[Rd] Aggregate function FR
Hi, I was wondering if it would be possible to add an argument to the aggreagte function to retain NA by categories?(default can not to in order to avoid breaking code) Please see below example: df = iris df$Species[5] = NA aggregate(`Petal.Width` ~ Species, df, sum) # does not include NA aggregate(`Petal.Width` ~ addNA(Species), df, sum) # include NA data.table and dplyr include NA by default. Python pandas has an aggreagate function inspired by base R aggregate. An option has been added to include NA. Thank you Best regards Morgan [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Bioc-devel] New package submission : No reviewer communication.
Dear Steffen and Lori, Steffen, many thanks for highlighting packages that are waiting review, including our packages. Lori, please, let us know what input you need from us to start the reviewing process for the different packages (i.e. struct, structToolbox, sbcms, pmp). We are keen on getting our packages included in the next release. What is the process to get involved in reviewing of other packages? We might be able to help out. Many thanks, Ralf On Wed, 20 Nov 2019 at 12:09, lori.sheph...@roswellpark.org < lori.sheph...@roswellpark.org> wrote: > Those are a special set of packages that were submitted by the same author > under a special circumstance. We are working with that author to work > through all the packages (which are related). > > All other packages aim to have a review and response within 2-3 weeks. > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > > From: Bioc-devel on behalf of Neumann, > Steffen > Sent: Wednesday, November 20, 2019 2:59 AM > To: Turaga, Nitesh ; ashku...@gatech.edu < > ashku...@gatech.edu>; bioc-devel@r-project.org > Subject: Re: [Bioc-devel] New package submission : No reviewer > communication. > > Hi, > > I think there is quite some backlog from September > > https://github.com/Bioconductor/Contributions/labels/1.%20awaiting%20moderation > Maybe the BioC team can use the momentum to assign more reviewers ? > > Yours, > Steffen > > On Tue, 2019-11-19 at 19:07 +, Turaga, Nitesh wrote: > > No problem at all! > > > > We are happy to help. If you have further questions feel free to ask. > > > > Best, > > > > Nitesh > > > > On 11/19/19, 1:58 PM, "Kumar, Ashwath" wrote: > > > > Hi Nitesh, > > > > Thanks a lot for the quick reply and clearing up the process. I > > completely understand that the process is tedious and takes a lot of > > time. I just wanted to clarify with people with previous experience > > submitting packages as this is my first time. > > > > Thanks, > > Ashwath > > > > -Original Message- > > From: Turaga, Nitesh > > Sent: Tuesday, November 19, 2019 1:56 PM > > To: Kumar, Ashwath ; > > bioc-devel@r-project.org > > Subject: Re: [Bioc-devel] New package submission : No reviewer > > communication. > > > > Hi, > > > > Please be patient in this regard. The reviewer will get to your > > package as soon as they can. Each package takes time to review, and > > each reviewer is reviewing multiple packages. > > > > As far as asking for support regarding your package, it is best > > to ask your questions on the "Issue" which was created for the > > package contribution. If you have general Bioconductor questions, > > the support site can help you as well, support.bioconductor.org. If > > you are unsure, bioc-devel mailing list is the right place. > > > > Best, > > > > Nitesh > > > > On 11/19/19, 1:47 PM, "Bioc-devel on behalf of Kumar, Ashwath" < > > bioc-devel-boun...@r-project.org on behalf of ashku...@gatech.edu> > > wrote: > > > > Hello all, > > > > I recently submitted a package to Bioconductor and I have not > > heard back from the reviewer about any feedback or acceptance or > > otherwise. The package has indeed passed all the automated tests and > > is awaiting the revision on the next stage of review process. Is > > there a recommended period of time I wait before requesting help in > > this regard and if so, how do I go about requesting support. Thanks a > > lot ! > > > > Thanks, > > Ashwath > > > > > >[[alternative HTML version deleted]] > > > > ___ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > > > > > This email message may contain legally privileged and/or > > confidential information. If you are not the intended recipient(s), > > or the employee or agent responsible for the delivery of this message > > to the intended recipient(s), you are hereby notified that any > > disclosure, copying, distribution, or use of this email message is > > prohibited. If you have received this message in error, please > > notify the sender immediately by e-mail and delete this email message > > from your computer. Thank you. > > > > > > > > > > This email message may contain legally privileged and/or confidential > > information. If you are not the intended recipient(s), or the > > employee or agent responsible for the delivery of this message to the > > intended recipient(s), you are hereby notified that any disclosure, > > copying, distribution, or use of this email message is > > prohibited. If you have received this message in error, please > > notify the sender immediately by e-mail and delete this email message > > from
Re: [Bioc-devel] New package submission : No reviewer communication.
Those are a special set of packages that were submitted by the same author under a special circumstance. We are working with that author to work through all the packages (which are related). All other packages aim to have a review and response within 2-3 weeks. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Neumann, Steffen Sent: Wednesday, November 20, 2019 2:59 AM To: Turaga, Nitesh ; ashku...@gatech.edu ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] New package submission : No reviewer communication. Hi, I think there is quite some backlog from September https://github.com/Bioconductor/Contributions/labels/1.%20awaiting%20moderation Maybe the BioC team can use the momentum to assign more reviewers ? Yours, Steffen On Tue, 2019-11-19 at 19:07 +, Turaga, Nitesh wrote: > No problem at all! > > We are happy to help. If you have further questions feel free to ask. > > Best, > > Nitesh > > On 11/19/19, 1:58 PM, "Kumar, Ashwath" wrote: > > Hi Nitesh, > > Thanks a lot for the quick reply and clearing up the process. I > completely understand that the process is tedious and takes a lot of > time. I just wanted to clarify with people with previous experience > submitting packages as this is my first time. > > Thanks, > Ashwath > > -Original Message- > From: Turaga, Nitesh > Sent: Tuesday, November 19, 2019 1:56 PM > To: Kumar, Ashwath ; > bioc-devel@r-project.org > Subject: Re: [Bioc-devel] New package submission : No reviewer > communication. > > Hi, > > Please be patient in this regard. The reviewer will get to your > package as soon as they can. Each package takes time to review, and > each reviewer is reviewing multiple packages. > > As far as asking for support regarding your package, it is best > to ask your questions on the "Issue" which was created for the > package contribution. If you have general Bioconductor questions, > the support site can help you as well, support.bioconductor.org. If > you are unsure, bioc-devel mailing list is the right place. > > Best, > > Nitesh > > On 11/19/19, 1:47 PM, "Bioc-devel on behalf of Kumar, Ashwath" < > bioc-devel-boun...@r-project.org on behalf of ashku...@gatech.edu> > wrote: > > Hello all, > > I recently submitted a package to Bioconductor and I have not > heard back from the reviewer about any feedback or acceptance or > otherwise. The package has indeed passed all the automated tests and > is awaiting the revision on the next stage of review process. Is > there a recommended period of time I wait before requesting help in > this regard and if so, how do I go about requesting support. Thanks a > lot ! > > Thanks, > Ashwath > > >[[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > This email message may contain legally privileged and/or > confidential information. If you are not the intended recipient(s), > or the employee or agent responsible for the delivery of this message > to the intended recipient(s), you are hereby notified that any > disclosure, copying, distribution, or use of this email message is > prohibited. If you have received this message in error, please > notify the sender immediately by e-mail and delete this email message > from your computer. Thank you. > > > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the > employee or agent responsible for the delivery of this message to the > intended recipient(s), you are hereby notified that any disclosure, > copying, distribution, or use of this email message is > prohibited. If you have received this message in error, please > notify the sender immediately by e-mail and delete this email message > from your computer. Thank you. > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Current bits of interest: * Advances in Plant and Food Metabolomics 10./11. and 12.12.2019 Workshop & Symposium https://www.wur.nl/en/activity/Advances-in-Plant-and-Food-Metabolomics-workshop.htm * European RFMF-Metabomeeting 2020 Toulouse, France, January 22-24 2020 https://rfmf-mpf-2020.sciencesconf.org * HUPO PSI spring meeting, 23.-25.03.2020, San Diego, CA Watch out: http://www.psidev.info/events --- IPB HalleAG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0
Re: [Rd] Why is matrix product slower when matrix has very small values?
Le 20/11/2019 à 09:56, Hilmar Berger a écrit : Hi Florian, just a guess, but couldn't it be that the multiplication of very small values leads to FP underflow exceptions which have to be handled by BLAS in a less efficient way than "normal" multiplications handled by SIMD instructions ? Another guess is that you are caught by what is called "denormal numbers" https://en.wikipedia.org/wiki/Denormal_number. Arithmetic operations on them are different and slower that those on "normal" numbers. Best, Serguei. Best regards, Hilmar On 19/11/2019 15:09, Florian Gerber wrote: Hi, I experience surprisingly large timing differences for the multiplication of matrices of the same dimension. An example is given below. How can this be explained? I posted the question on Stackoverflow: https://stackoverflow.com/questions/58886111/r-why-is-matrix-product-slower-when-matrix-has-very-small-values Somebody could reproduce the behavior but I did not get any useful explanations yet. Many thanks for hints! Florian ## disable openMP library(RhpcBLASctl); blas_set_num_threads(1); omp_set_num_threads(1) A <- exp(-as.matrix(dist(expand.grid(1:60, 1:60 summary(c(A)) # Min. 1st Qu. Median Mean 3rd Qu. Max. # 0.00 0.00 0.00 0.001738 0.00 1.00 B <- exp(-as.matrix(dist(expand.grid(1:60, 1:60)))*10) summary(c(B)) # Min. 1st Qu. Median Mean 3rd Qu. Max. # 0.000 0.000 0.000 0.0002778 0.000 1.000 identical(dim(A), dim(B)) ## [1] TRUE system.time(A %*% A) # user system elapsed # 2.387 0.001 2.389 system.time(B %*% B) # user system elapsed # 21.285 0.020 21.310 sessionInfo() # R version 3.6.1 (2019-07-05) # Platform: x86_64-pc-linux-gnu (64-bit) # Running under: Linux Mint 19.2 # Matrix products: default # BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 # LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Why is matrix product slower when matrix has very small values?
Hi Florian, just a guess, but couldn't it be that the multiplication of very small values leads to FP underflow exceptions which have to be handled by BLAS in a less efficient way than "normal" multiplications handled by SIMD instructions ? Best regards, Hilmar On 19/11/2019 15:09, Florian Gerber wrote: Hi, I experience surprisingly large timing differences for the multiplication of matrices of the same dimension. An example is given below. How can this be explained? I posted the question on Stackoverflow: https://stackoverflow.com/questions/58886111/r-why-is-matrix-product-slower-when-matrix-has-very-small-values Somebody could reproduce the behavior but I did not get any useful explanations yet. Many thanks for hints! Florian ## disable openMP library(RhpcBLASctl); blas_set_num_threads(1); omp_set_num_threads(1) A <- exp(-as.matrix(dist(expand.grid(1:60, 1:60 summary(c(A)) # Min. 1st Qu. Median Mean 3rd Qu. Max. # 0.00 0.00 0.00 0.001738 0.00 1.00 B <- exp(-as.matrix(dist(expand.grid(1:60, 1:60)))*10) summary(c(B)) # Min. 1st Qu.Median Mean 3rd Qu. Max. # 0.000 0.000 0.000 0.0002778 0.000 1.000 identical(dim(A), dim(B)) ## [1] TRUE system.time(A %*% A) #user system elapsed # 2.387 0.001 2.389 system.time(B %*% B) #user system elapsed # 21.285 0.020 21.310 sessionInfo() # R version 3.6.1 (2019-07-05) # Platform: x86_64-pc-linux-gnu (64-bit) # Running under: Linux Mint 19.2 # Matrix products: default # BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 # LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Dr. Hilmar Berger, MD Max Planck Institute for Infection Biology Charitéplatz 1 D-10117 Berlin GERMANY Phone: + 49 30 28460 430 Fax:+ 49 30 28460 401 E-Mail: ber...@mpiib-berlin.mpg.de Web : www.mpiib-berlin.mpg.de __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Bioc-devel] New package submission : No reviewer communication.
Hi, I think there is quite some backlog from September https://github.com/Bioconductor/Contributions/labels/1.%20awaiting%20moderation Maybe the BioC team can use the momentum to assign more reviewers ? Yours, Steffen On Tue, 2019-11-19 at 19:07 +, Turaga, Nitesh wrote: > No problem at all! > > We are happy to help. If you have further questions feel free to ask. > > Best, > > Nitesh > > On 11/19/19, 1:58 PM, "Kumar, Ashwath" wrote: > > Hi Nitesh, > > Thanks a lot for the quick reply and clearing up the process. I > completely understand that the process is tedious and takes a lot of > time. I just wanted to clarify with people with previous experience > submitting packages as this is my first time. > > Thanks, > Ashwath > > -Original Message- > From: Turaga, Nitesh > Sent: Tuesday, November 19, 2019 1:56 PM > To: Kumar, Ashwath ; > bioc-devel@r-project.org > Subject: Re: [Bioc-devel] New package submission : No reviewer > communication. > > Hi, > > Please be patient in this regard. The reviewer will get to your > package as soon as they can. Each package takes time to review, and > each reviewer is reviewing multiple packages. > > As far as asking for support regarding your package, it is best > to ask your questions on the "Issue" which was created for the > package contribution. If you have general Bioconductor questions, > the support site can help you as well, support.bioconductor.org. If > you are unsure, bioc-devel mailing list is the right place. > > Best, > > Nitesh > > On 11/19/19, 1:47 PM, "Bioc-devel on behalf of Kumar, Ashwath" < > bioc-devel-boun...@r-project.org on behalf of ashku...@gatech.edu> > wrote: > > Hello all, > > I recently submitted a package to Bioconductor and I have not > heard back from the reviewer about any feedback or acceptance or > otherwise. The package has indeed passed all the automated tests and > is awaiting the revision on the next stage of review process. Is > there a recommended period of time I wait before requesting help in > this regard and if so, how do I go about requesting support. Thanks a > lot ! > > Thanks, > Ashwath > > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > This email message may contain legally privileged and/or > confidential information. If you are not the intended recipient(s), > or the employee or agent responsible for the delivery of this message > to the intended recipient(s), you are hereby notified that any > disclosure, copying, distribution, or use of this email message is > prohibited. If you have received this message in error, please > notify the sender immediately by e-mail and delete this email message > from your computer. Thank you. > > > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the > employee or agent responsible for the delivery of this message to the > intended recipient(s), you are hereby notified that any disclosure, > copying, distribution, or use of this email message is > prohibited. If you have received this message in error, please > notify the sender immediately by e-mail and delete this email message > from your computer. Thank you. > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Current bits of interest: * Advances in Plant and Food Metabolomics 10./11. and 12.12.2019 Workshop & Symposium https://www.wur.nl/en/activity/Advances-in-Plant-and-Food-Metabolomics-workshop.htm * European RFMF-Metabomeeting 2020 Toulouse, France, January 22-24 2020 https://rfmf-mpf-2020.sciencesconf.org * HUPO PSI spring meeting, 23.-25.03.2020, San Diego, CA Watch out: http://www.psidev.info/events --- IPB HalleAG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
