga40,5),rep(loga30,5),rep(loga20,5),rep(0,5),rep(loga0,5)), Eg,Ee,k,h,delta,logbeta,logtau)), data = myE, na.action = na.exclude, start=list(loga40=-3.76,loga30=-2.63,loga20=-1.39,loga0=1.68, Eg=27000,Ee=200,k=0.16,h=0.47,delta=1.97,logbeta=2.2,logtau=-0.02) ) fit.re ## plot fit overlayed observations png(fitted-Re.png) plot(f_data, Re(E), type = p, col = mycol)# log=xy) lines(f_data, fitted(fit.re), col = grey80) #, log = xy dev.off() ## this gives an error ## probably due to the 5 curves do not share parameters. See 3rd panel in attached plot-raw-data.png fit.im - nls(Im(E) ~ Im(E_2S2P1D(f,c(rep(loga40,5),rep(loga30,5),rep(loga20,5),rep(0,5),rep(loga0,5)), Eg,Ee,k,h,delta,logbeta,logtau)), data = myE, na.action = na.exclude, start=list(loga40=-3.76,loga30=-2.63,loga20=-1.39,loga0=1.68, Eg=27000,Ee=200,k=0.16,h=0.47,delta=1.97,logbeta=2.2,logtau=-0.02) ) ## Now try abs() ## which works and gives allmost same estimates as for fit.re fit.abs - nls(abs(E) ~ abs(E_2S2P1D(f,c(rep(loga40,5),rep(loga30,5),rep(loga20,5),rep(0,5),rep(loga0,5)), Eg,Ee,k,h,delta,logbeta,logtau)), data = myE, na.action = na.exclude, start=list(loga40=-3.76,loga30=-2.63,loga20=-1.39,loga0=1.68, Eg=27000,Ee=200,k=0.16,h=0.47,delta=1.97,logbeta=2.2,logtau=-0.02)) fit.abs png(fitted-abs.png) plot(f_data, abs(E), type = p, col = mycol)# log=xy) lines(f_data, predict(fit.abs), col = grey80) #, log = xy dev.off() Yours sincerely / Med venlig hilsen Frede Aakmann Tøgersen Specialist, M.Sc., Ph.D. Plant Performance Modeling Technology Service Solutions T +45 9730 5135 M +45 2547 6050 fr...@vestas.com http://www.vestas.com Company reg. name: Vestas Wind Systems A/S This e-mail is subject to our e-mail disclaimer statement. Please refer to www.vestas.com/legal/notice If you have received this e-mail in error please contact the sender. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Andrea Graziani Sent: 9. februar 2014 23:46 To: r-help@r-project.org Subject: [R] Regression of complex-valued functions Hi everyone, I previously posted this question but my message was not well written and did not contain any code so I will try to do a better job this time. The goal is to perform a non-linear regression on complex-valued data. I will first give a short description of the data and then describe the complex- valued non-linear function. ***The Data Obtained from mechanical tests performed at 5 loading frequencies 0.1, 0.25, 1, 0.4 and 12 Hz, and at 5 temeperatures. The independent variable used in the regression is: f_data - rep(c(0.1,0.25,1,4,12),5) The measured values of the response variable are: E - c(289.7411+ 225.0708i , 386.4417+ 303.5021i , 671.5132+ 521.1253i , 1210.8638+ 846.6253i , 1860.9623+1155.4139i , 862.8984+ 636.2637i , 1159.0436+ 814.5609i , 1919.0369+1186.5679i , 3060.7207+1573.6088i , 4318.1781+1868.4761i , 2760.7782+1418.5450i , 3306.3013+1612.2712i , 4746.6958+1923.8662i , 6468.5769+2148.9502i , 8072.2642+2198.5344i , 6757.7680+2061.3110i , 7591.9787+2123.9168i , 9522.9471+2261.8489i , 11255.0952+2166.6411i , 12601.3970+2120.7178i , 11913.6543+2016.0828i , 12906.8294+2030.0610i , 14343.7693+1893.4877i , 15942.7703+1788.0910i , 16943.2261+1665.9847i) To visualize the data: plot(f_data,Re(E),log=xy) plot(f_data,Im(E),log=xy) plot(E) ***Non-linear regression function: Obtained
Re: [R] Regression of complex-valued functions
On 13/02/14 12:03, Andrea Graziani wrote: SNIP Using the same starting values, the two approaches bring to slightly different solutions: ### 1. Real part and Imaginary part fit$estimate [1] -3.8519181 -2.7342861 -1.4823740 1.7173982 4.4529298 1.4383334 0.1564904 0.4856774 2.2789567 3.9011926 0.1227758 ### 2. Modulus and argument fit$estimate [1] -3.8674680 -2.7250640 -1.4574350 1.6447868 4.4355748 1.2400092 0.1574215 0.4731295 2.0624878 3.7526197 0.1161640 Do you believe this is due only to “numerical reasons linked to how the nls() function works? I find it a bit surprising that there are differences in the third decimal place here. I would have thought that the results would be exactly the same, or ***very*** close to it. If you have done it right (I have not checked your code at all) the two approaches should amount to the same approach. I.e. Mod(z)^2 is equal to Re(z)^2 + Im(z)^2. Check your code carefully. Also it would be a good idea to try a toy example, something much less complicated than your real problem, and see what happens there. cheers, Rolf Turner __ 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.
[R] John M. Chambers Statistical Software Award 2014
The Statistical Computing Section of the American Statistical Association announces the competition for the John M. Chambers Statistical Software Award. In 1998 the Association for Computing Machinery presented its Software System Award to John Chambers for the design and development of S. Dr. Chambers generously donated his award to the Statistical Computing Section to endow an annual prize for statistical software written by, or in collaboration with, an undergraduate or graduate student. The prize carries with it a cash award of $1000, plus a substantial allowance for travel to the annual Joint Statistical Meetings (JSM) where the award will be presented. Teams of up to 3 people can participate in the competition, with the cash award being split among team members. The travel allowance will be given to just one individual in the team, who will be presented the award at JSM. To be eligible, the team must have designed and implemented a piece of statistical software. The individual within the team indicated to receive the travel allowance must have begun the development while a student, and must either currently be a student, or have completed all requirements for her/his last degree after January 1, 2013. To apply for the award, teams must provide the following materials: * Current CV's of all team members. * A letter from a faculty mentor at the academic institution of the individual indicated to receive the travel award. The letter should confirm that the individual had substantial participation in the development of the software, certify her/his student status when the software began to be developed (and either the current student status or the date of degree completion), and briefly discuss the importance of the software to statistical practice. * A brief, one to two page description of the software, summarizing what it does, how it does it, and why it is an important contribution. If the team member competing for the travel allowance has continued developing the software after finishing her/his studies, the description should indicate what was developed when the individual was a student and what has been added since. * An installable software package with its source code for use by the award committee. It should be accompanied by enough information to allow the judges to effectively use and evaluate the software (including its design considerations.) This information can be provided in a variety of ways, including but not limited to a user manual (paper or electronic), a paper, a URL, and online help to the system. All materials must be in English. We prefer that electronic text be submitted in Postscript or PDF. The entries will be judged on a variety of dimensions, including the importance and relevance for statistical practice of the tasks performed by the software, ease of use, clarity of description, elegance and availability for use by the statistical community. Preference will be given to those entries that are grounded in software design rather than calculation. The decision of the award committee is final. All application materials must be received by 5:00pm EST, Tuesday, February 18, 2014 at the address below. The winner will be announced in May and the award will be given at the 2014 Joint Statistical Meetings. Student Paper Competition c/o Aarti Munjal Colorado School of Public Health University of Colorado Denver aarti.mun...@ucdenver.edumailto:aarti.mun...@ucdenver.edu -- Aarti Munjal, Ph.D. Research Assistant Professor Department of Biostatistics and Informatics Colorado School of Public Health University of Colorado Denver Office Phone: 303-724-6273 [[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.
[R] Java 7.51 broke rJava?
Hi, after I updated Java to 7.51 on my Windows system, rJava can no longer load: library(rJava) Error : .onLoad failed in loadNamespace() for 'rJava', details: call: fun(libname, pkgname) error: No CurrentVersion entry in Software/JavaSoft registry! Try re-installing Java and make sure R and Java have matching architectures. Error: package or namespace load failed for ‘rJava’ My session info: sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_3.18.11 gage_2.12.1 Rcolombos_1.4.1 RJSONIO_1.0-3 RCurl_1.95-4.1 bitops_1.0-6 loaded via a namespace (and not attached): [1] BiocGenerics_0.8.0 Biostrings_2.30.1 digest_0.6.4 graph_1.40.1 httr_0.2 IRanges_1.20.6 [7] KEGGREST_1.2.0 parallel_3.0.2 png_0.1-7 stats4_3.0.2 stringr_0.6.2 tools_3.0.2 [13] XVector_0.2.0 Anyone knows how to fix this? Thanks. Yury __ 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.
[R] Help on best way to calculate and plot overall mean from dataset with two treatment groups
I am working on a dataset which has multiple species over several plots, categorised into two treatment groups. For example group_xy group_op plot species value x o 1 A 3 x o 1 A 5 x o 1 B 4 x o 2 A 3 x o 2 A 6 x o 2 A 3 y o 1 A 3 y o 1 A 5 y o 1 B 4 y o 2 A 3 y o 2 A 6 y o 2 A 3 x p 1 A 3 x p 1 A 5 x p 1 B 4 x p 2 A 3 x p 2 A 6 x p 2 A 3 y p 1 A 3 y p 1 A 5 y p 1 B 4 y p 2 A 3 y p 2 A 6 y p 2 A 3 What I would like to do is to take the mean of the species within each plot in each treatment group, then generate the mean for the species based upon the average of the values between plots. Thus the intermediate output would be group_xy group_op plot species mean_value standard_deviation x o 1 A 3 sd x o 1 B 4 sd x o 2 A 4 sd y o 1 A 3 sd y o 1 B 4 sd y o 2 A 4 sd x p 1 A 3 sd x p 1 B 4 sd x p 2 A 4 sd y p 1 A 3 sd y p 1 B 4 sd y p 2 A 4 sd Then eventually group_xy group_op species total_mean_value standard_deviation x o A 3.5 sd x o B 4 sd y o A 3.5 sd y o B 4 sd x p A 3.5 sd x p B 4 sd y p A 3.5 sd y p B 4 sd I am looking for an elegant code which would allow me to do this and generate plots. for all species for all treatment groups. Any help would be appreciated! [[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.
Re: [R] Java 7.51 broke rJava?
Have you investigated the suggestion in the error message yet? Architecture means 32bit vs 64bit... --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On February 12, 2014 3:09:33 PM PST, Yury V Bukhman ybukh...@glbrc.wisc.edu wrote: Hi, after I updated Java to 7.51 on my Windows system, rJava can no longer load: library(rJava) Error : .onLoad failed in loadNamespace() for 'rJava', details: call: fun(libname, pkgname) error: No CurrentVersion entry in Software/JavaSoft registry! Try re-installing Java and make sure R and Java have matching architectures. Error: package or namespace load failed for ‘rJava’ My session info: sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_3.18.11 gage_2.12.1 Rcolombos_1.4.1 RJSONIO_1.0-3 RCurl_1.95-4.1 bitops_1.0-6 loaded via a namespace (and not attached): [1] BiocGenerics_0.8.0 Biostrings_2.30.1 digest_0.6.4 graph_1.40.1 httr_0.2 IRanges_1.20.6 [7] KEGGREST_1.2.0 parallel_3.0.2 png_0.1-7 stats4_3.0.2 stringr_0.6.2 tools_3.0.2 [13] XVector_0.2.0 Anyone knows how to fix this? Thanks. Yury __ 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. __ 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.
[R] impossible to install package
Hi, I want to install languageR but is doesn't work. I tried it by two ways: (1) by writing the following command but there is a warning message in response: install.packages (LanguageR) Warning message: package LanguageR is not available (for R version 2.15.2) This problem appeared some weeks ago, but I was still able to install the package with the R package Installer with CRAN (binaries). (2) with the R package Installer which does not work since today. I tried different packages repository but it does not find LanguageR when I click on get list. The list remains empty. Could you please help me? Many thanks, Eve -- Eve Dupierrix Marie-Curie Research Fellow Queensland Brain Institute The University of Queensland St Lucia 4072 QLD Australia phone: +61 7 3346 3305 http://www.qbi.uq.edu.au/group-leader-mattingley http://webu2.upmf-grenoble.fr/LPNC/membre_eve_dupierrix [[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.
[R] Inquiry
Dear R users, Hello, this is Kei Takeuchi in Japan. I have started to use R(windows, version3.0.2) and have a problem. I think it is not difficlut but since I am beginner of R, I have no way to solve it. Where can I post my question? Thank you in advance. Kei Takeuchi __ 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.
Re: [R] impossible to install package
Dear Eve, See http://cran.r-project.org/web/packages/languageR/index.html The name of the package is languageR, not LanguageR. Best, Jorge.- On Thu, Feb 13, 2014 at 3:39 PM, Eve Dupierrix evedupier...@gmail.comwrote: Hi, I want to install languageR but is doesn't work. I tried it by two ways: (1) by writing the following command but there is a warning message in response: install.packages (LanguageR) Warning message: package 'LanguageR' is not available (for R version 2.15.2) This problem appeared some weeks ago, but I was still able to install the package with the R package Installer with CRAN (binaries). (2) with the R package Installer which does not work since today. I tried different packages repository but it does not find LanguageR when I click on get list. The list remains empty. Could you please help me? Many thanks, Eve -- Eve Dupierrix Marie-Curie Research Fellow Queensland Brain Institute The University of Queensland St Lucia 4072 QLD Australia phone: +61 7 3346 3305 http://www.qbi.uq.edu.au/group-leader-mattingley http://webu2.upmf-grenoble.fr/LPNC/membre_eve_dupierrix [[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]] __ 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.
Re: [R] Inquiry
Hi Kei, Welcome. I think you can first read an Introduction to R (http://cran.r-project.org/doc/manuals/R-intro.pdf) Then read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code, as requested when you ask a question to the R-help mailing list. Also, some specific questions have to be asked to specific mailing list: http://www.r-project.org/mail.html Hope this helps, Pascal On 13 February 2014 11:01, Kei_Takeuchi kt...@jari.or.jp wrote: Dear R users, Hello, this is Kei Takeuchi in Japan. I have started to use R(windows, version3.0.2) and have a problem. I think it is not difficlut but since I am beginner of R, I have no way to solve it. Where can I post my question? Thank you in advance. Kei Takeuchi __ 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. -- Pascal Oettli Project Scientist JAMSTEC Yokohama, Japan __ 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.
