Re: [R] nice report generator?
Sarah Goslee might want to chime in, but using odfWeave and appropriate LibreOffice templates, you can generate beautifully formatted tables, possibly in the style you wish, in LibreOffice, as well as add R figures. The R2wd package (which has a proprietary component) will also generate tables directly in Word (on windows machines) and their default theme is pretty attractive to me. I'm pretty sure even that is customizable. You can also put R plots directly into Word that way as well. Abhijit On 12/7/2011 3:21 PM, Michael wrote: > Thanks a lot Duncan! > > I did some home-work and found out that in terms of table looks, it's > neater to generate Excel 2010 style colorful tables, not the Latex > style plain/math-geek tables... > > Therefore, a report generator would hopefully generate Excel 2010 > style tables, plus R plots, etc. > > Any thoughts? > > Thanks a lot! > > On 12/7/11, Duncan Murdoch wrote: >> On 07/12/2011 1:14 PM, Michael wrote: >>> Hi all, >>> >>> I am looking for recommendations/pointers about best report generator you >>> think that are currently available? >>> >>> i.e. the package that can help turn console output into nice-looking neat >>> report to send to bosses? >> You might find the latex() command in Hmisc or the equivalent in the >> xtable package does what you want. For simple reports in a single table >> you don't need Sweave; for more complex ones it would make your life easier. >> >> My tables package (now on CRAN) might simplify the production of the >> table. It is set up to work with Hmisc currently. >> >> Duncan Murdoch >> > __ > 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] Proc Mixed to R
You need to use either the lme4 or nlme packages for mixed models.
(There are some other possibilities as well). See
http://glmm.wikidot.com/faq for MUCH more detail
On 10/27/2011 7:19 PM, Molly Hanlon wrote:
> Hi All,
>
> I'm working with some SAS code to analyze an experiment set up as follows:
> 66 subjects (colonies) treated with a random treatment (1-8) and measured at
> three time points.
> The data structure looks like:
>
> input colony tmt y1 y2 y3;
>
> y=y1; date=*1*; output;
>
> y=y2; date=*2*; output;
>
> y=y3; date=*3*; output;
>
> datalines;
>
> 1 3 6725 6750 925
>
> 2 8 6950 5800 11275
>
> 3 4 4200 6100 6475
>
>
> Procedure:
>
> *proc* *mixed* data=Nosema method=ml covtest;
>
> class colony tmt;
>
> model y=tmt date tmt*date / s;
>
> repeated / type=un subject=colony;
>
> random colony;
>
> lsmeans tmt/cl adjust=tukey;
>
>
> I am able to get something close by running aov on it, even closer by using
> Anova{car} and calling type=3. The problem I'm having is running the tukey
> and/or getting something similar to SAS's "Solution for Fixed Effects"
> table. Any idea what to do?
>
>
> Thanks,
>
>
> Molly
>
> [[alternative HTML version deleted]]
>
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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Re: [R] How to turn a LaTeX Sweave file (Rnw) into .HTML/.odf/.docx? (under windows)
So, I was playing around a bit on my Mac LyX can do Sweave (see http://wiki.lyx.org/LyX/LyxWithRThroughSweave), and will actually output HTML or ODT. However, on a cursory pass, I couldn't get the graphics to translate, since the Sweave driver translates the graphics as .ps or .pdf files, and I'm not sure the HTML translator looks for them or can accept them. The math actually translates nicely. So there is probably potential here. Abhijit On Sep 22, 2011, at 7:09 PM, Tal Galili wrote: > Hello dear R help members, > I have found several references on how to do this, my question is if anyone > is actually using them - and if there are some strong points on what to use, > and how well it is working out. > > My goal is to be able to easily create docs from R, but to be able to share > it with other researchers (who do not use LaTeX) so they could easily > copy/paste the tables and edit them for their needs (pdf is not solving this > for me). > > The only reasonable solution I came by so far is to use HTML markup coupled > with R2HTML (or odfWeave or R2wd). But nothing that can work with > LaTeX->HTML (easily) > > I have asked a similar question here: > http://stackoverflow.com/questions/7512897/how-to-turn-a-latex-sweave-file-rnw-into-html > And also noticed it was asked half a year ago here: > http://tex.stackexchange.com/questions/4145/workflow-for-converting-latex-into-open-office-ms-word-format > The general issue of TeX to HTML was discussed also in these places: > http://tex.stackexchange.com/questions/50/how-can-i-convert-math-less-latex-documents-into-microsoft-word > > And obviously the following page offers other good resources to consider: > http://cran.r-project.org/web/views/ReproducibleResearch.html > > p.s: I search the R-help for this topic, but "sweave html" didn't seem to > yield good results - my apologies if this has been heavily debated before - > links would be welcomed as well. > > > Tal > > > > Contact > Details:--- > Contact me: tal.gal...@gmail.com | 972-52-7275845 > Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | > www.r-statistics.com (English) > -- > > [[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] Hints for Data Mining
Please see the R Machine Learning Task View
(http://cran.r-project.org/web/views/MachineLearning.html) for a
starting point on decision trees.
On 9/14/2011 7:11 PM, Lorenzo Isella wrote:
> Dear All,
> I am recycling a previous email of mine where I asked some questions
> about clustering mixed numerical/categorical data. This time I am more
> into data mining. I am given a set of known statistical indexes {s_i},
> i=1,2...N for a N countries. These indexes in general are a both
> numerical and categorical variables. For each country, I also have a
> property x_i whose value is known, but that I also would like to be
> able to predict correctly using a model. This is needed in order to
> assess the importance of the various indexes in determining {x_i}.
> There are two cases of interest
>
> (1) all the {x_i} are numerical variables, e.g. the average life
> expectancy
>
> (2) all the {x_i} are categorical variables (e.g. the fact that the
> country joins treaty A, B or C). This reminds me of discrete choice
> models.
>
> Any suggestions about how to tackle this problems? In the past I used
> mclust, but it is limited to all the {s_i} being numerical variables.
>
> I saw an example of the use of glm for predicting binary variables
>
> http://www.ats.ucla.edu/stat/R/dae/probit.htm
>
> which may be relevant for (2). In general I know that some people use
> Weka for this sort of tasks, but I wonder if I can use R to get a
> decision tree and a confusion matrix and to be able to predict how the
> {x_i} would change by varying the value of one statistical index.
> Many thanks for your suggestions
>
> Lorenzo
>
> __
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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Re: [R] Avoiding for Loop for moving average
There is a recent blog post by Dirk Eddelbeutel on how to do something
similar using his Rcpp package and C++, with massive time improvements.
http://dirk.eddelbuettel.com/blog/
On 9/2/2011 12:43 PM, Noah Silverman wrote:
> Hello,
>
> I need to calculate a moving average and an exponentially weighted moving
> average over a fairly large data set (500K rows).
>
> Doing this in a for loop works nicely, but is slow.
>
> ewma<- data$col[1]
> N<- dim(data)[1]
> for(i in 2:N){
> data$ewma<- alpha * data$ewma[i-1] + (1-alpha) * data$value[i]
> }
>
>
> Since the moving average "accumulates" as we move through the data, I'm not
> sure on the best/fastest way to do this.
>
> Does anyone have any suggestions on how to avoid a loop doing this?
>
>
>
>
> --
> Noah Silverman
> UCLA Department of Statistics
> 8117 Math Sciences Building #8208
> Los Angeles, CA 90095
>
>
> [[alternative HTML version deleted]]
>
> __
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Opposite of paste function
or,
gsub('V','',vn)
On 8/10/2011 2:23 PM, Peter Langfelder wrote:
> On Wed, Aug 10, 2011 at 11:22 AM, Soyeon Kim wrote:
>> Dear All,
>>
>> I have vn variable
>>> vn
>> [1] "V300" "V376"
>> What I want to get is
>> 300 376
> as.numeric(substring(vn, 2))
>
> HTH
>
> Peter
>
> __
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> 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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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Storing and managing custom R functions for re-use
I think most of us are in a similar situation. I've usually kept mine in a file which is sourced when I start R. The main problem I have with this is that it clutters up my environment with a lot of stuff I don't need all the time. I'm in the process of creating a custom package which will be lazy-loaded. I believe a previous discussion of this topic suggested this as the preferred method. On 07/09/2011 07:30 AM, Simon Chamaillé-Jammes wrote: Dear all, sorry if this is a bit on the sidetrack for R-help. As a regular R user I have developed quite a lot of custom R functions, to the point of not always remembering what I have already programmed, where the file is and so on. I was wondering what other people do in this regards. A basic file with all your functions, or a custom R package, or directly integrated into a profile file ??? I'm considering that a blog with tagged posts may be a good solution (and really good ones could join R-bloggers maybe). If someone is happy to share what (s)he considers good practice, thanks. simon __ 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] Confidence bands in ggplot2
It's basically a question of layering, and the order in which the layers are
drawn. Draw the pointranges first and then the points:
qplot(x=as.factor(sch), y=est, ymin=lower.95ci, ymax=upper.95ci,
geom='pointrange')+
geom_point(aes(x=as.factor(sch), y=est), color='red')+...
On Jul 7, 2011, at 6:16 PM, Christopher Desjardins wrote:
> Thanks that worked perfectly. One thing if I may. Is it possible to make the
> center dot red and the lines connecting the dots black?
>
> Thanks,
> Chris
>
>
> On Jul 7, 2011, at 5:10 PM, Abhijit Dasgupta, PhD wrote:
>
>> You can easily do this by:
>>
>> qplot(x=as.factor(sch),y=est, geom='point', colour='red') +
>> geom_pointrange(aes(x=as.factor(sch), y=est, ymin=lower.95ci,
>> ymax=upper.95ci))+
>> xlab('School') + ylab("Value-added")+theme_bw()
>>
>>
>>
>>
>> On 07/07/2011 05:55 PM, Christopher Desjardins wrote:
>>> Hi,
>>> I have the following data:
>>>
>>>> est
>>> sch190 sch107 sch290 sch256 sch287 sch130
>>> sch139
>>> 4.16656026 2.64306071 4.22579866 6.12024789 4.49624748 11.12799127
>>> 1.17353917
>>> sch140 sch282 sch161 sch193 sch156 sch288
>>> sch352
>>> 3.48197696 -0.29659410 -1.99194986 10.23489859 7.77342138 6.77624539
>>> 9.66795001
>>> sch368 sch225 sch301 sch105 sch353 sch291
>>> sch179
>>> 7.20229569 4.41989204 5.61586860 5.99460203 -2.65019242 -9.42614560
>>> -0.25874193
>>> sch134 sch135 sch324 sch360 bb1
>>> 3.26432479 10.52555091 -0.09637968 2.49668858 -3.24173545
>>>
>>>> se
>>> sch190sch107sch290sch256sch287sch130sch139
>>> sch140
>>> 3.165127 3.710750 4.680911 6.335386 3.896302 4.907679 4.426284
>>> 4.266303
>>> sch282sch161sch193sch156sch288sch352sch368
>>> sch225
>>> 3.303747 4.550193 3.995261 5.787374 5.017278 7.820763 7.253183
>>> 4.483988
>>> sch301sch105sch353sch291sch179sch134sch135
>>> sch324
>>> 4.076570 7.564359 10.456522 5.705474 4.247927 5.671536 10.567093
>>> 4.138356
>>> sch360 bb1
>>> 4.943779 1.935142
>>>
>>>> sch
>>> [1] "190" "107" "290" "256" "287" "130" "139" "140" "282" "161" "193" "156"
>>> "288"
>>> [14] "352" "368" "225" "301" "105" "353" "291" "179" "134" "135" "324"
>>> "360" "BB"
>>>
>>>
>>> From this data I have created 95% confidence intervals assuming a normal
>>> distribution.
>>>
>>> lower.95ci<- est - se*qnorm(.975)
>>> upper.95ci<- est + se*qnorm(.975)
>>>
>>> What I'd like to do is plot the estimate (est) and have lines attach to the
>>> points located in lower.95ci and upper.95ci. Presently I am doing the
>>> following:
>>>
>>> qplot(x=as.factor(sch),y=lower.95ci) +
>>> geom_point(aes(x=as.factor(sch),y=upper.95ci),colour="black") +
>>> geom_point(aes(x=as.factor(sch), y=est),colour="red") + ylab("Value-Added")
>>> + xlab("School") + theme_bw()
>>>
>>> Which creates this graph --->
>>> http://dl.dropbox.com/u/1501309/value_added_test.pdf
>>>
>>> That's fine except that it doesn't connect the points vertically. Does
>>> anyone know how I could make the 'black' points connect to the 'red' point,
>>> i.e. show confidence bands?
>>>
>>> Thanks,
>>> Chris
>>>
>>>
>>> [[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.
>
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Confidence bands in ggplot2
You can easily do this by:
qplot(x=as.factor(sch),y=est, geom='point', colour='red') +
geom_pointrange(aes(x=as.factor(sch), y=est, ymin=lower.95ci, ymax=upper.95ci))+
xlab('School') + ylab("Value-added")+theme_bw()
On 07/07/2011 05:55 PM, Christopher Desjardins wrote:
Hi,
I have the following data:
est
sch190 sch107 sch290 sch256 sch287 sch130
sch139
4.16656026 2.64306071 4.22579866 6.12024789 4.49624748 11.12799127
1.17353917
sch140 sch282 sch161 sch193 sch156 sch288
sch352
3.48197696 -0.29659410 -1.99194986 10.23489859 7.77342138 6.77624539
9.66795001
sch368 sch225 sch301 sch105 sch353 sch291
sch179
7.20229569 4.41989204 5.61586860 5.99460203 -2.65019242 -9.42614560
-0.25874193
sch134 sch135 sch324 sch360 bb1
3.26432479 10.52555091 -0.09637968 2.49668858 -3.24173545
se
sch190sch107sch290sch256sch287sch130sch139sch140
3.165127 3.710750 4.680911 6.335386 3.896302 4.907679 4.426284 4.266303
sch282sch161sch193sch156sch288sch352sch368sch225
3.303747 4.550193 3.995261 5.787374 5.017278 7.820763 7.253183 4.483988
sch301sch105sch353sch291sch179sch134sch135sch324
4.076570 7.564359 10.456522 5.705474 4.247927 5.671536 10.567093 4.138356
sch360 bb1
4.943779 1.935142
sch
[1] "190" "107" "290" "256" "287" "130" "139" "140" "282" "161" "193" "156"
"288"
[14] "352" "368" "225" "301" "105" "353" "291" "179" "134" "135" "324" "360"
"BB"
From this data I have created 95% confidence intervals assuming a normal
distribution.
lower.95ci<- est - se*qnorm(.975)
upper.95ci<- est + se*qnorm(.975)
What I'd like to do is plot the estimate (est) and have lines attach to the
points located in lower.95ci and upper.95ci. Presently I am doing the
following:
qplot(x=as.factor(sch),y=lower.95ci) + geom_point(aes(x=as.factor(sch),y=upper.95ci),colour="black") +
geom_point(aes(x=as.factor(sch), y=est),colour="red") + ylab("Value-Added") +
xlab("School") + theme_bw()
Which creates this graph --->
http://dl.dropbox.com/u/1501309/value_added_test.pdf
That's fine except that it doesn't connect the points vertically. Does anyone
know how I could make the 'black' points connect to the 'red' point, i.e. show
confidence bands?
Thanks,
Chris
[[alternative HTML version deleted]]
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Re: [R] trying to import xls or xlsx files
Gabor's answer explains the error perfectly. You might want to look at the xlsx
package as well as the RODBC package if you're on Windows. RODBC is really
fast, if you can use it.
Abhijit
On Jun 23, 2011, at 2:00 PM, wwreith wrote:
> library(xlsReadWrite)
> mydata<-read.xls("file path", header=TRUE)
>
> however if I change xls to csv it works just fine. Any ideas what I'm doing
> wrong? I have have also using the package gdata with the exact same error.
>
> Below is the error that pops up.
>
> Error in findPerl(verbose = verbose) :
> perl executable not found. Use perl= argument to specify the correct path.
> Error in file.exists(tfn) : invalid 'file' argument
>
>
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/trying-to-import-xls-or-xlsx-files-tp3620580p3620580.html
> Sent from the R help mailing list archive at Nabble.com.
>
> __
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> and provide commented, minimal, self-contained, reproducible code.
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Re: [R] new to R need urgent help!
On Jun 23, 2011, at 4:42 PM, elisheva corn wrote: > hi all- > > I am doing some research, have never used R before until today and need to > understand the following program for a project. > if some one could PLEASE help me understand this program ASAP i would > GREATLY appreciate it (any syntax/ statistic comments would be great) > > PLEASE PLEASE HELP!! THANKYOU!!! > -on a side note, it seems to me that R doesnt include the pv, and it was > calculated seperatly, is this true? > > > fit=gee(foci~as.factor(time)*cond,id=exper,data=drt,family=poisson(link = > "log")) You apparently have count data (foci) which is measured repeatedly within exper, and you're interested in how foci changes with time and condition including their interaction. The code fits a generalized estimating equation (GEE) model, which can be an appropriate model for repeated measures data. See, for example, Diggle, Liang, Zeger & Heagerty for background. > Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 > running glm to get initial regression estimate > (Intercept) as.factor(time)24 > 3.051177 -2.705675 > condHypoxia as.factor(time)24:condHypoxia >-0.402259 1.429034 >> pv=2*(1-pnorm(abs(summary(fit)$coef[,5]))) >> data.frame(summary(fit)$coef,pv) The gee package doesn't compute the value directly, though other functions like lm, glm and others do. What the code does is use the robust z statistic, which is the estimate/robust se, and relate it to the standard normal distribution. > Estimate Naive.S.E. Naive.z Robust.S.E. > Robust.z > (Intercept)3.051177 0.02221052 137.37527 0.04897055 > 62.306363 > as.factor(time)24 -2.705675 0.10890056 -24.84537 0.19987174 > -13.537057 > condHypoxia -0.402259 0.03907961 -10.29332 0.10661248 > -3.773095 > as.factor(time)24:condHypoxia 1.429034 0.12549576 11.38711 0.17867421 > 7.997988 >pv > (Intercept) 0.00e+00 > as.factor(time)24 0.00e+00 > condHypoxia 1.612350e-04 > as.factor(time)24:condHypoxia 1.332268e-15 >> ftable(table(drt$cond,drt$time,predict(fit))) > 0.345501643340608 1.37227675004058 2.64891772174934 > 3.05117673373261 > > > Oxia0.5 00 > 0 485 >24 3150 > 00 > Hypoxia 0.5 00 > 3460 >24 0 449 > 00 >> ## 3-th term gives the difference between the Hypoxia/Oxia at time=0.5 >> ## the difference between Hypoxia/Oxia at time=24 >> L=matrix(c(0,0,1,1),nrow=1) >> fit$coef[L==1] > condHypoxia as.factor(time)24:condHypoxia >-0.402259 1.429034 >> L%*%fit$coef > [,1] > [1,] 1.026775 >> wald.test(fit$robust.variance,fit$coef,L=L) > Wald test: > -- > > Chi-squared test: > X2 = 23.8, df = 1, P(> X2) = 1.1e-06 >> > >[[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-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] Summarize by two or more attributes
One possibility is:
library(doBy)
summaryBy(Rate~Source+Bin, data=Df, FUN=sum)
On 5/17/2011 12:48 PM, LCOG1 wrote:
> Okay everyone heres a likely softball for someone.
>
> Consider the following data frame:
>
> #Create data
> x<-rep(c(1,15),10)
> y<-rnorm(20)
> z<-c(rep("auto",10),rep("bus",10))
> a<-rep(c(1,1,2,2,3,3,4,4,5,5),2)
> #Create Data frame
> Df<-data.frame(Source=x,Rate=y,Bin=a,Type=z)
>
>
> I want to create a new column the equals the sum of the Rates for each type
> (1,15) by Bin.
>
> A related question: I have been using R for a while now and usually
> manipulate my data in data frames but i know lists are better for R so
> perhaps the above should be done using lists. Feel free to offer
> suggestions coming from that angle.
>
> Thanks guys
>
> JR-
>
>
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/Summarize-by-two-or-more-attributes-tp3529825p3529825.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.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] combine lattice plot and standard R plot
Hi,
All of the components in the grid.arrange statement are from ggplot2 and
lattice, which are both in turn based on the grid package. What
grid.arrange is able to do is use the grid framework to arrange the
individual plots on a page. The base graphics are not based on grid, and
so won't work (afaik) with grid.arrange
Abhijit
On 5/4/2011 2:47 PM, Scott Chamberlain wrote:
> What about the example in gridExtra package:
>
> require(ggplot2); require(lattice); require(gridExtra)
> grid.arrange(qplot(1:10), xyplot(1:10~1:10), tableGrob(head(iris)), nrow=2,
> as.table=TRUE, main="test main", sub=textGrob("test sub", gp=gpar(font=2)))
> On Wednesday, May 4, 2011 at 1:44 PM, Jonathan Daily wrote:
> If you read the help documentation, lattice is not really compatible
>> with standard graphics.
>>
>> library("lattice")
>> ?lattice
>>
>> 2011/5/4 Lucia Cañas:
>>> Dear R users,
>>>
>>> I would like to combine lattice plot (xyplot) and standard R plot (plot and
>>> plotCI) in an unique figure.
>>>
>>> I use the function "par()" to combine plot and plotCI and I use the
>>> function "print()" to combine xyplot. I tried to use these functions to
>>> combine xyplot and plotCI and plots but they do not work. Does anybody know
>>> how I can do this?
>>>
>>> Thank you very much in advance.
>>>
>>>
>>>
>>>
>>> LucÃa Cañás Ferreiro
>>>
>>> Instituto Español de OceanografÃa
>>> Centro Oceanográfico de A coruña
>>> Paseo MarÃtimo Alcalde Francisco Vázquez, 10
>>> 15001 - A Coruña, Spain
>>>
>>> Tel: +34 981 218151 Fax: +34 981 229077
>>> lucia.ca...@co.ieo.es
>>> http://www.ieo.es
>>>
>>>
>>>
>>> [[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.
>>
>>
>> --
>> ===
>> Jon Daily
>> Technician
>> ===
>> #!/usr/bin/env outside
>> # It's great, trust me.
>>
>> __
>> 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.
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] linear regression in a data.frame using recast -- A fortunes candidate??
Seconded On 03/16/2011 05:37 PM, Bert Gunter wrote: Ha! -- A fortunes candidate? -- Bert If this is really a time series, then you will have serious validity problems due to auto-correlation among non-independent units. (But if you are just searching for a way to pull the wool over the eyes of the statistically uninformed, then I guess there's no stopping you.) -- David Winsemius, MD West Hartford, CT __ 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] value of W seems to be suspicious in the mann-whitney wilcox related test. what could be the problem
You need to read up on the Wilcoxon signed-rank test and the output from wilcox.test!!! The confidence interval is of the difference of medians, which can certainly be negative. In fact, your estimate is -33, and the confidence interval is (-68, 0) which is reasonable. The value of W is a positive number, in general, and isn't restricted to [0,1] Abhijit > > On 3/14/2011 11:07 AM, taby gathoni wrote: >> my output is as follows: >> wilcox.test(main_samp$SCORE~main_samp$GENDER, conf.int = TRUE) >> >> Wilcoxon rank sum test with continuity correction >> >> data: main_samp$SCORE by main_samp$GENDER >> W = 2780.5, p-value = 0.04829 >> alternative hypothesis: true location shift is not equal to 0 >> 95 percent confidence interval: >> -6.85e+01 -2.056837e-05 >> sample estimates: >> difference in location >> -33.3 >> result of W seems suspicious since i expect the result to be between 0 and >> 1. >> >> and the confidence intervals are also -ves what could be the challenge? >> Thanks Taby >> >> >> >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> >> >> __ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guidehttp://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] value of W seems to be suspicious in the mann-whitney wilcox related test. what could be the problem
You need to read up on the Wilcoxon signed-rank test and the output from wilcox.test!!! The confidence interval is of the difference of medians, which can certainly be negative. In fact, your estimate is -33, and the confidence interval is (-68, 0) which is reasonable. The value of W is a positive number, in general, and isn't restricted to [0,1] Abhijit On 3/14/2011 11:07 AM, taby gathoni wrote: > my output is as follows: > wilcox.test(main_samp$SCORE~main_samp$GENDER, conf.int = TRUE) > > Wilcoxon rank sum test with continuity correction > > data: main_samp$SCORE by main_samp$GENDER > W = 2780.5, p-value = 0.04829 > alternative hypothesis: true location shift is not equal to 0 > 95 percent confidence interval: > -6.85e+01 -2.056837e-05 > sample estimates: > difference in location > -33.3 > result of W seems suspicious since i expect the result to be between 0 and > 1. > > and the confidence intervals are also -ves what could be the challenge? > Thanks Taby > > > > > > > > > [[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] Rstudio question
Seconded. Go to the support forum at www.rstudio.org and post your question/bug/suggestion. Those folks have been excellent in their response times and feedback. On 3/4/2011 9:14 AM, Shige Song wrote: > Why don't you post the question to the RStudio support forum? The > folks there are quite responsive and very helpful. > > Shige > > On Fri, Mar 4, 2011 at 9:05 AM, Robert Kinley wrote: >> I really like RStudio ... >> >> ... but I wish it wouldn't automatically reload the last .RData it had. >> >> Anyone know how to fix this ... ? >> >> Also - does anyone know is there an Rstudio-user email-list forum thingy >> out there ? >> >> ta. >> >> Robert Kinley >> >> [[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-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] Plot with same font like in LaTeX
The tikzDevice package can do this. On 3/2/2011 6:48 AM, Jonas Stein wrote: > Hi, > > i want to make my plots look uniform in LaTeX documents. > > - usage of the same font on axes and in legend like LaTeX uses >(for example "Computer Modern") > > - put real LaTeX formulas on the axes > > Have you any hints how i can achieve that? > I had no luck two years ago, but i want to try it again now. > > kind regards, > [[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] Revolution Analytics reading SAS datasets
I'm sure the legal ground is tricky. However, OpenOffice and LibreOffice and KWord have been able to open the (proprietary) MS Word doc format for a while now, and they are open source (and Libre Office might even be GPL'd), so the algorithm is in fact "published" in Jeremy's sense, and has been for several years. I figure the reason for keeping the SAS reading functionality proprietary is Revolution's (perfectly legitimate) wish to make money by separating their product from GNU R and adding features that would make people want to buy rather than just download from CRAN. Within GNU R there are of course sas.get in the Hmisc package (which requires SAS). It should also be quite easy to write a wrapper around dsread, a command-line closed source product freely downloadable in a limited form which will convert sas7bdat files to csv or tsv format (and SQL if you pay). This latter path won't require SAS locally. I'm also sure that SAS has a way to export its datasets into R, since the current version of IML Studio will in fact interact with R. On 02/10/2011 03:11 PM, Jeremy Miles wrote: On 10 February 2011 12:01, Matt Shotwell wrote: On Thu, 2011-02-10 at 10:44 -0800, David Smith wrote: The SAS import/export feature of Revolution R Enterprise 4.2 isn't open-source, so we can't release it in open-source Revolution R Community, or to CRAN as we do with the ParallelR packages (foreach, doMC, etc.). Judging by the language of Dr. Nie's comments on the page linked below, it seems unlikely this feature is the result of a licensing agreement with SAS. Is that correct? There was some discussion of this on the SAS email list. People who seem to know what they were talking about said that they would have had to reverse engineer it to decode the file format. It's slightly tricky legal ground - the file format can't be copyrighted but publishing the algorigthm might not be allowed. I guess if they release it as open source, that could be construed as publishing the algorithm. (SPSS and WPS both can open SAS files, and I'd be surprised if SAS licensed to them. [Esp WPS, who SAS are (or were) suing for all kinds of things in court in London.) Jeremy __ 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] How to reshape wide format data.frame to long format?
As for your second question, you could certainly do
newcodesM = transform(newcodesM, variable1 =
unlist(strsplit(variable,'\\.'))[1], variable2 = unlist(strsplit(variable,
'\\.'))[2], variable3 = unlist(strsplit(variable,'\\.'))[3])
though I'm sure there is a more efficient use of strsplit in this context.
Abhijit
On Jan 20, 2011, at 10:51 AM, Fredrik Karlsson wrote:
> Dear list,
>
> I need to convert this data.frame
>
>> names(codesM)
> [1] "key""AMR.pa1.M" "AMR.pa2.M" "AMR.pa3.M" "AMR.pa4.M"
> [6] "AMR.pa5.M" "AMR.pa6.M" "AMR.pa7.M" "AMR.pa8.M" "AMR.pa9.M"
> [11] "AMR.pa10.M" "AMR.ta1.M" "AMR.ta2.M" "AMR.ta3.M" "AMR.ta4.M"
> [16] "AMR.ta5.M" "AMR.ta6.M" "AMR.ta7.M" "AMR.ta8.M" "AMR.ta9.M"
> [21] "AMR.ta10.M" "AMR.ka1.M" "AMR.ka2.M" "AMR.ka3.M" "AMR.ka4.M"
> [26] "AMR.ka5.M" "AMR.ka6.M" "AMR.ka7.M" "AMR.ka8.M" "AMR.ka9.M"
> [31] "AMR.ka10.M" "SMR.pa1.M" "SMR.pa2.M" "SMR.pa3.M" "SMR.pa4.M"
> [36] "SMR.pa5.M" "SMR.pa6.M" "SMR.pa7.M" "SMR.pa8.M" "SMR.pa9.M"
> [41] "SMR.pa10.M" "SMR.ta1.M" "SMR.ta2.M" "SMR.ta3.M" "SMR.ta4.M"
> [46] "SMR.ta5.M" "SMR.ta6.M" "SMR.ta7.M" "SMR.ta8.M" "SMR.ta9.M"
> [51] "SMR.ta10.M" "SMR.ka1.M" "SMR.ka2.M" "SMR.ka3.M" "SMR.ka4.M"
> [56] "SMR.ka5.M" "SMR.ka6.M" "SMR.ka7.M" "SMR.ka8.M" "SMR.ka9.M"
> [61] "SMR.ka10.M"
>> dim(codesM)
> [1] 42 61
>
> into a 3 x 2501 data.frame where the "key" variable is kept, the
> values in columns 2-61 above is inserted into a "values" column and
> the name of the column is inserted in a third column ("variable"
> perhaps).
>
> Like
>
> key variable value
> POSTOFF_1_1AMR.pa1.M 5
> POSTOFF_1_1AMR.pa2.M 3
>
>
> I think I should be able to do this using the "reshape" function, but
> I cannot get it to work. I think I need some help to understand
> this...
>
>
> (If I could split the "variable" into three separate columns splitting
> by ".", that would be even better.)
>
> I appreciate all the help I could get.
>
> /Fredrik
>
> --
> "Life is like a trumpet - if you don't put anything into it, you don't
> get anything out of it."
>
> __
> 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] How to reshape wide format data.frame to long format?
I would think that the following code should work:
newcodesM = reshape(codesM, id=1)
If other variables in the data.frame are factors, reshape thinks all of them
are ID variables and tries to use all of them as "keys". Specifying the id
variable you want to keep (I used id=1 since "key" is in the 1st column) will
probably solve the issue.
Abhijit
On Jan 20, 2011, at 10:51 AM, Fredrik Karlsson wrote:
> Dear list,
>
> I need to convert this data.frame
>
>> names(codesM)
> [1] "key""AMR.pa1.M" "AMR.pa2.M" "AMR.pa3.M" "AMR.pa4.M"
> [6] "AMR.pa5.M" "AMR.pa6.M" "AMR.pa7.M" "AMR.pa8.M" "AMR.pa9.M"
> [11] "AMR.pa10.M" "AMR.ta1.M" "AMR.ta2.M" "AMR.ta3.M" "AMR.ta4.M"
> [16] "AMR.ta5.M" "AMR.ta6.M" "AMR.ta7.M" "AMR.ta8.M" "AMR.ta9.M"
> [21] "AMR.ta10.M" "AMR.ka1.M" "AMR.ka2.M" "AMR.ka3.M" "AMR.ka4.M"
> [26] "AMR.ka5.M" "AMR.ka6.M" "AMR.ka7.M" "AMR.ka8.M" "AMR.ka9.M"
> [31] "AMR.ka10.M" "SMR.pa1.M" "SMR.pa2.M" "SMR.pa3.M" "SMR.pa4.M"
> [36] "SMR.pa5.M" "SMR.pa6.M" "SMR.pa7.M" "SMR.pa8.M" "SMR.pa9.M"
> [41] "SMR.pa10.M" "SMR.ta1.M" "SMR.ta2.M" "SMR.ta3.M" "SMR.ta4.M"
> [46] "SMR.ta5.M" "SMR.ta6.M" "SMR.ta7.M" "SMR.ta8.M" "SMR.ta9.M"
> [51] "SMR.ta10.M" "SMR.ka1.M" "SMR.ka2.M" "SMR.ka3.M" "SMR.ka4.M"
> [56] "SMR.ka5.M" "SMR.ka6.M" "SMR.ka7.M" "SMR.ka8.M" "SMR.ka9.M"
> [61] "SMR.ka10.M"
>> dim(codesM)
> [1] 42 61
>
> into a 3 x 2501 data.frame where the "key" variable is kept, the
> values in columns 2-61 above is inserted into a "values" column and
> the name of the column is inserted in a third column ("variable"
> perhaps).
>
> Like
>
> key variable value
> POSTOFF_1_1AMR.pa1.M 5
> POSTOFF_1_1AMR.pa2.M 3
>
>
> I think I should be able to do this using the "reshape" function, but
> I cannot get it to work. I think I need some help to understand
> this...
>
>
> (If I could split the "variable" into three separate columns splitting
> by ".", that would be even better.)
>
> I appreciate all the help I could get.
>
> /Fredrik
>
> --
> "Life is like a trumpet - if you don't put anything into it, you don't
> get anything out of it."
>
> __
> 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] Reading large SAS dataset in R
Santanu, I second Phil's suggestion. sas.get is actually quite nice. Another current option is using a command-line utility called dsread (http://www.oview.co.uk/dsread/) to convert the sas7bdat file to a csv or tsv format, which can then easily be read into R using read.table and its derivatives. Frank Harrell (author of the Hmisc package) commented positively on this approach on the list a couple of months back. Abhijit On Jan 5, 2011, at 5:51 PM, Phil Spector wrote: > Santanu - > If you have sas installed on your computer, you may find using > the sas.get function of the Hmisc package useful. > If the only message that read.ssd produced was "Sas failed", it > would be difficult to figure out what went wrong. Usually the location of > the log file, which would explain the error more thoroughly, is included in > the error message. > > - Phil Spector >Statistical Computing Facility >Department of Statistics >UC Berkeley >spec...@stat.berkeley.edu > > > On Wed, 5 Jan 2011, Santanu Pramanik wrote: > >> Hi all, >> >> I have a large (approx. 1 GB) SAS dataset (test.sas7bdat) located in the >> server (?R:/? directory). I have SAS 9.1 installed in my PC and I can read >> the SAS dataset in SAS, under a windows environment, after assigning libname >> in "R:\" directory. >> >> >> >> Now I am trying to read the SAS dataset in R (R 2.12.0) using the read.ssd >> function of the ?foreign? package, but I get an error message ?SAS failed?. >> I believe I have specified the paths correctly (after reading some previous >> posts I made sure that I do it right). Below is the small code: >> >> >> >> sashome<- "C:/Program Files/SAS/SAS 9.1" >> >> read.ssd(libname="R:/", sectionnames="test", sascmd=file.path(sashome, >> "sas.exe")) >> >> >> >> Please let me know where I am making the mistake. Is it because of the size >> of the file or the location of the file (in server instead of local hard >> drive)? >> >> >> >> Thanks in advance, >> >> Santanu >> >> >> -- >> >> Santanu Pramanik >> Survey Statistician >> NORC at the University of Chicago >> Bethesda, MD >> >> [[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-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] How to Read a Large CSV into a Database with R
Thanks On 11/16/2010 12:41 PM, Seth Falcon wrote: > Hi Abhijit, > > [I've cc'd R-help to keep the discussion on the list] > > On Tue, Nov 16, 2010 at 8:06 AM, Abhijit Dasgupta > wrote: > >> Seth, >> >> I was looking for something like this too. I've a question. If >> you're reading the data from a connection, does R start reading the >> next chunk of data right after the previous chunk, or do we need to >> keep track of things using "skip" >> > The purpose of using a file connection is to allow R to keep its place > in the file as it reads and not have to re-read or skip. This is > considerably more efficient. > > > > [[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] Several lattice plots on one page
Another solution is using grid.arrange in the gridExtra package. This works
like the par(mfrow=...) command, but for grid-based graphics like lattice and
ggplot2
On Nov 8, 2010, at 1:19 PM, Marcus Drescher wrote:
> Dear all,
>
> I am trying (!!!) to generate pdfs that have 8 plots on one page:
>
>
> df = data.frame(
> day = c(1,2,3,4),
> var1 = c(1,2,3,4),
> var2 = c(100,200,300,4000),
> var3 = c(10,20,300,4),
> var4 = c(10,2,3,4000),
> var5 = c(10,20,30,40),
> var6 = c(0.001,0.002,0.003,0.004),
> var7 = c(123,223,123,412),
> var8 = c(213,123,234,435),
> all = as.factor(c(1,1,1,1)))
>
> pdf("test1.pdf", width=20, heigh=27, paper="a4")
>print(plot(groupedData(var1 ~ day | all, data = df), main = "var1",
> xlab="", ylab=""), split=c(1,1,2,4), more=TRUE)
>print(plot(groupedData(var2 ~ day | all, data = df), main = "var2",
> xlab="", ylab=""), split=c(1,2,2,4), more=TRUE)
>print(plot(groupedData(var3 ~ day | all, data = df), main = "var3",
> xlab="", ylab=""), split=c(1,3,2,4), more=TRUE)
>print(plot(groupedData(var4 ~ day | all, data = df), main = "var4",
> xlab="", ylab=""), split=c(1,4,2,4), more=TRUE)
>print(plot(groupedData(var5 ~ day | all, data = df), main = "var5",
> xlab="", ylab=""), split=c(2,1,2,4), more=TRUE)
>print(plot(groupedData(var6 ~ day | all, data = df), main = "var6",
> xlab="", ylab=""), split=c(2,2,2,4), more=TRUE)
>print(plot(groupedData(var7 ~ day | all, data = df), main = "var7",
> xlab="", ylab=""), split=c(2,3,2,4), more=TRUE)
>print(plot(groupedData(var8 ~ day | all, data = df), main = "var8",
> xlab="", ylab=""), split=c(2,4,2,4))
> dev.off()
>
>
> My problem is that the separate plots all have different sizes. (Some are
> tall, but very small, or the other way around. The target is to have equally
> tall and wide graphs. (The variables have different scales. Grouping does not
> work.)
>
> Optimally, the plots would use the complete pdf page.
>
> Any ideas how to adjust height and width?
>
> Best
> Marcus
>
> __
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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Re: [R] ggplot output
The other way (in the same spirit as par(mfrow = ...) in base graphics) is to use the grid.arrange function in the gridExtra package. See it's documentation for examples. On Nov 4, 2010, at 9:36 AM, ashz wrote: > > Dear All, > > I have this script: > > dat <- data.frame(Month = hstat$Date,C_avg = hstat$C.avg,C_stdev = > hstat$C.stdev) > ggplot(data = dat, aes(x = Month, y = C_avg, ymin = C_avg - C_stdev, ymax = > C_avg + C_stdev)) + > geom_point() + > geom_line() + > geom_errorbar() > > dat <- data.frame(Month = hstat$Date,K_avg = hstat$K.avg,K_stdev = > hstat$K.stdev) > ggplot(data = dat, aes(x = Month, y = K_avg, ymin = K_avg - K_stdev, ymax = > K_avg + K_stdev)) + > geom_point() + > geom_line() + > geom_errorbar() > > dat <- data.frame(Month = hstat$Date,S_avg = hstat$S.avg,S_stdev = > hstat$S.stdev) > ggplot(data = dat, aes(x = Month, y = S_avg, ymin = S_avg - S_stdev, ymax = > S_avg + S_stdev)) + > geom_point() + > geom_line() + > geom_errorbar() > > Running the script generates 3 separate graphs, how can I output them next > to each other? > > Thanks > > -- > View this message in context: > http://r.789695.n4.nabble.com/ggplot-output-tp3027026p3027026.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] ForestPlot or similar
You need to use a print statement
print(forestplot())
Lattice and ggplot2 need to be explicitly printed to get output into
jpeg. I believe Matt's function only provides the graphics object and
not the printed version.
Abhijit
On 11/2/2010 4:32 PM, Mestat wrote:
> Thanks Matt,
> I am having a problem now to use this function. The function separately
> works fine. But the problem is that I am working with a simulation, so i
> placed the CREDPLOT function in my program and added the following commands
> according my data:
>
> #MY DATA, ESTIMATES, LOWER AND UPPER INTERVALS
> rw_cibas_quantile_ori_m<-rw_quantile_app_ori[-51:-1000]
> rw_cibas_low_quantile_ori_l<-rw_cibas_low_quantile_ori[-51:-1000]
> rw_cibas_up_quantile_ori_u<-rw_cibas_up_quantile_ori[-51:-1000]
>
> #GRAPHIC
> jpeg ('Nfp_rw_bas_quantile_ori.jpeg')
> forestplot(rw_cibas_quantile_ori_m,rw_cibas_low_quantile_ori_l,rw_cibas_up_quantile_ori_u,cen=403.677)
> dev.off()
>
> My program is running fine, but I am not getting any graphic. I did the
> graphic using the function FORESTPLOT, but the graphic provided by the
> function CREDPLOT is much better. Here is my code:
>
> rw_ciper_gini_ori_m<-rw_gini_app_ori[-51:-1000]
> rw_ciper_low_gini_ori_l<-rw_ciper_low_gini_ori[-51:-1000]
> rw_ciper_up_gini_ori_u<-rw_ciper_up_gini_ori[-51:-1000]
> tabletext<-cbind(c(rep(" ",50),NA))
> rw_ciper_gini_ori_m<-c(rw_ciper_gini_ori_m,NA)
> rw_ciper_low_gini_ori_l<-c(rw_ciper_low_gini_ori_l,NA)
> rw_ciper_up_gini_ori_u<-c(rw_ciper_up_gini_ori_u,NA)
> jpeg ('Sfp_rw_per_gini_ori.jpeg')
> forestplot(tabletext,rw_ciper_gini_ori_m,rw_ciper_low_gini_ori_l,rw_ciper_up_gini_ori_u,zero=0.4,col=meta.colors(box="royalblue",line="darkblue"))
> dev.off()
>
> Any information about whats is missing/wrong in order to obtain the graphic
> with the function CREDPLOT is welcomed.
> Thanks is advance,
> Marcio
>
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Re: [R] Question about ggplot2
from where you are, year.plot+ylim(0,0.1) Abhijit On Nov 2, 2010, at 9:57 AM, Shige Song wrote: > Dear All, > > I am trying to graph a simple scatter plot where the x axis is year > and the y axis is a percentage (percentage of infant death). Instead > of plotting the raw data, I want to plot summary statistics such as > mean and median. Here is the problem: the value range of y is between > 0 and 1, but since infant death is a rare event, the mean and median > is very low (something like 5%), which shows up as a horizontal line > at the bottom of the figure. My question is: how do I change the scale > of the y-axis so that it does not have the range between 0 and 1 but > between 0 and 0.1? Many thanks. > > By the way, I am using ggplot2, and here is my code: > > --- > year.plot <- ggplot(d, aes(year, rate)) > year.plot + stat_summary(fun.y = "mean", geom = "line") > --- > > Best, > Shige > > __ > 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] Fwd: ForestPlot or similar
> From: Abhijit Dasgupta
> Date: October 31, 2010 1:30:02 AM EDT
> To: Matt Shotwell
> Subject: Re: [R] ForestPlot or similar
>
> I just did something very similar using ggplot's pointrange geom. In the
> following, I'm plotting hazard ratios, for which the nominal value is 1 and
> not 0. x has 5 columns: drug, hr, hr.lcb, hr.ucb, and group, and I'm faceting
> by group. If you want the plots horizontal, add coord_flip() to the command
> --- as it stands the plots are vertically oriented.
>
>require(ggplot2)
>p <- ggplot(x, aes(x=drug, y = hr, ymin=hr.lcb, ymax=hr.ucb))+
>geom_pointrange()+ facet_grid(.~group)
>p <- p + xlab('Drug') + ylab('Hazard ratio')+
>geom_hline(y=1, col='red', lty=2)
>
>
> Abhijit
> On Oct 30, 2010, at 5:31 PM, Matt Shotwell wrote:
>
>> Here is a small function for forest plots in R, with an example:
>>
>> http://biostatmatt.com/wiki/r-credplot
>>
>> -Matt
>>
>> On Sat, 2010-10-30 at 11:40 -0400, Mestat wrote:
>>> Here is one example:
>>> I have three vectors (mean,lower interval, upper interval)
>>> mean<-c(2,4,6,8)
>>> l<-c(1,2,3,4)
>>> u<-c(4,8,12,16)
>>> How would I plot that if I want to use the FORESTPLOT function. I dont need
>>> to use the TABLETEXT option.
>>> I am working in something like this:
>>> tabletext<-c(NA,NA,NA,NA,NA)
>>> mean<-c(NA,2,4,6,8)
>>> l<-c(NA,1,2,3,4)
>>> u<-c(NA,4,8,12,16)
>>> forestplot(tabletext,mean,l,u,zero=0)
>>> But I am having a problem with the length of the dimension...
>>> Thanks in advance,
>>> Marcio
>>>
>>
>> --
>> Matthew S. Shotwell
>> Graduate Student
>> Division of Biostatistics and Epidemiology
>> Medical University of South Carolina
>>
>> __
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>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
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Re: [R] Programmaticly finding number of processors by R code
If you have installed multicore (for unix/mac), you can find the number of cores by /*multicore:::detectCores()*/ On 10/3/10 1:03 PM, Ajay Ohri wrote: > Dear List > > Sorry if this question seems very basic. > > Is there a function to pro grammatically find number of processors in > my system _ I want to pass this as a parameter to snow in some serial > code to parallel code functions > > Regards > > Ajay > > > > Websites- > http://decisionstats.com > http://dudeofdata.com > > > Linkedin- www.linkedin.com/in/ajayohri > > __ > 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. -- Abhijit Dasgupta, PhD Director and Principal Statistician ARAASTAT Ph: 301.385.3067 E: adasgu...@araastat.com W: http://www.araastat.com [[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] Creating R objects in Java
On 10/1/10 9:18 AM, lord12 wrote: How do you call R methods from Java? I want to create a GUI using Swing in Jaa that calls R methods in Java. Look in the documentation for the rJava package -- Abhijit Dasgupta, PhD Director and Principal Statistician ARAASTAT Ph: 301.385.3067 E: adasgu...@araastat.com W: http://www.araastat.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] R Code for paper?
Reading Gilbert's paper and references, and going on the web, I see that Gilbert provided Fortran source code for his method as well as Tarone's method. It might be possible to wrap this in R On 09/30/2010 06:40 PM, Jim Silverton wrote: Does anyone has the Rcode for Gilbert's 2005 paper on the discrete FDR and Tarone's 1990 paper? And Storey's pFDR? __ 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] R Code for paper?
Look at the "qvalue" package by Dabney and Storey, which might satisfy your last query On 09/30/2010 06:40 PM, Jim Silverton wrote: Does anyone has the Rcode for Gilbert's 2005 paper on the discrete FDR and Tarone's 1990 paper? And Storey's pFDR? __ 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] speeding up regressions using ddply
There has been a recent addition of parallel processing capabilities
to plyr (I believe v1.2 and later), along with a dataframe iterator
construct. Both have improved performance of ddply greatly for
multicore/cluster computing. So we now have the niceness of plyr's
grammar with pretty good performance. From the plyr NEWS file:
Version 1.2 (2010-09-09)
--
NEW FEATURES
* l*ply, d*ply, a*ply and m*ply all gain a .parallel argument that when
TRUE,
applies functions in parallel using a parallel backend registered
with the
foreach package:
x <- seq_len(20)
wait <- function(i) Sys.sleep(0.1)
system.time(llply(x, wait))
# user system elapsed
# 0.007 0.005 2.005
library(doMC)
registerDoMC(2)
system.time(llply(x, wait, .parallel = TRUE))
# user system elapsed
# 0.020 0.011 1.038
On 9/22/10 10:41 AM, Ista Zahn wrote:
Hi Alison,
On Wed, Sep 22, 2010 at 11:05 AM, Alison Macalady wrote:
Hi,
I have a data set that I'd like to run logistic regressions on, using ddply
to speed up the computation of many models with different combinations of
variables.
In my experience ddply is not particularly fast. I use it a lot
because it is flexible and has easy to understand syntax, not for it's
speed.
I would like to run regressions on every unique two-variable
combination in a portion of my data set, but I can't quite figure out how
to do using ddply.
I'm not sure ddply is the tool for this job.
The data set looks like this, with "status" as the
binary dependent variable and V1:V8 as potential independent variables in
the logistic regression:
m<- matrix(rnorm(288), nrow = 36)
colnames(m)<- paste('V', 1:8, sep = '')
x<- data.frame( status = factor(rep(rep(c('D','L'), each = 6), 3)),
as.data.frame(m))
You can use combn to determine the combinations you want:
Varcombos<- combn(names(x)[-1], 2)
> From there you can do a loop, something like
results<- list()
for(i in 1:dim(Varcombos)[2])
{
log.glm<- glm(as.formula(paste("status ~ ", Varcombos[1,i], " + ",
Varcombos[2,i], sep="")), family=binomial(link=logit),
na.action=na.omit, data=x)
glm.summary<-summary(log.glm)
aic<- extractAIC(log.glm)
coef<- coef(glm.summary)
results[[i]]<- list(Est1=coef[1,2], Est2=coef[3,2], AIC=aic[2])
#or whatever other output here
names(results)[i]<- paste(Varcombos[1,i], Varcombos[2,i], sep="_")
}
I'm sure you could replace the loop with something more elegant, but
I'm not really sure how to go about it.
I used melt to put my data frame into a more workable format
require(reshape)
xm<- melt(x, id = 'status')
Here is the basic shape of the function I'd like to apply to every
combination of variables in the dataset:
h<- function(df)
{
attach(df)
log.glm<- (glm(status ~ value1+ value2 , family=binomial(link=logit),
na.action=na.omit)) #What I can't figure out is how to specify 2 different
variables (I've put value1 and value2 as placeholders) from the xm to
include in the model
glm.summary<-summary(log.glm)
aic<- extractAIC(log.glm)
coef<- coef(glm.summary)
list(Est1=coef[1,2], Est2=coef[3,2], AIC=aic[2]) #or whatever other output
here
}
And then I'd like to use ddply to speed up the computations.
require(pplyr)
output<-dddply(xm, .(variable), as.data.frame.function(h))
output
I can easily do this using ddply when I only want to use 1 variable in the
model, but can't figure out how to do it with two variables.
I don't think this approach can work. You are saying "split up xm by
variable" and then expecting to be able to reference different levels
of variable within each split, an impossible request.
Hope this helps,
Ista
Many thanks for any hints!
Ali
Alison Macalady
Ph.D. Candidate
University of Arizona
School of Geography and Development
& Laboratory of Tree Ring Research
______
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Abhijit Dasgupta, PhD
Director and Principal Statistician
ARAASTAT
Ph: 301.385.3067
E: adasgu...@araastat.com
W: http://www.araastat.com
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Re: [R] aggregate, by, *apply
I would approach this slightly differently. I would make func a
function of x and y.
func <- function(x,y){
m <- median(x)
return(m > 2 & m < y)
}
Now generate tmp just as you have. then:
require(plyr)
res <- daply(tmp, .(z), summarise, res=func(x,y))
I believe this does the trick
Abhijit
On 9/15/10 5:45 PM, Mark Ebbert wrote:
Dear R gurus,
I regularly come across a situation where I would like to apply a function to a
subset of data in a dataframe, but I have not found an R function to facilitate
exactly what I need. More specifically, I'd like my function to have a context
of where the data it's analyzing came from. Here is an example:
### BEGIN ###
func<-function(x){
m<-median(x$x)
if(m> 2& m< x$y){
return(T)
}
return(F)
}
tmp<-data.frame(x=1:10,y=c(rep(34,3),rep(35,3),rep(34,4)),z=c(rep("a",3),rep("b",3),rep("c",4)))
res<-aggregate(tmp,list(z),func)
### END ###
The values in the example are trivial, but the problem is that only one column
is passed to my function at a time, so I can't determine how 'm' relates to
'x$y'. Any tips/guidance is appreciated.
Mark T. W. Ebbert
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--
Abhijit Dasgupta, PhD
Director and Principal Statistician
ARAASTAT
Ph: 301.385.3067
E: adasgu...@araastat.com
W: http://www.araastat.com
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Re: [R] Creating publication-quality plots for use in Microsoft Word
On 9/15/10 10:38 AM, dadrivr wrote:
Hi everyone,
I am trying to make some publication-quality plots for use in Microsoft
Word, but I am having trouble creating high-quality plots that are supported
by Microsoft Word.
If I use the R plot function to create the figure, the lines are jagged, and
the picture is not of high quality (same with JPEG(), TIFF(), and PNG()
functions). I have tried using the Cairo package, but it distorts my dashed
lines, and the win.metafile results in a picture of terrible quality. The
only way I have succeeded in getting a high quality picture in a file is by
using the pdf() function to save the plot as a pdf file, but all my attempts
to convert the image in the pdf file to a TIFF or other file type accepted
by Word result in considerably degraded quality. Do you have any
suggestions for creating publication-quality plots in R that can be placed
in Word documents? What packages, functions (along with options), and/or
conversions would you use? Thanks so much for your help!
Another option I've used is to export to PDF (which seems to give the
best quality) and then use the (free) Imagemagick program to convert the
PDF to high-resolution PNG. This worked for some involved heatmaps that
were submitted to a journal. Imagemagick can be downloaded directly for
Windows or via Cygwin.
Suppose your figure is in fig1.pdf. You can use the following command
(once Imagemagick is downloaded and in your path):
system("convert -density 300x300 fig1.pdf fig1.png")
--
Abhijit Dasgupta, PhD
Director and Principal Statistician
ARAASTAT
Ph: 301.385.3067
E: adasgu...@araastat.com
W: http://www.araastat.com
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Re: [R] Saving/loading custom R scripts
You can create a .First function in your .Rprofile file (which will
be in ~/.Rprofile). For example
.First <- function(){
source("Friedman-Test-with-Post-Hoc.r.txt")
}
You can also create your own package ("mylibrary") down the line (see
the R manual for creating extensions at
http://cran.fhcrc.org/doc/manuals/R-exts.pdf) which will be a collection
of your custom scripts that you have written, and then you can
automatically load them using
.First <- function(){
library("mylibrary")
}
Hope this helps.
Abhijit
On 9/8/10 3:25 AM, DrCJones wrote:
Hi,
How does R automatically load functions so that they are available from the
workspace? Is it anything like Matlab - you just specify a directory path
and it finds it?
The reason I ask is because I found a really nice script that I would like
to use on a regular basis, and it would be nice not to have to 'copy and
paste' it into R on every startup:
http://www.r-statistics.com/wp-content/uploads/2010/02/Friedman-Test-with-Post-Hoc.r.txt
This would be for Ubuntu, if that makes any difference.
Cheers
--
Abhijit Dasgupta, PhD
Director and Principal Statistician
ARAASTAT
Ph: 301.385.3067
E: adasgu...@araastat.com
W: http://www.araastat.com
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Re: [R] Something similar to layout in lattice or ggplot
Thank you all for the suggestions. They have all been immensely helpful. Abhijit On 9/7/10 10:44 AM, ONKELINX, Thierry wrote: Dear Abhijit, In ggplot you can use facetting (facet_grid() or facet_wrap()) to create subplot based on the same dataset. Or you can work with viewport() if you want several independent plots. HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek team Biometrie& Kwaliteitszorg Gaverstraat 4 9500 Geraardsbergen Belgium Research Institute for Nature and Forest team Biometrics& Quality Assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens Abhijit Dasgupta Verzonden: dinsdag 7 september 2010 16:38 Aan: r-help@r-project.org Onderwerp: [R] Something similar to layout in lattice or ggplot Hi, Is there a function similar to the layout function in base graphics in either lattice or ggplot? I'm hoping someone has written a function wrapper to the appropriate commands in grid that would make this easier :) Abhijit [[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. Druk dit bericht a.u.b. niet onnodig af. Please do not print this message unnecessarily. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. -- Abhijit Dasgupta, PhD Director and Principal Statistician ARAASTAT Ph: 301.385.3067 E: adasgu...@araastat.com W: http://www.araastat.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] Something similar to layout in lattice or ggplot
Hi Thierry, It's really the latter I want..independent plots. I use faceting quite a bit, but I need things like a page of plots for simulations under different conditions. I suppose I can still use faceting combined with reshape, but I'd rather not go that route if I can help it. Abhijit On 9/7/10 10:44 AM, ONKELINX, Thierry wrote: Dear Abhijit, In ggplot you can use facetting (facet_grid() or facet_wrap()) to create subplot based on the same dataset. Or you can work with viewport() if you want several independent plots. HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek team Biometrie& Kwaliteitszorg Gaverstraat 4 9500 Geraardsbergen Belgium Research Institute for Nature and Forest team Biometrics& Quality Assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens Abhijit Dasgupta Verzonden: dinsdag 7 september 2010 16:38 Aan: r-help@r-project.org Onderwerp: [R] Something similar to layout in lattice or ggplot Hi, Is there a function similar to the layout function in base graphics in either lattice or ggplot? I'm hoping someone has written a function wrapper to the appropriate commands in grid that would make this easier :) Abhijit [[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. Druk dit bericht a.u.b. niet onnodig af. Please do not print this message unnecessarily. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. -- Abhijit Dasgupta, PhD Director and Principal Statistician ARAASTAT Ph: 301.385.3067 E: adasgu...@araastat.com W: http://www.araastat.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] Something similar to layout in lattice or ggplot
Hi, Is there a function similar to the layout function in base graphics in either lattice or ggplot? I'm hoping someone has written a function wrapper to the appropriate commands in grid that would make this easier :) Abhijit [[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] Problems in snow: can't open connection with nodes
This is a problem a few of us have experienced with snow, and there is a
discussion on the R-hpc list about this. No solution yet, as far as I
can tell.
Abhijit
On 9/7/2010 9:18 AM, bfoubert wrote:
> I'm working with snow and created a local cluster. So far, the same code has
> always worked (please see below). However, now I receive a message that the
> connection with the nodes cannot be opened. I restarted my workstation but
> that didn't help. Is there a known solution for this problem? Thanks a lot
> for any help.
>
> bram foubert
>
>
> library(snow)
> cl =
> makeSOCKcluster(c("localhost","localhost","localhost","localhost","localhost","localhost","localhost"))
> nrslaves = length(cl)
>
> CreateData= function(path){
> ...
> }
>
> clusterApply(cl,c("bgcdata1.txt","bgcdata2.txt","bgcdata3.txt","bgcdata4.txt","bgcdata5.txt","bgcdata6.txt","bgcdata7.txt"),CreateData)
> Error in checkForRemoteErrors(val) :
>7 nodes produced errors; first error: cannot open the connection
>
>
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Re: [R] ggplot inside cycle
You haven't wrapped p in the print command, which is one of the ways to
make sure the plot gets printed when we need it.
print(p+geom_point(aes(size=3))) does the trick
On 08/26/2010 06:08 AM, Petr PIKAL wrote:
Dear all
I want to save several ggplots in one pdf document. I tried this
for (i in names(iris)[2:4]) {
p<-ggplot(iris, aes(x=Sepal.Length, y=iris[,i], colour=Species))
p+geom_point(aes(size=3))
}
with different variations of y input but was not successful. In past I
used qplot in similar fashion which worked
for(i in names(mleti)[7:15]) print(qplot(sito, mleti1[,i],
facets=~typ,ylab=i, geom=c("point", "line"), colour=ordered(minuty),
data=mleti1))
So I wonder if anybody used ggplot in cycle and how to solve input of
variables throughout cycle
Thank you
Petr
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Re: [R] How to remove rows based on frequency of factor and then difference date scores
The paste-y argument is my usual trick in these situations. I forget that tapply can take multiple ordering arguments :) Abhijit On 08/24/2010 02:17 PM, David Winsemius wrote: On Aug 24, 2010, at 1:59 PM, Abhijit Dasgupta, PhD wrote: The only problem with this is that Chris's unique individuals are a combination of Type and ID, as I understand it. So Type=A, ID=1 is a different individual from Type=B,ID=1. So we need to create a unique identifier per person, simplistically by uniqueID=paste(Type, ID, sep=''). Then, using this new identifier, everything follows. I see your point. I agree that a tapply method should present both factors in the indices argument. > new.df <- txt.df[ -which( txt.df$nn <=1), ] > new.df <- new.df[ with(new.df, order(Type, ID) ), ] # and possibly needs to be ordered? > new.df$diffdays <- unlist( tapply(new.df$dt2, list(new.df$ID, new.df$Type), function(x) x[1] -x) ) > new.df Type ID Date Valuedt2 nn diffdays 1A 1 16/09/2020 8 2020-09-16 30 2A 1 23/09/2010 9 2010-09-23 3 3646 4B 1 13/5/2010 6 2010-05-13 30 But do not agree that you need, in this case at least, to create a paste()-y index. Agreed, however, such a construction can be useful in other situations. -- Abhijit Dasgupta, PhD Director and Principal Statistician ARAASTAT Ph: 301.385.3067 E: adasgu...@araastat.com W: http://www.araastat.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] How to remove rows based on frequency of factor and then difference date scores
The only problem with this is that Chris's unique individuals are a combination of Type and ID, as I understand it. So Type=A, ID=1 is a different individual from Type=B,ID=1. So we need to create a unique identifier per person, simplistically by uniqueID=paste(Type, ID, sep=''). Then, using this new identifier, everything follows. On 08/24/2010 01:53 PM, David Winsemius wrote: On Aug 24, 2010, at 1:19 PM, Chris Beeley wrote: Hello- A basic question which has nonetheless floored me entirely. I have a dataset which looks like this: Type ID DateValue A 116/09/2020 8 A 1 23/09/2010 9 B 3 18/8/20107 B 1 13/5/20106 There are two Types, which correspond to different individuals in different conditions, and loads of ID labels (1:50) corresponding to the different individuals in each condition, and measurements at different times (from 1 to 10 measurements) for each individual. I want to perform the following operations: 1) Delete all individuals for whom only one measurement is available. In the dataset above, you can see that I want to delete the row Type B ID 3, and Type B ID 1, but without deleting the Type A ID 1 data because there is more than one measurement for Type A ID 1 (but not for Type B ID1) 2) Produce difference scores for each of the Dates, so each individual (Type A ID1 and all the others for whom more than one measurement exists) starts at Date "1" and goes up in integers according to how many days have elapsed. I just know there's some incredibly cunning R-ish way of doing this but after many hours of fiddling I have had to admit defeat. Not sure about terribly cunning. Let's assume your dataframe was read in with stringsAsFactors=FALSE and is called txt.df: > txt.df$dt2 <- as.Date(txt.df$Date, format="%d/%m/%Y") > txt.df Type ID Date Valuedt2 1A 1 16/09/2020 8 2020-09-16 2A 1 23/09/2010 9 2010-09-23 3B 3 18/8/2010 7 2010-08-18 4B 1 13/5/2010 6 2010-05-13 > txt.df$nn <- ave(txt.df$ID,txt.df$ID, FUN=length) > txt.df Type ID Date Valuedt2 nn 1A 1 16/09/2020 8 2020-09-16 3 2A 1 23/09/2010 9 2010-09-23 3 3B 3 18/8/2010 7 2010-08-18 1 4B 1 13/5/2010 6 2010-05-13 3 > txt.df[ -which( txt.df$nn <=1), ] Type ID Date Valuedt2 nn 1A 1 16/09/2020 8 2020-09-16 3 2A 1 23/09/2010 9 2010-09-23 3 4B 1 13/5/2010 6 2010-05-13 3 # Task #1 accomplished > tapply(txt.df$dt2, txt.df$ID, function(x) x[1] -x) $`1` Time differences in days [1]0 3646 3779 $`3` Time difference of 0 days > unlist( tapply(txt.df$dt2, txt.df$ID, function(x) x[1] -x) ) 11 12 133 0 3646 37790 > txt.df$diffdays <- unlist( tapply(txt.df$dt2, txt.df$ID, function(x) x[1] -x) ) > txt.df Type ID Date Valuedt2 nn diffdays 1A 1 16/09/2020 8 2020-09-16 30 2A 1 23/09/2010 9 2010-09-23 3 3646 3B 3 18/8/2010 7 2010-08-18 1 3779 4B 1 13/5/2010 6 2010-05-13 30 > I would be very grateful for any words of advice. Many thanks, Chris Beeley, Institute of Mental Health, UK __ 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. David Winsemius, MD West Hartford, CT __ 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. -- Abhijit Dasgupta, PhD Director and Principal Statistician ARAASTAT Ph: 301.385.3067 E: adasgu...@araastat.com W: http://www.araastat.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] How to remove rows based on frequency of factor and then difference date scores
An answer to 1)
> x = data.frame(Type=c('A','A','B','B'), ID=c(1,1,3,1), Date =
c('16/09/2010','23/09/2010','18/8/2010','13/5/2010'), Value=c(8,9,7,6))
> x
Type ID Date Value
1A 1 16/09/2010 8
2A 1 23/09/2010 9
3B 3 18/8/2010 7
4B 1 13/5/2010 6
> x$Date = as.Date(x$Date,format='%d/%m/%Y')
> library(plyr)
> x$uniqueID = paste(x$Type, x$ID, sep='')
> nobs = daply(x, ~uniqueID, nrow)
> keep = names(nobs)[nobs>1]
> newx = x[x$uniqueID %in% keep,]
An answer to 2)
> require(plyr)
> ddply(newx, ~uniqueID, transform, newDate = as.numeric(Date -
min(Date)+1))
On 08/24/2010 01:19 PM, Chris Beeley wrote:
Hello-
A basic question which has nonetheless floored me entirely. I have a
dataset which looks like this:
Type ID DateValue
A 116/09/2020 8
A 1 23/09/2010 9
B 3 18/8/20107
B 1 13/5/20106
There are two Types, which correspond to different individuals in
different conditions, and loads of ID labels (1:50) corresponding to
the different individuals in each condition, and measurements at
different times (from 1 to 10 measurements) for each individual.
I want to perform the following operations:
1) Delete all individuals for whom only one measurement is available.
In the dataset above, you can see that I want to delete the row Type B
ID 3, and Type B ID 1, but without deleting the Type A ID 1 data
because there is more than one measurement for Type A ID 1 (but not
for Type B ID1)
2) Produce difference scores for each of the Dates, so each individual
(Type A ID1 and all the others for whom more than one measurement
exists) starts at Date "1" and goes up in integers according to how
many days have elapsed.
I just know there's some incredibly cunning R-ish way of doing this
but after many hours of fiddling I have had to admit defeat.
I would be very grateful for any words of advice.
Many thanks,
Chris Beeley,
Institute of Mental Health, UK
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--
Abhijit Dasgupta, PhD
Director and Principal Statistician
ARAASTAT
Ph: 301.385.3067
E: adasgu...@araastat.com
W: http://www.araastat.com
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Re: [R] Sweave
No, the \setkeys statement should be in the main body of the Sweave file,
not in the R code part.
On Aug 18, 2010 9:20 AM, "Randall Wrong" wrote:
Thanks Karen and Abhijit.
I have read the section 4.1.2 of the Sweave user manual. Actually the manual
lacks example code.
I would like to change the option in "includegraphics", not to change the
true sizes of the pictures.
This is what I usually do :
\begin{figure}
\centering
<>=
print( acfplot( x ) )
@
\end{figure}
Should I write :
\begin{figure}
\setkeys{Gin}{width=0.7\textwidth}
\centering
<>=
print( acfplot( x ) )
@
\end{figure}
?
Thanks for your help,
Randall
2010/8/18 Karen Kotschy
> Dear Randall
>
> I do it like this:
>
> \begin{center}
> \setkeys{Gin}{width=0.7\textwidth}
> \begin{Scode}{fig=T, echo=F}
> ...
> \end{Scode}
> \end{center}
>
> Hope this helps.
>
> Karen
>
> On Wed 18Aug10, Randall Wrong wrote:
> > Dear R users,
> >
> > I am using Sweave.
> >
> > I woul...
> http://www.R-project.org/posting-guide.html<
http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
> >
> >
> > --
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Re: [R] Sweave
Please read the Sweave documentation. The default is set to 0.8\textwidth.
You have to change a \SweaveOpt.
On Aug 17, 2010 7:00 PM, "Randall Wrong" wrote:
Dear R users,
I am using Sweave.
I would like to use the width option for the graphics :
\begin{figure}[h!]
\centering
\includegraphics[width=0.7\textwidth]{x}
\end{figure}
How do I get this ?
Thank you very much,
Randall
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Re: [R] ESS question. How to get rid of ess-smart-underscore?
I bogged about 3 possible solutions recently (statbandit.wordpress.com). Possibly the 2nd most recent post. Abhijit On Aug 9, 2010 8:28 AM, "W Eryk Wolski" wrote: Hi, ESS replaces "_" by "<-". How can I switch off this feature? I need to be able to type the underscore Thanks Eryk -- Witold Eryk Wolski Heidmark str 5 D-28329 Bremen tel.: 04215261837 __ 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] How to apply apply?!
For 1, an easy way is dat <- transform(dat, CLOSE2=2*CLOSE) For 2: apply(dat,1,fun) On 08/06/2010 03:06 PM, Raghuraman Ramachandran wrote: guRus I have say a dataframe, d and I wish to do the following: 1) For each row, I want to take one particular value of the row and multiply it by 2. How do I do it. Say the data frame is as below: OPEN HIGH LOW CLOSE 1931.2 1931.2 1931.2 1931.2 0 0 0 999.05 0 0 0 1052.5 0 0 0 987.8 0 0 0 925.6 0 0 0 866 0 0 0 1400.2 0 0 0 754.5 0 0 0 702.6 0 0 0 653.25 0 0 0 348 0 0 0 801 866.55 866.55 866.55 866.55 783.1 783.1 742.25 742.25 575 575 575 575 0 0 0 493 470 470 420 425 355 360 343 360 312.05 312.05 274 280.85 257.35 257.35 197 198.75 182 185.95 137 150.75 120.25 129 90.7 101.25 91.85 91.85 57 66.6 How do I multiply only the close of every row using the 'apply' function? And once multiplied how do I obtain a new table that also contains the new 2*CLOSE column (without cbind?). 2) Also, how do I run a generic function per row. Say for example I want to calculate the Implied Volatility for each row of this data frame ( using the RMterics package). How do I do that please using the apply function? I am focusing on apply because I like the vectorisation concept in R and I do not want to use a for loop etc. Many thanks for the enlightment, Raghu [[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. -- Abhijit Dasgupta, PhD Director and Principal Statistician ARAASTAT Ph: 301.385.3067 E: adasgu...@araastat.com W: http://www.araastat.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] How to extract se(coef) from cph?
if the cph model fit is m1, you can try sqrt(diag(m1$var)) This is coded in print.cph.fit (library(rms)) On 08/05/2010 04:03 PM, Biau David wrote: Hello, I am modeling some survival data wih cph (Design). I have modeled a predictor which showed non linear effect with restricted cubic splines. I would like to retrieve the se(coef) for other, linear, predictors. This is just to make nice LateX tables automatically. I have the coefficients with coef(). How do I do that? Thanks, David Biau. [[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. -- Abhijit Dasgupta, PhD Director and Principal Statistician ARAASTAT Ph: 301.385.3067 E: adasgu...@araastat.com W: http://www.araastat.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] snow makeCluster (makeSOCKcluster) not working in R-2.11
Hello,
I was using snow to parallel-process some code in R-2.10 (32-bit
windows. ). The code is as follows:
require(foreach)
require(doSNOW)
cl <- makeCluster(6, type='SOCK')
registerDoSNOW(cl)
bl2 <- foreach(i=icount(length(unqmrno))) %dopar% {
(some code here)
}
stopCluster(cl)
When I run the same code in Windows R-2.11 (either 32-bit or 64-bit), R
hangs at cl<-makeCluster(6, type='SOCK') and no R processes are spawned.
I was wondering if others have encountered this problem, and any
suggestions on solving this would be greatly appreciated.
--
Abhijit Dasgupta, PhD
Statistician | Clinical Sciences Section | NIAMS/NIH
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[R] Hmisc summary.formula.reverse
Hello, Can summary.formula.reverse be customized to allow other summary statistics to be reported rather than the quartiles and mean +/- sd? The "fun" option apparently doesn't apply when method='reverse' Thanks -- Abhijit Dasgupta, PhD Statistician | Clinical Sciences Section | NIAMS/NIH __ 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] tkrplot installation problems
Hello,
I'm running R 2.8.1 on Ubuntu Hardy. I'm trying to install tkrplot.
Using r-cran-tkrplot from the repository, I'm getting the following error:
> library(tkrplot)
Loading required package: tcltk
Loading Tcl/Tk interface ... done
Error in structure(.External("dotTcl", ..., PACKAGE = "tcltk"), class =
"tclObj") :
[tcl] version conflict for package "Tcl": have 8.5.0, need exactly 8.4.
Error in library(tkrplot) : .First.lib failed for 'tkrplot'
This tries to install tkrplot version 0.0.16
However, installing R2.8.1 from the repositories automatically installs
tcl8.5. In fact, if I try and remove tcl8.5 using synaptic, it also
removes R.
I also tried to install the package from source, both by using
install.packages as well as downloading source (tkrplot 0.0.18). This
fails to install.
Can someone please help. My ultimate objective is to use the
TeachingDemos package.
> sessionInfo()
R version 2.8.1 (2008-12-22)
i486-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] tcltk stats graphics grDevices utils datasets methods
[8] base
Thanks.
Abhijit
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Re: [R] Output Nicely formatted tables from R
Please look at http://biostat.mc.vanderbilt.edu/twiki/pub/Main/StatReport/latexFineControl.pdf for ways to do fine control of tabular data formatting via Sweave. Bill Cunliffe wrote: Hi there, I've spent a while searching for ways of outputting table data from R in presentable formats, such as colored backgrounds for column headings, bold fonts etc. It appears that this is not possible, but I would be interested to learn if in fact there was a way of achieving this. Many thanks! [[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-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] apply with a division
Won't scale(x,center=F, scale=x[1,]) do the trick?
--
Abhijit
Quoting Gabor Grothendieck <[EMAIL PROTECTED]>:
> This should work whether your data, x, is a data frame or a matrix:
>
> x / x[rep(1, nrow(x)),]
>
>
> On Thu, Jul 3, 2008 at 6:04 PM, Greg Kettler <[EMAIL PROTECTED]>
wrote:
>> Hi,
>> I'd like to normalize a dataset by dividing each row by the first
row.
>> Very simple, right?
>> I tried this:
>>
>>> expt.fluor
>> X1 X2 X3
>> 1 124 120 134
>> 2 165 163 174
>> 3 52 51 43
>> 4 179 171 166
>> 5 239 238 235
>>
>>> first.row <- expt.fluor[1,]
>>> normed <- apply(expt.fluor, 1, function(r) {r / first.row})
>>> normed
>> [[1]]
>> X1 X2 X3
>> 1 1 1 1
>>
>> [[2]]
>> X1 X2 X3
>> 1 1.330645 1.358333 1.298507
>>
>> [[3]]
>> X1 X2 X3
>> 1 0.4193548 0.425 0.3208955
>>
>> [[4]]
>> X1 X2 X3
>> 1 1.443548 1.425 1.238806
>>
>> [[5]]
>> X1 X2 X3
>> 1 1.927419 1.98 1.753731
>>
>> Ugly! The values are right, but why didn't I get another 2D array
>> back? Shouldn't the division in my inline function return a
vector?
>>
>> Thanks,
>> Greg
>>
>> __
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>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> __
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Re: [R] get formatted regression output
library(Hmisc) has latex and html functions to convert the output into latex (then to pdf, if you wish), and into html. A useful link for this is http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/SweaveConvert Bunny, lautloscrew.com wrote: Hi everybody, I have a simple regression summary created by summary.lm and I wonder how i can export it to another file format which can be used on the web. .pdf would be possible, a html table would be nicer than your momma on your birthday. any suggestions ? thx so much in advance matthias __ 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] how to extract object from stats test output (cor.test)?
First of all, you need to store as a list not a vector if you;re storing the
entire output. Otherwise, you can just store, for example, cor.test(...)$p.value
On Thu, 19 Jun 2008 11:01:42 -0400
"Patrick Ayscue" <[EMAIL PROTECTED]> wrote:
> Hello,
>
> Is there a way to extract output objects from a stats test without viewing
> the entire output? I am trying to do so in the following:
>
> define a vector of length j
>
> for( i in 1: length (vector)) {
> vector[i] = cor.test (datavector1, datavector2[i], method=("spearman"))
> }
>
> I would like the reported Spearman's rho to be saved in a vector. I have
> tried a few different ways of doing this but seem unable to figure out how
> to get only that output without looking at each report and copying by hand.
>
>
> Any help would be appreciated.
>
>
> Thanks,
> Patrick
>
> [[alternative HTML version deleted]]
>
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> and provide commented, minimal, self-contained, reproducible code.
--
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Re: [R] Problem in Binning of a data set
One issue you will have is that, if you're using the same cutpoints for the binning for all three tables, you'll probably get different numbers of values from each column in each bin, so you won't be able to form a "matrix". Of course, I might be misunderstanding what you mean by "binning" :) Abhijit sumit gupta wrote: Hello, I am having problem with binning the data. I have a 50X3 matrix and I binned the data for all the 3 columns. Using table command I got the total no. of elements in a particular bin. Could you please tell me how to see that what all elements are there in a particular bin and then create a different matrix for each bin? Thanks. Regards, Sumit [[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-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] shell command
Yes, see ?system samitj wrote: Hi, Can we execute a unix shell command from within R shell? thanks, Sam __ 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] A curious bug in read.xls
I believe read.xls has a colClasses argument. If you import using read.xls(filename, colClasses='character') everything will be imported as a string, and you can re-convert after importing Alberto Monteiro wrote: I found a curious bug in read.xls. I don't know if it's reproducible. It's like this: suppose I do a read.xls in a spreadsheet. A column begins with a number. Then, any strings below it will be rendered as NA. If the column begins with a string, then it will be rendered correctly. Alberto Monteiro __ 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] Usefulness of "scale" function
Type ?scale in R for the answer :)
Gundala Viswanath wrote:
Hi all,
I found this snippet in a gene expression
clustering code.
__BEGIN__
temp <- readLines("GSE1110_series_matrix.txt");
cat(temp[-grep("^!|^\"$", temp)], file="GSE1110clean.txt", sep="\n");
mydata <- read.delim("GSE1110clean.txt", header=T, sep="\t")
mydatascale <- t(scale(t(mydata)))
I am wondering, in general:
1. What is the purpose of 'scale' function?
2. When one should use it?
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Re: [R] favorite useful tools?
The two sets of packages I use a lot for their utility functions and for
making my day-to-day analysis and reporting easier are Hmisc and Design
by Frank Harrell and {gdata,gmodels,gplots} by Greg Warnes. Frank's
packages have good documentation and cover a pretty good range of
regression methods as well as a refined set of report-writing tools (see
http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/RS for more). These
aren't "obscure" or "small" tools, but very useful and "cool" tools I
use regularly.
Greg and Frank can thank me later for the free plug :-D :-D
Abhijit
Carl Witthoft wrote:
Hi,
I'm relatively new to R, so I don't know the full list of base (or
popular add-on packages) functions and tools available. For example,
I tripped across mention of rle() in a message about some other
problem. rle() turned out to be a handy shortcut to splitting some of
my data by magnitude (vaguely like a sequence-based histogram).
So I thought I'd ask: what small, or obscure, tools and functions in R
do you find handy or 'cool' to use in your work?
Thanks
Carl
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Re: [R] R + Linux
I've had R on an Ubuntu system for about 18 months now, and getting R up and running was a breeze. (I didn't realize it earlier, but Dirk certainly gets my vote of thanks for his efforts in making this process as easy as it is). Specially in terms of dependencies and the like, the Ubuntu packaging system has made things specially easy. I've also had the experience of installing R on a RedHat Enterprise System on a new server at university, and the dependencies issues was much more problematic (albeit, I wasn't allowed to use yum because of the way our IT people had set it up), specially at the compiler level. Just my limited experience in this area. In any case, I'm not going back to Windows now if not forced; I've been quite happy with my experience in the Linux world. Abhijit Markus Jäntti wrote: > I have both Debian, Ubuntu, RedHat and CentOS systems, and primary run R > on the Debian and RedHat machines. I have encountered few problems > running R on RedHat/CentOS, but I do think the Debian/Ubuntu package > management system, combined with the kind provision of packages, makes > life a lot simpler. (Yes, many thanks to Dirk!). > > Also, the ease of installing and maintaining among with the highly > useful user forums of Ubuntu would lead me to recommend that particular > distribution. > > Regards, > > Markus > > On Fri, 2008-06-06 at 14:13 -0400, steven wilson wrote: > >> Dear all; >> >> I'm planning to install Linux on my computer to run R (I'm bored of >> W..XP). However, I haven't used Linux before and I would appreciate, >> if possible, suggestions/comments about what could be the best option >> install, say Fedora, Ubuntu or OpenSuse which to my impression are the >> most popular ones (at least on the R-help lists). The computer is a PC >> desktop with 4GB RAM and Intel Quad-Core Xeon processor and will be >> used only to run R. >> >> Thanks >> Steven >> >> __ >> 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] Correlated Columns in data frame
The line in question randomly decides which of the two correlated
columns to drop. If C1 and C2 are correlated you could drop either one,
the code decides which randomly, which is a principled way to do this.
This does mean that repeated runs of this code will give you different
results, but the final result is what you want in all cases: the columns
of the resultant data.frame do not have pairwise correlation above a
threshold. I guess the point here is that starting from the same
data.frame there are several resultant data.frames possible which
satisfy the property you desire, so are equally valid from that
criterion's perspective.
A simple code for your more recent query is :
cor.mat=cor(/data.frame/)
ind = which(abs(cor.mat) Dear all,
> Sorry to post my query once again in the list, since I did
> not get attention from anyone in my previous mail to this
> list.
> Now I make it simple here that please give me a code for
> find out the columns of a dataframe whose correlation
> coefficient is below a pre-determined threshold. (For
> detailed query please see my previous message to this list,
> pasted hereunder)
>
> Thanks and regards,
> B.Nataraj
>
> Following is my previous message to this list to which I do
> not get any reply.
>
> Dear all,
> For removing correlated columns in a data frame,df.
> I found a code written in R in the page
> http://cheminfo.informatics.indiana.edu/~rguha/code/R/ of
> Mr.Rajarshi Guha.
> The code is
> #
> r2test <- function(df, cutoff=0.8) {
> if (cutoff > 1 || cutoff <= 0) {
> stop(" 0 <= cutoff < 1")
> }
> if (!is.matrix(d) && !is.data.frame(d)) {
> stop("Must supply a data.frame or matrix")
> }
> r2cut = sqrt(cutoff);
> cormat <- cor(d);
> bad.idx <- which(abs(cormat)>r2cut,arr.ind=T);
> bad.idx <- matrix( bad.idx[bad.idx[,1] > bad.idx[,2]],
> ncol=2);
> drop.idx <- ifelse(runif(nrow(bad.idx)) > .5,
> bad.idx[,1], bad.idx [,2]);
> if (length(drop.idx) == 0) {
> 1:ncol(d)
> } else {
> (1:ncol(d))[-unique(drop.idx)]
> }
> }
>
> Now the problem is the code return different output (i.e.
> different column number) for a different call. I could not
> understood why it happens from that code, but I can
> understand the logic in code except the line
>
> drop.idx <- ifelse(runif(nrow(bad.idx)) > .5, bad.idx[,1],
> bad.idx [,2]);
>
> what it means by comparing > 0.5 of nrow(bad.idx).
> So I am looking for anyone to help me for different output
> generation between the different function call as well as
> meaning of the line which I mentioned above.
>
> Thanks!
> B.Nataraj
>
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> and provide commented, minimal, self-contained, reproducible code.
>
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Re: [R] How to swap and rearrange rows?
Another possibility:
# Generate the months in sequential order:
m <- months(seq(as.Date('2000/1/1'), by='month',length=12),abbreviate=T)
# Concatenate the data
est=rbind(est31,est30,est28)
# generate the right order
ind <- match(substr(rownames(est),1,3),m)
# reorder the rows
est <- est[ind,]
BTW, Richard meant "rbind" instead of "cbind" in his code, which I'm sure you
knew.
Abhijit
On Fri, 16 May 2008 10:09:22 +0100
[EMAIL PROTECTED] wrote:
> > How to swap and rearrange the row so that I will have
> > Jan-Dec in order?
> > > est31
> > p0 est.alpha est.beta est.rate
> > Jan 0.8802867 0.7321440 7.241757 0.1380880
> > Mar 0.8598566 0.7096567 7.376367 0.1355681
> > May 0.6204301 0.8657272 6.036106 0.1656697
> > July 0.5032258 0.9928488 4.027408 0.2482986
> > Aug 0.5322581 0.9625738 4.103121 0.2437169
> > Oct 0.6792115 0.8526226 5.105218 0.1958780
> > Dec 0.8397849 0.7490287 7.070349 0.1414357
> > > est30
> > p0 est.alpha est.beta est.rate
> > Apr 0.7296296 0.7929348 6.303877 0.1586325
> > Jun 0.5574074 0.8588608 5.695905 0.1755647
> > Sept 0.607 0.9031150 4.594891 0.2176330
> > Nov 0.7725926 0.7600906 5.636366 0.1774193
> > > est28
> > p0 est.alpha est.beta est.rate
> > Feb 0.877262 0.6567584 8.708051 0.1148363
> > Thank you so much.
>
> First, concatenate the data frames:
> est <- cbind(est31, est30, est28)
>
> Now you can sort the resulting data frame using order, as described in FAQ
> on R 7.23.
> months <- factor(rownames(est), levels=c("Jan", "Feb", "Mar", "Apr",
> "May", "Jun", "July", "Aug", "Sept", "Oct", "Nov", "Dec"))
> sortedest <- est[order(months),]
>
> (You might also want to recode 'July' to 'Jul' and 'Sept' to 'Sep' to be
> consistent with the other months.)
>
> Regards,
> Richie.
>
> Mathematical Sciences Unit
> HSL
>
>
>
> ATTENTION:
>
> This message contains privileged and confidential info...{{dropped:12}}
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Re: [R] Newbie question about vector matrix multiplication
Won't diag(w)%*%co%*%diag(w) do it?
Dan Stanger wrote:
Hello All,
I have a covariance matrix, generated by read.table, and cov:
co<-cov(read.table("c:/r.x"))
XYZ
X 0.0012517684 0.0002765438 0.0007887114
Y 0.0002765438 0.0002570286 0.0002117336
Z 0.0007887114 0.0002117336 0.0009168750
And a weight vector generated by
w<- read.table("c:/r.weights")
X Y Z
1 0.5818416 0.2158531 0.2023053
I want to compute the product of the matrix and vectors termwise to
generate a 3x3 matrix, where m[i,j]=w[i]*co[i,j]*w[j].
0.000423773 7.47216E-08 4.41255E-08
7.47216E-08 1.96566E-11 4.29229E-11
4.41255E-08 4.29229E-11 4.11045E-11
Is this possible without writing explicit loops?
Thank you,
Dan Stanger
Eaton Vance Management
200 State Street
Boston, MA 02109
617 598 8261
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Re: [R] Can R handle large dataset?
I believe this is determined by how much memory your computer has, not particularly by R itself. Mingjun Huang wrote: Hello, I am new to R, can anyone give me an idea of how R handle a large dataset (e.g. couple of Gbytes)? Thanks a lot! Best, Mingjun __ 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] anova p value extraction
What works, amazingly, is summary(pb)$"Pr(>F)" [note the quotes] Abhijit On Wed, 07 May 2008 18:17:09 -0700 "H. Paul Benton" <[EMAIL PROTECTED]> wrote: > Yea the anova object seems to be odd. It's not S4 so that's why I tried > originally the attr() funtion but > > summary(pb)$Pr(>F) > > Error: unexpected '>' in "summary(pb)$Pr(>" > > summary(pb)$Pr > > NULL > > summary(pb)@Pr(>F) > > Error: unexpected '>' in "summary(pb)@Pr(>" > > summary(pb)@Pr(F) > > Error: no slot of name "Pr" for this object of class "summary.aov" > In addition: Warning message: > trying to get slot "Pr" from an object (class "summary.aov") that is > not an S4 object > > > > Research Programmer & Technician > The Scripps Research Institute > Mass Spectrometry Core Facility > o The > / > o Scripps > \ > o Research > / > o Institute > > > > [EMAIL PROTECTED] wrote: > > Hi: it's probably the Pr(> F) element so just access it by > > > > sum<-summary(whatever). > > > > then sum$Pr(>F) will probably work. But make sure that's it because > > usually the name is pval or pvalue etc so I'm > > surprised about the weird name. > > > > > > > > > > On Wed, May 7, 2008 at 8:47 PM, Paul Benton wrote: > > > >> hello all, > >> > >> Quick question, how do I get the p value out of the anova? > >> > >> Thanks, > >> > >> Paul > >> > >>> pb<-aov(as.numeric(diff[5,16:33]) ~ grF) > >>> summary(pb) > >> Df Sum SqMean Sq F value Pr(>F) > >> grF 3 2.7860e+10 9.2867e+09 4.2236 0.02534 * > >> Residuals 14 3.0783e+10 2.1988e+09 > >> --- > >> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 > >>> str(summary(pb)) > >> List of 1 > >> $ :Classes 'anova' and 'data.frame': 2 obs. of 5 variables: > >> ..$ Df : num [1:2] 3 14 > >> ..$ Sum Sq : num [1:2] 2.79e+10 3.08e+10 > >> ..$ Mean Sq: num [1:2] 9.29e+09 2.20e+09 > >> ..$ F value: num [1:2] 4.22 NA > >> ..$ Pr(>F) : num [1:2] 0.0253 NA > >> - attr(*, "class")= chr [1:2] "summary.aov" "listof" > >>> attr(summary(pb), "Pr(>F)") > >> NULL > >> > >> __ > >> 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. -- Abhijit Dasgupta __ 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] CRAN and Multiple Linear Regression
Multiple linear regression is handled by the function lm() in the default installation of R. This takes inputs as lm(y~x1+x2+x3). If you're going to be using R regularly, there are several books which cover the basic statistical analyses available in R (and then some), including those by Peter Daalgard and by Brian Ripley, who are very regular contributors to this list. Abhijit Anja und Th. Sponsel wrote: Hello I have to solve a multiple linear regression. Most programs like Excel or Mathlab only support 5-10 dimensions. Now I have installed CRAN and I have no clue what to do next. At the moment I am entering my data into an excelsheet (for quick copy- paste). The Y-array will be 20 columns (=dimensions) and 128 rows (=variables). The X-array may also be 128 rows in Excel. Which package do I need - or does it work without any package? What commands do I have to enter? I'm not familiar with CRAN and I didn't find any example. Best regards, Thomas __ 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] howto import .xls and .ods
I've written a little python script that converts ods and xls to csv, and a wrapper in R that imports a sheet of the ods and/or xls into a data.frame in R. If this is a FAQ and there is an existing solution, great. Actually, for xls, the library gdata has a read.xls function that uses a perl function underneath. Abhijit Dasgupta, Ph.D Assistant Professor | Division of Biostatistics Dept of Pharmacology and Experimental Therapeutics | Thomas Jefferson University 1015 Chestnut St | Suite M100 | Philadelphia PA 19107 Ph: (215) 503-9201 | Fax: (215) 503-3804 adasgupt (at) mail (dot) jci (dot) tju (dot) edu The documents accompanying this transmission may contain confidential health or business information. This information is intended for the use of the individual or entity named above. If you have received this information in error, please notify the sender immediately and arrange for the return or destruction of these documents. Jonas Stein wrote: Hi, i want to import data from .ods and .xls files in R on a linux system. Seems it was a faq in the past, but i found only solutions for Windows. Is there a handy solution for linux? The best would be something like mytab <-read.ods(...) Any hints? Thanks a lot for reading so far, __ 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] a simple question of importing data
Or you could use the read.xls program in the gdata library that uses a
perl script underneath.
Charles Danko wrote:
> try:
> var <- read.table("weekly.txt", sep="\t", header=TRUE)
>
> Charles
>
> On Thu, Apr 24, 2008 at 3:29 PM, tzsmile <[EMAIL PROTECTED]> wrote:
>
>> i just want to read data from Excel and i copied it and pasted into a txt
>> file.
>> then i want to use "read.table" to read it. but however i tried, it doesn't
>> work.
>> can someone help me?
>> data is attached.
>> thanks http://www.nabble.com/file/p16851853/weekly.txt weekly.txt
>> --
>> View this message in context:
>> http://www.nabble.com/a-simple-question-of-importing-data-tp16851853p16851853.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.
>
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Re: [R] Ubuntu vs. Windows
My naive understanding of this (I switched to Ubuntu a year ago from WinXP for similar reasons) is that Ubuntu as an OS uses less memory than WinXP, thus leaving more memory for computation, swap space, etc. In other words, Ubuntu is "lighter" than XP on system resources. Abhijit Doran, Harold wrote: > Dear List: > > I am very much a unix neophyte, but recently had a Ubuntu box installed > in my office. I commonly use Windows XP with 3 GB RAM on my machine and > the Ubuntu machine is exactly the same as my windows box (e.g., > processor and RAM) as far as I can tell. > > Now, I recently had to run a very large lmer analysis using my windows > machine, but was unable to due to memory limitations, even after > increasing all the memory limits in R (which I think is a 2gig max > according to the FAQ for windows). So, to make this computationally > feasible, I had to sample from my very big data set and then run the > analysis. Even still, it would take something on the order of 45 mins to > 1 hr to get parameter estimates. (BTW, SAS Proc nlmixed was even worse > and kept giving execution errors until the data set was very small and > then it ran for a long time) > > However, I just ran the same analysis on the Ubuntu machine with the > full, complete data set, which is very big and lmer gave me back > parameter estimates in less than 5 minutes. > > Because I have so little experience with Ubuntu, I am quite pleased and > would like to understand this a bit better. Does this occur because R is > a bit friendlier with unix somehow? Or, is this occuring because unix > somehow has more efficient methods for memory allocation? > > I wish I knew enough to even ask the right questions. So, I welcome any > enlightenment members may add. > > __ > 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] Skipping specified rows in scan or read.table
Hi Ravi, One thing I tend to do is, when using read.table, specify the option 'colClasses='character''. This forces everything to be read as a character. From there, as.numeric works fine, and you don't have to deal with factors and reconverting them. Hope this helps Abhijit Ravi Varadhan wrote: > Hi, > > > > I have a data file, certain lines of which are character fields. I would > like to skip these rows, and read the data file as a numeric data frame. I > know that I can skip lines at the beginning with read.table and scan, but is > there a way to skip a specified sequence of lines (e.g., 1, 2, 10, 11, 19, > 20, 28, 29, etc.) ? > > > > If I read the entire data file, and then delete the character fields, the > values are still kept as factors, with each value denoted by its level. > Since, I have continuous variables, there are as many levels as there are > values. I am unable to coerce this to "numeric" mode. Is there a way to do > this so that I can then manipulate the numeric data frame? > > > > Thanks for any help. > > Best, > > Ravi. > > > --- > > Ravi Varadhan, Ph.D. > > Assistant Professor, The Center on Aging and Health > > Division of Geriatric Medicine and Gerontology > > Johns Hopkins University > > Ph: (410) 502-2619 > > Fax: (410) 614-9625 > > Email: [EMAIL PROTECTED] > > Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html > > > > > > > > > > [[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-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] vectorized way to combine levels of a factor
For your first problem, you can probably do it in 2 statements:
V3 = ifelse(V2==A,V2,V3)
V3 = ifelse(V2==B|V2==C,D,V3)
If you want to split V1 into (0,a],(a,b],(b,c],(c,1], you can do, quite simply
V1.factor = cut(V1, c(0,a,b,c,1))
Abhijit
On Wed, 9 Apr 2008 13:58:17 -0700
Chang Liu <[EMAIL PROTECTED]> wrote:
>
> Hi Gurus:
>
> If I have a large dataset of the form of:
>
> > x <- data.frame(V1 = runif(10), V2 = sample(c('A','B','C'),10,T)) > x
> >V1 V21 0.2691580 A2 0.8711267 B3 0.2674728 C4 0.3278876 A5
> > 0.1809152 A6 0.2499651 C7 0.9155174 A8 0.8004974 B9 0.7885516 A10
> > 0.9301630 A
> And I want a V3 that =V2 if V2=A, and =D if V2=B or C. In other words I want
> to use a vectorized way to combine some levels, rather than having to loop
> through a large dataset.
>
> Similarly, if I want to group V1 into levels, what is a fast way to do it?
>
> Thank you!
> Karen
> _
> If you like crossword puzzles, then you'll love Flexicon, a game which
> comb[[elided Hotmail spam]]
>
> [[alternative HTML version deleted]]
>
> __
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
Abhijit Dasgupta
__
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Re: [R] Sweave - print \n ?
you haven't escaped the \ for the \n, I think. Your line should be
cat("\\hline \\n"). You did escape the \ for hline, though.
Abhijit Dasgupta, Ph.D
Assistant Professor | Division of Biostatistics
Dept of Pharmacology and Experimental Therapeutics | Thomas Jefferson
University
1015 Chestnut St | Suite M100 | Philadelphia PA 19107
Ph: (215) 503-9201 | Fax: (215) 503-3804
adasgupt (at) mail (dot) jci (dot) tju (dot) edu
The documents accompanying this transmission may contain confidential
health or business information. This information is intended for the use
of the individual or entity named above. If you have received this
information in error, please notify the sender immediately and arrange
for the return or destruction of these documents.
Werner Wernersen wrote:
> Hi,
>
> this is probably quite stupid but I have no clue
> what's wrong. Let's say I write the function
> hline <- function() {
> cat("\\hline \n")
> }
> and call hline() from within a Sweave chunk. Why is
> there no carriage return after the \hline in the
> resulting tex file?
>
> if I call hline() hline() in the chunk, then I get
> \hline \hline
> in the tex code without a linebreak in between.
>
> Thanks for any hints,
> Werner
>
>
> E-Mails jetzt auf Ihrem Handy.
>
> __
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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Re: [R] Recode factors
Another suggestion is:
blah = as.character(aa)
blah=gsub('[a-z]','0',blah,ignore.case=T)
aa = as.factor(blah)
I've found changing factors to characters rather than numeric is
generally safer.
Abhijit
Doran, Harold wrote:
> Perfect. My headache is gone. Thanks.
>
>
>> -Original Message-
>> From: Henrique Dallazuanna [mailto:[EMAIL PROTECTED]
>> Sent: Thursday, March 27, 2008 12:50 PM
>> To: Doran, Harold
>> Cc: r-help@r-project.org
>> Subject: Re: [R] Recode factors
>>
>> If I understand, you can try this:
>>
>> levels(x)[is.na(as.numeric(levels(x)))] <- 0
>>
>> On 27/03/2008, Doran, Harold <[EMAIL PROTECTED]> wrote:
>>
>>> I know this comes up, but I didn't see my exact issue in
>>>
>> the archives.
>>
>>> I have variables in a dataframe that need to be recoded.
>>>
>> Here is what
>>
>>> I'm dealing with
>>>
>>> I have a factor called aa
>>>
>>> > class(aa)
>>> [1] "factor"
>>> > table(aa)
>>> aa
>>> *0123ABCDLNT
>>>00 1908 725 208900 6700216
>>>
>>> I need to recode everything that is not a numeric value
>>>
>> into a 0. So,
>>
>>> for example
>>>
>>> > mm <- ifelse(aa == 'B', 0, aa)
>>> > table(mm)
>>> mm
>>>0345 11 12 13
>>> 67 1908 725 2089216
>>>
>>> The recoding works, but the values are no longer what they were
>>> previously. For example, what was a '1' is now a '4' etc.
>>>
>> Is there a
>>
>>> way to recode factors and also keep the values the same as
>>>
>> they were before?
>>
>>> That is, a '1' would remain a '1' after the recode?
>>>
>>> After the recoding, I need to convert to a numeric
>>>
>> variable. I can do
>>
>>> this as
>>>
>>> mm <- as.numeric(as.character(aa))
>>>
>>> Harold
>>>
>>>
>>> > sessionInfo()
>>> R version 2.6.2 (2008-02-08)
>>> i386-pc-mingw32
>>>
>>> locale:
>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>>> States.1252;LC_MONETARY=English_United
>>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets
>>>
>> methods base
>>
>>> other attached packages:
>>> [1] gdata_2.4.0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] gtools_2.4.0
>>> >
>>>
>>> __
>>> 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.
>>>
>>>
>> --
>> Henrique Dallazuanna
>> Curitiba-Paraná-Brasil
>> 25° 25' 40" S 49° 16' 22" O
>>
>>
>
> __
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>
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[R] OdfWeave and contingency tables
Hi, I would like to use odfWeave to output some contingency tables (the output of "table") into OOo. I know I can do this in LaTex (using "latex" in the Hmisc package), but I was wondering if it is possible in OdfWeave. My documentation to odfTable says inputs can only be vector, matrix or data.frame, and I'm having a hard time converting my table into one of these formats. Regards Abhijit __ 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.
