Re: [R] submitting R scripts with command_line_arguments to PBS HPC clusters

2017-07-11 Thread Bogdan Tanasa
Dear Peter, that is very very helpful, many thanks for your suggestions ;) ! On Tue, Jul 11, 2017 at 11:34 PM, Anthoni, Peter (IMK) < peter.anth...@kit.edu> wrote: > Hi, > > The problem is most likely, you need to call a R CMD BATCH with your > arguments and the R-script inside of a shell script

Re: [R] submitting R scripts with command_line_arguments to PBS HPC clusters

2017-07-11 Thread Anthoni, Peter (IMK)
Hi, The problem is most likely, you need to call a R CMD BATCH with your arguments and the R-script inside of a shell script that you submit to your qsub. Unfortunately we don't use qsub anymore so can't test it, but it should be as follows: R-script eg. test.R: > ##First read in the arguments

Re: [R] submitting R scripts with command_line_arguments to PBS HPC clusters

2017-07-11 Thread Jeff Newmiller
This sounds like an operating system specific question, in that "submit the R script to a PBS HPC scheduler" would be the kind of action that would run R with very different environment variables and possibly different access credentials than your usual interactive terminal. A thorough reading

[R] submitting R scripts with command_line_arguments to PBS HPC clusters

2017-07-11 Thread Bogdan Tanasa
Dear all, please could you advise me on the following : I've written a R script that reads 3 arguments from the command line, i.e. : " args <- commandArgs(TRUE) TUMOR <- args[1] GERMLINE <- args[2] CHR <- args[3] ". when I submit the R script to a PBS HPC scheduler, I do the following (below), b

Re: [R] Problems with time formats when importing data using readHTMLTable

2017-07-11 Thread David Winsemius
Sent from my iPhone > On Jul 11, 2017, at 10:00 AM, Cristina Silva wrote: > > Dear David, > > Thank you very much. You have solved my problem, not of importing in the > right format but the date conversion. It works for me, and if I specify the > timezone tz='GMT', I get exactly the same ti

Re: [R] Extracting sentences with combinations of target words/terms from cancer patient text medical records

2017-07-11 Thread Bert Gunter
Have you looked at the CRAN Natural Language Processing Task View? If not, why not? If so, why were the resources described there inadequate? Bert On Jul 11, 2017 10:49 AM, "Paul Miller via R-help" wrote: > Hello All, > > I need some help figuring out how to extract combinations of target > wor

[R] Multivariate random forests in R - how to obtain variance explained for multiple responses in randomForestSRC package - or other package

2017-07-11 Thread Alice Eldridge
Hello, I am wanting to use MRF to do multivariate regression. We are testing whether acoustic indices can predict structure (relative abundances) of vocalising avian community in UK and Ecuador. There are 26 acoustic indices, 65 UK species and 95 Ecuadorian species. I want to build a model for ea

[R] Extracting sentences with combinations of target words/terms from cancer patient text medical records

2017-07-11 Thread Paul Miller via R-help
Hello All, I need some help figuring out how to extract combinations of target words/terms from cancer patient text medical records. I've provided some sample data and code below to illustrate what I'm trying to do. At the moment, I'm trying to extract sentences that contain the word "breast" p

Re: [R] Problems with time formats when importing data using readHTMLTable

2017-07-11 Thread Cristina Silva
Dear David, Thank you very much. You have solved my problem, not of importing in the right format but the date conversion. It works for me, and if I specify the timezone tz='GMT', I get exactly the same time of the webpage. Sincerely yours, Cristina On Tue, 11 Jul 2017 07:15:43 -0700, Davi

Re: [R] Problems with time formats when importing data using readHTMLTable

2017-07-11 Thread David Winsemius
> On Jul 11, 2017, at 6:25 AM, Cristina Silva wrote: > > Dear Jeff, > > I am sorry, I didn't notice that it was not plain text. I hope that it is now > in the correct format. I explain the problem again, now with more detais. > I am collecting the track positions of our research vessel from >

Re: [R] Problems with time formats when importing data using readHTMLTable

2017-07-11 Thread Cristina Silva
Dear Jeff, I am sorry, I didn't notice that it was not plain text. I hope that it is now in the correct format. I explain the problem again, now with more detais. I am collecting the track positions of our research vessel from www.marinetraffic.com. In the page, the data appear in a table:

Re: [R] fit lognorm to cdf data

2017-07-11 Thread peter dalgaard
You can have any expression on the RHS, and list the parameters to optimize over in start=. The only reason to restrict to SSfpl and friends is that they are SelfStarting, i.e., they contain methods to compute reasonable starting values, but you were giving start= anyway. - pd > On 11 Jul 2017

Re: [R] dplyr help

2017-07-11 Thread Jeff Newmiller
A better thanks would be to post the solution that met your needs... particularly since in spite of our efforts it appears we may not have understood your problem. A small sample data set generated with dput along with your code would be helpful in making sure others learn along with you. -- S

Re: [R] dplyr help

2017-07-11 Thread Mangalani Peter Makananisa
Thank you very much for the support. I just used the reshape library and my problem was solved. Kind regards, Peter -Original Message- From: PIKAL Petr [mailto:petr.pi...@precheza.cz] Sent: 10 July 2017 11:17 AM To: Mangalani Peter Makananisa; r-help@r-project.org Cc: Vito Ricci (vito

Re: [R] dplyr help

2017-07-11 Thread Mangalani Peter Makananisa
Thank you very much for the support. I have just used the reshape library and my problem was solved. Kind regards, Peter -Original Message- From: Jeff Newmiller [mailto:jdnew...@dcn.davis.ca.us] Sent: 10 July 2017 03:52 PM To: r-help@r-project.org; Mangalani Peter Makananisa; r-help@r