[R] formatting a result table (number of digits)
Hello,
Is there an easy way to format the output of a result table that R
generates from a regression? I like the table, but would like to
limit the number of decimal points in the entries if possible.
For instance I would like only 3 digits of precision for the Value,
Std.Error. (And if it would be easy to get rid of scientific notation,
that would be good to know too). So ideally keep the table/headers etc,
but chance the entries.
I've looked at format and print without much success.
I'm using R 2.10.1 in a Linux environment.
Thanks,
Esmail
Below's an example of generating the table I am trying to format:
load('data.rda')
library(nlme)
ic - lme(Ind_Cntrbn ~
D_Clb_Pbl+D_Club+Round+Ind_cntr_1+GR_cntr_1+D_Success_1+IndEarngs_1+D_Unfair_cntr_1+D_1st10rnds+D_Female+D_econ_gov+D_mjr_social+D_frshmn+D_junior+D_senior+UrbanArea+ParentEducation+Empathy+Lcs_Cntrl_Intn+Trust,
random=~1|Group, data=Dataset)
s=summary(ic)
t=s$tTable
t
Value Std.Error DF t-value p-value
(Intercept) 5.683020304 0.78867419 2237 7.20578963 7.853134e-13
D_Clb_Pbl0.193187682 0.25494452 22 0.75776363 4.566332e-01
D_Club 0.112745107 0.09636280 2237 1.17000650 2.421230e-01
Round -0.096400805 0.0181 2237 -5.31948107 1.144272e-07
Ind_cntr_1 0.340706093 0.04002901 2237 8.51147920 3.097981e-17
GR_cntr_10.033215293 0.01271829 2237 2.61161545 9.071799e-03
D_Success_1 2.210964800 0.38904872 2237 5.68300241 1.496038e-08
IndEarngs_1 -0.277758214 0.03903289 2237 -7.11600506 1.489839e-12
D_Unfair_cntr_1 -0.535979858 0.18280685 2237 -2.93194624 3.402644e-03
D_1st10rnds -0.479775417 0.19375663 2237 -2.47617547 1.335331e-02
D_Female 0.07269 0.12354518 2237 0.62055250 5.349573e-01
D_econ_gov -0.282679230 0.12023002 2237 -2.35115350 1.880165e-02
D_mjr_social 0.149134543 0.12572505 2237 1.18619595 2.356709e-01
D_frshmn-0.149157208 0.20609463 2237 -0.72373166 4.693062e-01
D_junior-0.112917886 0.17455488 2237 -0.64689045 5.177692e-01
D_senior-0.107570461 0.15088326 2237 -0.71293835 4.759583e-01
UrbanArea -0.364410559 0.11988827 2237 -3.03958489 2.396486e-03
ParentEducation 0.098237171 0.05350248 2237 1.83612365 6.647201e-02
Empathy 0.042232476 0.08248236 2237 0.51201825 6.086888e-01
Lcs_Cntrl_Intn 0.132131306 0.08841098 2237 1.49451240 1.351828e-01
Trust -0.003872427 0.08468412 2237 -0.04572789 9.635312e-01
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[R] Comparing matrices
Hello all,
I have two matrices, pop and pop2, each the same number of rows and
columns that I want to compare for equality. I am concerned about
efficiency in this operation.
I've tried a few things without success so far. Doing something simple like:
if (pop==pop2) { cat('equal') } else { cat('NOT equal') }
results in the warning:
1: In if (pop == pop2) { :
the condition has length 1 and only the first element will be used
so it seems to look only at the first element.
print(pop==pop2) gives me a listing of TRUE/FALSE values for each
element.
I am really only looking for a single TRUE or FALSE value to tell me
if the two populations (ie pop and pop2) are the same or different. In
my application there will be about 200 columns and 50 rows and this
comparison will happen very frequently (possibly a few thousand
times), so I am concerned about efficiency.
I am appending the code I used to generate my matrices and some things
I tried (mentioned above) and also the output get so far.
FWIW, Linux environment, R 2.10.1.
Thanks,
Esmail
ps: Am I correct that if I do the assignment
pop2 = pop
I create a totally separate instance/(deep)copy of the
data? I tried a few tests that seem to confirm this, but I'd
rather be sure.
--- code
# create a binary vector of size len
create_bin_Chromosome - function(len)
{
sample(0:1, len, replace=T)
}
# create popsize members, each of length len
create_pop_2 - function(popsize, len)
{
datasize=len*popsize
npop - matrix(0, popsize, len, byrow=T)
for(i in 1:popsize)
npop[i,] = create_bin_Chromosome(len)
npop
}
POP_SIZE = 3
LEN = 8
pop = create_pop_2(POP_SIZE, LEN)
pop2 = pop
print(pop==pop2)
if (pop==pop2) { cat('equal\n') } else { cat('NOT equal\n') }
print(pop)
print(pop2)
pop[2,5] = 99
pop2[3,3] = 77
print(pop==pop2)
if (pop==pop2) { cat('equal\n') } else { cat('NOT equal\n') }
print(pop)
print(pop2)
-- output ---
source('popc.R')
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[2,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[3,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
equal
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,]01010110
[2,]01100000
[3,]01001011
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,]01010110
[2,]01100000
[3,]01001011
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[2,] TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE
[3,] TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE
equal
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,]01010110
[2,]0110 99000
[3,]01001011
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,]01010110
[2,]01100000
[3,]01 7701011
Warning messages:
1: In if (pop == pop2) { :
the condition has length 1 and only the first element will be used
2: In if (pop == pop2) { :
the condition has length 1 and only the first element will be used
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[R] sprintf + integer(0) problem
Hello all,
I am stuck with R v2.8.0 under Linux for the time being and I am
running into a small problem that doesn't exist under 2.9.x and 2.10.x
with sprintf.
If I have the following code segment to help me determine the column
number for a specific column header/label:
nn = names(Dataset)
s = Group
c = which(nn==s)
cat(sprintf('found %s in col %d\n', s, c))
If the string s is found as a column header, sprintf works fine.
However if the string isn't found, c contains integer(0) which then
causes a program abort with the following message under 2.8.0
Error in sprintf(found %s in col %d\n, s, c) : zero-length argument
Is there an easy work around? I tried using %s (in place of %d) hoping
it would just print integer(0) - which is better than a crash - but
that didn't work.
I am developing and testing my code under 2.9 and 2.10 but then
transferring it to a faster system that unfortunately still uses 2.8.0
.. I'd rather not have to keep modifying the source each time I upload it.
I'm hoping someone has an easy fix.
Thanks
Esmail
PS: in v 2.10.1 no output at all is generated when the string isn't found
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Re: [R] sprintf + integer(0) problem
Henrique Dallazuanna wrote: You can try this: cat(sprintf(ifelse(any(grepl(s, nn)), 'found %s in col %d\n', 'Column %s not found'), s, match(s, nn))) Wow .. one can always learn something new .. that looks pretty complex, I have a bunch of print statements. I was hoping for a simpler solution so I guess for now I'll just comment out the sections that might cause problems under 2.8.0 (too bad, because it's useful to have some of this info displayed - which it does during development/testing, so it's ok). If anyone has a alternate solution, please let me know. In the meantime I'm going to try to use this code to determine if I should display the info or not: min = version[[minor]] maj = version[[major]] ver = paste(maj, '.',min, sep='') if (ver == 2.8.0) ... Cheers, Esmail -- View this message in context: http://n4.nabble.com/sprintf-integer-0-problem-tp1567829p1568357.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] sprintf + integer(0) problem
On 24-Feb-10 20:03, Henrique Dallazuanna wrote:
You can use tryCatch also:
cat(tryCatch(sprintf('found %s in col %d\n', s, c), error =
function(x)cat('Not Found\n')))
Ah .. one more way .. thanks, I've saved it away in my set of
R tricks!
Best,
Esmail
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[R] lint for R? and debugging
Good morning .. sorry if this is a basic question, but is there a lint-like utility for R to check for suspicious language constructs? And along the same lines, any type of interactive debugging utility for R? My main use of R is under Linux (though I run code sometimes under Window XP). R versions 2.9-2.10 Thanks, Esmail __ 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] lint for R? and debugging
On 16-Feb-10 09:03, Karl Ove Hufthammer wrote: On Tue, 16 Feb 2010 08:00:09 -0500 Esmailesmail...@gmail.com wrote: And along the same lines, any type of interactive debugging utility for R? See this article in R News: 'Debugging Without (Too Many) Tears' http://cran.r-project.org/doc/Rnews/Rnews_2003-3.pdf#page=29 Thanks for the pointer, that looks very interesting. Any lint-like utilities out there? I miss a lot of the development tools I have available for Python or Java with R, esp once the code starts to grow beyond a few hundred lines. Esmail __ 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] argh .. if/else .. why?
Hello, would someone please help explain the following inconsistency
in the if/else statement to me?
The format of the if/else #3 below is ok, but if/else #1 is not? (I get
an unexpected else type error.) In order for it to work I have to use
if/else #2
Thanks .. maybe there is some reason for this, but this looks very
inconsistent to me.
R version 2.10.1 (2009-12-14)
Ubuntu 9.04
Esmail
---
#if (ZELIG) if/else #1
# cat(sprintf(Zelig for %d runs - timeR\n, RUNS))
#else
# cat(sprintf(lme for %d runs - timeR\n, RUNS))
if (ZELIG){ ### if/else #2
cat(sprintf(Zelig for %d runs - timeR\n, RUNS))
} else
{
cat(sprintf(lme for %d runs - timeR\n, RUNS))
}
cat(date(), start - timeR\n)
for(i in 1:RUNS)
{
if (ZELIG) # if/else #3
do_Zelig()
else
do_lme()
cat(i, ' - ', date(),\n)
}
cat(date(), end - timeR\n)
sink()
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Re: [R] argh .. if/else .. why?
On 15-Feb-10 09:13, jim holtman wrote: This is a common question. The problem is basically when input commands at the command line, when you hit the carriage return it is assuming there is a complete command. Within a function, or a block like the 'for' loop, the statement is not complete until the closing bracket, so internally it will be parsed correctly, but just get into the habit of making sure the if/else are on the same line or bracket. Ah .. so the fact that this is inside a block (in this case a function) makes a difference .. I see .. well this is certainly different from other languages I have worked with, but the explanation is clear. Thanks you! Esmail __ 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] argh .. if/else .. why?
On 15-Feb-10 09:27, lee.ad...@luminant.com wrote: I, personally, utilize the ifelse(test,statement,statement) function when possible over the methodology outlined. Haven't used that construct before, I'll check it out. Thanks. And mystery solved. Esmail __ 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] a fast way to get AIC, BIC and logLik?
Hello all, Disclaimer, I know very little about statistics :-| I am running a series of regressions for friends, the goal being to determine the AIC, BIC and logLik values from the result/summary of each regression. We are doing this as part of an evolutionary algorithm, so it is important that the regression step be as quick as possible. We initially used the Zelig library, but this was running rather slow (we may have up to 210 variables in our equation). The call looked like this: IndContr_1 - zelig(Y ~ var1 + var2 + .. + varN +tag(1|Group), data=Dataset, model=ls.mixed) My friends then suggested using the nlme library instead, so our call looks like this now: IndContr_2 - lme(Y ~ var1 + var2 + .. varN, random=~1|Group, data=Dataset) This runs much faster, in about 25-30% of the time of the zelig (at least my preliminary timing seems to indicate this) Is there a faster way yet to get the AIC/BIC/logLik values? (I hope this question makes sense) Thanks, Esmail __ 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] lme4 and function 'cholmod_start' not provided by package 'Matrix' / Ubuntu
Hello all, Using Ubuntu 9.04 and R 2.8.1. For a project I need to use the Zelig package, which in turn wants to use the lme4 package. When trying to use Zelig and it tries to its required packages I get the following error message. Error in dyn.load(file, DLLpath = DLLpath, ...) : function 'cholmod_start' not provided by package 'Matrix' Error in loadModelDeps(model) : This model depends on package lme4. Please install this package and try again However, library() lists this package: Packages in library '/usr/lib/R/site-library': codaOutput analysis and diagnostics for MCMC lme4Linear mixed-effects models using S4 classes Matrix Sparse and Dense Matrix Classes and Methods MCMCpackMarkov chain Monte Carlo (MCMC) Package mvtnorm Multivariate Normal and t Distributions sandwichRobust Covariance Matrix Estimators VGAMVector Generalized Linear and Additive Models Zelig Everyone's Statistical Software zoo ... Trying to load lme4 directly with library(lme4) yields: Error in dyn.load(file, DLLpath = DLLpath, ...) : function 'cholmod_start' not provided by package 'Matrix' Error: package/namespace load failed for 'lme4' I have looked on the web for quite a bit, but not found a solution, what am I missing? lme4 wants matrix version = 0.999375-11, I have Matrix_0.999375-17, and R = 2.7 (I have 2.8.1). I notice that in the functions listings for Matrix cholmod_start is not found. (also for some odd reason, my system installs version Zelig 3.3-1 instead of 3.4-5, don't think this is a factor though) Here are some specifics about my setup, I tried to be complete but I am happy to provide more information if it would help. Thanks! Esmail Ubuntu 9.04 Linux t61 2.6.28-17-generic #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009 i686 GNU/Linux library(lme4) Loading required package: Matrix Loading required package: lattice Attaching package: 'Matrix' The following object(s) are masked from package:stats : xtabs The following object(s) are masked from package:base : colMeans, colSums, rcond, rowMeans, rowSums Error in dyn.load(file, DLLpath = DLLpath, ...) : function 'cholmod_start' not provided by package 'Matrix' Error: package/namespace load failed for 'lme4' sessionInfo() R version 2.8.1 (2008-12-22) i486-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Matrix_0.999375-17 lattice_0.17-26 loaded via a namespace (and not attached): [1] grid_2.8.1 Information on package 'lme4' Description: Package: lme4 Version: 0.999375-28 Date: 2008-12-13 Title: Linear mixed-effects models using S4 classes Author:Douglas Bates ba...@stat.wisc.edu, Martin Maechler maech...@r-project.org and Bin Dai d...@stat.wisc.edu Maintainer:Douglas Bates ba...@stat.wisc.edu Description: Fit linear and generalized linear mixed-effects models. Depends: methods, R(= 2.7.0), Matrix(= 0.999375-11), lattice LinkingTo: Matrix, stats Imports: graphics, stats Suggests: mlmRev, MEMSS LazyLoad: yes LazyData: yes License: GPL (=2) URL: http://lme4.r-forge.r-project.org/ Packaged: Sat Dec 13 20:07:38 2008; maechler Built: R 2.8.0; i486-pc-linux-gnu; 2008-12-15 13:16:45; unix Information on package 'Matrix' Description: Package: Matrix Version: 0.999375-17 Date: 2008-12-10 Title:Sparse and Dense Matrix Classes and Methods Author: Douglas Bates ba...@stat.wisc.edu and Martin Maechler maech...@stat.math.ethz.ch Maintainer: Doug and Martin matrix-auth...@r-project.org Description: Classes and methods for dense and sparse matrices and operations on them using Lapack and SuiteSparse. Depends: R (= 2.6.0), stats, methods, utils, lattice Imports: graphics, lattice, grid, stats Enhances: graph, SparseM SystemRequirements: GNU make LazyLoad: yes LazyData: no LazyDataNote: no longer available, since we use data/*.R *and* our classes all.equal-methods Matrix Methods for Function all.equal() atomicVector-class Virtual Class atomicVector of Atomic Vectors bandExtract bands of a matrix bdiag Construct a Block Diagonal Matrix cBind Versions
Re: [R] lme4 and function 'cholmod_start' not provided by package 'Matrix' / Ubuntu
On 10-Jan-10 12:12, Dieter Menne wrote: Esmail Bonakdarian-4 wrote: Using Ubuntu 9.04 and R 2.8.1. For a project I need to use the Zelig package, which in turn wants to use the lme4 package. When trying to use Zelig and it tries to its required packages I get the following error message. Error in dyn.load(file, DLLpath = DLLpath, ...) : function 'cholmod_start' not provided by package 'Matrix' Error in loadModelDeps(model) : This model depends on package lme4. Please install this package and try again Looks like a version mismatch. It's probably easiest if you update to R 2.10.1 and try again; you will have to reinstall all your packages, because of the change help format in 2.9.x Dieter Ok, I'll give this a try (probably not a bad idea to be more up-to-date. Hopefully that will make the problem go away. Thanks, Esmail __ 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] lme4 and function 'cholmod_start' not provided by package 'Matrix' / Ubuntu
On 10-Jan-10 12:40, Douglas Bates wrote: As Dieter points out, this is likely a mismatch between the versions of the lme4 and the Matrix packages, which are very closely linked together. It appears that the version of the lme4 package is too old for the version of the Matrix package, which is hard to catch in the dependencies (lme4 depends on Matrix but not the other way around). As Dieter suggests, it would be best to install the most recent version of R which can then pull in the most recent versions of the lme4 and Matrix packages. Hi, Yes, you were both right on the money. I took your suggestion and upgraded R to 2.10.1 and I had to install lme4 and zelig from source to get the current packages. Thanks again! Esmail __ 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] Learning R
Julia Cains wrote: Dear R helpers, Almost 15 days back I have become member of this very active and wonderful group. So far I have been only raising queries and in turn got them solved too and I really thank for the spirit this group member show when it comes to the guidance. I wish to learn R language and I have given 2 months time for this. Can anyone please guide me as how do I begin i.e. from basics to advance. R is such a vast thing to learn, so I wish to learn it step by step without getting lost at any stage. Please guide me where do I start and upgrade myself to higher level step by step. Regards Julia I heard some time back that O'Reilly is coming out with a book on R .. not sure if that's out yet, or how good it might be. Worth looking into ... Esmail ps: Just checked, 'R in a Nutshell': http://oreilly.com/catalog/9780596801717 release date dec 2009/jan 2010 __ 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] Google's R Style Guide
hadley wickham wrote: Perhaps most of you have already seen this? http://google-styleguide.googlecode.com/svn/trunk/google-r-style.html Comments/Critiques? I made my own version that reflects my personal biases: http://had.co.nz/stat405/resources/r-style-guide.html thanks for sharing, I'll check it out. Cheers, Esmail __ 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] Google's R Style Guide
Duncan Murdoch wrote: On 8/28/2009 8:59 AM, Esmail wrote: Perhaps most of you have already seen this? http://google-styleguide.googlecode.com/svn/trunk/google-r-style.html Comments/Critiques? The rules are mostly reasonable, though they aren't the ones followed in the R source. One bad rule is the one on curly braces: An opening curly brace should never go on its own line; a closing curly brace should always go on its own line. The problem is the second part. If the closing brace is followed by an else clause, the else should go on the same line as the brace, or things will parse differently when pasted than they do in a function. F Excellent point, thanks, this has caused me some problems in the past too. Esmail __ 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] Google's R Style Guide
(Ted Harding) wrote: On 28-Aug-09 12:59:24, Esmail wrote: Perhaps most of you have already seen this? http://google-styleguide.googlecode.com/svn/trunk/google-r-style.html Comments/Critiques? I think it is grossly over-prescriptive. For example: function names have initial capital letters and no dots is violated throughout R itself. Thanks Ted, the way I look at these is as recommendations that I can choose to follow .. if something strikes me as silly I will happily ignore it ;-) Best, Esmail __ 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] Google's R Style Guide
Kingsford Jones wrote: A few thoughts: ... -- It's nice that people have made these guides available Agreed .. it helps those relatively new to the language (and possible other language biases) get their orientation. Cheers, Esmail __ 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] Google's R Style Guide
Barry Rowlingson wrote: On Fri, Aug 28, 2009 at 5:11 PM, hadley wickhamh.wick...@gmail.com wrote: In my view, that's the purpose of indenting - you see scope from indenting. *cough* python *cough* :-) (my favorite language at the moment) __ 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] Best R text editors?
Jonathan Greenberg wrote: Quick informal poll: what is everyone's favorite text editor for working with R? Emacs+ESS __ 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] Google's R Style Guide
Perhaps most of you have already seen this? http://google-styleguide.googlecode.com/svn/trunk/google-r-style.html Comments/Critiques? Thanks, Esmail ps: Reminds me of PEP 8 for Python http://www.python.org/dev/peps/pep-0008/ Maybe not that surprising since Python is also one of the main languages used by Google. __ 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] using optimize() correctly ...
Berend Hasselman wrote: If you do resopt - optim(-5,f, method=SANN,control=list(fnscale=-1)) you will get the global maximum. SANN: simulated annealing. But starting in -4 takes you to the local maximum. So if I understand correctly, this method would also yield the same sort of result (ie non-guaranteed global max or min over the range -10 to 10). But the help for optim recommends optimize for one-dimensional maximization. Yes, I recall reading this. As far as I know there is no general foolproof method for finding a global optimum except trying different initial points. No method can really replace one's own knowledge about a function. Agreed, however, I am testing a genetic algorithm's ability to find the global maximum/minimum and was looking for another independent tool to verify the results I am getting for f(x) and f(x, y), ie my various test functions which will be more complex than the one I posted (and many will be multi-modal since those present a challenge for any algorithm). Since R has proven to be quite capable in the past I thought I would check and see if it could easily do this. I was hoping to avoid having to plot and re-run various functions repeatedly over various ranges or starting points. Thanks again for the help/information, much appreciated. Esmail __ 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] using optimize() correctly ...
Hi Ravi! Ravi Varadhan wrote: Yes. Most classical optimization methods (e.g. gradient-type, Newton-type) are local, i.e. they do not attempt to locate the global optimum. Ah .. I see. The primary difficulty with global optimization is that there are no mathematical conditions that characterize global optimum in multi-modal problems. .. A simplistic strategy to find global optimum is to use local methods with multiple starting values. :-) .. well, that is somewhat similar to the approach the genetic algorithm uses, well, at least with respect of having many starting points. Again the problem is that you don't have any guarantee that you have found the global optimum. Well, then it looks like I am out of luck if I wanted to plug in a function and provide end ranges and get the global max/min. I was hoping this would provide a way for me to verify the workings of a genetic algorithm I am testing. I appreciate you taking the time to explain this so clearly, thanks again, Esmail __ 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] using optimize() correctly ...
Hello Berend, Berend Hasselman wrote: Your function is not unimodal. The help for optimize states: If f is not unimodal, then optimize() may approximate a local, but perhaps non-global, minimum to the same accuracy. Ah ok, I didn't read the manual page carefully enough. Do you know if R has a function to find the global maximum/minimum of a function of x over a given interval? nlminb(), optim(), in particular the option `method = L-BFGS-B' or the function spg() in BB package were recommended to use if I wanted to optimize a function over x and y given their respective intervals. Will they also potentially only give me the local maxima/minima? I am not a regular R user, so my knowledge is clearly not where is could/should be. Thanks, Esmail __ 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] optimizing function over x,y
Hello all, I would like to maximize or minimize a given math function over a specific set of values. I was checking out Wolfram Alpha (http://www70.wolframalpha.com/) and it can do simple optimization problems in math, such as maximize 15*x - x**2 over 0 to 15 (http://www70.wolframalpha.com/input/?i=maximize+15*x+-+x**2+over+0+to+15) which finds the maximum value and input for x in the range 0 to 15. Very cool. (This is of course a very simple example). Reading the R documentation I found out that with R I can do this: f-function(x) (15*x)-x**2 optimize(f, c(0,15), lower=0,upper=15, maximum=TRUE) which works very nicely too! What I would like to do, but what Wolfram Alpha apparently can't do (according to a post in their community forum) is to maximize (or minimize) functions that contain two variables, x and y, or more. So for example a very simple example would be minimize x**2 + y**2 over x:0 to 15, y:0-12 -- this does not work -- though I'm unclear about -- the correct syntax too. Is there a way to do this in R in just a neat and easy way as R optimizes a 1-D function? For this particular instance I am interested in the minimum of x * sin(4*x) + 1.1 * sin(2*y), where x,y in range 0-10 so an example of this in R would be great, though in other problems the range may not be identical for x and y. Thanks, Esmail ps: Has anyone written any programs in Python that they then have used to call R functions? I am thinking of writing some of my scripts in Python, but then accessing some of R's functions. __ 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] using optimize() correctly ...
Hi, I am trying to use the optimize function to optimize a function. The results I am getting don't agree with what I compute on my own and when I look at the graph of f(x) = 100 + ((x-10)**2 + (x-10)) * cos(x-10), where -10 = x = 10 in gnuplot. I suspect I am making a mistake in the usage of the R optimize function, perhaps someone could point out where? f-function(x) 100 + ((x-10)**2 + (x-10)) * cos(x-10) to MAXIMIZE: result=optimize(f, c(-10,10), lower = -10, upper=10, maximum=TRUE) result $maximum [1] -2.728743 $objective [1] 247.3284 to MINIMIZE result=optimize(f, c(-10,10), lower = -10, upper=10, maximum=FALSE) result $minimum [1] 6.290112 $objective [1] 91.52681 However, I believe the correct values should be minimize: x = -5.838 val= -133.020 maximize: x = -8.957 val= 438.448 Thanks, Esmail This is w/ R version 2.8.1 (2008-12-22) under Ubuntu 9.04 __ 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] optimizing function over x,y
Ravi Varadhan wrote: Look at nlminb() or optim(), in particular the option `method = L-BFGS-B' or the function spg() in BB package. With these you can optimize over any number of variables. Ravi. Hi Ravi, Thanks for the leads, I'll take a look, though right now I have run into problems with even the simple (?) optimize function, so I'll first have to figure out what I'm doing wrong with it. Best, Esmail __ 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] running R on netbooks/minis?
Erin Hodgess wrote: Dear R People: Is it possible to run R on a netbook/mini, please? I have run this in my MSI Wind w/ 2GB RAM under XP and also Linux (in VirtualBox) w/o problems - though of course it's much slower than on a 'real' desktop or laptop :-) The Atom processor's forte is not speed, but frugal power consumption. HTH, Esmail __ 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] 3 questions regarding matrix copy/shuffle/compares
Hello David,
Let me try again, I don't think this was the best post ever I've made :-)
Hopefully this is clearer, or otherwise I may break this up into
three separate simple queries as this may be too long.
== is not an assignment operator in R, so the answer is that it
would do neither. - and = can do assignment. In neither case
would it be a deep copy.
It was late when I posted the code, I made a mistake with regard to
the assignment operator and used the boolean compare instead -- thanks
for catching that.
It should have been:
keep_pop[1:POP_SIZE] = pop[1:POP_SIZE]
Here's an edited and clearer version I hope:
The basic idea is that I am trying to keep track of a number of bitrings.
Therefore I am creating a matrix (named 'pop') whose rows are made up
of bit vectors (ie my bitstrings). I only initialize half of the rows
with my bitstrings of random 1s and 0s, the rest of the rows are set
to all zeros).
So I use following function call to create a matrix and fill it with
bit strings:
pop=create_pop_2(POP_SIZE, LEN)
where
POP_SIZE refers to the number of rows
LEN to the columns (length of my bitstrings)
This is the code I call:
# create a random binary vector of size len
#
create_bin_Chromosome - function(len)
{
sample(0:1, len, replace=T)
}
## create_population ###
# create population of chromosomes of length len
# the matrix contains twice as much space as popsize
#
create_pop_2 - function(popsize, len)
{
datasize=len*popsize
print(datasize)
npop - matrix(0, popsize*2, len, byrow=T)
for(i in 1:popsize)
npop[i,] = create_bin_Chromosome(len)
npop
}
My 3 questions:
(1) If I did
keep_pop[1:POP_SIZE] = pop[1:POP_SIZE]
to keep a copy of the original data structure before manipulating
'pop' potentially, would this make a deep copy or just shallow? Ie
if I change something in pop would keep_pop change too? I would
like two independent copies so that 'keep_pop' stays intact while
'pop' may change.
- and = can do assignment. In neither case would it be a
deep copy.
Is there a deepcopy operator, or would I have to have two nested
loops and iterate through them? Or is there a nice R-idiomatic way
to do this?
(2) If I wanted to change the order of rows in my matrix 'pop', is
there an easy way to shuffle these? I.e., I don't want to change
any of the bitstrings vectors/rows, just the order of the rows in the
matrix 'pop'. (E.g., in Python I could just say something like
suffle(pop)) - is there an equivalent for R?
So if pop [ [0, 0, 0]
[1, 1, 1]
[1, 1, 0] ]
after the shuffle it may look like
[ [1, 1, 0](originally at index 2)
[1, 1, 1](originally at index 1)
[0, 0, 0] ] (originally at index 0)
the rows themselves remained intact, just their order changes.
This is a tiny example, in my case I may have 100 rows (POPS_SIZE)
and rows of LEN 200.
(3) I would like to compare the contents of 'keep_pop' (a copy of the
original 'pop') with the current 'pop'. Though the order of rows
may be different between the two, it should not matter as long as
the same rows are present. So for the example given above, the
comparison should return True.
For instance, in Python this would be simply
if sorted(keep_pop) == sorted(pop):
print 'they are equal'
else
print 'they are not equal'
Is there an equivalent R code segment?
I hope this post is clearer than my original one. Thank you David for
pointing out some of the shortcomings of my earlier post.
Thanks,
Esmail
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Re: [R] 3 questions regarding matrix copy/shuffle/compares
David Winsemius wrote: Yes. As I said before I am going to refrain from posting speculation until you provide valid R code that will create an object that can be the subject of operations. The code I have provided works, here is a run that may prove helpful: POP_SIZE = 6 LEN = 8 pop=create_pop_2(POP_SIZE, LEN) print(pop) [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [1,]01011001 [2,]00000000 [3,]11001000 [4,]00000001 [5,]00110010 [6,]10000010 [7,]00000000 [8,]00000000 [9,]00000000 [10,]00000000 [11,]00000000 [12,]00000000 I want to (1) create a deep copy of pop, (2) be able to shuffle the rows only, and (3) be able to compare two copies of these objects for equality and have it return True if only the rows have been shuffled. __ 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] 3 questions regarding matrix copy/shuffle/compares
David,
Good news! It seems that R has deep copy by default. I ran this simplified
test and it seems I can change 'pop' without changing the saved version.
POP_SIZE = 4
LEN = 8
pop=create_pop_2(POP_SIZE, LEN)
cat('printing original pop\n')
print(pop)
keep_pop = pop
pop[1,1] = 99
cat('printing changed pop\n')
print(pop)
cat('printing keep_pop\n')
print(keep_pop)
---
source('mat.R')
[1] 32
printing original pop
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,]01101001
[2,]10100011
[3,]01011101
[4,]00010100
[5,]00000000
[6,]00000000
[7,]00000000
[8,]00000000
printing changed pop
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,] 991101001
[2,]10100011
[3,]01011101
[4,]00010100
[5,]00000000
[6,]00000000
[7,]00000000
[8,]00000000
printing keep_pop
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,]01101001
[2,]10100011
[3,]01011101
[4,]00010100
[5,]00000000
[6,]00000000
[7,]00000000
[8,]00000000
Re Shuffle
I tried using sample based on your earlier post, but your example
really helped, thanks! That solves the shuffling issue.
dx - sample(1:POP_SIZE, POP_SIZE)
cat('shuffled index:')
print(dx)
print(pop[dx,])
cat('shuffled pop')
pop[1:POP_SIZE,] = pop[dx,]
print(pop)
re compare:
I am unclear why you would not create an original and a copy,
Well .. that I wanted to do from the start (hence my question about
deep copy :-)
work on the copy, and compare with the original that is also sorted
by the external index.
That's a great idea, hadn't thought of keeping the index around for
this, I'll give this a try.
Final question, how do I compare these two structures so that I get
one result, true or false? Right now
keep == pop yields all these individual comparisons:
pop==keep
[,1] [,2] [,3] [,4] [,5]
[1,] FALSE TRUE FALSE TRUE FALSE
[2,] FALSE TRUE FALSE TRUE FALSE
[3,] TRUE TRUE TRUE TRUE TRUE
[4,] TRUE TRUE TRUE TRUE TRUE
[5,] TRUE TRUE TRUE TRUE TRUE
[6,] TRUE TRUE TRUE TRUE TRUE
Thanks for the help, much appreciated.
Esmail
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Re: [R] 3 questions regarding matrix copy/shuffle/compares
hadley wickham wrote: I want to (1) create a deep copy of pop, I have already said *I* do not know how to create a deep copy in R. Creating a deep copy is easy, because all copies are deep copies. You need to try very hard to create a reference in R. Hi Hadley Right you are .. I discovered this now too. It's really confusing to go back and forth between different languages. I have been programming in Python for the last 2 months and everything there is a reference .. so I have to worry about deep copy etc. Thanks! Esmail __ 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] 3 questions regarding matrix copy/shuffle/compares
David Winsemius dwinsem...@comcast.net wrote: My understanding of the OP's request was for some sort of copy which did change when entries in the original were changed; the sort of behavior that might be seen in a spreadsheet that had a copy by reference. You misunderstood (my phrasing wasn't probably the best), but I was clear about wanting two independent copies. From my earlier post: (1) If I did keep_pop[1:POP_SIZE] = pop[1:POP_SIZE] to keep a copy of the original data structure before manipulating 'pop' potentially, would this make a deep copy or just shallow? Ie if I change something in 'pop' would it be reflected in 'keep_pop' too? (I don't think so, but just wanted to check). I would like two independent copies. Regardless, the net outcome was new knowledge, so this is a good outcome. Esmail __ 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] comparing matrices
I'm trying to compare two matrices made up of bits.
doing a simple comparison of
matA == matB
yields this sort of output.
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] FALSE TRUE FALSE TRUE TRUE FALSE
[2,] TRUE TRUE TRUE TRUE TRUE TRUE
[3,] FALSE TRUE FALSE FALSE FALSE TRUE
[4,] FALSE TRUE TRUE FALSE FALSE FALSE
[5,] TRUE TRUE TRUE TRUE FALSE FALSE
[6,] TRUE TRUE TRUE TRUE FALSE FALSE
I really would like just one comprehensive value to say TRUE or FALSE.
This is the hack (rather ugly I think) I put together that works,
but there has to be a nicer way, no?
res=pop[1:ROWS,] == keep[1:ROWS,]
if ((ROWS*COL) == sum(res))
{
cat('they are equal\n')
}else
cat('they are NOT equal\n')
Thanks!
Esmail
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Re: [R] comparing matrices
baptiste auguie wrote: I'm not sure I'm following you but have you tried, identical(matrix(c(1,1,1,1),ncol=2), matrix(c(1,1,1,1),ncol=2)) ?all.equal ?isTRUE ?identical and possibly the compare package, compare(matrix(c(1,1,1,1),ncol=2),matrix(c(1,1,1,1),ncol=2)) HTH, baptiste Hi Babtiste, Thanks for pointing out the various options that exist. R is a very rich language indeed and it's good to know how to accomplish tasks in various ways. Cheers, Esmail __ 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] comparing matrices
ONKELINX, Thierry wrote: Have a look at all.equal matA - matrix(1:4, ncol = 2) matB - matA all.equal(matA, matB) matB[1,1] - -10 all.equal(matA, matB) Hi Thierry, Thanks, all.equal does indicate if it's all equal so that works great! Much nicer than my hack - thanks, Esmail __ 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] 3 questions regarding matrix copy/shuffle/compares
Hello all,
I have the following function call to create a matrix of POP_SIZE rows
and fill it with bit strings of size LEN:
pop=create_pop_2(POP_SIZE, LEN)
I have 3 questions:
(1) If I did
keep_pop[1:POP_SIZE] == pop[1:POP_SIZE]
to keep a copy of the original data structure before manipulating
'pop' potentially, would this make a deep copy or just shallow? Ie
if I change something in 'pop' would it be reflected in 'keep_pop'
too? (I don't think so, but just wanted to check). I would like
two independent copies.
(2) If I wanted to change the order of *rows* in my matrix 'pop', is there
an easy way to shuffle these? I don't want to change anything in the
columns, just the complete rowsn (E.g., in Python I could just say
something like suffle(pop) assuming pop is a list of list) - is there
an equivalent for R?
(3) I would like to compare the contents of 'keep_pop' with 'pop'. Though
the order of rows may be different it should not matter as long as
the same rows are present. Again, in Python this would be simply
if sorted(keep_pop) == sorted(pop):
print 'they are equal'
else
print 'they are not equal'
Is there an equivalent R code segment?
Thanks,
Esmail
--- the code called above -
# create a binary vector of size len
#
create_bin_Chromosome - function(len)
{
sample(0:1, len, replace=T)
}
## create_population ###
# create population of chromosomes of length len
# the matrix contains twice as much space as popsize
#
create_pop_2 - function(popsize, len)
{
datasize=len*popsize
print(datasize)
npop - matrix(0, popsize*2, len, byrow=T)
for(i in 1:popsize)
npop[i,] = create_bin_Chromosome(len)
npop
}
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[R] flip certain bits in vector
I have a string of binary values, and I would like to flip certain bits in a set of positions. Let's say the vector p contains position [1, 3, 5, 7] vector b contains bits [1, 0, 1, 0, 1, 0, 1, 0, 1, 0] result r should be [0, 1, 0, 0, 0, 0, 0, 0, 1, 0] in pseudo code this would be something like --- r = c() for (i in 1:10) if (i in p) r = c(r, flip[i]) r doesn't work :-) R doesn't like the if statement. Is there a nice, concise way to do this? The vector contents and size will vary, but length of p = b. Thanks, Esmail __ 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] flip certain bits in vector
David Winsemius wrote: I do not think your wetware processed the inputs correctly. The second bit should not have been flipped: Ooops .. yes you are right! Try this loop free index based solution: b - c( 1, 0, 1, 0, 1, 0, 1, 0, 1, 0) r - b r[p] - 0 + !r[p] # adding 0 converts logical TRUE/FALSE to 0/1 r [1] 0 0 0 0 0 0 0 0 1 0 Great! .. thanks ... I appreciate the hlep, Esmail __ 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] flip certain bits in vector
jim holtman wrote: try this: b - c(1, 0, 1, 0, 1, 0, 1, 0, 1, 0) p - c(1, 3, 5, 7) b[p] - ifelse(b[p] == 0, 1, 0) I'll have to look up the ifelse operator, looks like the ternary operator used in C b[p] = b[p]==0?1:0 Cool - thanks! Esmail __ 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] difference between assignment syntax - vs =
Patrick Burns wrote: 'The R Inferno' page 78 is one source you can look at. Patrick Burns wow .. nice! .. thanks for posting this reference. Esmail __ 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] Sorting rows in a matrix based on vector of indecies
Hello I have a matrix of size rows x cols. I also have a vector of size rows. The vector contains index values that corresponds to rows in the matrix. I would like to re-arrange/sort the contents of the matrix according to the entries in the vector. Can this be done efficiently in R and possibly in place? Or would it be better to allocate another whole matrix? Simple example: matrix: ff aa zz bb vector: 2, 4, 1, 3 new matrix: aa bb ff zz I suppose I could allocate another matrix and loop through the vector of indecies placing entries into the new matrix. Do I have to worry about deallocating the memory space of the first matrix or will it automagically go away if I assign the new matrix to the old matrix identifier (assuming nothing else is pointing at it)? Thanks, Esmail __ 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] Sorting rows in a matrix based on vector of indecies
Hi David, This was useful, thanks. The example was just that, there are no as, b,s etc I was just trying to show what I was trying to do. Using m[v,] where m was the matrix in my example and v the vector of index values works great as you suggested Thanks. R is quite a powerful language as I am starting to discover (and folks on the list here are very helpful). Regards, Esmail David Winsemius wrote: See if this helps: mtx-matrix( rep(letters[1:4], 6), nrow=4) mtx [,1] [,2] [,3] [,4] [,5] [,6] [1,] a a a a a a [2,] b b b b b b [3,] c c c c c c [4,] d d d d d d mtx[c(2, 4, 1, 3), ] [,1] [,2] [,3] [,4] [,5] [,6] [1,] b b b b b b [2,] d d d d d d [3,] a a a a a a [4,] c c c c c c You can do with that result whatever you want: assign it, m2 - mtx[c(2, 4, 1, 3), ] __ 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] Python and R
Doran, Harold wrote: lm(y ~ x-1) solve(crossprod(x), t(x))%*%y# probably this can be done more efficiently You could do crossprod(x,y) instead of t(x))%*%y that certainly looks more readable (and less error prone) to an R newbie like myself :-) __ 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] Python and R
Hi Kenn, Thanks for the suggestions, I'll have to see if I can figure out how to convert the relatively simple call to lm with an equation and the data file to the functions you mention (or if that's even feasible). Not an expert in statistics myself, I am mostly concentrating on the programming aspects of R. Problem is that I suspect my colleagues who are providing some guidance with the stats end are not quite experts themselves, and certainly new to R. Cheers, Esmail Kenn Konstabel wrote: lm does lots of computations, some of which you may never need. If speed really matters, you might want to compute only those things you will really use. If you only need coefficients, then using %*%, solve and crossprod will be remarkably faster than lm # repeating someone else's example # lm(DAX~., EuStockMarkets) y - EuStockMarkets[,DAX] x - EuStockMarkets x[,1]-1 colnames(x)[1] - Intercept lm(y ~ x-1) solve(crossprod(x), t(x))%*%y# probably this can be done more efficiently # and a naive timing system.time( for(i in 1:1000) lm(y ~ x-1)) user system elapsed 14.640.33 32.69 system.time(for(i in 1:1000) solve(crossprod(x), crossprod(x,y)) ) user system elapsed 0.360.000.36 Also lsfit() is a bit quicker than lm or lm.fit. Regards, Kenn __ 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] Python and R
Gabor Grothendieck wrote: On Wed, Feb 18, 2009 at 7:27 AM, Esmail Bonakdarian esmail...@gmail.com wrote: Gabor Grothendieck wrote: See ?Rprof for profiling your R code. If lm is the culprit, rewriting your lm calls using lm.fit might help. Yes, based on my informal benchmarking, lm is the main bottleneck, the rest of the code consists mostly of vector manipulations and control structures. I am not familiar with lm.fit, I'll definitely look it up. I hope it's similar enough to make it easy to substitute one for the other. Thanks for the suggestion, much appreciated. (My runs now take sometimes several hours, it would be great to cut that time down by any amount :-) Yes, the speedup can be significant. e.g. here we cut the time down to 40% of the lm time by using lm.fit and we can get down to nearly 10% if we go even lower level: Wow those numbers look impressive, that would be a nice speedup to have. I took a look at the manual and found the following at the top of the description for lm.fit: These are the basic computing engines called by lm used to fit linear models. These should usually not be used directly unless by experienced users. I am certainly not an experienced user - so I wonder how different it would be to use lm.fit instead of lm. Right now I cobble together an equation and then call lm with it and the datafile. I.e., LM.1 = lm(as.formula(eqn), data=datafile) s=summary(LM.1) I then extract some information from the summary stats. I'm not really quite sure what to make of the parameter list in lm.fit I will look on-line and see if I can find an example showing the use of this - thanks for pointing me in that direction. Esmail system.time(replicate(1000, lm(DAX ~.-1, EuStockMarkets))) user system elapsed 26.850.07 27.35 system.time(replicate(1000, lm.fit(EuStockMarkets[,-1], EuStockMarkets[,1]))) user system elapsed 10.760.00 10.78 system.time(replicate(1000, qr.coef(qr(EuStockMarkets[,-1]), EuStockMarkets[,1]))) user system elapsed 3.330.003.34 lm(DAX ~.-1, EuStockMarkets) Call: lm(formula = DAX ~ . - 1, data = EuStockMarkets) Coefficients: SMI CAC FTSE 0.55156 0.45062 -0.09392 # They call give the same coefficients: lm.fit(EuStockMarkets[,-1], EuStockMarkets[,1])$coef SMI CACFTSE 0.55156141 0.45062183 -0.09391815 qr.coef(qr(EuStockMarkets[,-1]), EuStockMarkets[,1]) SMI CACFTSE 0.55156141 0.45062183 -0.09391815 __ 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] Python and R
Gabor Grothendieck wrote: See ?Rprof for profiling your R code. If lm is the culprit, rewriting your lm calls using lm.fit might help. Yes, based on my informal benchmarking, lm is the main bottleneck, the rest of the code consists mostly of vector manipulations and control structures. I am not familiar with lm.fit, I'll definitely look it up. I hope it's similar enough to make it easy to substitute one for the other. Thanks for the suggestion, much appreciated. (My runs now take sometimes several hours, it would be great to cut that time down by any amount :-) Esmail __ 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] Python and R
Hello all, I am just wondering if any of you are doing most of your scripting with Python instead of R's programming language and then calling the relevant R functions as needed? And if so, what is your experience with this and what sort of software/library do you use in combination with Python to be able to access R's functionality. Is there much of a performance hit either way? (as both are interpreted languages) Thanks, Esmail __ 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] Python and R
Hello! On Tue, Feb 17, 2009 at 5:58 PM, Warren Young war...@etr-usa.com wrote: Esmail Bonakdarian wrote: I am just wondering if any of you are doing most of your scripting with Python instead of R's programming language and then calling the relevant R functions as needed? No, but if I wanted to do such a thing, I'd look at Sage: http://sagemath.org/ ah .. thanks for the pointer, I had not heard of Sage, I was just starting to look at SciPy. It'll give you access to a lot more than just R. Is there much of a performance hit either way? (as both are interpreted languages) Are you just asking, or do you have a particular execution time goal, which if exceeded would prevent doing this? I ask because I suspect it's the former, and fast enough is fast enough. I put together a large'ish R program last year, but I think I would be happier if I could code it in say Python - but I would rather not do that at the expense of execution time. Thanks again for telling me about Sage. Esmail __ 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] Python and R
On Tue, Feb 17, 2009 at 6:05 PM, Barry Rowlingson b.rowling...@lancaster.ac.uk wrote: 2009/2/17 Esmail Bonakdarian esmail...@gmail.com: When I need to use the two together, it's easiest with 'rpy'. This lets you call R functions from python, so you can do: from rpy import r r.hist(z) wow .. that is pretty straight forward, I'll have to check out rpy for sure. to get a histogram of the values in a python list 'z'. There are some complications converting structured data types between the two but they can be overcome, and apparently are handled better with the next generation Rpy2 (which I've not got into yet). Google for rpy for info. Will do! Is there much of a performance hit either way? (as both are interpreted languages) Not sure what you mean here. Do you mean is: R sum(x) faster than Python sum(x) and how much worse is: Python from rpy import r Python r.sum(x) Well, I have a program written in R which already takes quite a while to run. I was just wondering if I were to rewrite most of the logic in Python - the main thing I use in R are its regression facilities - if it would speed things up. I suspect not since both of them are interpreted, and the bulk of the time is taken up by R's regression calls. Esmail __ 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 randomly eliminate half the entries in a vector?
Hello all,
I need some help with a nice R-idiomatic and efficient solution to a
small problem.
Essentially, I am trying to eliminate randomly half of the entries in
a vector that contains index values into some other vectors.
More details:
I am working with two strings/vectors of 0s and 1s. These will contain
about 200 elements (always the same number for both)
I want to:
1. determines the locations of where the two strings differ
-- easy using xor(s1, s2)
2. *randomly* selects *half* of those positions
-- not sure how to do this. I suppose the result would be
a list of index positions of size sum(xor(s1, s2))/2
3. exchange (flip) the bits in those random positions for both strings
-- I have something that seems to do that, but it doesn't look
slick and I wonder how efficient it is.
Mostly I need help for #2, but will happily accept suggestions for #3,
or for that matter anything that looks odd.
Below my partial solution .. the HUX function is what I am trying
to finish if someone can point me in the right direction.
Thanks
Esmail
--
rm(list=ls())
# create a binary vector of size len
#
create_bin_Chromosome - function(len)
{
sample(0:1, len, replace=T)
}
# HUX - half uniform crossover
#
# 1. determines the locations of where the two strings
#differ (easy xor)
#
# 2. randomly selects half of those positions
#
# 3. exchanges (flips) the bits in those positions for
#both
#
HUX - function(b1, b2)
{
# 1. find differing bits
r=xor(b1, b2)
# positions where bits differ
different = which(r==TRUE)
cat(\nhrp: , different, \n)
# 2. ??? how to do this best so that each time
#a different half subset is selected? I.e.,
#sum(r)/2 positions.
# 3. this flips *all* positions, should really only flip
#half of them (randomly selected half)
new_b1 = b1
new_b2 = b2
for(i in different) # should contain half the entries (randomly)
{
new_b1[i] = b2[i]
new_b2[i] = b1[i]
}
result - matrix(c(new_b1, new_b2), 2, LEN, byrow=T)
result
}
LEN = 5
b1=create_bin_Chromosome(LEN)
b2=create_bin_Chromosome(LEN)
cat(b1, \n)
cat(b2, \n)
idx=HUX(b1, b2)
cat(\n\n)
cat(idx[1,], \n)
cat(idx[2,], \n)
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[R] how to randomly eliminate half the entries in a vector?
(sorry if this is a duplicate-problems with posting at my end)
Hello all,
I need some help with a nice R-idiomatic and efficient solution to a
small problem.
Essentially, I am trying to eliminate randomly half of the entries in
a vector that contains index values into some other vectors.
More details:
I am working with two strings/vectors of 0s and 1s. These will contain
about 200 elements (always the same number for both)
I want to:
1. determines the locations of where the two strings differ
-- easy using xor(s1, s2)
2. *randomly* selects *half* of those positions
-- not sure how to do this. I suppose the result would be
a list of index positions of size sum(xor(s1, s2))/2
3. exchange (flip) the bits in those random positions for both strings
-- I have something that seems to do that, but it doesn't look
slick and I wonder how efficient it is.
Mostly I need help for #2, but will happily accept suggestions for #3,
or for that matter anything that looks odd.
Below my partial solution .. the HUX function is what I am trying
to finish if someone can point me in the right direction.
Thanks
Esmail
--
rm(list=ls())
# create a binary vector of size len
#
create_bin_Chromosome - function(len)
{
sample(0:1, len, replace=T)
}
# HUX - half uniform crossover
#
# 1. determines the locations of where the two strings
#differ (easy xor)
#
# 2. randomly selects half of those positions
#
# 3. exchanges (flips) the bits in those positions for
#both
#
HUX - function(b1, b2)
{
# 1. find differing bits
r=xor(b1, b2)
# positions where bits differ
different = which(r==TRUE)
cat(\nhrp: , different, \n)
# 2. ??? how to do this best so that each time
#a different half subset is selected? I.e.,
#sum(r)/2 positions.
# 3. this flips *all* positions, should really only flip
#half of them (randomly selected half)
new_b1 = b1
new_b2 = b2
for(i in different) # should contain half the entries (randomly)
{
new_b1[i] = b2[i]
new_b2[i] = b1[i]
}
result - matrix(c(new_b1, new_b2), 2, LEN, byrow=T)
result
}
LEN = 5
b1=create_bin_Chromosome(LEN)
b2=create_bin_Chromosome(LEN)
cat(b1, \n)
cat(b2, \n)
idx=HUX(b1, b2)
cat(\n\n)
cat(idx[1,], \n)
cat(idx[2,], \n)
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Re: [R] how to randomly eliminate half the entries in a vector?
Gene Leynes wrote: This is my first help post, hope it works! Just check out the sample function At the command line type: ?sample I think it will be pretty clear from the documentation. Yes, most excellent suggestion and quite helpful! Thanks, Esmail __ 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] running R-code outside of R
Jim Porzak wrote: The user of your R script sees only the outputs you create. The R source is hidden. Ah .. that sounds great .. I wish I had known about this a month ago! I'll have to check it out - thanks! Esmail HTH, Jim Porzak .. Would the R script that is being run be hidden from the user, or would the user be able to view/download/save the R source code - or could it be hidden so they just run the code, but never see it? Esmail __ 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] running R-code outside of R
Spencer Graves wrote: If you want to hide the fact that you are using R -- especially if you charge people for your software that uses R clandestinely -- that's a violation of the license (GPL). No on both accounts .. but thanks for pointing this out none the less. __ 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] Programming Concepts and Philosophy
hadley wickham wrote: 2008/6/20 [EMAIL PROTECTED] [EMAIL PROTECTED]: If you do nothing to your code, in 18 months time its performance will have doubled because computers will have become faster. Your code will not get easier to understand by itself. Very nicely put .. and true too! __ 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] replace column headers
Paul Adams wrote: Hello everyone,=I have a question as to how to remove the column headers in a data file and then replace those with titles from another file in this case the file labeled ann ( in which the titles are all in one column). Maybe this will help partially. I am not sure on how to read your new column names from a file into a vector but if you can get them into that format this should let you accomplish your goal. Esmail load(Data/simpleTestData2.rda) df Y X1 X2 X3 X4 X5 X6 1 74.9 10 49.8 0.2 99 50 57 2 79.8 11 49.6 0.4 69 91 57 3 84.4 12 48.8 1.2 30 38 58 4 88.8 13 47.6 2.4 77 87 58 colnames(df) [1] Y X1 X2 X3 X4 X5 X6 altnames=c(A, B1, B2, B3, B4, B5, B6) colnames(df)=altnames df A B1 B2 B3 B4 B5 B6 1 74.9 10 49.8 0.2 99 50 57 2 79.8 11 49.6 0.4 69 91 57 3 84.4 12 48.8 1.2 30 38 58 4 88.8 13 47.6 2.4 77 87 58 save(df, file=example.rda) # new file will contain the new column headers. __ 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] searching for specific row in matrix
Hi,
I have matrix of bits and a target vector. Is there an
efficient way to search the rows of the matrix for the target?
I am interested in the first row index where target is found.
Example:
source(lookup.R)
[,1] [,2] [,3] [,4] [,5]
[1,]10110
[2,]11010
[3,]00100
[4,]10011
[5,]10111
[6,]11001
[7,]10011
[8,]00111
[9,]01101
[10,]00010
target: 1 1 0 1 1
Should return -1 (or some other indicator) since the
target was not found in any of the rows.
source(lookup.R)
[,1] [,2] [,3] [,4] [,5]
[1,]00110
[2,]10000
[3,]10000
[4,]11000
[5,]11100
[6,]00110
[7,]01110
[8,]00110
[9,]11011
[10,]10100
target: 1 1 0 1 1
Should return 9 since the target was found in row 9
If the target is found, it is no longer necessary to keep
searching the rest of the matrix (which may be quite large)
The data/size etc may change of course, but target will
always have the same number of columns as the matrix.
I tried variations of which, and a for loop
comparing pop[i,] to target without much success, nor
did google yield any results. I am hoping someone here
can provide a suggestion.
Thanks,
EB
-
# Here is the code that generates the above data
create_bin_string - function(len)
{
sample(0:1, len, replace=T)
}
ROWS = 10
COLS = 5
pop = matrix(create_bin_string(ROWS*COLS), ROWS, COLS, byrow=T)
target=c(1, 1, 0, 1, 1)
# my population
print(pop)
# I am looking for the index of this in pop
# if present (else -1?)
cat(\ntarget: , target, \n)
##
## this is NOT working
## plus it would continue to search
## after it found the target
##
for(i in ROWS)
if (pop[i,] == target)
cat(\nfound in row: , i, \n\n)
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Re: [R] searching for specific row in matrix
Henrique Dallazuanna wrote:
Try this:
which(apply(t(m) == target, 2, all))
Wow! .. talk about concise! Neat! Thanks.
This will return all matches correct? So if I only wanted
the first I'd simply subscript [1] into it.
Do you think the fact that it searches the whole matrix instead
of stopping when it finds a match may slow it down?
This is my own solution I came up with in the meantime,
looks rather pedestrian compared to your one line, but it will
drop out immediately once if finds the target. Yours looks (based
simply on appearance :-) faster. Having no feel for the language
I may just have to time them.
I would assume that your solution would be faster simple since it's
using built-in language constructs which are optimized (and implemented
in C?) instead of my own interpreted way.
# return index of target in pop, else -1
searchPop - function(pop, target)
{
rows = length(pop[1,])
for(i in 1:rows)
{
result = (pop[i,] == target)
if (sum(which(result==FALSE)) == 0)
return(i)
}
return (-1)
}
idx=searchPop(pop, target)
if (idx 0)
{
cat(NOT found\n)
} else
cat(Found at position , idx, \n)
Esmail
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
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Re: [R] searching for specific row in matrix
Dimitris Rizopoulos wrote:
try this:
match.pat - function (mat, target, nomatch = -1) {
f1 - do.call(paste, c(as.data.frame(mat), sep = \r))
f2 - paste(target, collapse = \r)
ind - f1 %in% f2
if (any(ind)) which(ind)[1] else nomatch
}
Thanks! More R for me to sink my teeth in :-) My own solution
doesn't seem to work quite correctly as I found out from some
further testing .. so the solutions posted here are much appreciated!
Esmail
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Re: [R] searching for specific row in matrix
# determine which data matches matches - t(pop) == target # 't' due to matching in column order # colSums equal to COLS will indicate matches which(colSums(matches) == COLS) Neat! .. somewhat similar to the solution I came up with in the meantime, only yours works :-) Thanks Jim. Esmail __ 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] Adding new columns to (output) data - e.g., read 5 cols write 8
Hello, I have the following task I'd like to accomplish: A file contains 5 columns of data (several hundred rows), let's call them a, b, c, d and e (ie these are their column headers) I also have a set of definitions, e.g., f = a + b g = a * 3 h = c + d etc. I would like to write out a new .rda file that contains columns a b c d e f g h etc. I.e. , the original data plus new columns (with headers and data). It seems that there ought to be a simple way to do this, could someone provide some guidance on the best way to accomplish this task? (I tried a few things as this seemed rather trivial, but did not succeed. I still hope/assume this is a trivial thing to do if one knows R well) Thanks, Esmail ps: I want to thank everyone again who posted their solutions to my previous query. Seeing different solutions for the same problem is a tremendously effective way to learn something new. __ 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] Adding new columns to (output) data - e.g., read 5 cols write 8
Hi Erik, Erik Iverson wrote: Esmail - Are these 5 vectors of data stored in a data.frame? I assume so. Yes, I do a simple load() call first to read the .rda file ... test2 - transform(test, d = 2*a + b, e = 3*c) save(test2, file = test2.Rdata) Does this help? Yes it does .. this is just what I needed. I'll probably do it in this way: df=transform(df, X5=X1+X2) df=transform(df, X6=X1-X2) etc ... building it up the df line by line since the definitions have been provided one per line (instead of queuing them up in one line like you showed). I'll have to write a little awk or ruby script to take the original definitions and wrap them into the transform call, but then I should be all set to go. Thanks again! Esmail __ 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] Adding new columns to (output) data - e.g., read 5 cols write 8
jim holtman wrote: yourDF - cbind(yourDF, f=yourDF$a+yourDF$b, g=yourDF$a * 3, h=yourDF$c + yourDF$d) Thanks Jim, I also learned about the transform() method from Erik which will also work beautifully. Esmail __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R + Linux
steven wilson wrote: I'm planning to install Linux on my computer to run R (I'm bored of W..XP). However, I haven't used Linux before and I would appreciate, if possible, suggestions/comments about what could be the best option install, Hi, I have used Linux since the early 1990s starting with the original slackware distribution, followed by various versions of Red Hat, Gentoo (compiled from source), Fedora and now Ubuntu. Ubuntu is my choice for having the least troublesome install and maintenance. It has a very nice package manager, and if your goal is to *use* a Linux system rather than tinker with it, you could do much worse than Ubuntu. I installed R via the package manger a month ago or so, very easy and trouble free. Hope that helps, Esmail __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R + Linux
FWIW, those who are curious about Linux but are not willing or ready to abandon the Windows platform can now very easily try out Ubuntu without having to repartition their hard drive. Wubi is a project that installs Ubuntu under Windows so that it can be uninstalled easily and requires no messing around with hard drive partitions. From the Wubi web site: Wubi is an officially supported Ubuntu installer for Windows users that can bring you to the Linux world with a single click. Wubi allows you to install and uninstall Ubuntu as any other Windows application, in a simple and safe way. Are you curious about Linux and Ubuntu? Trying them out has never been easier! For more information see: http://wubi-installer.org/ Esmail __ 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] Improving data processing efficiency
hadley wickham wrote: Hi, I tried this suggestion as I am curious about bottlenecks in my own R code ... Why not try profiling? The profr package provides an alternative display that I find more helpful than the default tools: install.packages(profr) install.packages(profr) Warning message: package ‘profr’ is not available any ideas? Thanks, Esmail library(profr) p - profr(fcn_create_nonissuing_match_by_quarterssinceissue(...)) plot(p) That should at least help you see where the slow bits are. Hadley __ 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] Improving data processing efficiency
Esmail Bonakdarian wrote: hadley wickham wrote: Hi, I tried this suggestion as I am curious about bottlenecks in my own R code ... Why not try profiling? The profr package provides an alternative display that I find more helpful than the default tools: install.packages(profr) install.packages(profr) Warning message: package ‘profr’ is not available I selected a different mirror in place of the Iowa one and it worked. Odd, I just assumed all the same packages are available on all mirrors. __ 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] Thank you
Tubin wrote: In the past few weeks I have had to give myself a crash course in R, in order to accomplish some necessary tasks for my job. During that time, I've found this forum to be helpful time and time again - usually I find the answer to my problem by searching the archives; once or twice I've posted questions and been given near-immediate solutions. I just wanted to thank the forum participants for all of their contributions over the years! Hear hear! .. I've benefited greatly from reading the postings here and some of the members have been very generous with their knowledge too! Esmail __ 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 do you exit a function in R?
Bill Cunliffe wrote:
For example, based on a certain condition, I may want to exit my code early:
# Are there the same number of assets in prices and
positions?
if (nAssetPositions != nAssetPrices) {
cat(Different number of assets! \n\n)
exit function
I've wondered about that myself
Have you tried return() ? It would return NULL I think, as long as that
doesn't cause a problem it should exit the method.
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Re: [R] hash or other quick lookup function?
Hi Duncan,
Duncan Murdoch wrote:
Duncan Murdoch wrote:
Esmail Bonakdarian wrote:
Hello all,
I have a matrix of bit values.
I compute certain values based on the bits in each row. There may be
*duplicate* entries in the matrix, ie several rows may be identical.
These rows change over time, and identical entries may not be next to
each other.
Computing these values is time consuming, so I would like a way to
store a value once it's computed. That way I would be able to look up the value
based on a given bitstring (row in the matrix) and avoid having to
re-compute the same value.
So, my thought is a hash function based on a bit string - does R have such
a thing? Or is there an alternative approach that would do the same in R?
The lookup should be quick, otherwise the gains from avoiding
recomputing identical values would be lost to some extent.
Environments can be hashed. To use this, you'd convert the bit string
into a character string, and use that as the name of a variable in an
environment.
For example,
cache - new.env(hash=TRUE, parent=emptyenv())
...
bits - '0101'
if (exists(bits, cache)) {
return(get(bits, cache))
} else {
value - long.computation()
assign(bits, value)
Whoops, that assignment should have been in the cache:
assign(bits, value, envir=cache)
return(value)
}
Thank you for posting this, I'll have to give it a try.
If I can get this to work it should save some some time
spent on recomputing values.
(Sorry for the delayed reply, I was traveling for the
whole last day - suffering from some reverse jet lag at
the moment :-)
Can anyone else think of other alternatives? Always happy
to learn something new.
Thanks!
Esmail
ps: do you think the conversion to a character string
before comparison/search will cause a noticeable
performance hit? I still lack an intuitive feel for
R the programming language. I'd have more of an idea
with regular high-level programming languages.
Duncan Murdoch
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Re: [R] How to make R running faster
Neil Shephard wrote: Loops are not massively efficient within R. Look into using the apply() family of functions (eapply()/lapply()/mapply/rapply()/tapply()). Didn't someone post not too long ago that apply is internally represented as a for-loop? Or am I not remembering this correctly? The reason for apply was that it was more concise but not necessarily more efficient. Esmail __ 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] recompute values repeatedly, or new file for glm()?
Hello all, I need to tap into the collective wisdom of the group re an issue of efficiency. A sketch of the situation: Let's say 4000 observations in variables Y, X1, X2 , X3 and X4. I would like to feed various combinations of this expression Y ~ X1+X2+X3+X4 + I(X1^2)+I(X2^2)+I(X3^2)+I(X4^2) + X1*X2 + X1*X3 + X1*X4 + X2*X3 + X2*X4 + X3*X4 repeatedly to glm(). (I really have little knowledge about how R or glm() works internally) Let's say I call glm() 200 times with various combinations does it make sense to compute these various factors based on X1 .. X4 and store them in a file along with the original data, and then use that file for the glm() calls or will the overhead of computing these factors be so small that it's not worth computing these values ahead of time and storing them in a file? This is simplified example, I actually have 20 original variables rather than the 4 I show above. I hope this made some sense. Thanks, Esmail ps: If it makes sense to preprocess X1,X2,X3 and X4 to generate a new file that contains the values for X1, X2, X3, X4, I(X1^2), I(X2^2), I(X3^2), I(X4^2), X1*X2, X1*X3, X1*X4 ,X2*X3, X2*X4, X3*X4 is there an easy way to take the expression at the top of the message and convert the values in the original dataframe and compute them so that I can write them out to a new file? __ 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] Printing output in STDOUT
Edward Wijaya wrote: Hi, Currently the R script I have is executed with this command: $ R CMD BATCH mycode.R And the output is stored in mycode.Rout. Is there a way I can issue command from shell (like above) so that the output is printed to STDOUT? It's troublesome to open the Rout file every time to debug. Under a Unix system you could try to pipe the command into tail -f i.e., $ R CMD BATCH mycode.R | tail -f That should display the file as it gets written. I don't have access to a Unix system right now to give this a try but it should be a work around until someone who knows more about R can come up with an answer. HTH Esmail __ 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] Printing output in STDOUT
Prof Brian Ripley wrote: On Tue, 20 May 2008, Esmail Bonakdarian wrote: Edward Wijaya wrote: Hi, Currently the R script I have is executed with this command: $ R CMD BATCH mycode.R And the output is stored in mycode.Rout. Is there a way I can issue command from shell (like above) so that the output is printed to STDOUT? It's troublesome to open the Rout file every time to debug. Under a Unix system you could try to pipe the command into tail -f i.e., $ R CMD BATCH mycode.R | tail -f That should display the file as it gets written. Buffering may get in the way -- so 'gets written' may be much later than when it is output by R. Yes, that's quite likely to be the case .. I like your suggestions below much better - saved away for future reference too. Esmail __ 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] Format integer
Anh Tran wrote: Hi, What's one way to convert an integer to a string with preceding 0's? such that '13' becomes '013' to be put into a string I've tried formatC, but they removes all the zeros and replace it with blanks Hi, try sprintf: i=13 cat(sprintf(%05d\n, i)) 00013 HTH, Esmail __ 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] test
Tony Plate wrote: You probably should check this section in your R-help subscription options (via https://stat.ethz.ch/mailman/options/r-help/, I think): Receive your own posts to the list? Tony, Like jt I too have it set to receive my own messages, but I too don't see them. I wonder if it has to do with the fact that both of us use gmail to post to the list? In any case, regardless if we see them, they are getting posted, which is what matters :) Cheers, Esmail __ 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] test
Charilaos Skiadas wrote: On May 13, 2008, at 5:52 AM, Esmail Bonakdarian wrote: Tony Plate wrote: You probably should check this section in your R-help subscription options (via https://stat.ethz.ch/mailman/options/r-help/, I think): Receive your own posts to the list? Tony, Like jt I too have it set to receive my own messages, but I too don't see them. I wonder if it has to do with the fact that both of us use gmail to post to the list? Bingo! Well, I don't know if this happens with the web interface to gmail, but if you use POP to access your gmail account, then any emails you send to any kind of list will not get back to you Yup, I use Thunderbird to read/process my gmail :-) (Problem being, sort of, that gmail groups things in Conversations, and in this case will remember the email you sent out and use that copy in the conversation, instead of the one sent through the list. Except that part of the conversation sits in my sent folder rather than being nicely threaded into the conversation. Not a very good excuse in my opinion, and a particularly irritating feature.). agreed! In the rare occasions where my waiting powers get exhausted before someone on this very helpful list replies to my email, I just use the online archives to check whether my email was sent or not. Yes, I did that initially when I wasn't sure if my message was getting out. Often thought I don't have to do this because the helpful folks on this list have already replied to my posting. Best, Esmail __ 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] Random number generation
Greg Snow wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Esmail Bonakdarian Sent: Sunday, May 11, 2008 7:25 AM To: Prof Brian Ripley Cc: [EMAIL PROTECTED] Subject: Re: [R] Random number generation [snip] What I read doesn't seem to be incorrect however (it may even have been an archived message here), the *language* itself does not seem to support block *comments*. Using conditional constructs, or an IDE/editor to achieve similar results is a work around - but not the same. I don't mean to nitpick, but as a computer scientist I see this as different :-) I am not a computer scientist, so correct me if I am wrong, but from what I remember (and a quick glance at my copy of Kernighan Ritchie), the C *language* itself does not support block *comments*, rather the preproccessor Hi there, Yes, while that may be true, many other languages that don't use an explicit pre-processor mechanism (though internally will go through a similar process) do support block comments. It's a moot point anyway, since when you compile a C program the preprocessor also runs (just like the linker etc) unless you specifically ask for something differently via command line switches. As far as the programmer is concerned the semantics are those of a language that provides block comments with the simple use of /* */ , and not dependent on if-statements or editor/IDE tricks. Since R is optimized for interactive use rather than compilation, running everything through a preproccessor is not really an option. However as an additional work around My use then may be not typical since I am trying to write scripts in R and only use R directly to try out functions/language constructs. you could always run your R scripts through the C preproccessor and have it strip the block comments for you. Too much work, call me old school, but I like the computer do work for me, rather than the other way around :-) Given the complexity of implementing block commenting (even deciding on the syntax) and the ease of current work arounds, the cost benefit ratio probably puts this very near the bottom of the priority list. I couldn't possibly offer an opinion on that .. I'll happily defer to you and the other experts here for this. Cheers, Esmail __ 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] [OT] xemacs on windows vista
Wensui Liu wrote: Hi, dear all, I just switch to vista (ultimate) and have heard there is some problem for the installation of xemacs on vista. Is there any insight or experience that you could share? I really appreciate any input. thank you so much! Hi, I don't know about XEmacs, but I am using a specially bundled version of GNU Emacs by Vincet Goulet which is great. I was using a plain-vanilla version of GNU Emacs before, but this one has ESS and spell check support built in :-) I am using it under XP .. I believe this also works under Vista Check out: http://vgoulet.act.ulaval.ca/en/ressources/emacs/ HTH, Esmail __ 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] Random number generation
Stephan Kolassa wrote: Have you tried successively removing/commenting parts of the script before the sample() command until the problem goes away? That way you should be able to pinpoint the offending script command. Hi, This brings up a question I have .. is there a way to do *block* comments with scripts? A la /* ... */ like it's done in Java or C/C++? Ie comment more than just one line at a time. From what I have read this is not possible in R (at least not easily), but I am eager for someone to contradict me :-) Thanks, Esmail __ 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] Random number generation
Hello there,
Prof Brian Ripley wrote:
On Sun, 11 May 2008, Esmail Bonakdarian wrote:
Stephan Kolassa wrote:
Have you tried successively removing/commenting parts of the script
before the sample() command until the problem goes away? That way you
should be able to pinpoint the offending script command.
Hi,
This brings up a question I have .. is there a way to do *block* comments
with scripts? A la /* ... */ like it's done in Java or C/C++? Ie comment
more than just one line at a time.
From what I have read this is not possible in R (at least not easily),
but
I am eager for someone to contradict me :-)
if(FALSE) {
...
}
Any good editor can do block commenting, e.g. ESS.
You didn't tell us what you read, but I have never seen this in a
reputable source.
I don't remember the source as I was reading widely all over the place
trying to get up to speed with R in a hurry (having found this group
was one of the best sources).
What I read doesn't seem to be incorrect however (it may even have been an
archived message here), the *language* itself does not seem to support block
*comments*. Using conditional constructs, or an IDE/editor to achieve similar
results is a work around - but not the same. I don't mean to nitpick, but
as a computer scientist I see this as different :-)
I'll have to look at ESS though.
Thanks,
Esmail
ps: Ah, I seem Meta-; works as a toggle in emacs/ESS .. thanks for encouraging
me to look at that some more.
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[R] which.max2()
Hello,
which.max() only returns one index value, the one for the
maximum value. If I want the two index values for the two
largest values, is this a decent solution, or is there a
nicer/better R'ish way?
max2 -function(v)
{
m=which.max(v)
v[m] = -v[m]
m2=which.max(v)
result=c(m, m2)
result
}
Seems to work ok.
Thanks,
Esmail
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Re: [R] which.max2()
Dimitris Rizopoulos wrote: try this: v - rnorm(10) v order(v, decreasing = TRUE)[1:2] Wow .. that is slick! First I thought, wait .. I don't want to reorder the elements, but this doesn't - it just returns the index values in order. I don't really get that from reading the documentation, it's probably there, but not that clear to me. Thanks for showing me something more R'ish. Esmail __ 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] which.max2()
Marc Schwartz wrote:
I might be tempted to take a more generic approach, where one can
provide an argument to the function to indicate that I want the 'top x'
maximum values and to give the user the option of returning the indices
or the values themselves.
Perhaps:
which.max2 - function(x, top = 1, values = FALSE)
{
if (values)
rev(sort(x))[1:top]
else
order(x, decreasing = TRUE)[1:top]
}
Very cool too! .. Thanks Marc. Again, I did not get this from the
order documentation (ie that it manipulate index values rather than
the values themselves). Great to see examples.
Best,
Esmail
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[R] building a formula string bit by bit ..
Hello,
Still a newbie with R, though I have learned a lot from reading
this list. I'm hoping someone can help with this question:
I have two vectors, one for variables, and one for bits.
I want to build a string (really a formula) based on the values in my
vector of 1s and 0s in bits. If I have a one, I want to include the
corresponding entry in the vars vector, otherwise ignore it. Of course
the bits vector will not stay the same.
So for example:
vars=c('X.1', 'X.2', 'X.3', 'X.4', 'X.5')
bits=c(1, 0, 1, 1, 0)
ones=which(bits==1)
should yield:
X.1 + X.3 + X.4
where as
bits=c(1, 1, 0, 0, 0)
would yield
X.1 + X.2
the which operator gives me the index values, is there an easy and
*efficient* way to build this string so that I can pass it on to glm?
I can probably hack some ugly code together to do this, but it won't
be efficient, and it won't be elegant :-)
Can anyone help?
Thanks!
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Re: [R] building a formula string bit by bit ..
Jorge Ivan Velez wrote:
Hi Esmail,
Try this:
vars=c('X.1', 'X.2', 'X.3', 'X.4', 'X.5')
bits=c(1, 0, 1, 1, 0)
paste(vars[which(bits==1)],collapse=+)
HTH,
Jorge
Wow .. that is beautiful :-) .. and exactly what I was looking
for (and suspected existed).
I ended up doing this:
eqn=(paste(vars[which(bits==1)],collapse= + ))
eqn=paste(c(Y.data ~), eqn)
GLM.9 - glm(as.formula(eqn) , family=gaussian(identity), data=simpleData)
For some reason I couldn't collapse the two eqn/paste statements into one
statement but this seems to work.
Thank again Jorge and everyone else .. this group is a big help.
Esmail
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[R] Automatically generating new column names (and columns)
Once again I need to tap into the collective knowledge here.
Let's say I have the following columns and data below
Y X1 X2 X3 X4
I would like to generate additional new columns and column names
(ie the data would be squared - and I'd like the column names to
reflect this) like:
Y X1 X2 X3 X4 X1^2 X2^2 X3^2 X4^2
I believe I can compute the values correctly with the code below, but
I am unable to generate the column names. (This is a short example, in
reality I have many more columns and more complicated names)
for(i in 2:5)
{
name=get(paste(names(simpleData)[i],^2, sep=))
simpleData- transform(simpleData, name=(simpleData[,i]^2))
}
print(simpleData)
Any suggestions/hints .. I've searched the FAQ and web (this is how I
came across the get() function) but no luck so far.
Thanks,
Esmail
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[R] efficiency profiling? (was: Why R is 200 times slower than Matlab ?)
This has been an interesting discussion, and brings up two questions for me: Is there a good collection of hints/suggestions for R language idoms in terms of efficiency? For instance I read not to use for-loops, so I used apply only to later read that apply is internally implemented as a for so nothing gained here. Warnings about pitfalls (such as nested loops), hints, suggestions would be great. The second question - is there some sort of profiling tool available that would make it easy to recognize where the script is spending most of its time? Might be especially useful for newbies like me. Thanks all, Esmail __ 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. _ Spell a grand slam in this game where word skill meets World Series. Get in the game. 08 [[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] efficiency profiling?
See ?Rprof for the tool. For the tips, I think you just need to hang around here a while. I don't know of a nice collection (but I'm sure there are several.) Duncan Murdoch Hi, thanks .. several folks pointed me to Rprof, I'll take a look. Yes, I have been reading the list, the amount of messages per day is simply amazing, I can hardly keep up. Do most of you read this on the web or get it as digest? I am getting them as individual e-mails (thank god for filters) ... :-) Esmail _ Back to work after babyhow do you know when youre ready? 5797498ocid=T067MSN40A0701A [[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] Documentation General Comments
I realize the R developers are probably overwhelmed and have little time for this, but the documentation really needs some serious reorganizaton. A good through description of basic variable types would help a lot, e.g. the difference between lists, arrays, matrices and frames. Agreed, esp since I am right now at this moment struggling with the differences of lists, arrays and vectors. (I have two vectors that I am trying to return from a function as an array of two rows - for some reason that's not working) I just started with the R last week , and I am trying to get up to speed with this language. And while I have many years of experience with various programming languages, many which I have learned on my own, I am encountering a number of things that are slowing me down. I have downloaded the various intro/reference materials. I am super-happy to have found this list though, everyone seems friendly and helpful, and I am learning a lot from it. Any new/additional documentation would be much welcome. _ esh_getintouch_042008 [[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] Documentation General Comments
Thank you Rob, I just downloaded it and it looks very useful. In the meantime I think I solved my immediate problem (and while pluggin' away also deepened my understanding - or so I will at least claim :-) Esmail I don't know if you will find this helpful, but one of the better online chapters on R Data Objects that I've found is by Tomas Aragon and Wayne Enanoria. Among other nice attributes it has some tables that summarize improtant functions for working with different data objects. The URL is: http://www.medepi.net/epir/epir_chap02.pdf Rob Baer _ Pack up or back upuse SkyDrive to transfer files or keep extra copies. Learn how. sh_skydrive_packup_042008 [[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] representing binary data for Genetic Algorithm in R
Hello all, I am trying to implement a simple Genetic Algorithm. I am doing this in R since I want access to the statistical functions (eg lm) it provides. I'm not new to programming, or GAs, but I am totally new to R (the package and the language), and I am hoping someone could help with these questions: 1. I am going to use a binary representation, it seems that vectors of Factors would be what I should use? I would specify values of TRUE/FALSE instead? Or is there a better choice for manipulating binary strings? Does this seem like a legitimate way to create a random one: sample(0:1, vec_size, replace=T) 2. Am I correct in assuming that R is interpreted (and hence is going to be noticeably slower than compiled languages)? 3. Is there some sort of debugging facility? 4. Does anyone know how to do an effective search for R in google (or other search engines). The fact that this is a single letters seems to have most applications ignore this input. This might help me in finding answers to some other basic questions I have (such as is there an equivalent function to printf in R? cat and print are not quite working right for me -- but I need to dig deeper into the documentation) I am not sure if this belongs into the help or development group, so I'm giving this a try. If this is the wrong group to post in, please let me know and I'll repost. There will probably be more elementary questions (I am reading the various manuals too .. but if anyone has some other favorite sites they want to recommend please do so) Thanks, Esmail ps: I there a USENET group dedicated to R? pps: I am also exploring ways of calling R functions from Java, if anyone has any comments regarding that please share. _ Going green? See the top 12 foods to eat organic. 1N1653A [[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] representing binary data for Genetic Algorithm in R
Hello! Dear Esmail, you really have to have a look at some introduction to R (e.g. http://cran.r-project.org/doc/manuals/R-intro.pdf), but see the Manual section in R website (http://www.r-project.org/). That would answer many of your questions. point well taken, I am a bit in a hurry with a project I inherited unexpectedly, so I was trying to take some shortcuts in trying to get up to speed intending to dig into the documentation more in depth as soon as possible. I do have the documents you mention and have been trying to scan them. thanks for your post, Esmail _ Going green? See the top 12 foods to eat organic. 1N1653A [[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.
