Re: [R] [Rd] I do not want that R CMD build removes temp directory
Dear Uwe, Unfortunately there isn't much of an output. This is all what I have: $ R CMD INSTALL --log prolfqua Warning: unknown option '--log' * installing to library 'C:/Users/witoldwolski/AppData/Local/R/win-library/4.2' * installing *source* package 'prolfqua' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ERROR: lazy loading failed for package 'prolfqua' * removing 'C:/Users/witoldwolski/AppData/Local/R/win-library/4.2/prolfqua' Also with --no-test-load option the install is failing : $ R CMD INSTALL --clean --no-test-load prolfqua * installing to library 'C:/Users/witoldwolski/AppData/Local/R/win-library/4.2' * installing *source* package 'prolfqua' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ERROR: lazy loading failed for package 'prolfqua' * removing 'C:/Users/witoldwolski/AppData/Local/R/win-library/4.2/prolfqua' And including "--no-clean-on-error" also does not help because the installation directory is empty. Tested the install, on macos M1, linux ARM64, linux x86, Windows 64, and it works everywhere except Parallels Windows 64 on ARM M1. R version 4.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) best regards Witek On Fri, 16 Dec 2022 at 11:24, Uwe Ligges wrote: > > > > On 15.12.2022 21:47, Witold E Wolski wrote: > > Thank you Simon, > > > > It seems not to be related to the R package but rather to the OS, > > (just got the same error when installing the shiny R package from > > CRAN). > > I am on an M1 mac running Windows ARM in Parallels. Installed a > > x86_64-w64 R version. > > > > > > > > "** byte-compile and prepare package for lazy loading > > ERROR: lazy loading failed for package 'shiny' > > * removing 'C:/Users/witoldwolski/AppData/Local/R/win-library/4.2/shiny' > > Warning in install.packages :" > > Can we please have the full output? > > Best, > Uwe Ligges > > > > > On Thu, 15 Dec 2022 at 19:09, Simon Urbanek > > wrote: > >> > >> Yes: > >> > >> $ R CMD INSTALL --help | grep error > >>--no-clean-on-error do not remove installed package on error > >> > >> But probably more commonly used way is to install the package from its > >> unpacked directory as that avoids the use of temporary directories in the > >> first place. > >> > >> In you case you can also use --no-test-load and the non-functional package > >> will still be installed so you can inspect it. > >> > >> Cheers, > >> Simon > >> > >> PS: please don't cross-post > >> > >> > >>> On Dec 16, 2022, at 7:01 AM, Witold E Wolski wrote: > >>> > >>> I am getting a package build error, and can not figure out the problem. > >>> The error is > >>> " > >>> ERROR: lazy loading failed for package 'prolfqua' > >>> * removing 'C:/Users/ > >>> " > >>> However since R CMD build removes the temp directory and does not give > >>> any other errors how can I find out what the build problem is? > >>> > >>> Is there a way to disable the temp directory removal? > >>> > >>> Best Regards > >>> Witek > >>> -- > >>> Witold Eryk Wolski > >>> > >>> __ > >>> r-de...@r-project.org mailing list > >>> https://stat.ethz.ch/mailman/listinfo/r-devel > >>> > >> > > > > -- Witold Eryk Wolski __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] [Rd] I do not want that R CMD build removes temp directory
Thank you Simon, It seems not to be related to the R package but rather to the OS, (just got the same error when installing the shiny R package from CRAN). I am on an M1 mac running Windows ARM in Parallels. Installed a x86_64-w64 R version. "** byte-compile and prepare package for lazy loading ERROR: lazy loading failed for package 'shiny' * removing 'C:/Users/witoldwolski/AppData/Local/R/win-library/4.2/shiny' Warning in install.packages :" On Thu, 15 Dec 2022 at 19:09, Simon Urbanek wrote: > > Yes: > > $ R CMD INSTALL --help | grep error > --no-clean-on-error do not remove installed package on error > > But probably more commonly used way is to install the package from its > unpacked directory as that avoids the use of temporary directories in the > first place. > > In you case you can also use --no-test-load and the non-functional package > will still be installed so you can inspect it. > > Cheers, > Simon > > PS: please don't cross-post > > > > On Dec 16, 2022, at 7:01 AM, Witold E Wolski wrote: > > > > I am getting a package build error, and can not figure out the problem. > > The error is > > " > > ERROR: lazy loading failed for package 'prolfqua' > > * removing 'C:/Users/ > > " > > However since R CMD build removes the temp directory and does not give > > any other errors how can I find out what the build problem is? > > > > Is there a way to disable the temp directory removal? > > > > Best Regards > > Witek > > -- > > Witold Eryk Wolski > > > > __ > > r-de...@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > -- Witold Eryk Wolski __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] I do not want that R CMD build removes temp directory
I am getting a package build error, and can not figure out the problem. The error is " ERROR: lazy loading failed for package 'prolfqua' * removing 'C:/Users/ " However since R CMD build removes the temp directory and does not give any other errors how can I find out what the build problem is? Is there a way to disable the temp directory removal? Best Regards Witek -- Witold Eryk Wolski __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Package installation for 4.1 on windows.
Dear Duncan, Thank you. Indeed I did had the R_LIBS_USER env. variable defined. Best regards Witold On Mon, 7 Jun 2021 at 17:48, Duncan Murdoch wrote: > > On 07/06/2021 10:37 a.m., Witold E Wolski wrote: > > Hello, > > > > I just installed R 4.1 and now trying to update install some packages. > > > > R version 4.1.0 (2021-05-18) -- "Camp Pontanezen" > > Copyright (C) 2021 The R Foundation for Statistical Computing > > > > But when installing packages I read: > > > > Installing packages into ‘C:/Users/wolski/Documents/R/win-library/4.0’ > > > > Should not be a win-library/4.1. package directory be used by default? > > > > I suspect something in your local setup specifies that directory. The > usual place to install is the directory where R was installed; it only > switches to the user home directory if that fails, or the user requests it. > > Duncan Murdoch -- Witold Eryk Wolski __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Package installation for 4.1 on windows.
Hello, I just installed R 4.1 and now trying to update install some packages. R version 4.1.0 (2021-05-18) -- "Camp Pontanezen" Copyright (C) 2021 The R Foundation for Statistical Computing But when installing packages I read: Installing packages into ‘C:/Users/wolski/Documents/R/win-library/4.0’ Should not be a win-library/4.1. package directory be used by default? Best regards Witold -- Witold Eryk Wolski __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] brms does not work with R4.0.2
Hello, Got the following info from the brms package Maintainer. "This is a caused by a problem in the current rstan CRAN version on Windows and is not related to brms. You can find various threads that deal with that topic on https://discourse.mc-stan.org/. For now, it may be easiest to revert to rstan 2.19.3." Thanks Witek On Mon, 13 Jul 2020 at 15:41, Witold E Wolski wrote: > > Hello, > > I upgraded today to R4.0.2 from 3.6.3 on my Windows machine (actually > 2 of them - first desktop and then laptop just to verify the problem) > and on both of them I am getting the following error when running the > brms::brm function example code. > > ``` > > bprior1 <- prior(student_t(5,0,10), class = b) + > + prior(cauchy(0,2), class = sd) > > fit1 <- brm(count ~ zAge + zBase * Trt + (1|patient), > + data = epilepsy, family = poisson(), prior = bprior1) > Compiling the C++ model > > > > fit1 > Error: object 'fit1' not found > ``` > > I tried to get some more information by setting `silent = FALSE` but > nothing is being printed. > All I see is: > > ``` > > brm(count ~ zAge + zBase * Trt + (1|patient), > + data = epilepsy, family = poisson(), prior = bprior1, silent=FALSE) > Compiling the C++ model > > > ``` > > R tools is installed and I did test that they work properly. > Also: > > ``` > system.file(package = "StanHeaders") > [1] "C:/Users/wewol/OneDrive/Documents/R/win-library/4.0/StanHeaders" > ``` > > Help highly appreciated. > > Witek > -- > Witold Eryk Wolski -- Witold Eryk Wolski __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] brms does not work with R4.0.2
Hello, I upgraded today to R4.0.2 from 3.6.3 on my Windows machine (actually 2 of them - first desktop and then laptop just to verify the problem) and on both of them I am getting the following error when running the brms::brm function example code. ``` > bprior1 <- prior(student_t(5,0,10), class = b) + + prior(cauchy(0,2), class = sd) > fit1 <- brm(count ~ zAge + zBase * Trt + (1|patient), + data = epilepsy, family = poisson(), prior = bprior1) Compiling the C++ model > > fit1 Error: object 'fit1' not found ``` I tried to get some more information by setting `silent = FALSE` but nothing is being printed. All I see is: ``` > brm(count ~ zAge + zBase * Trt + (1|patient), + data = epilepsy, family = poisson(), prior = bprior1, silent=FALSE) Compiling the C++ model > ``` R tools is installed and I did test that they work properly. Also: ``` system.file(package = "StanHeaders") [1] "C:/Users/wewol/OneDrive/Documents/R/win-library/4.0/StanHeaders" ``` Help highly appreciated. Witek -- Witold Eryk Wolski __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] smoothScatter() and the KernSmooth package
Hello, I am getting the following error when running a package check ``` Error in loadNamespace(name) : there is no package called 'KernSmooth' Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ``` The error happens in a function which calls graphics::smoothScatter I found this e-mail on the r-devel list where this problem is also reported. https://stat.ethz.ch/pipermail/r-devel/2015-February/070671.html So I could add KernSmooth to Suggest in the DESCRIPTION but I have a few questions: (and I am citing from the e-mail above to which I could not find a reply): "I have a few questions: isn't it unusual the way smoothScatter calls grDevices:::.smoothScatterCalcDensity() and KernSmooth::bkde2D(), i.e., without requiring the packages? Shouldn't "graphics" suggest "KernSmooth"? " best regards Witek -- Witold Eryk Wolski __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] decomposing a string representing a valid mathematical expression?
Hello, I would like to decompose a string i.e. "a - b" or "a +b" into an array or list ["a","-","b"] Since R knows how to parse expressions these type of expressions I would like to reuse some existing functions and not to use gsub or strsplit etc. Thank you Witek -- Witold Eryk Wolski __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] stats::power.t.test error
Dear Peter, Yes, It is a technical issue and a matter of diddling around. And I agree with your comment regarding the 2 observations. I have several thousands variance estimates for which I need to compute the sample sizes automatically. Using try statements is typically the last thing I would like to resort too. Is there an alternative implementation of power.t.test on CRAN which could the diddling for me and return plausible sample sizes i.e. integers. best regards Witek On Fri, 4 Oct 2019 at 16:28, peter dalgaard wrote: > > This is mainly a technical issue with uniroot trying to go outside of its > interval: (2, 1e7) > > It is fairly easy to find an approximate solution by diddling a little by > hand: > > > power.t.test(delta = 0.5849625, sd=0.01, n=1.04, sig.level=0.05)$power > [1] 0.8023375 > > Notice, however, that 1.04 observations in each group makes no sense at all. > In order to actually do a t-test you need at least 2 observations per group > (since we assume equal group sizes) or you have no variance estimate. Already > at sd=0.1, you are crossing the n=2 border, so for any smaller sd, you will > just get higher power with n=2. (Also, anything with single-digit degrees of > freedom for variance is probably expecting rather much regarding to Gaussian > distribution of your data.) > > -pd > > > On 4 Oct 2019, at 14:30 , Witold E Wolski wrote: > > > > Hi, > > > > power.t.test works for some range of input parameters but fails otherwise. > > > >> power.t.test(delta = 0.5849625, sd=0.1, power=0.8, sig.level=0.05)$n > > [1] 1.971668 > >> power.t.test(delta = 0.5849625, sd=0.05, power=0.8, sig.level=0.05)$n > > [1] 1.620328 > >> power.t.test(delta = 0.5849625, sd=0.01, power=0.8, sig.level=0.05)$n > > Error in uniroot(function(n) eval(p.body) - power, c(2, 1e+07), tol = tol, > > : > > did not succeed extending the interval endpoints for f(lower) * f(upper) > > <= 0 > > In addition: Warning message: > > In qt(sig.level/tside, nu, lower.tail = FALSE) : NaNs produced > > > > I guessing that sd is very small compared with delta, hence the > > problem. But what are allowed values (ratios) of delta and sd? > > > > Best > > Witek > > > > > > > > > > > > > > -- > > Witold Eryk Wolski > > > > __ > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > > 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. > > -- > Peter Dalgaard, Professor, > Center for Statistics, Copenhagen Business School > Solbjerg Plads 3, 2000 Frederiksberg, Denmark > Phone: (+45)38153501 > Office: A 4.23 > Email: pd@cbs.dk Priv: pda...@gmail.com > > > > > > > > > -- Witold Eryk Wolski __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] stats::power.t.test error
Hi, power.t.test works for some range of input parameters but fails otherwise. > power.t.test(delta = 0.5849625, sd=0.1, power=0.8, sig.level=0.05)$n [1] 1.971668 > power.t.test(delta = 0.5849625, sd=0.05, power=0.8, sig.level=0.05)$n [1] 1.620328 > power.t.test(delta = 0.5849625, sd=0.01, power=0.8, sig.level=0.05)$n Error in uniroot(function(n) eval(p.body) - power, c(2, 1e+07), tol = tol, : did not succeed extending the interval endpoints for f(lower) * f(upper) <= 0 In addition: Warning message: In qt(sig.level/tside, nu, lower.tail = FALSE) : NaNs produced I guessing that sd is very small compared with delta, hence the problem. But what are allowed values (ratios) of delta and sd? Best Witek -- Witold Eryk Wolski __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] linear model contrast in R
I am looking for a function to compute contrasts with a interface similar to that of lmerTest::contest multcomp::glht i.e. taking the model and a contrast vector or matrix as an argument, but for linear models, and without the multiple testing adjusted made by multcomp::glht. Thank you -- Witold Eryk Wolski __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] isSingular for lm?
lme4 has a function isSingular to check if the fitted model is Singular, Although lm has the parameter singular.ok = TRUE by defualt, I could not find a function to check if the fitted model is singular. What would be the correct way to implement such a function for and lm object? Check if df.residuals == 0 Thanks Witek -- Witold Eryk Wolski __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] randomForest out of bag prediction
Hello,
I am just not sure what the predict.RandomForest function is doing...
I confused.
I would expect the predictions for these 2 function calls to predict the same:
```{r}
diachp.rf <- randomForest(quality~.,data=data,ntree=50, importance=TRUE)
ypred_oob <- predict(diachp.rf)
dataX <- data %>% select(-quality) # remove response.
ypred <- predict( diachp.rf, dataX )
ypred_oob == ypred
```
These are both out of bag predictions but ypred and ypred_oob are
actually they are very different.
> table(ypred_oob , data$quality)
ypred_oob01
0 1324 346
1 493 2837
> table(ypred , data$quality)
ypred01
0 18170
10 3183
What I find even more disturbing is that 100% accuracy for ypred.
Would you agree that this is rather unexpected?
regards
Witek
--
Witold Eryk Wolski
__
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and provide commented, minimal, self-contained, reproducible code.
[R] Visualizing contrasts for lmer models
Hello, Is there an R-package which implements visualizations of estimated coefficients and the data for lmer models similar to those shown here: http://genomicsclass.github.io/book/pages/interactions_and_contrasts.html in sections: Examining the estimated coefficients (ideally with ggplot) ??? I find these visualizations (especially those for contrasts) very helpful but despite R -package searches I failed to find a generic implementation. best regards Witek Witold Eryk Wolski __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] See section 'Good practice' in '?data'.
To which document
"See section 'Good practice' in '?data'."
refers too?
Found the following calls to data() loading into the global environment:
File 'bibliospec/R/annotateClass.R':
data("AminoAcids")
See section 'Good practice' in '?data'.
Thanks
--
Witold Eryk Wolski
__
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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.
[R] Error: XYZ is not an exported object
I am wrting a package and would like to be able to export it to access it with: packagename::dataset This is how my roxygen doc for the data object looks like: #' Data frame with amino acid masses #' #' @name AminoAcids #' @docType data #' @keywords data #' @export NULL It does end up in the namespace file with: export(AminoAcids) the data is in the data/ folder of the package. and I can load it with data(AminoAcid) Still R CMD build gives me the error: Error : 'AminoAcids' is not an exported object from 'namespace:bibliospec' because I am trying to access it with bibliospec::AminoAcids Help highly appreciated. Thank you -- Witold Eryk Wolski __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] create n suffixes of length 1:n from string of length n
Is there a build in function, which creates n suffixes of length 1:n
from string of length n?
e.g given abcd
produces
"a"
"ab"
"abc"
FAST.
equally nice to have would be:
e.g.
given c("a", "b", "c")
produces
"a"
"a","b"
"a","b","c"
Thank you
Witold
--
Witold Eryk Wolski
__
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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.
[R] rstudio mailing list
Is there a mailing list for Rstudio related questions? I searched the web but did not find one. Thank you -- Witold Eryk Wolski __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] documenting R reference class methods with roxygen2
I would like to document function arguments in R reference classes and I do not know how. I know that methods description can be provided by adding a string below the function declaration. But how to document the function arguments in similar fashion like the arguments of R functions (which can be documented with @param). Thank you. PS. Sorry if for some this question is off topic but I did not found a mailing list dedicated to roxygen2. -- Witold Eryk Wolski __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] [FORGED] Splitting data.frame into a list of small data.frames given indices
Hi Bert,
My reply is inline:
On 1 July 2016 at 17:02, Bert Gunter <bgunter.4...@gmail.com> wrote:
> Inline.
>
> Cheers,
> Bert
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> On Fri, Jul 1, 2016 at 7:40 AM, Witold E Wolski <wewol...@gmail.com> wrote:
>> Hi William,
>>
>> I tested plyrs dlply function, and it seems to have have an O(N*
>> log(R)) complexity (tested for R=N) so I do not know if N is the
>> number of rows or nr of categories.
>>
>> For the data.frame example with 2e5 rows and 2e5 categories it is
>> approx. 10 times faster than split. Still, it is 10 seconds on an
>> i7-5930K 3.5GHz Intel.
>>
>> It would be nice if the documentation would contain runtime
>> complexity information and the documentation of base package function
>> would point to function which should be used instead.
>
> It would, indeed -- but these things are very dependent on exact data
> context, the hardware in use, the OS, etc. Moreover, how could base
> documentation possibly keep track of what all other packages are
> doing?! -- that seems unreasonable on the face of it.
Old methods need to stay for backward compatibility but why not
include new packages, which are a clear improvement over the old ones,
into the default packages and reference them?
I know that
> from time to time R docs do mention base algorithmic complexity (e.g.
> ?sort and the data.table package, I believe), but generally it is
> preferable to omit such details, imho: access to a function should be
> through its relatively fixed API, while the underlying machinery may
> be subject to considerable change.
Just take a look how the C++ stl or the python documents functions for
working with containers. They do provide information about complexity
of operations, or algorithms. Such information is needed to make
reasonable decisions, including not to use a function or a container
type.
If there is a new implementation that changes complexity this
information needs to be updated.
Obviously, there are circumstances
> where something still could (and perhaps should) be said about
> efficiency -- and R docs often do say it -- but I think the level of
> detail you request is unrealistic and might often even mislead.
>
> Obviously, just my opinion, so contrary views welcome.
>
> Cheers,
> Bert
>
>
>>
>> Thanks
>>
>>
>>
>>
>> On 29 June 2016 at 16:13, William Dunlap <wdun...@tibco.com> wrote:
>>> I won't go into why splitting data.frames (or factors) uses time
>>> proportional to the number of input rows times the number of
>>> levels in the splitting factor, but you will get much better mileage
>>> if you call split individually on each 'atomic' (numeric, character, ...)
>>> variable and use mapply on the resulting lists.
>>>
>>> The plyr and dplyr packages were developed to deal with this
>>> sort of problem. Check them out.
>>>
>>>
>>> Bill Dunlap
>>> TIBCO Software
>>> wdunlap tibco.com
>>>
>>> On Wed, Jun 29, 2016 at 6:21 AM, Witold E Wolski <wewol...@gmail.com> wrote:
>>>>
>>>> Hi,
>>>>
>>>> Here is an complete example which shows the the complexity of split or
>>>> by is O(n^2)
>>>>
>>>> nrows <- c(1e3,5e3, 1e4 ,5e4, 1e5 ,2e5)
>>>> res<-list()
>>>>
>>>> for(i in nrows){
>>>> dum <- data.frame(x = runif(i,1,1000), y=runif(i,1,1000))
>>>> res[[length(res)+1]]<-(system.time(x<- split(dum, 1:nrow(dum
>>>> }
>>>> res <- do.call("rbind",res)
>>>> plot(nrows^2, res[,"elapsed"])
>>>>
>>>> And I can't see a reason why this has to be so slow.
>>>>
>>>>
>>>> cheers
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 29 June 2016 at 12:00, Rolf Turner <r.tur...@auckland.ac.nz> wrote:
>>>> > On 29/06/16 21:16, Witold E Wolski wrote:
>>>> >>
>>>> >> It's the inverse problem to merging a list of data.frames into a large
>>>> >> data.frame just discussed in the "performance of do.call("rbind")"
>>>> >> thread
>>>> >>
>>>> >> I would like to split a data.frame into a list of data.frames
>>>&
Re: [R] [FORGED] Splitting data.frame into a list of small data.frames given indices
Hi William,
I tested plyrs dlply function, and it seems to have have an O(N*
log(R)) complexity (tested for R=N) so I do not know if N is the
number of rows or nr of categories.
For the data.frame example with 2e5 rows and 2e5 categories it is
approx. 10 times faster than split. Still, it is 10 seconds on an
i7-5930K 3.5GHz Intel.
It would be nice if the documentation would contain runtime
complexity information and the documentation of base package function
would point to function which should be used instead.
Thanks
On 29 June 2016 at 16:13, William Dunlap <wdun...@tibco.com> wrote:
> I won't go into why splitting data.frames (or factors) uses time
> proportional to the number of input rows times the number of
> levels in the splitting factor, but you will get much better mileage
> if you call split individually on each 'atomic' (numeric, character, ...)
> variable and use mapply on the resulting lists.
>
> The plyr and dplyr packages were developed to deal with this
> sort of problem. Check them out.
>
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
> On Wed, Jun 29, 2016 at 6:21 AM, Witold E Wolski <wewol...@gmail.com> wrote:
>>
>> Hi,
>>
>> Here is an complete example which shows the the complexity of split or
>> by is O(n^2)
>>
>> nrows <- c(1e3,5e3, 1e4 ,5e4, 1e5 ,2e5)
>> res<-list()
>>
>> for(i in nrows){
>> dum <- data.frame(x = runif(i,1,1000), y=runif(i,1,1000))
>> res[[length(res)+1]]<-(system.time(x<- split(dum, 1:nrow(dum
>> }
>> res <- do.call("rbind",res)
>> plot(nrows^2, res[,"elapsed"])
>>
>> And I can't see a reason why this has to be so slow.
>>
>>
>> cheers
>>
>>
>>
>>
>>
>>
>>
>> On 29 June 2016 at 12:00, Rolf Turner <r.tur...@auckland.ac.nz> wrote:
>> > On 29/06/16 21:16, Witold E Wolski wrote:
>> >>
>> >> It's the inverse problem to merging a list of data.frames into a large
>> >> data.frame just discussed in the "performance of do.call("rbind")"
>> >> thread
>> >>
>> >> I would like to split a data.frame into a list of data.frames
>> >> according to first column.
>> >> This SEEMS to be easily possible with the function base::by. However,
>> >> as soon as the data.frame has a few million rows this function CAN NOT
>> >> BE USED (except you have A PLENTY OF TIME).
>> >>
>> >> for 'by' runtime ~ nrow^2, or formally O(n^2) (see benchmark below).
>> >>
>> >> So basically I am looking for a similar function with better
>> >> complexity.
>> >>
>> >>
>> >> > nrows <- c(1e5,1e6,2e6,3e6,5e6)
>> >>>
>> >>> timing <- list()
>> >>> for(i in nrows){
>> >>
>> >> + dum <- peaks[1:i,]
>> >> + timing[[length(timing)+1]] <- system.time(x<- by(dum[,2:3],
>> >> INDICES=list(dum[,1]), FUN=function(x){x}, simplify = FALSE))
>> >> + }
>> >>>
>> >>> names(timing)<- nrows
>> >>> timing
>> >>
>> >> $`1e+05`
>> >>user system elapsed
>> >>0.050.000.05
>> >>
>> >> $`1e+06`
>> >>user system elapsed
>> >>1.482.984.46
>> >>
>> >> $`2e+06`
>> >>user system elapsed
>> >>7.25 11.39 18.65
>> >>
>> >> $`3e+06`
>> >>user system elapsed
>> >> 16.15 25.81 41.99
>> >>
>> >> $`5e+06`
>> >>user system elapsed
>> >> 43.22 74.72 118.09
>> >
>> >
>> > I'm not sure that I follow what you're doing, and your example is not
>> > reproducible, since we have no idea what "peaks" is, but on a toy
>> > example
>> > with 5e6 rows in the data frame I got a timing result of
>> >
>> >user system elapsed
>> > 0.379 0.025 0.406
>> >
>> > when I applied split(). Is this adequately fast? Seems to me that if
>> > you
>> > want to split something, split() would be a good place to start.
>> >
>> > cheers,
>> >
>> > Rolf Turner
>> >
>> > --
>> > Technical Editor ANZJS
>> > Department of Statistics
>> > University of Auckland
>> > Phone: +64-9-373-7599 ext. 88276
>>
>>
>>
>> --
>> Witold Eryk Wolski
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> 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.
>
>
--
Witold Eryk Wolski
__
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Re: [R] [FORGED] Splitting data.frame into a list of small data.frames given indices
Hi,
Here is an complete example which shows the the complexity of split or
by is O(n^2)
nrows <- c(1e3,5e3, 1e4 ,5e4, 1e5 ,2e5)
res<-list()
for(i in nrows){
dum <- data.frame(x = runif(i,1,1000), y=runif(i,1,1000))
res[[length(res)+1]]<-(system.time(x<- split(dum, 1:nrow(dum
}
res <- do.call("rbind",res)
plot(nrows^2, res[,"elapsed"])
And I can't see a reason why this has to be so slow.
cheers
On 29 June 2016 at 12:00, Rolf Turner <r.tur...@auckland.ac.nz> wrote:
> On 29/06/16 21:16, Witold E Wolski wrote:
>>
>> It's the inverse problem to merging a list of data.frames into a large
>> data.frame just discussed in the "performance of do.call("rbind")"
>> thread
>>
>> I would like to split a data.frame into a list of data.frames
>> according to first column.
>> This SEEMS to be easily possible with the function base::by. However,
>> as soon as the data.frame has a few million rows this function CAN NOT
>> BE USED (except you have A PLENTY OF TIME).
>>
>> for 'by' runtime ~ nrow^2, or formally O(n^2) (see benchmark below).
>>
>> So basically I am looking for a similar function with better complexity.
>>
>>
>> > nrows <- c(1e5,1e6,2e6,3e6,5e6)
>>>
>>> timing <- list()
>>> for(i in nrows){
>>
>> + dum <- peaks[1:i,]
>> + timing[[length(timing)+1]] <- system.time(x<- by(dum[,2:3],
>> INDICES=list(dum[,1]), FUN=function(x){x}, simplify = FALSE))
>> + }
>>>
>>> names(timing)<- nrows
>>> timing
>>
>> $`1e+05`
>>user system elapsed
>>0.050.000.05
>>
>> $`1e+06`
>>user system elapsed
>>1.482.984.46
>>
>> $`2e+06`
>>user system elapsed
>>7.25 11.39 18.65
>>
>> $`3e+06`
>>user system elapsed
>> 16.15 25.81 41.99
>>
>> $`5e+06`
>>user system elapsed
>> 43.22 74.72 118.09
>
>
> I'm not sure that I follow what you're doing, and your example is not
> reproducible, since we have no idea what "peaks" is, but on a toy example
> with 5e6 rows in the data frame I got a timing result of
>
>user system elapsed
> 0.379 0.025 0.406
>
> when I applied split(). Is this adequately fast? Seems to me that if you
> want to split something, split() would be a good place to start.
>
> cheers,
>
> Rolf Turner
>
> --
> Technical Editor ANZJS
> Department of Statistics
> University of Auckland
> Phone: +64-9-373-7599 ext. 88276
--
Witold Eryk Wolski
__
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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.
[R] Splitting data.frame into a list of small data.frames given indices
It's the inverse problem to merging a list of data.frames into a large
data.frame just discussed in the "performance of do.call("rbind")"
thread
I would like to split a data.frame into a list of data.frames
according to first column.
This SEEMS to be easily possible with the function base::by. However,
as soon as the data.frame has a few million rows this function CAN NOT
BE USED (except you have A PLENTY OF TIME).
for 'by' runtime ~ nrow^2, or formally O(n^2) (see benchmark below).
So basically I am looking for a similar function with better complexity.
> nrows <- c(1e5,1e6,2e6,3e6,5e6)
> timing <- list()
> for(i in nrows){
+ dum <- peaks[1:i,]
+ timing[[length(timing)+1]] <- system.time(x<- by(dum[,2:3],
INDICES=list(dum[,1]), FUN=function(x){x}, simplify = FALSE))
+ }
> names(timing)<- nrows
> timing
$`1e+05`
user system elapsed
0.050.000.05
$`1e+06`
user system elapsed
1.482.984.46
$`2e+06`
user system elapsed
7.25 11.39 18.65
$`3e+06`
user system elapsed
16.15 25.81 41.99
$`5e+06`
user system elapsed
43.22 74.72 118.09
--
Witold Eryk Wolski
__
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Re: [R] performance of do.call("rbind")
Hi Bert,
You are most likely right. I just thought that do.call("rbind", is
somehow more clever and allocates the memory up front. My error. After
more searching I did find rbind.fill from plyr which seems to do the
job (it computes the size of the result data.frame and allocates it
first).
best
On 27 June 2016 at 18:49, Bert Gunter <bgunter.4...@gmail.com> wrote:
> The following might be nonsense, as I have no understanding of R
> internals; but
>
> "Growing" structures in R by iteratively adding new pieces is often
> warned to be inefficient when the number of iterations is large, and
> your rbind() invocation might fall under this rubric. If so, you might
> try issuing the call say, 20 times, over 10k disjoint subsets of the
> list, and then rbinding up the 20 large frames.
>
> Again, caveat emptor.
>
> Cheers,
> Bert
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> On Mon, Jun 27, 2016 at 8:51 AM, Witold E Wolski <wewol...@gmail.com> wrote:
>> I have a list (variable name data.list) with approx 200k data.frames
>> with dim(data.frame) approx 100x3.
>>
>> a call
>>
>> data <-do.call("rbind", data.list)
>>
>> does not complete - run time is prohibitive (I killed the rsession
>> after 5 minutes).
>>
>> I would think that merging data.frame's is a common operation. Is
>> there a better function (more performant) that I could use?
>>
>> Thank you.
>> Witold
>>
>>
>>
>>
>> --
>> Witold Eryk Wolski
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> 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.
--
Witold Eryk Wolski
__
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and provide commented, minimal, self-contained, reproducible code.
[R] refclasses question - Defining accessor function
Are accessors a fancy feature that do not work?
I wanted to use accessor functions in a R refclass to hide the classes
implementation where I am using sqlite.
What I did observe is, that if I access in a method any of the fields
(in the example below field .data in method printExample) all the
accessor functions are called (even those not accessed by the function
: in this case funnydata is not accessed).
That means if any of the accessor functions is slow (in the example
the funnydata accessor sleeps for 3 s) all the fields and all
functions accessing any fields will be slow.
In the example below accessing .data or calling printExample will take 3s.
It's easy enough not to use accessor functions, so not a big deal.
Still, I lost quite a bit of time wondering what is happening.
Test <-setRefClass("Test",
fields = list( .data = "list",
funnydata = function(x){
Sys.sleep(3)
if(missing(x)){
Sys.sleep(3)
}
}
),
methods = list(
initialise=function(){ .data <<- list(a="a")},
printExample = function(){
print("print Example")
print(.data)}
)
)
test<-Test()
test$printExample()
test$.data
--
Witold Eryk Wolski
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[R] performance of do.call("rbind")
I have a list (variable name data.list) with approx 200k data.frames
with dim(data.frame) approx 100x3.
a call
data <-do.call("rbind", data.list)
does not complete - run time is prohibitive (I killed the rsession
after 5 minutes).
I would think that merging data.frame's is a common operation. Is
there a better function (more performant) that I could use?
Thank you.
Witold
--
Witold Eryk Wolski
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and provide commented, minimal, self-contained, reproducible code.
[R] numeric inputs to sweep produce NaN...
I have two inputs to sweep which are numeric (with a few NA's) but the output is NaN. How Why? > sum(!is.numeric(unlist(protquant))) [1] 0 > sum(!is.numeric(normalize)) [1] 0 > normprotquant <- sweep(protquant, 2, normalize, "-" ) > sum(is.nan(unlist(normprotquant))) [1] 31 version R 3.3.0 best regards Witold -- Witold Eryk Wolski __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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 manipulate ... in the argument list
Duncan suggested to use the argument explicitly and combine it with
the missing function which is for this problem also my preferred
solution:
image.2 <- function(x, col , breaks, ...){
# function is manipulating colors (adding a few)
# since it changes colors it needs to update breaks if defined.
if( !missing(breaks) ){
#manipulate breaks
image(x, col, breaks ,...)
}else{
image(x,col ,...)
}
}
It is good to know that I also could have used do.call.
I also learned yesterday that it is better to search for dot dot dot
argument or for elipsis instead of ...
best
On 11 May 2016 at 15:45, Vito M. R. Muggeo <vito.mug...@unipa.it> wrote:
> Hi Witold,
> use do.call()
>
> list.args<-list(...)
>
> #modify 'list.args' (add/delete/modify)
>
> do.call(image, list.args)
>
> best,
> vito
>
>
> Il 11/05/2016 10.45, Witold E Wolski ha scritto:
>>
>> Hi,
>>
>> I am looking for a documentation describing how to manipulate the
>> "..." . Searching R-intro.html gives to many not relevant hits for
>> "..."
>>
>> What I want to do is something like this :
>>
>>
>> image.2 <- function(x, col , ...){
>> # function is manipulating colors (adding a few)
>> # since it changes colors it needs to update breaks if defined.
>>
>>breaks <- list(...)$breaks
>>
>> if( !is.null( list(...)$breaks ) ){
>> #manipulate breaks
>>
>> image(x, col, breaks = breaks ,...)
>>
>>}else{
>> image(x,col ,...)
>>}
>> }
>>
>> but in order to get it working I will need to remove breaks from ...
>> since otherwise I am getting multiple defined argument for breaks.
>>
>> So how to manipulate the "..." argument? Or should I use a different
>> pattern
>>
>> best
>>
>>
>>
>
> --
> ==
> Vito M.R. Muggeo
> Dip.to Sc Statist e Matem `Vianelli'
> Università di Palermo
> viale delle Scienze, edificio 13
> 90128 Palermo - ITALY
> tel: 091 23895240
> fax: 091 485726
> http://dssm.unipa.it/vmuggeo
> Associate Editor, Statistical Modelling
> ===
--
Witold Eryk Wolski
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] how to manipulate ... in the argument list
Hi,
I am looking for a documentation describing how to manipulate the
"..." . Searching R-intro.html gives to many not relevant hits for
"..."
What I want to do is something like this :
image.2 <- function(x, col , ...){
# function is manipulating colors (adding a few)
# since it changes colors it needs to update breaks if defined.
breaks <- list(...)$breaks
if( !is.null( list(...)$breaks ) ){
#manipulate breaks
image(x, col, breaks = breaks ,...)
}else{
image(x,col ,...)
}
}
but in order to get it working I will need to remove breaks from ...
since otherwise I am getting multiple defined argument for breaks.
So how to manipulate the "..." argument? Or should I use a different pattern
best
--
Witold Eryk Wolski
__
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and provide commented, minimal, self-contained, reproducible code.
[R] packaging an R-application
Dear List, What I am seeking advice for is how to best package an R installation with all the packages required? Scenario: I need to deliver an R script which will have quite a bit of package dependencies, to packages which are not necessarily stable, are not on cran and might dissapear in the near future. It should be possible to execute the R-script without any changes during the next 3 years. What I did look into is packrat. But if I am correct it pulls the r-packages from cran so if a package was from somewhere else or isn't available anymore it will fail. what I have also found is R on an USB stick: http://personal.bgsu.edu/~mrizzo/Rmisc/usbR.htm Would this work? Or is there anything on the lines of pyinstaller (http://www.pyinstaller.org/) for R? Thank you -- Witold Eryk Wolski __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] conditionally disable evaluation of chunks in Rmarkdown...
I do have an Rmd where I would like to conditionally evaluate the second part.
So far I am working with :
```{r}
if(length(specLibrary@ionlibrary) ==0){
library(knitr)
opts_chunk$set(eval=FALSE, message=FALSE, echo=FALSE)
}
```
Which disables the evaluation of subsequent chunks.
However my RMD file contains also these kind of snippets : `r `
How do I disable them?
regards
--
Witold Eryk Wolski
__
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[R] r-markdown - keeping figures
I am running r-markdown from r-studio and can't work out how to keep the figures. I mean I have a few figures in the document and would like to have them as separate pdf's too as I have been used to have them when using Sweave. best regards Witold -- Witold Eryk Wolski __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] names in R list's
Hi Jeff,
Indeed there was something about plain-text in the r-help posting
guide although I can't find it there anymore.
https://www.r-project.org/posting-guide.html
Is it still an requirement?
Jeff, thanks for you constructive contribution ;) . Glad that you know
about plain text mode in e-mails, beside doing some perl programming.
I forgot about both. Even the linux admin's I know use python and
thunderbird or some webmail nowadays not pine and perl, but I do not
much networking, so what do I know.
I think the question I am asking is legitimate. The access complexity
of datastructures is specified in the documentation in case of python
datastructures, java collections or stl containers.
I guess this information is available for name access on R-list but I
just can't find it.
regards
On 7 September 2015 at 16:37, Jeff Newmiller <jdnew...@dcn.davis.ca.us> wrote:
> You puzzle me. Why does someone who cannot figure out how to post an email in
> plain text after so many messages on this mailing list get all worried about
> access time for string indexing?
>
> Environment objects have those properties. They do not solve all problems
> though, because they are rather heavyweight... you need a lot of lookups to
> pay for their overhead. R5 objects and the hash package both use them, but I
> have never found three need to use them. Yes, I do program in Perl so I know
> where you are coming from, but the vector-based name lookup used in R works
> quite effectively for data where the number of list items is short or where I
> plan to access every element as part of my data processing anyway.
> ---
> Jeff NewmillerThe . . Go Live...
> DCN:<jdnew...@dcn.davis.ca.us>Basics: ##.#. ##.#. Live Go...
> Live: OO#.. Dead: OO#.. Playing
> Research Engineer (Solar/BatteriesO.O#. #.O#. with
> /Software/Embedded Controllers) .OO#. .OO#. rocks...1k
> ---
> Sent from my phone. Please excuse my brevity.
>
> On September 7, 2015 3:34:53 AM PDT, Witold E Wolski <wewol...@gmail.com>
> wrote:
>>What is the access time for R lists given a name of list element, is it
>>linear, log, or constant?
>>
>>Than what are to rules for names in R-lists
>>
>>That reusing names is possible makes me wonder.
>>
>>tmp <- as.list(c(1,2,3,4))
>>names(tmp) = c("a","a","b","b")
>>tmp
>>tmp$a
>>
>>
>>What I am looking for is a standard R data structure which will allow
>>me
>>for fast and name lookup.
>
--
Witold Eryk Wolski
__
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and provide commented, minimal, self-contained, reproducible code.
[R] names in R list's
What is the access time for R lists given a name of list element, is it
linear, log, or constant?
Than what are to rules for names in R-lists
That reusing names is possible makes me wonder.
tmp <- as.list(c(1,2,3,4))
names(tmp) = c("a","a","b","b")
tmp
tmp$a
What I am looking for is a standard R data structure which will allow me
for fast and name lookup.
--
Witold Eryk Wolski
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] registerDoParallel and R CMD check --as-cran errors
To answer my own question. Dono if it's the right way to do... In the example code I am using a single CPU and it works. regards PS. Should I have asked this question on the devel list? On 2 September 2015 at 14:39, Witold E Wolski <wewol...@gmail.com> wrote: > I am testing a package with > > R CMD check > and > R CMD check --as-cran > > some code which is run in the examples section uses the foreach and > doParallel package. > > > When run with --as-cran I have an error. > registerDoParallel function causes an error. > > Error in .check_ncores(length(names)) : 6 simultaneous processes spawned > Calls: annotatePeptides ... registerDoParallel -> makeCluster -> > makePSOCKcluster -> .check_ncores > > > What should can I do to prevent this error and pas the --as-cran check? > > best regards > Witold > > > -- > Witold Eryk Wolski > > -- Witold Eryk Wolski [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] registerDoParallel and R CMD check --as-cran errors
I am testing a package with R CMD check and R CMD check --as-cran some code which is run in the examples section uses the foreach and doParallel package. When run with --as-cran I have an error. registerDoParallel function causes an error. Error in .check_ncores(length(names)) : 6 simultaneous processes spawned Calls: annotatePeptides ... registerDoParallel -> makeCluster -> makePSOCKcluster -> .check_ncores What should can I do to prevent this error and pas the --as-cran check? best regards Witold -- Witold Eryk Wolski [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] data - stringAsFactors = FALSE
I have a tab delimited table in the data directory of a package. I would like that when loading this data with data(tablename) in the example section the strings are not coerced to factors. How can I achieve it? Or should I move this tables to the inst/extdata directory and load them with read.table? regards -- Witold Eryk Wolski [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] compiling Rmd - can't find tex file....
to answer my own question. I did not find out what knit2pdf is good for but rmarkdown::render does the job. regards On 26 August 2015 at 11:46, Witold E Wolski wewol...@gmail.com wrote: I am using from within R-studio and the .Rmd file builds nicely. However, when I try to compile the fiel using : knit2pdf( specL.Rmd, output=file.path(res.12345,specL.pdf) ) I am getting tex errors (see below). When I wan't to check what's wrong I can't find the tex file. Any ideas? Thank you PS: Errors: |.. | 95% label: writepepProt |.| 100% ordinary text without R code *output file: res.12345/specL.pdf* *Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : * * Running 'texi2dvi' on 'specL.pdf' failed.* *LaTeX errors:* *! Missing $ inserted.* *inserted text * *$* *to be read again * * _* *! Missing $ inserted.* *inserted text * *$* *to be read again * * \par * *! You can't use `macro parameter character #' in horizontal mode.* *l.15 #* -- Witold Eryk Wolski -- Witold Eryk Wolski [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] compiling Rmd - can't find tex file....
I am using from within R-studio and the .Rmd file builds nicely. However, when I try to compile the fiel using : knit2pdf( specL.Rmd, output=file.path(res.12345,specL.pdf) ) I am getting tex errors (see below). When I wan't to check what's wrong I can't find the tex file. Any ideas? Thank you PS: Errors: |.. | 95% label: writepepProt |.| 100% ordinary text without R code *output file: res.12345/specL.pdf* *Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : * * Running 'texi2dvi' on 'specL.pdf' failed.* *LaTeX errors:* *! Missing $ inserted.* *inserted text * *$* *to be read again * * _* *! Missing $ inserted.* *inserted text * *$* *to be read again * * \par * *! You can't use `macro parameter character #' in horizontal mode.* *l.15 #* -- Witold Eryk Wolski [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Faster text search in document database than with grep?
I have a database of text documents (letter sequences). Several thousands of documents with approx. 1000-2000 letters each. I need to find exact matches of short 3-15 letters sequences in those documents. Without any regexp patterns the search of one 3-15 letter words takes in the order of 1s. So for a database with several thousand documents it's an the order of hours. The naive approach would be to use mcmapply, but than on a standard hardware I am still in the same order and since R is an interactive programming environment this isn't a solution I would go for. But aren't there faster algorithmic solutions? Can anyone point me please to an implementation available in R. Thank you Witold -- Witold Eryk Wolski [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Faster text search in document database than with grep?
Dear Duncan, This is a model of the data I work with. database - replicate(5, paste(sample(letters,rexp(1,1/500), rep=TRUE), collapse=)) words - replicate(1,paste(sample(letters,rexp(1,1/70), rep=TRUE), collapse=)) NumberOfWords - 10 system.time(lapply(words[1: NumberOfWords], grep, database)) user system elapsed 5.002 0.003 5.005 The model reproduces the running times I have to cope with. To use grep in this context is rather naive and I am wondering if there are better solutions availabe in R. On 3 August 2015 at 15:13, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 03/08/2015 5:25 AM, Witold E Wolski wrote: I have a database of text documents (letter sequences). Several thousands of documents with approx. 1000-2000 letters each. I need to find exact matches of short 3-15 letters sequences in those documents. Without any regexp patterns the search of one 3-15 letter words takes in the order of 1s. So for a database with several thousand documents it's an the order of hours. The naive approach would be to use mcmapply, but than on a standard hardware I am still in the same order and since R is an interactive programming environment this isn't a solution I would go for. But aren't there faster algorithmic solutions? Can anyone point me please to an implementation available in R. You haven't shown us what you did, but it sounds far slower than I'd expect. I just used the code below to set up a database of 1 documents of 2000 letters each, and searching those documents for abc takes about 70 milliseconds: database - replicate(1, paste(sample(letters, 2000, rep=TRUE), collapse=)) grep(abc, database, fixed=TRUE) Duncan Murdoch -- Witold Eryk Wolski [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] sort order of a character sequence is different on windose and linux (linux result)
From my reading of http://r.789695.n4.nabble.com/internal-string-comparison-Scollate-td4687584.html they have good arguments to ask for Scollate whatever it is in the R public API. And from my point of view R would benefit from a tight integration of data.table. Without data.table R is very impractical to use, with data which is avaiable today. On 6 July 2014 14:15, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 06/07/2014, 7:56 AM, Witold E Wolski wrote: This is the info I got from the data.table developers... Seems that they did have tried to find a more elegant solution solution.: From my reading of the response below, data.table doesn't use R's sort() function to do their sorting. You should use whatever sort function they use if you want to match their sort order. Duncan Murdoch data.table used to support this until 1.8.6. But since Scollate became not a part of authorised R-API (IIUC) anymore at some point, data.table only supports sort/order under the C-locale. data.table's ordering/sorting is over 10-20x faster than base's and the only way right now (IIUC) to sort by locale is to use base's sort/order. This post may give some more insight. http://r.789695.n4.nabble.com/internal-string-comparison-Scollate-td4687584.html In summary, we support only C-locale. On 6 July 2014 13:33, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 06/07/2014, 7:19 AM, Witold E Wolski wrote: It seems that the package I am developing depends on the locale C because of interactions with other packages (data.table). So I would like to set the locale to C as soon as the package is loaded. Where can I do it .. I could of course set it in every function in my package but... As the help page says, you can't do it reliably on all platforms, and you really shouldn't even try: that will affect other things that the user does. You will need to find another solution to your problem. Duncan Murdoch -- Witold Eryk Wolski __ 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] sort order of a character sequence is different on windose and linux (linux result)
This is the result of sorting a character sequence on a linux box (with R . 3.10) bla = read.table(xx.txt,stringsAsFactors=F) bla = bla[,1] bla[1:10] [1] 1000_DGFVALSK_2_run0 1000_DGFVALSK_2_run0 1000_DGFVALSK_2_run0 1000_DGFVALSK_2_run0 1000_DGFVALSK_2_run0 [6] 1000_DGFVALSK_2_run0 1001_DGGAWGTEQR_2_run0 1001_DGGAWGTEQR_2_run0 1001_DGGAWGTEQR_2_run0 1001_DGGAWGTEQR_2_run0 sort(bla)[1:10] [1] 1000_DGFVALSK_2_run0 1000_DGFVALSK_2_run0 1000_DGFVALSK_2_run0 1000_DGFVALSK_2_run0 1000_DGFVALSK_2_run0 [6] 1000_DGFVALSK_2_run0 1001_DGGAWGTEQR_2_run0 1001_DGGAWGTEQR_2_run0 1001_DGGAWGTEQR_2_run0 1001_DGGAWGTEQR_2_run0 I will send the result of sorting the content of xx.txt on windows from the windows box in a moment. the file xx.txt can be found at: https://github.com/wolski/imsbInfer/blob/master/xx.txt -- Witold Eryk Wolski __ 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] sort order of a character sequence is different on windose and linux (windows result)
And here is the result when sorting the same sequence on a windows box: bla = read.table(xx.txt,stringsAsFactors=F) bla = bla[,1] bla[1:10] [1] 1000_DGFVALSK_2_run0 1000_DGFVALSK_2_run0 1000_DGFVALSK_2_run0 1000_DGFVALSK_2_run0 [5] 1000_DGFVALSK_2_run0 1000_DGFVALSK_2_run0 1001_DGGAWGTEQR_2_run0 1001_DGGAWGTEQR_2_run0 [9] 1001_DGGAWGTEQR_2_run0 1001_DGGAWGTEQR_2_run0 sort(bla)[1:10] [1] 1_AAALQAK_2_run0 1_AAALQAK_2_run0 1_AAALQAK_2_run0 1_AAALQAK_2_run0 [5] 1_AAALQAK_2_run0 1_AAALQAK_2_run0 10_AAATAEEPDPK_2_run0 10_AAATAEEPDPK_2_run0 [9] 10_AAATAEEPDPK_2_run0 10_AAATAEEPDPK_2_run0 -- Witold Eryk Wolski __ 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] sort order of a character sequence is different on windose and linux (linux result)
It seems that the package I am developing depends on the locale C because of interactions with other packages (data.table). So I would like to set the locale to C as soon as the package is loaded. Where can I do it .. I could of course set it in every function in my package but... __ 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] sort order of a character sequence is different on windose and linux (linux result)
This is the info I got from the data.table developers... Seems that they did have tried to find a more elegant solution solution.: data.table used to support this until 1.8.6. But since Scollate became not a part of authorised R-API (IIUC) anymore at some point, data.table only supports sort/order under the C-locale. data.table's ordering/sorting is over 10-20x faster than base's and the only way right now (IIUC) to sort by locale is to use base's sort/order. This post may give some more insight. http://r.789695.n4.nabble.com/internal-string-comparison-Scollate-td4687584.html In summary, we support only C-locale. On 6 July 2014 13:33, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 06/07/2014, 7:19 AM, Witold E Wolski wrote: It seems that the package I am developing depends on the locale C because of interactions with other packages (data.table). So I would like to set the locale to C as soon as the package is loaded. Where can I do it .. I could of course set it in every function in my package but... As the help page says, you can't do it reliably on all platforms, and you really shouldn't even try: that will affect other things that the user does. You will need to find another solution to your problem. Duncan Murdoch -- Witold Eryk Wolski __ 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 does a valid subscript can produce an subscript out of bounds error?
Thank you. You example helped to FIX IT. The problem is I guess somehow related to: class(msexp$pepinfo$transition_group_id) [1] factor and the whole R type conversion , riddle. For subscripts my intuition is: either require integer or do the cast to the rowname type (character). However, it seems that R somehow prefers to cast factors to integers... it seems that %in% casts both vectors to the same type. But to which one? Oh, I guess all this is neatly explained in the R standard ... but websearching for it just returns: standard deviation a frustrated R user. On 5 July 2014 02:18, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 04/07/2014, 6:35 PM, Witold E Wolski wrote: how does a valid subscript (see first 2 lines) can produce an subscript out of bounds error (see line 4)? 1 sum(!rownames(msexp$rt) %in% msexp$pepinfo$transition_group_id) [1] 0 2 sum(!msexp$pepinfo$transition_group_id %in% rownames(msexp$rt)) [1] 0 3 class(msexp$rt) [1] matrix 4 msexp$rt = as.matrix(msexp$rt[msexp$pepinfo$transition_group_id,]) Error in msexp$rt[msexp$pepinfo$transition_group_id, ] : subscript out of bounds x - matrix(1,1,1) rownames(x) - colnames(x) - 23 23 %in% rownames(x) [1] TRUE x[23,] Error in x[23, ] : subscript out of bounds -- Witold Eryk Wolski __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] data.table merge question...
Actually the question is regarding differences in behaviour on windows in linux. The 2 lines of code produce on linux all TRUE on windows this looks heterogenous... Using merge.data.frame produces on all platforms TRUE ... msexp$pepinfo = data.frame(merge(tt,msexp$pepinfo,by=transition_group_id),stringsAsFactors=FALSE) tt$transition_group_id == msexp$pepinfo$transition_group_id [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE [23] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE [45] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [67] FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [89] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [111] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE ... -- Witold Eryk Wolski __ 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] how does a valid subscript can produce an subscript out of bounds error?
how does a valid subscript (see first 2 lines) can produce an subscript out of bounds error (see line 4)? 1 sum(!rownames(msexp$rt) %in% msexp$pepinfo$transition_group_id) [1] 0 2 sum(!msexp$pepinfo$transition_group_id %in% rownames(msexp$rt)) [1] 0 3 class(msexp$rt) [1] matrix 4 msexp$rt = as.matrix(msexp$rt[msexp$pepinfo$transition_group_id,]) Error in msexp$rt[msexp$pepinfo$transition_group_id, ] : subscript out of bounds -- Witold Eryk Wolski __ 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] How to document an S3 class?
Hi, How do I document an S3 class with roxygen2? I create the class at the end of the method with: class(res) - myclass but how do I create an documentation entry for this class, where I can describe the fields of the class (in case of myclass these are just list entries)? regards -- Witold Eryk Wolski __ 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] correlation given p value and sample size
Hi, Looking for and function which produces the minimum r (pearson correlation) so that H0 (r=0) can be rejected, given sample size and p-value? Witold -- Witold Eryk Wolski __ 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] Rscript and roxygen error
I do want to run a R script (runrox.sh) containing two commands: library(roxygen2) roxygenize(imsbInfer) When pasting these 2 lines into R they run with no error. But when calling: Rscript runrox.sh the script produces this error: roxygen fails with Error: Failure in roxygen block beginning analyzeDuplicatedPeptides.R:1 could not find function is Execution halted -- Witold Eryk Wolski __ 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] Rscript and roxygen error
the same script which is not working with Rscript does work with R CMD BATCH. I thought the main difference between Rscript and R CMD BATCH is where the ouptut gets redirected and that Rscript should preferred over the old R CMD BATCH. On 26 May 2014 15:12, Witold E Wolski wewol...@gmail.com wrote: I do want to run a R script (runrox.sh) containing two commands: library(roxygen2) roxygenize(imsbInfer) When pasting these 2 lines into R they run with no error. But when calling: Rscript runrox.sh the script produces this error: roxygen fails with Error: Failure in roxygen block beginning analyzeDuplicatedPeptides.R:1 could not find function is Execution halted -- Witold Eryk Wolski -- Witold Eryk Wolski __ 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] How to build and check an package on a system without tex latex?
This is what I tried: R CMD check $(PKGNAME)_$(PKGVERS).tar.gz --no-manual --no-rebuild-vignettes R CMD build --no-manual --no-rebuild-vignettes $(PKGSRC) But still somehow the R CMD build attempts to build the vignettes (OK with me), but also run texi2dvi on them producing the error message below: Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'AExample2.tex' failed. Messages: sh: 1: /usr/bin/texi2dvi: not found Calls: Anonymous - texi2pdf - texi2dvi Execution halted make: *** [build] Error 1 -- Witold Eryk Wolski __ 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] Documenting docType data
Hi, I am Trying to document data using roxygen2 by following the stackoverflow question: http://stackoverflow.com/questions/9561684/documenting-dataset-with-roxygen2 And although my data resigin in mypackage/data has extension .rda and .csv I am getting the same error as in the stackoverlfow issue: ** testing if installed package can be loaded Error in namespaceExport(ns, exports) : undefined exports: feature_alignment_requant Error: loading failed Execution halted ERROR: loading failed best regards Witold -- Witold Eryk Wolski __ 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] Documenting docType data
Thanks a lot. I still had an @export. On 20 May 2014 14:34, Hadley Wickham h.wick...@gmail.com wrote: Don't export the dataset? (as mentioned in the answer to that question). If that doesn't help, please supply a minimal reproducible example. Hadley On Tue, May 20, 2014 at 3:35 AM, Witold E Wolski wewol...@gmail.com wrote: Hi, I am Trying to document data using roxygen2 by following the stackoverflow question: http://stackoverflow.com/questions/9561684/documenting-dataset-with-roxygen2 And although my data resigin in mypackage/data has extension .rda and .csv I am getting the same error as in the stackoverlfow issue: ** testing if installed package can be loaded Error in namespaceExport(ns, exports) : undefined exports: feature_alignment_requant Error: loading failed Execution halted ERROR: loading failed best regards Witold -- Witold Eryk Wolski __ 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. -- http://had.co.nz/ -- Witold Eryk Wolski __ 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] dist like function but where you can configure the method
Dear Jari,
Thanks for your reply...
The overhead would be
2 for loops
for(i in 1:dim(x)[2])
for(j in i:dim(x)[2])
isn't it? Or are you seeing a different way to implement it?
A for loop is pretty expensive in R. Therefore I am looking for an
implementation similar to apply or lapply were the iteration is made
in native code.
On 16 May 2014 15:57, Jari Oksanen jari.oksa...@oulu.fi wrote:
Witold E Wolski wewolski at gmail.com writes:
Looking for an fast dist implementation
where I could pass my own dist function to the method parameter
i.e.
mydistfun = function(x,y){
return(ks.test(x,y)$p.value) #some mystique implementation
}
wow = dist(data,method=mydistfun)
I think it is best to write that function yourself.
The dist object is a vector corresponding to a lower triangle
(without the diagonal) of a symmetric matrix and with attributes.
The attributes are class which should be c(mydist, dist), Size
which is the length(x), Labels (optional) which are the
names of your items and if given, should have length(x),
call = match.call(), Diag = FALSE, Upper = FALSE and method name.
All you need is a vector with attributes.
All this will add very little overhead to your calculation, so
for all practical purposes this implementation is just as fast as
is your mystique implementation of pairwise distances. Your
example (ks.test()) probably would be pretty slow. If you can
vectorize your distance, it can be really fast, even if you
calculate the full symmetric matrix and throw away the diagonal and
upper triangle.
Cheers, Jari Oksanen
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and provide commented, minimal, self-contained, reproducible code.
--
Witold Eryk Wolski
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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] dist like function but where you can configure the method
Ouch,
First : my question was not how to implement dist but if there is a
more generic dist function than stats:dist.
Secondly: ks.test is ment as a placeholder (see the comment in the
code I did send) for any other function taking two vector arguments.
Third: I do subscribe to the idea that a function call is easier to
read and understand than a for loop. @Bert apply is a native C
function and the loop is not interpreted AFAIK
@Rui @Barry @Jari What do you benchmark? an empty loop?
Look at the trivial benchmarks below: _apply_ clearly outperforms a
for loop in R , It always has, it outperforms even an empty for
# an empty unrealistic for loop as suggested by Rui , Barry and Jari
f1 - function(n){
for(i in 1:n){
for(j in 1:n){
}
}}
myfunc = function(x,y=x){x-y}
# a for loop which does actually something
f2 - function(n){
mm - matrix(0,ncol=n,nrow=n)
for(i in 1:n){
for(j in 1:n){
mm[i,j] = myfunc(i,j)
}
}
return(mm)
}
# and array
f3 = function(n){
res = rep(0,n*n)
for(i in 1:(n*n))
{
res[i] = myfunc(i)
}
}
n = 1000
system.time(f1(n))
system.time(f2(n))
system.time(f3(n))
system.time(apply(t(1:(n*n)),1,myfunc))
system.time(f1(n))
User System verstrichen
0.280.000.28
system.time(f2(n))
User System verstrichen
6.800.007.09
system.time(f3(n))
User System verstrichen
5.830.005.98
system.time(apply(t(1:(n*n)),1,myfunc))
User System verstrichen
0.190.000.19
On 16 May 2014 20:55, Rui Barradas ruipbarra...@sapo.pt wrote:
Hello,
The compiler package is good at speeding up for loops but in this case the
gain is neglectable. The ks test is the real time problem.
library(compiler)
f1 - function(n){
for(i in 1:100){
for(i in 1:100){
ks.test(runif(100),runif(100))
}
}
}
f1.c - cmpfun(f1)
system.time(f1())
user system elapsed
3.500.003.53
system.time(f1.c())
user system elapsed
3.470.003.48
Rui Barradas
Em 16-05-2014 17:12, Barry Rowlingson escreveu:
On Fri, May 16, 2014 at 4:46 PM, Witold E Wolski wewol...@gmail.com
wrote:
Dear Jari,
Thanks for your reply...
The overhead would be
2 for loops
for(i in 1:dim(x)[2])
for(j in i:dim(x)[2])
isn't it? Or are you seeing a different way to implement it?
A for loop is pretty expensive in R. Therefore I am looking for an
implementation similar to apply or lapply were the iteration is made
in native code.
No, a for loop is not pretty expensive in R -- at least not compared
to doing a k-s test:
system.time(for(i in 1:1){ks.test(runif(100),runif(100))})
user system elapsed
3.680 0.012 3.697
3.68 seconds to do 1 ks tests (and generate 200 runifs)
system.time(for(i in 1:1){})
user system elapsed
0.000 0.000 0.001
0.000s time to do 1 loops. Oh lets nest it for fun:
system.time(for(i in 1:100){for(i in
1:100){ks.test(runif(100),runif(100))}})
user system elapsed
3.692 0.004 3.701
no different. Even a ks-test with only 5 items is taking me 2.2 seconds.
Moral: don't worry about the for loops.
Barry
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and provide commented, minimal, self-contained, reproducible code.
--
Witold Eryk Wolski
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[R] dist like function but where you can configure the method
Looking for an fast dist implementation
where I could pass my own dist function to the method parameter
i.e.
mydistfun = function(x,y){
return(ks.test(x,y)$p.value) #some mystique implementation
}
wow = dist(data,method=mydistfun)
thanks
--
Witold Eryk Wolski
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and provide commented, minimal, self-contained, reproducible code.
[R] S3 - how to implement colnames-
Have a class for which I would like to provide a colnames-.myclass function so that colnames(myintsance) - c(a,b,c) can be called. Witold -- Witold Eryk Wolski [[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] S3 - how to implement colnames-
Hi
So how would I actually implement it - what is the signature?
dimnames-.myclass - function(data,newnames){
colnames(data) = newnames
return(data)
}
?
On 14 May 2014 11:53, Martin Maechler maech...@stat.math.ethz.ch wrote:
DO *NOT* post to both R-help and R-devel !!
That is considered *very* impolite.
As this is a question for R-help only, i.e., not fit for
R-devel anyway :
Witold E Wolski wewol...@gmail.com
on Wed, 14 May 2014 10:57:09 +0200 writes:
Have a class for which I would like to provide a colnames-.myclass
function so that
colnames(myintsance) - c(a,b,c)
can be called.
This is not easily possible, as `colnames-` is *not* a generic
function. OTOH, this is not necessary either, as
colnames, rownames are basically just short cuts for dimnames anyway:
As `dimnames-` *is* a generic function,
so you write methods for `dimnames-`.
Martin
--
Witold Eryk Wolski
[[alternative HTML version deleted]]
^^
Hmm,...
--
Witold Eryk Wolski
[[alternative HTML version deleted]]
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[R] roxygen2 question
How to document S3Methods with roxygen so that I have only 1 entry in
the package documentation page per S3Method.
In the package documentation page they show up than as follows
read2msExperiment read 2 feature alginer long format and generate an
msexperiment
read2msExperiment.data.frame convert data.frame 2 msexperiment
read2msExperiment.default read 2 feature alginer long format and
generate an msexperiment
I did alias read2msExperiment in the documentation of
read2msExperiment.default but this only helps that read2msExperiment
points to the documentation of read2msExperiment.default.
What I would like to have is one entry in the package documentation
page for all s3Methods:
This is my roxygen code at the moment.
#' @export
read2msExperiment=function(obj,...){
UseMethod('read2msExperiment')
}
#' read 2 feature alginer long format and generate an msexperiment
#' @aliases read2msExperiment
#' @param filename filename to read (can't be compressed)
#' @return msexperiment
#' @export
read2msExperiment.default=function(filename){
print(read2msExperiment.default)
aligtable=fread(filename)
data = convertLF2Wideformat(aligtable)
data = convert2msExperiment(data)
return(data)
}
--
Witold Eryk Wolski
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and provide commented, minimal, self-contained, reproducible code.
[R] installing r on ubuntu ?
Hi, trying to install newest R on ubuntu I follow the instructions at: http://cran.at.r-project.org/bin/linux/ubuntu/ I added: deb http://cran.r-mirror.de/bin/linux/ubuntu saucy/ to: /etc/apt/sources.list running : sudo apt-get update produces : W: GPG error: http://cran.r-mirror.de saucy/ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 51716619E084DAB9 ?? regards Witold -- Witold Eryk Wolski __ 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] how to check capabilities of an graphics device?
Before plotting to an device, I would like check which capabilities/properties it has to avoid warnings such as: In plot.xy(xy, type, ...) : semi-transparency is not supported on this device: reported only once per page -- Witold Eryk Wolski __ 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] Can't write to an device after catching a warning.
I have some code to handle warnings thrown because a device does not
support some features:
bla = tryCatch(
plot(d$ratio,-log10(d$pvals),col=#0033,pch=19,xlab=xlab,
ylab=ylab),
warning=function(bla){dev.off(); return(1)}
)
if(!is.null(bla)){
plot(d$ratio,-log10(d$pvals),col=1,pch=19,xlab=xlab, ylab=ylab)
}
Problem with the code above is that I need to call dev.off() in the
function handling warnings
function(bla){dev.off(); return(1)}
The dev.off() in the tryCatch closes the device and alle commands send
to the device (i.e. par(mforw=c(2,2)) are lost.
However, if I don't call dev.off(), all what I write to the device
next (i.e. in the subsequent if statment) is'nt plotted. The device
appears to be blocked.
regard
--
Witold Eryk Wolski
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and provide commented, minimal, self-contained, reproducible code.
[R] data.table - How do I transform a set of column?
I started to use the data.table to subset, reshape large data. But how do I transform a set of columns? # for a data.frame I would do: df = data.frame(a = c(a,b,c,d), b = 1:4,c = 1:4) df[,2:3] = df[,2:3]^2 # but with data.table this somehow similar code produces an error. dt = data.table(a = c(a,b,c,d), b = 1:4,c = 1:4) dt[, 2:3 , with=FALSE ] = x[,2:3,with=FALSE]^2 By the way. I need the columns selection 2:3 because column 1 in data.table contains the keys. With data.frame, matrix I would store the keys as rownames. and just write: df = df^2 (easier to read) Is there syntactic sugar in data.table to be able to say something like: transform all nonkey columns, replace all nonkey columns? best regards Witold -- Witold Eryk Wolski __ 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] data.table and R package check
Hi, using data.table in package code i.e setkey(aligtable,transition_group_id,align_origfilename) aligtable = aligtable[CJ(unique(transition_group_id), unique(align_origfilename))] When I do run R package check I got warnings such as: convert2msExperiment: no visible binding for global variable 'transition_group_id' and more and more and MORE I can't suppress those warnings by putting transition_group_id into quotes because this would break this code: aligtable = aligtable[CJ(unique(transition_group_id), unique(align_origfilename))] Any alternatives? regards -- Witold Eryk Wolski __ 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] stats::runmed - crashes R - session
R version 3.0.1 (2013-05-16) -- Good Sport Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) length(log2ro) [1] 16152 summary(log2ro) Min. 1st Qu. MedianMean 3rd Qu.Max.NA's -10 0 0 Inf 0 Inf 10461 tmpInt = runmed( log2ro,k=501) No output shown since segfault. Does anyone from R Core would like to look into it? I can provide the dataset. regards -- Witold Eryk Wolski __ 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] match - returns a vector of the positions of (first) matches - looking for All positions.
Looking for a build in function which returns a vector of the positions of _ALL_ matches. -- Witold Eryk Wolski __ 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] match - returns a vector of the positions of (first) matches - looking for All positions.
Hi Petr, I was actually citing the match (%in%) docu - match returns the positions of (first) matches. I am looking for something returning ALL matches (sure it's easy to write a function which does it ... my intuition however is, that there is already such a function in R - is there something which isn't already implemented in R? Not that I know of. ) regarding : which(table == match) in case table is a vector the output produced is going to be: Warning message: In table == match : longer object length is not a multiple of shorter object length regards On 3 February 2014 11:36, PIKAL Petr petr.pi...@precheza.cz wrote: Hi which(table == match) or which(table %in% match) Petr -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Witold E Wolski Sent: Monday, February 03, 2014 11:19 AM To: r-help@r-project.org Subject: [R] match - returns a vector of the positions of (first) matches - looking for All positions. Looking for a build in function which returns a vector of the positions of _ALL_ matches. -- Witold Eryk Wolski __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny pouze jeho adresátům. Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze svého systému. Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat. Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či zpožděním přenosu e-mailu. V případě, že je tento e-mail součástí obchodního jednání: - vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, a to z jakéhokoliv důvodu i bez uvedení důvodu. - a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany příjemce s dodatkem či odchylkou. - trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným dosažením shody na všech jejích náležitostech. - odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu případně osobě, kterou adresát zastupuje, předloženy nebo jejich existence je adresátovi či osobě jím zastoupené známá. This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients. If you received this e-mail by mistake, please immediately inform its sender. Delete the contents of this e-mail with all attachments and its copies from your system. If you are not the intended recipient of this e-mail, you are not authorized to use, disseminate, copy or disclose this e-mail in any manner. The sender of this e-mail shall not be liable for any possible damage caused by modifications of the e-mail or by delay with transfer of the email. In case that this e-mail forms part of business dealings: - the sender reserves the right to end negotiations about entering into a contract in any time, for any reason, and without stating any reasoning. - if the e-mail contains an offer, the recipient is entitled to immediately accept such offer; The sender of this e-mail (offer) excludes any acceptance of the offer on the part of the recipient containing any amendment or variation. - the sender insists on that the respective contract is concluded only upon an express mutual agreement on all its aspects. - the sender of this e-mail informs that he/she is not authorized to enter into any contracts on behalf of the company except for cases in which he/she is expressly authorized to do so in writing, and such authorization or power of attorney is submitted to the recipient or the person represented by the recipient, or the existence of such authorization is known to the recipient of the person represented by the recipient. -- Witold Eryk Wolski __ 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] match - returns a vector of the positions of (first) matches - looking for All positions.
Thank you. That's what I was looking for.
I am wondering what does the documentation means by (first) than?
match {base}
match returns a vector of the positions of (first) matches of its
first argument in its second.
On 3 February 2014 15:02, PIKAL Petr petr.pi...@precheza.cz wrote:
Hi
Posting questions without context may result in answers unrelated to your
problem.
Anyway it works for me without problem
table-sample(letters[1:5], 20, replace=T)
which(table %in% a)
[1] 1 2 19
version
_
platform i386-w64-mingw32
arch i386
os mingw32
system i386, mingw32
status Under development (unstable)
major 3
minor 1.0
year 2013
month 12
day19
svn rev64488
language R
version.string R Under development (unstable) (2013-12-19 r64488)
nickname Unsuffered Consequences
Regards
Petr
-Original Message-
From: Witold E Wolski [mailto:wewol...@gmail.com]
Sent: Monday, February 03, 2014 1:07 PM
To: PIKAL Petr
Cc: r-help@r-project.org
Subject: Re: [R] match - returns a vector of the positions of (first)
matches - looking for All positions.
Hi Petr,
I was actually citing the match (%in%) docu - match returns the
positions of (first) matches.
I am looking for something returning ALL matches (sure it's easy to
write a function which does it ...
my intuition however is, that there is already such a function in R -
is there something which isn't already implemented in R? Not that I
know of. )
regarding :
which(table == match)
in case table is a vector the output produced is going to be:
Warning message:
In table == match :
longer object length is not a multiple of shorter object length
regards
On 3 February 2014 11:36, PIKAL Petr petr.pi...@precheza.cz wrote:
Hi
which(table == match)
or
which(table %in% match)
Petr
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of Witold E Wolski
Sent: Monday, February 03, 2014 11:19 AM
To: r-help@r-project.org
Subject: [R] match - returns a vector of the positions of (first)
matches - looking for All positions.
Looking for a build in function which returns a vector of the
positions of _ALL_ matches.
--
Witold Eryk Wolski
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-
guide.html and provide commented, minimal, self-contained,
reproducible code.
Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a
jsou určeny pouze jeho adresátům.
Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě
neprodleně jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho
kopie vymažte ze svého systému.
Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento
email jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat.
Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou
modifikacemi či zpožděním přenosu e-mailu.
V případě, že je tento e-mail součástí obchodního jednání:
- vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření
smlouvy, a to z jakéhokoliv důvodu i bez uvedení důvodu.
- a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně
přijmout; Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky
ze strany příjemce s dodatkem či odchylkou.
- trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve
výslovným dosažením shody na všech jejích náležitostech.
- odesílatel tohoto emailu informuje, že není oprávněn uzavírat za
společnost žádné smlouvy s výjimkou případů, kdy k tomu byl písemně
zmocněn nebo písemně pověřen a takové pověření nebo plná moc byly
adresátovi tohoto emailu případně osobě, kterou adresát zastupuje,
předloženy nebo jejich existence je adresátovi či osobě jím zastoupené
známá.
This e-mail and any documents attached to it may be confidential and
are intended only for its intended recipients.
If you received this e-mail by mistake, please immediately inform its
sender. Delete the contents of this e-mail with all attachments and its
copies from your system.
If you are not the intended recipient of this e-mail, you are not
authorized to use, disseminate, copy or disclose this e-mail in any
manner.
The sender of this e-mail shall not be liable for any possible damage
caused by modifications of the e-mail or by delay with transfer of the
email.
In case that this e-mail forms part of business dealings:
- the sender reserves the right to end negotiations about entering
into a contract in any time, for any reason, and without stating any
reasoning.
- if the e-mail contains an offer, the recipient is entitled to
immediately accept such offer; The sender
[R] image plot with color scale
I am plotting an image of correlations but need to add a color scale... dat-matrix(rnorm(1000),ncol=5) labels=c(a,b,c,d,e) cortmp - cor(dat) image(cortmp , axes = F ) axis( 1, at=seq(0,1,length=length(labels)) , labels=labels , cex.axis=0.8 ,srt = 45,las=2,cex=1) axis( 2, at=seq(0,1,length=length(labels)) , labels=labels , cex.axis=0.8 ,srt = -45,las=1,cex=1) tried image.plot from package fields but : image.plot(cortmp , axes = F ) axis( 1, at=seq(0,1,length=length(labels)) , labels=labels , cex.axis=0.8 ,srt = 45,las=2,cex=1) axis( 2, at=seq(0,1,length=length(labels)) , labels=labels , cex.axis=0.8 ,srt = -45,las=1,cex=1) but adding the axis fails... (the axis appears but the labls are not shown. Can anyone can suggest an easy to use image function in R? best Witold -- Witold Eryk Wolski __ 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] writing blobs with RDBI
How to write a blob with RDBI? assuming I have x - 1:10 * 0.1 How do I store it in a sql table as an blob? regards -- Witold Eryk Wolski __ 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] pairs plot
my data are matrix with 3 numeric columns. would like to have pairs plot with scatterplots in the upper with hist at the diag and with correlation at the lower. actually default pairs does almost what I want but looks semi awesome. Especially, i didn't find out how to remove the axes from the lower part where I do only want to display the numeric values correlations there and somehow axes don't fit. Hence I am looking at ggpairs from GGally and calling it without parameters looks almost perfect : but I cant find out how they got the Corr: in the upper, so I can't put it in the lower, and I do not know how to put the hist in the diag. please help -- Witold Eryk Wolski __ 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] how to pairs plot without axes
In the pairs help is an example how to plot the correlation as txt.
How do I get rid of the axes
in the upper panel?
regards
## put (absolute) correlations on the upper panels,
## with size proportional to the correlations.
panel.cor - function(x, y, digits = 3, prefix = , cex.cor,axis=F, ...)
{
tt-cbind(x,y)
idx-apply(tt,1,function(x){sum(is.na(x))==0})
x-x[idx]
y-y[idx]
usr - par(usr); on.exit(par(usr))
par(usr = c(0, 1, 0, 1))
r - abs(cor(x, y))
print(r)
txt - format(c(r, 0.123456789), digits = digits)[1]
txt - paste0(prefix, txt)
if(missing(cex.cor)) cex.cor - 0.8/strwidth(txt)
text(0.5, 0.5, txt, cex = r^20*cex.cor)
}
--
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and provide commented, minimal, self-contained, reproducible code.
[R] igraph vertex.label.font sans serif
Would like to plot vertex labels without serif. there is vertex.label.font param but he lets me choose only between one font type in normal bold and emph. any suggestions welcome. -- Witold Eryk Wolski __ 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] igraph vertex.label.font sans serif
recall. it's: vertex.label.family sorry On 20 August 2013 17:30, Witold E Wolski wewol...@gmail.com wrote: Would like to plot vertex labels without serif. there is vertex.label.font param but he lets me choose only between one font type in normal bold and emph. any suggestions welcome. -- Witold Eryk Wolski -- Witold Eryk Wolski __ 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] parcor package example for adalasso.net fails.
Hi, I am a bit surprised that an example code from an R-package installed from CRAN can fail: n-20 p-10 X-matrix(rnorm(n*p),ncol=p) pc-adalasso.net(X,k=5) Performing local (adaptive) lasso regressions Vertex no Error in glmnet(XXtrain, ytrain, type.gaussian = type, standardize = FALSE) : x should be a matrix with 2 or more columns regards -- Witold Eryk Wolski __ 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] storing multidimensional arrays - save and load -
I am have a procedure which generates multidimensional arrays. To compute them is expensive so I want to store them in order to be able to analyse them later. I am using at the moment problem is that the array is always assigned to a variable ma (the computation is in a loop). Than I generate a file name and store it (i.e) save(ma, file=ma1.txt) save(ma, file=ma2.txt) ... problem starts when I want to load it load(ma1.RData) # loads in ma load(ma2.RData) # overrides ma How can i prevent this behaviour. Is there a better way to store multidimensional arrays? regards -- Witold Eryk Wolski __ 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] breaks argument in heatmap.2 doesn't do what it should I think
I do set the breaks parameter in heatmap.2 I would expect that the color.key and the histogram (the thing in the top left of the plot) are aligned. Just that everyone can reproduce the problem: mypalette-brewer.pal(11,RdYlBu) ddd - rnorm(400,0,0.1) mdd - matrix(ddd,ncol=50) hm - heatmap.2(mdd,col=mypalette,scale=row) #this is used to produce the breaks, (and here it works fine) mdd - t(scale(t(mdd))) heatmap.2(mdd,col=mypalette,scale=none,breaks=hm$breaks) # take a look and you will see that the colors are not aligned with the breaks although the documentation states breaks: (optional) Either a numeric vector indicating the splitting points for binning ‘x’ into colors, or a integer number of break points to be used, in which case the break points will be spaced equally between ‘min(x)’ and ‘max(x)’. -- Witold Eryk Wolski __ 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.start
Does anyone also observes with R 3.1 (on linux) that the help.start function frequently blocks the R session (never returns) ? Can I do anything or just waith for R3.1.1? -- Witold Eryk Wolski __ 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] help.start
Dear Martin I mean R version 3.0.1 (2013-05-16) -- Good Sport On 6 August 2013 16:55, Martin Maechler maech...@stat.math.ethz.ch wrote: Witold E Wolski wewol...@gmail.com on Tue, 6 Aug 2013 16:40:42 +0200 writes: Does anyone also observes with R 3.1 (on linux) that the help.start there's no R 3.1 . What do you mean really? R 3.0.1 ? or do you mean the current R under development which (quite rarely) also shows as 3.1.0 and will be changed quite a bit before eventually be released as 3.1.0 in 2014 ?? Witold, reallly, you should know better, I think function frequently blocks the R session (never returns) ? Can I do anything or just waith for R3.1.1? -- Witold Eryk Wolski -- Witold Eryk Wolski __ 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] When scale is applied in heatmap
When clustering I would do something like plot(hclust(dist(scale(X In case of heatmap and heatmap.2 it seems to me that for the dendrograms plot(hclust(dist(X))) is done while for the heatmap image(scale(X)) is done. I would say this is a bug however, because this is consistent among the heatmap functions, can anyone enlighten me why this is so? -- Witold Eryk Wolski __ 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] heatmap scale parameter question
I do not want to use the b word, but can anyone who also subscribes to the r-developer list forward my observation regarding heatmap? I am pretty confident that the behaviour of heatmap in R 3.0.1 is not that one intended. On 31 July 2013 14:03, Witold E Wolski wewol...@gmail.com wrote: Would anyone of the more experienced r-users explain to me the behaviour of the scale parameter in the heatmap function. different options for scale (R 3.0.1) do change only the colors but do not affect the dendrograms. Please see for yourself executing the following code: d - matrix(rnorm(100),nrow=20) stats::heatmap(d) X11() heatmap(d,scale=column) X11() heatmap(d,scale=row) X11() heatmap(d,scale=none) In all four above cases the dendrograms look exactly the same However, scaling clearly affects clustering. see: d - scale(d) heatmap(d,scale=none) best regards R version 3.0.1 (2013-05-16) -- Good Sport ciao -- Witold Eryk Wolski -- Witold Eryk Wolski -- Witold Eryk Wolski __ 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] heatmap scale parameter question
Would anyone of the more experienced r-users explain to me the behaviour of the scale parameter in the heatmap function. different options for scale (R 3.0.1) do change only the colors but do not affect the dendrograms. Please see for yourself executing the following code: d - matrix(rnorm(100),nrow=20) stats::heatmap(d) X11() heatmap(d,scale=column) X11() heatmap(d,scale=row) X11() heatmap(d,scale=none) In all four above cases the dendrograms look exactly the same However, scaling clearly affects clustering. see: d - scale(d) heatmap(d,scale=none) best regards R version 3.0.1 (2013-05-16) -- Good Sport ciao -- Witold Eryk Wolski -- Witold Eryk Wolski __ 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] heatmap scale parameter
does change only the colors but dendrograms are unaffected. d - matrix(rnorm(100),nrow=20) heatmap(d) heatmap(d,scale=column) heatmap(d,scale=row) heatmap(d,scale=none) However scaling clearly affects clustering. see: d - scale(d) heatmap(d,scale=none) R version 3.0.1 (2013-05-16) -- Good Sport Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) ciao -- Witold Eryk Wolski __ 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] function 2 convert matrix to long-format?
I would like to convert this (output of tapply) , , minus B6 S9 T0 0.1416 0.12235 T1 0.1049 0.11890 T2 0.1328 0.15510 , , plus B6 S9 T0 0.14225 0.16875 T1 0.09295 0.09900 T2 0.13350 0.14560 to long-format : T0 B6 minus 0.1416 T0 S9 minus 0.12235 T0 B6 plus 0.14225 T0 S9 plus 0.16875 ... whats the default way in R? best -- Witold Eryk Wolski __ 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] function 2 convert matrix to long-format?
RECALL : found the answer: use aggregate instead of tapply thx On 24 July 2013 12:00, Witold E Wolski wewol...@gmail.com wrote: I would like to convert this (output of tapply) , , minus B6 S9 T0 0.1416 0.12235 T1 0.1049 0.11890 T2 0.1328 0.15510 , , plus B6 S9 T0 0.14225 0.16875 T1 0.09295 0.09900 T2 0.13350 0.14560 to long-format : T0 B6 minus 0.1416 T0 S9 minus 0.12235 T0 B6 plus 0.14225 T0 S9 plus 0.16875 ... whats the default way in R? best -- Witold Eryk Wolski -- Witold Eryk Wolski __ 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] anti off diagonal min max mean - how to rotate matrix by 90 degree
How can id do this efficiently in R ? 1 0 0 0 2 0 0 0 3 rotate right 0 0 1 0 2 0 3 0 0 rotate left 0 0 3 0 2 0 1 0 0 What I want to do is described here: http://stackoverflow.com/questions/13049575/r-min-max-and-mean-of-off-diagonal-elements-in-a-matrix but I want do to it for all off-anti-diagonals. I am also concerned that the method described on stackoverflow isn't necessarily efficient. I work with matrices of size 3k * 3k. -- Witold Eryk Wolski __ 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] cut into groups of equal nr of elements...
I would like to cut a vector into groups of equal nr of elements. looking for a function on the lines of cut but where I can specify the size of the groups instead of the nr of groups. -- Witold Eryk Wolski __ 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] robust smoothing - median smoothing.
Looking for robust smoothing methods available in R... a robust version of lowess or smooth.spline. Was searching for median and smoothing but the search engine isn't calibrated . -- Witold Eryk Wolski __ 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] file.stem?
Looking for a function which returns the stem of the filename given a path. i.e. file.stem(/the/path/to/afile.txt) afile regards -- Witold Eryk Wolski [[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] file.stem?
Rui, Thank you
On 15 July 2013 16:32, Rui Barradas ruipbarra...@sapo.pt wrote:
Hello,
You can use ?basename to write a file.stem function:
basename(/the/path/to/afile.txt)
file.stem - function(x){
bn - basename(x)
gsub(\\..*$, , bn)
}
file.stem(/the/path/to/afile.txt)
Hope this helps,
Rui Barradas
Em 15-07-2013 15:23, Witold E Wolski escreveu:
Looking for a function which returns the stem of the filename given a
path.
i.e.
file.stem(/the/path/to/afile.txt)
afile
regards
--
Witold Eryk Wolski
__
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and provide commented, minimal, self-contained, reproducible code.
[R] disabling vignette creation in R CMD build
While developing a package I would like to disable vignette creation when executing R CMD build. The vignette creation is costly so I would prefer not to have to regenerate it every time. regards -- Witold Eryk Wolski [[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] create index for tapply or by
Is there a build in function to create an index for tapply or by given a
a numeric vector x an a vector of breaks?
What I want to do is:
x - 1:100
breaks - c(0,10,20,50,99,110)
y - rep(0,length(x))
for(i in 2:length(breaks)){
y[which(xbreaks[i-1] x = breaks[i])] - i
}
by(x,y,sum)
but I find the code especially th for loop unneRving.
--
Witold Eryk Wolski
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
[R] write table without quotation marks in column names....
Hi write.table likes to quote () the column and row names. Is there a way to switch it off? Witold [[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] sweave xtable and driver RweaveHTML
Hi,
So far I used Sweave to create pdf reports. I used xtable to create some
tables in the report.
But now I would like to use the same snw file to generate an HTML version.
The xtable output breaks the RweaveHTML driver.
library(R2HTML)
Sweave('analyseLFQ.Snw', driver = RweaveHTML)
Error in match.arg(options$results, c(Robj, html, hide)) :
'arg' should be one of Robj, html, hide
Any suggestions would be highly recommended. I.e. I am wondering can I
include dynamically generated tables in Sweave output,
using syntax independent of the renderer?
regards
Witold
--
Witold Eryk Wolski
Triemlistrasse 155
8047 Zuerich
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
[R] Sweave - if \Sexpr{} than \SweaveInput{my.Rnw}
Depending on an R computation I would like to include an Sweave documents
in the main Sweave document.
How can I do it?
So I was thinking to use Latex features :
\newif\ifpaper
\ifpaper
\SweaveInput{my1.Rnw}
\else
\SweaveInput{my2.Rnw}
\fi
But how do I set paper to true or false given an \Sexpr ??
\papertrue % or
\paperfalse
Any ideas?
cheers
--
Witold Eryk Wolski
Triemlistrasse 155
8047 Zuerich
[[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.
