search for: trailingonly

...that somebody will be able to figure out how to make it faster, either through parallelisation, or by making changes. I've marked the places where Rprof showed me it was slowing down: currencyCorrelation <- function(lagtime = 1) { require(quantmod) dataTrack <- getSymbols(commandArgs(trailingOnly=T)[1], from='2009-11-21', to='2011-04-03') stockData <- get(dataTrack) currencies <- row.names(oanda.currencies[grep(pattern='oz.', fixed=T, x =as.vector(oanda.currencies$oanda.df.1.length.oanda.df...2....1.)) == F]) correlations <- vector() values <- lis...

Hi, $ cat commandArgs.R args=commandArgs(trailingOnly=TRUE) args[1]+10 I have the above code. But the following command line gives me an error. I am wondering what is the correct way to convert a string to a vector? $ Rscript commandArgs.R 1:3 > args=commandArgs(trailingOnly=TRUE) > args[1]+10 Error in args[1] + 10 : non-numeric argument to bi...

Hola. Tengo un script con la siguiente estructura. #!/usr/bin/env Rscript args = commandArgs(trailingOnly=TRUE) source("carga-datos.R") source("modelo.R") y quiero llamar a mi script desde consola con Rscript --vanilla miscript.R datos1.csv De forma que se guarde como argumento el nombre del fichero que quiero cargar y se pase a al script carga-datos.R. El problema es que aun...

dear R experts--- I am experimenting with multicore processing, so far with pretty disappointing results. Here is my simple example: A <- 100000 randvalues <- abs(rnorm(A)) minfn <- function( x, i ) { log(abs(x))+x^3+i/A+randvalues[i] } ?## an arbitrary function ARGV <- commandArgs(trailingOnly=TRUE) if (ARGV[1] == "do-onecore") { ?library(foreach) ?discard <- foreach(i = 1:A) %do% uniroot( minfn, c(1e-20,9e20), i ) } else if (ARGV[1] == "do-multicore") { ?library(doMC) ?registerDoMC() ?cat("You have", getDoParWorkers(), "cores\n") ?...

...from Rscript, but not to run if the same file is being source()d, or submitted via ESS, etc. As a gloss I would like to write a file that looks somewhat like: #!/usr/bin/env Rscript my.func <- function(...) { #do something... } if ( #is.running.Rscript# ) { do.call(my.func, commandArgs(trailingOnly=TRUE)) } If it helps, I'm thinking of something similar to the Python idiom of writing #!/usr/bin/env python #class, function definitions if (__name__=='__main__'): #code to be executed when running this file directly The intent is to use R's debugging facilities to help sol...

...I know Rscript has the option to run in --vanilla. Where exactly do I insert the --vanilla option? When I do something like this: ./nameOfRScript --vanilla arg1 arg2 ... And I try to access the commandArgs, the first argument is --vanilla which isn't what I want. I tried to do commandArgs(trailingOnly=TRUE) with ./nameOfRScript --vanilla --args arg1 arg2 ... But I sitll have the first argument as --vanilla. Does anyone know how to get around this? Thanks, Fong [[alternative HTML version deleted]]

I have examined the documentation for batch mode use of R: R CMD BATCH [options] infile [outfile] The documentation for this seems rather spartan. Running "R CMD BATCH --help" gives me info on only two options: one for getting help and the other to get the version. I see, further on, that there are options for retoring and saving sessions (which I do not need to do in this case),

Is there a better way to do the following? I have data in a number of tab delimited files. I am using read.delim() to read them, in a loop. I am invoking my code on Linux Fedora 20, from the BASH command line, using Rscript. The code I'm using looks like: arguments <- commandArgs(trailingOnly=TRUE); # initialize the capped_data data.frame capped_data <- data.frame(lpar="NULL", started=Sys.time(), ended=Sys.time(), stringsAsFactors=FALSE); # and empty it. capped_data <- capped_data[-1,]; # # Read in the...

...having some trouble getting my shell script to work. I've checked out the Intro to R Manual and a host of other websites, but I still can't get the script to work when I submit the job to the cluster. Here is my main R code: ##Load Libraries ##... ## Load Time Data Args <- commandArgs(trailingOnly = TRUE); print(Args); timeDat <- read.flowSet(files=NULL, path=Args[1]); save(timeDat,file = Args[2]); Here is my shell script file #!/bin/bash #$ -cwd #$ -q all.q R --slave --vanilla --file="/home/jpura/Desktop/FDA_Trial_Data/testscript.R" --args "/home/jpura/Desktop/FDA_Tria...

I am a beginner in R and know only a little about it yet. I have a script written in R language, named as "a.txt" for example. I am using a Linux machine, at present I only know that I can type "R" in the terminal and then copy-paste the content in "a.txt" to the R's interface to execute the program. However, I want to know if there is any method that allows me to

Dear all, When running R CMD check on Windows XP to test my package I get the following warning message: "* checking line endings in C/C++/Fortran sources/headers ... WARNING Found the following sources/headers with CR or CRLF line endings: src/xpsDict.h" The problem is that this file is created by the compiler AUTOMATICALLY during the compilation process, and since the file is

Hi, I know that I can use the following script to get the command line options for an R script. But the output shows two many irrelevant arguments. For example, I only want to pass "a", "b" and "c" to the script. The first 5 elements in the variable 'args' are not what I want. I am wondering what is the correct way to pass command line options to an R script.

...IS_OPT_OUTMAP_GLM $GIS_OPT_FSTATS $GIS_FLAG_M $GIS_OPT_SPP $GIS_OPT_SPA $GIS_OPT_FAM $GIS_OPT_TERMS $GIS_FLAG_Q $GIS_OPT_OUTMAP_PROJ $GIS_OPT_ENV_PROJ $GIS_OPT_KFOLD $GIS_OPT_SFOLD In the R script, I use the commandArgs function to capture the arguments supplied to Rscript: args <- commandArgs(trailingOnly=TRUE) The problem is that args only contains the first 12 arguments (up to and including $GIS_OPT_OUTPUT_PROJ). I also tried using a call to R instead of Rscript: R --no-save --no-restore --no-site-file --no-init-file --args "${GIS_OPT_INMAP}" "${GIS_OPT_PRES}" "${GIS_OP...

Dear R People: I have used ./R --no-save -q -f e.in >stuff.out with great success on SUSE10.1 with R-2.7.1. My question is, please: is there a way to pass in a variable to the e.in file? I'm fairly sure that the answer is no, but thought I'd double check. Thanks in advance, Sincerely, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences

Hi, I am struggling with using R CMD BATCH command. Kindly suggest solution to the following problem. I have a function named CinC with accept two input parameters. This can be shown as: CinC <- function(start, end) where start and end both are character strings. Please suggest me how can I run this function using command R CMD BATCH. Currently I am trying to do like this -> R CMD

...f the required packages print("Loading Libraries??") library(intamap) # also loads sp, gstat, rgdal, akima, automap, mvtnorm, MASS, evd, lattice library(extremevalues) library(fBasics) library(geoR) library(graphics) library(plotrix) ################### get arguments Args = commandArgs(trailingOnly=TRUE) print(Args) currentWS_RCMD = Args[1] indata_RCMD = sub(".shp","",Args[2], ignore.case = TRUE) # strip extension from the file name R_output_RCMD = Args[3] ################################################### In the Arc Script tool, the parameters are: currentWS: Data T...

He encontrado la respuesta. EL ejemplo que puse era trivial, ya que es obvio que if(i ==0) entonces next, pero me referia a sin saber si va a ser error el modelo o no. Para esto he encontrado la solución for(i in -3:3){ tryCatch({ z<-1/i > z<-z*z > modelo<-lm(z~1) }, error=function(e){print("es un error"}) } Gracias de todas maneras!!!!! Jesús

...tion above, with the pipe and tail combo. # This file becomes the program read into R. If it is set chmod+x then you can execute this file. pp=function(...) paste(sep="",...) script="scriptdemo.rsh" usage=pp(script,": put help info here") argv = commandArgs(trailingOnly=TRUE) # --help if(any(argv=="--help")) { cat(usage) quit(save="no",status=0) } # 2nd point of note: this is how to read stdin inside a script: # # slurp in all the input r=readLines("stdin") bad=grep("^#",r) # remove comments # wri...

A couple of weeks ago I asked how it is possible to run an R script (not a function) passing some parameters. Someone suggested the function "commandArgs()". I read the on-line help and found no clarifying example. Therefore I do not know how to use it appropriately. I noticed this function returns the pathname of the R executable which is not what I need. I meant to ask if it is

Thanks for your pointer. Is there any way in R how to replace " ' " with " /' " programmatically? My actual string is quite lengthy, so changing it manually may not be possible. I am aware of gsub() function, however not sure I can apply it directly on my original string. Regards, On Tue, Jul 18, 2017 at 10:27 PM, John McKown <john.archie.mckown at gmail.com>