Re: [R] How can I make my functions run faster
Greetings,
I am a newbie too. I will share what I do normally for speeding up the code.
1. Restrict defining too many variables (Global/ Local)
2. Use apply functions (apply,sapply,lapply,tapply, etc.) whenever feasible
3. Having multiple user defined functions doesn't help. Try to compact
everything in minimum number of functions
4. The in-memory of R is just 10% of your total RAM (Correct me if wrong).
Make sure most of it is used for processing and not storing
Hope this will help. Kindly suggest if I have misunderstood anything.
Thanks and Regards,
Heramb Gadgil
2013/8/19 Laz lmra...@ufl.edu
Yes Bert, I am a beginner in writing R functions. I just don't know what
to avoid or what to use in order to make the R functions faster.
When I run the individual functions, they run quite well.
However, calling all of them using the final function it becomes too slow.
So I don't know how to make it faster.
I used system.time()
Regards,
Laz
On 8/19/2013 10:13 AM, Bert Gunter wrote:
... and read the R Language Definition manual. I noticed unnecessary
constructs
(e.g., z - f(something); return(z)) that suggest you have more basics
to learn to write efficient, well-structured R code.
-- Bert
On Mon, Aug 19, 2013 at 3:55 AM, Michael Dewey i...@aghmed.fsnet.co.uk
wrote:
At 10:28 19/08/2013, Laz wrote:
Dear R users,
I have written a couple of R functions, some are through the help of
the R
group members. However, running them takes days instead of minutes or a
few
hours. I am wondering whether there is a quick way of doing that.
Your example code is rather long for humans to profile. Have you thought
of
getting R to tell where it is spending most time? The R extensions manual
tells you how to do this.
Here are all my R functions. The last one calls almost all of the
previous
functions. It is the one I am interested in most. It gives me the
correct
output but it takes several days to run only 1000 or 2000 simulations!
e.g. system.time(test1-finalF(**designs=5,swaps=20));test1
will take about 20 minutes to run but
system.time(test1-finalF(**designs=5,swaps=50));test1 takes about 10
hours
and system.time(test1-finalF(**designs=25,swaps=2000));test1 takes
about 3
days to run
Here are my functions
##**##**
#
ls() # list all existing objects
rm(list = ls()) # remove them all
rm(list = ls()[!grepl(global.var.A, ls())])
# refresh memory
gc()
ls()
### Define a function that requires useful input from the user
#b=4;g=seq(1,20,1);rb=5;cb=4;**s2e=1; r=10;c=8
##**###
##**##
# function to calculate heritability
herit-function(varG,varR=1)
{
h-4*varG/(varG+varR)
return(c(heritability=h))
}
##**#
# function to calculate random error
varR-function(varG,h2)
{
varR- varG*(4-h2)/h2
return(c(random_error=varR))
}
##**
# function to calculate treatment variance
varG-function(varR=1,h2)
{
varG-varR*h2/(4-h2)
return(c(treatment_variance=**varG))
}
##**#
# calculating R inverse from spatial data
rspat-function(rhox=0.6,rhoy=**0.6)
{
s2e-1
R-s2e*eye(N)
for(i in 1:N) {
for (j in i:N){
y1-y[i]
y2-y[j]
x1-x[i]
x2-x[j]
R[i,j]-s2e*(rhox^abs(x2-x1))***(rhoy^abs(y2-y1)) # Core
AR(1)*AR(1)
R[j,i]-R[i,j]
}
}
IR-solve(R)
IR
}
ped-read.table(ped2new.txt**,header=FALSE)
# Now work on the pedigree
## A function to return Zinverse from pedigree
ZGped-function(ped)
{
ped2-data.frame(ped)
lenp2-length(unique(ped2$V1))**;lenp2 # how many Genotypes in
total in
the pedigree =40
ln2-length(g);ln2#ln2=nrow(**matdf)=30
# calculate the new Z
Zped-model.matrix(~ matdf$genotypes -1)# has order N*t = 180 by 30
dif-(lenp2-ln2);dif # 40-30=10
#print(c(lenp2,ln2,dif))
zeromatrix-zeros(nrow(matdf),**dif);zeromatrix # 180 by 10
Z-cbind(zeromatrix,Zped) # Design Matrix for random effect
(Genotypes):
180 by 40
# calculate the new G
M-matrix(0,lenp2,lenp2) # 40 by 40
for (i in 1:nrow(ped2)) { M[ped2[i, 1], ped2[i, 2]] - ped2[i, 3] }
G-s2g*M # Genetic Variance covariance matrix for pedigree 2: 40 by
40
IG-solve(G)
return(list(IG=IG, Z=Z))
}
##
##Required packages#
library(gmp)
library(knitr) # load this packages for publishing results
library(matlab)
library(Matrix)
library(psych)
library(foreach)
library(epicalc)
library(ggplot2)
library(xtable)
library(gdata)
library(gplots)
#b=6;g=seq(1,30,1);rb=5;cb=6;**r=15;c=12;h2=0.3;rhox=0.6;**
rhoy=0.6;ped=0
setup-function(b,g,rb,cb,r,c,**h2,rhox=0.6,rhoy=0.6,ped=F)
{
# where
# b = number of blocks
# t = number of treatments
Re: [R] How can I make my functions run faster
Greetings, Thanks Jeff. I appreciate your 'to the point' explanation. Will read into it more. Best, Heramb Gadgil 2013/8/19 Jeff Newmiller jdnew...@dcn.davis.ca.us 1. Keeping the number of variables down encourages you to structure your data, which allows you to re-use code more efficiently. However, I don't believe that the number of variables intrinsically slows down your code significantly.. e.g. storing a computed value in a local variable is almost always better than repeating the calculation. 2. Apply functions are not primarily intended for performance optimization; they are effective for compactly expressing the idea of your algorithms. Using vectorization and indexing is much more effective for enhancing performance (and in my mind is even better at expressing algorithms than using apply functions). 3. Agree that too many functions can slow things down, but that is normally less the fault of the functions than of the way some programmers handle data. It is more productive to focus on the positive idea of using vectors to compute as much as possible rather than the negative idea of eliminating functions. 4. I don't think I agree that this statement about memory usage generally applies to all uses of R. However, it can be crucial to learn to avoid mixing input/output with data processing if you are interested in performance. To the OP: I will pass on trying to analyse your large code base... it is requested in the Posting Guide that you isolate your issues and ask specific questions. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. Heramb Gadgil heramb.gad...@gmail.com wrote: Greetings, I am a newbie too. I will share what I do normally for speeding up the code. 1. Restrict defining too many variables (Global/ Local) 2. Use apply functions (apply,sapply,lapply,tapply, etc.) whenever feasible 3. Having multiple user defined functions doesn't help. Try to compact everything in minimum number of functions 4. The in-memory of R is just 10% of your total RAM (Correct me if wrong). Make sure most of it is used for processing and not storing Hope this will help. Kindly suggest if I have misunderstood anything. Thanks and Regards, Heramb Gadgil 2013/8/19 Laz lmra...@ufl.edu Yes Bert, I am a beginner in writing R functions. I just don't know what to avoid or what to use in order to make the R functions faster. When I run the individual functions, they run quite well. However, calling all of them using the final function it becomes too slow. So I don't know how to make it faster. I used system.time() Regards, Laz On 8/19/2013 10:13 AM, Bert Gunter wrote: ... and read the R Language Definition manual. I noticed unnecessary constructs (e.g., z - f(something); return(z)) that suggest you have more basics to learn to write efficient, well-structured R code. -- Bert On Mon, Aug 19, 2013 at 3:55 AM, Michael Dewey i...@aghmed.fsnet.co.uk wrote: At 10:28 19/08/2013, Laz wrote: Dear R users, I have written a couple of R functions, some are through the help of the R group members. However, running them takes days instead of minutes or a few hours. I am wondering whether there is a quick way of doing that. Your example code is rather long for humans to profile. Have you thought of getting R to tell where it is spending most time? The R extensions manual tells you how to do this. Here are all my R functions. The last one calls almost all of the previous functions. It is the one I am interested in most. It gives me the correct output but it takes several days to run only 1000 or 2000 simulations! e.g. system.time(test1-finalF(**designs=5,swaps=20));test1 will take about 20 minutes to run but system.time(test1-finalF(**designs=5,swaps=50));test1 takes about 10 hours and system.time(test1-finalF(**designs=25,swaps=2000));test1 takes about 3 days to run Here are my functions ##**##** # ls() # list all existing objects rm(list = ls()) # remove them all rm(list = ls()[!grepl(global.var.A, ls())]) # refresh memory gc() ls() ### Define a function that requires useful input from the user #b=4;g=seq(1,20,1);rb=5;cb=4;**s2e=1; r=10;c=8 ##**### ##**## # function
Re: [R] how to get a value from a list (using paste function)?
I am not sure why Never ever! Can you please elaborate. What are the negatives about the method Warm Regards, Heramb M. Gadgil On Thu, Dec 27, 2012 at 3:50 PM, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: On 27.12.2012 08:09, Heramb Gadgil wrote: eval(parse(text=paste0(**cvtest$,lambda.rule))) No, never ever! There is an R idiom made for it: cvtest[[lambda.rule]] Uwe Ligges I hope this works. On Wed, Dec 19, 2012 at 12:57 AM, Thomas Stewart tgs.public.m...@gmail.com**wrote: Soyeon- A possible solution: get(lambda.rule,envir=**list2env(cvtest)) On Tue, Dec 18, 2012 at 12:34 PM, Soyeon Kim yunni0...@gmail.com wrote: Dear my R friends, I want to get a number from a list using paste function. In my example, lambda.rule - lambda.1se cvtest is a list (result from cv.glmnet) and cvtest$lambda.1se [1] 1.308973 I want to call the value using paste function. I used get function but there was an error. test - get(paste(cvtest$,lambda.**rule, sep=)) Error in get(paste(cvtest$, lambda.rule, sep = )) : object 'cvtest$lambda.1se' not found Do you guys know how to solve this issue? Thank you so much in advance and merry Christmas! Soyeon __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/**posting-guide.htmlhttp://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/**posting-guide.htmlhttp://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to get a value from a list (using paste function)?
Agreed. But the initial question was to get the output with paste function. That is the reason why I went for eval. Please let me know in case I am going the wrong way On Thu, Dec 27, 2012 at 4:34 PM, Jessica Streicher j.streic...@micromata.de wrote: Well for one, if ever someone looks at your code, cvtest[[lambda.rule]] is much easier to read and understand than eval(parse(text=paste0(cvtest$,lambda.rule))) On 27.12.2012, at 11:44, Heramb Gadgil wrote: I am not sure why Never ever! Can you please elaborate. What are the negatives about the method Warm Regards, Heramb M. Gadgil On Thu, Dec 27, 2012 at 3:50 PM, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: On 27.12.2012 08:09, Heramb Gadgil wrote: eval(parse(text=paste0(**cvtest$,lambda.rule))) No, never ever! There is an R idiom made for it: cvtest[[lambda.rule]] Uwe Ligges I hope this works. On Wed, Dec 19, 2012 at 12:57 AM, Thomas Stewart tgs.public.m...@gmail.com**wrote: Soyeon- A possible solution: get(lambda.rule,envir=**list2env(cvtest)) On Tue, Dec 18, 2012 at 12:34 PM, Soyeon Kim yunni0...@gmail.com wrote: Dear my R friends, I want to get a number from a list using paste function. In my example, lambda.rule - lambda.1se cvtest is a list (result from cv.glmnet) and cvtest$lambda.1se [1] 1.308973 I want to call the value using paste function. I used get function but there was an error. test - get(paste(cvtest$,lambda.**rule, sep=)) Error in get(paste(cvtest$, lambda.rule, sep = )) : object 'cvtest$lambda.1se' not found Do you guys know how to solve this issue? Thank you so much in advance and merry Christmas! Soyeon __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-help https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/**posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-help https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/**posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-help https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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. [[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] how to get a value from a list (using paste function)?
Thanks a lot for the explaination. Much appreciated. :-) On Thu, Dec 27, 2012 at 10:31 PM, William Dunlap wdun...@tibco.com wrote: Can you please elaborate. What are the negatives about the method Here are a few examples of eval(parse(text=paste())) failing: cvtest - list(Test-1=1, Bozo=2, Joe's Test=3) lambda.rule - Test-1 eval(parse(text=paste0(cvtest$, lambda.rule))) # want 1 [1] 0 lambda.rule - Joe's Test eval(parse(text=paste0(cvtest$, lambda.rule))) # want 3 Error in parse(text = paste0(cvtest$, lambda.rule)) : text:1:11: unexpected INCOMPLETE_STRING 1: cvtest$Joe's Test ^ and here is an example of $ giving a suboptimal result: cvtest$B # want NULL (there is no component named B) [1] 2 [[ gives the correct result in all cases: lambda.rule - Test-1 cvtest[[lambda.rule]] [1] 1 lambda.rule - B cvtest[[lambda.rule]] NULL lambda.rule - Bozo cvtest[[lambda.rule]] [1] 2 lambda.rule - Joe's Test cvtest[[lambda.rule]] [1] 3 Also, I find it hard to read code involving eval(parse(text=paste(...))). Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Heramb Gadgil Sent: Thursday, December 27, 2012 2:44 AM To: Uwe Ligges Cc: Thomas Stewart; r-help Subject: Re: [R] how to get a value from a list (using paste function)? I am not sure why Never ever! Can you please elaborate. What are the negatives about the method Warm Regards, Heramb M. Gadgil On Thu, Dec 27, 2012 at 3:50 PM, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: On 27.12.2012 08:09, Heramb Gadgil wrote: eval(parse(text=paste0(**cvtest$,lambda.rule))) No, never ever! There is an R idiom made for it: cvtest[[lambda.rule]] Uwe Ligges I hope this works. On Wed, Dec 19, 2012 at 12:57 AM, Thomas Stewart tgs.public.m...@gmail.com**wrote: Soyeon- A possible solution: get(lambda.rule,envir=**list2env(cvtest)) On Tue, Dec 18, 2012 at 12:34 PM, Soyeon Kim yunni0...@gmail.com wrote: Dear my R friends, I want to get a number from a list using paste function. In my example, lambda.rule - lambda.1se cvtest is a list (result from cv.glmnet) and cvtest$lambda.1se [1] 1.308973 I want to call the value using paste function. I used get function but there was an error. test - get(paste(cvtest$,lambda.**rule, sep=)) Error in get(paste(cvtest$, lambda.rule, sep = )) : object 'cvtest$lambda.1se' not found Do you guys know how to solve this issue? Thank you so much in advance and merry Christmas! Soyeon __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r- helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/**posting-guide.htmlhttp://www.R- project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r- helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/**posting-guide.htmlhttp://www.R- project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r- helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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. [[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] Renaming column names according to another dataframe
try this: colnames(df)-df_names[1:ncol(df),name] On Sun, Dec 23, 2012 at 8:41 PM, radhi radhikum...@yahoo.in wrote: Hi, I've got a dataframe having a code as column name. Addtionally I have another dataframe with a two columns (and lots of rows), the first containing the code and the second some Text (real name). Now I'd like to use the information (pairs of code and name) of the second dataframe to rename all the columnnames in the first dataframe. How is it possible to achieve that? Here a small example of the two dataframes: df - data.frame(A=(1:10),B=(1:10),C=(1:10)) df_names - data.frame(code=c(A,B,C,D,E),name=c(Col A,Col B,Col C,Col D,Col E)) click here http://totalltelugumovies.blogspot.in -- View this message in context: http://r.789695.n4.nabble.com/Renaming-column-names-according-to-another-dataframe-tp4653824.html Sent from the R help mailing list archive at Nabble.com. [[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. [[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] how to read different files into different objects in one time?
You can try this one too.
#Set the directory to a path where all the files to be read are stored
TabletoRead=list.files(pattern=.txt)
I_Step=unlist(lapply(TabletoRead,function(tab){
srno-ifelse(exists(srno),(1+srno),1)
Temp=read.table(tab,header=T,sep=#Seperator)
makeActiveBinding(paste(Table,srno,sep=_),
function() Temp, .GlobalEnv)
}))
rm(I_Step)
Ref_Table=cbind(Orignial=TabletoRead,Stored_As=paste(Table,1:length(TabletoRead),sep=_))
#When required you can check the Ref_Table to get the required table
On Thu, Dec 20, 2012 at 10:41 AM, Jeff Newmiller
jdnew...@dcn.davis.ca.uswrote:
The short answer is: don't try. You really don't want dozens of different
objects in memory that you didn't name yourself.
What you want instead is a list of objects. You can start with a vector of
filenames and use lapply to create another list containing the data frames.
For convenience you can then set the list element names to the names of the
files.
fnames - list.files()
dta - lapply( fnames, function(i){read.table(i, header= TRUE) })
names(dta) - fnames
You can access these data frames using the $ or [[ operators.
dta$G1.txt
dta[[G1.txt]]
or
dta[[2]]
Read more about it in the Introduction to R document supplied with R.
---
Jeff NewmillerThe . . Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live
Go...
Live: OO#.. Dead: OO#.. Playing
Research Engineer (Solar/BatteriesO.O#. #.O#. with
/Software/Embedded Controllers) .OO#. .OO#. rocks...1k
---
Sent from my phone. Please excuse my brevity.
Yao He yao.h.1...@gmail.com wrote:
Dear All
I have a lot of files in a directory as follows:
02-03.txt 03-04.txt 04-05.txt 05-06.txt 06-07.txt
07-08.txt 08-09.txt
09-10.txt G0.txt G1.txt raw_ped.txt
..
I want to read them into different objects according to their
filenames,such as:
02-03-read.table(02-03.txt,header=T)
03-04-read.table(03-04.txt,header=T)
I don't want to type hundreds of read.table(),so how I read it in one
time?
I think the core problem is that I can't create different objects'
name in the use of loop or sapply() ,but there may be a better way to
do what I want.
Thanks a lot
Yao He
Yao He
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Re: [R] how to get a value from a list (using paste function)?
eval(parse(text=paste0(cvtest$,lambda.rule))) I hope this works. On Wed, Dec 19, 2012 at 12:57 AM, Thomas Stewart tgs.public.m...@gmail.comwrote: Soyeon- A possible solution: get(lambda.rule,envir=list2env(cvtest)) On Tue, Dec 18, 2012 at 12:34 PM, Soyeon Kim yunni0...@gmail.com wrote: Dear my R friends, I want to get a number from a list using paste function. In my example, lambda.rule - lambda.1se cvtest is a list (result from cv.glmnet) and cvtest$lambda.1se [1] 1.308973 I want to call the value using paste function. I used get function but there was an error. test - get(paste(cvtest$,lambda.rule, sep=)) Error in get(paste(cvtest$, lambda.rule, sep = )) : object 'cvtest$lambda.1se' not found Do you guys know how to solve this issue? Thank you so much in advance and merry Christmas! Soyeon __ 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. [[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. [[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] install.packages on windows
You can look for different versions of that package and try manually installing the lower version. On Fri, Sep 28, 2012 at 11:25 PM, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: On 28.09.2012 00:32, Duncan Murdoch wrote: On 12-09-27 2:53 PM, Anju R wrote: Sometimes when I try to install certain packages I get a warning message. For example, I tried to install the package Imtest on windows R version 2.15.1 and got the following message: Warning message: package Imtest is not available (for R version 2.15.1) How can I install the above package? Why do I get the above Warning message? It probably means exactly what it says, except that the information is about the mirror you are using. I would try another mirror. If that doesn't solve it, then it probably means that the package is really not available for 2.15.1. You can look on the cran.r-project.org website for information about it, and probably download the source from there, but you will probably need to fix whatever is wrong with it before it will work. Or in other words: There is no such package Imtest on CRAN, perhaps you are looking for lmtest? Uwe Ligges Duncan Murdoch __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/**posting-guide.htmlhttp://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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] mapping data from table to .csv template
Try the following code.
It is basic but effective;
*setwd(/home/user2/Documents)*
*Test_matrix=read.csv(Trial.csv,header=T) # The 1st table that you have
considered
*
*Test_matrix=as.matrix(Test_matrix)*
*Writer=function(mat){u=unique(mat[,Subject])*
*l=length(u)*
*dummy=lapply(1:l,FUN=function(x){string=u[x]*
*step1=unlist(strsplit(string,))*
*file_name=substring(string,(which(step1==[)+1),(which(step1==])-1))*
*m=mat[which(mat[,Subject]==string),]*
*dummy_matrix=matrix(rep(0,11*11),nrow=11)*
*colnames(dummy_matrix)=#Names of all the 11 ppl.*
*rownames(dummy_matrix)=#Names of all the 11 ppl.*
*for(i in 1:11)*
*{for(j in 1:11)*
*
{index=which(m[,Receiver]==rownames(dummy)[i]m[,Sender]==colnames(dummy)[j])
*
*count=length(index)*
*dummy_matrix[i,j]=count}}*
*
write.csv(dummy_matrix,paste('/home/hduser/',file_name,'_counts','.csv',sep=''))
*
*write.csv(m,paste('/home/hduser/',file_name,.csv,sep=))*
*})}*
*I hope this helps,*
*Best,*
*Heramb
*
On Tue, Sep 25, 2012 at 12:29 PM, PIKAL Petr petr.pi...@precheza.cz wrote:
Hi
your data are difficult to read so I make my own
set.seed(111)
sender-sample(letters[1:5], 20, replace=T)
receiver-sample(letters[1:5], 20, replace=T)
xtabs(~sender+receiver)
receiver
sender a b c d e
a 1 1 3 1 0
b 0 1 0 1 1
c 1 3 2 2 0
d 0 1 0 0 1
e 0 0 0 1 0
If you want such result from each subject of your table }presumably
data.frame just split and lapply it
untested
lapply(split(your.data, by a column), function (x)
xtabs(~x$sender+x$receiver))
Regards
Petr
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of s.s.m. fauzi
Sent: Tuesday, September 25, 2012 4:06 AM
To: r-help@r-project.org
Subject: [R] mapping data from table to .csv template
I have a .csv table named mailing.csv as below. It consist a receiver,
subject and sender.
Receiversubject sender
1 Adrian ColeRE: [WHIRR-117] Composable servicesTom White
2 Adrian ColeRE: [WHIRR-117] Composable servicesTom White
3 Adrian ColeRE: [WHIRR-117] Composable services Adrian Cole
4 Adrian ColeRE: [WHIRR-117] Composable services Adrian Cole
5 Adrian ColeRE: [WHIRR-117] Composable servicesTom White
6 Adrian ColeRE: [WHIRR-117] Composable services Adrian Cole
7 Adrian ColeRE: [WHIRR-117] Composable servicesTom White
8 Adrian ColeRE: [WHIRR-117] Composable servicesTom White
9 Adrian ColeRE: [WHIRR-117] Composable services Adrian Cole
10 Adrian ColeRE: [WHIRR-117] Composable services Adrian Cole
11 Adrian ColeRE: [WHIRR-117] Composable servicesTom White
12 Adrian ColeRE: [WHIRR-117] Composable servicesTom White
13 Adrian ColeRE: [WHIRR-117] Composable servicesTom White
14 Adrian ColeRE: [WHIRR-117] Composable servicesTom White
15 Patrick Hunt RE: [WHIRR-123] Cassandra integration Tom White
16 Patrick Hunt RE: [WHIRR-123] Cassandra integration Andrei Savu
17 Patrick Hunt RE: [WHIRR-123] Cassandra integration Andrei Savu
18 Patrick Hunt RE: [WHIRR-123] Cassandra integration Tom White
19 Patrick Hunt RE: [WHIRR-123] Cassandra integration Tom White
20 Patrick Hunt RE: [WHIRR-123] Cassandra integration Adrian Cole
21 Patrick Hunt RE: [WHIRR-123] Cassandra integration Tom White22
Patrick Hunt RE: [WHIRR-123] Cassandra integration Patrick Hunt
What I would like to do is to update/map the information from table
above to .csv template (namedAC_template.csv), and save it in a
separate file using subject details in backet as file name (for
instance AC_WHIRR-117). As for table above, it should create two new
files name as AC_WHIRR-117and AC_WHIRR-123.
sample .csv template (AC_template.csv) is as below:
Adrian.Cole Patrick.Hunt Andrei.Savu Bruno.Dumon
Edward.J..Yoon Eugene.Koontz Jakob.Homan Kelvin.Kakugawa Tom.White
Adrian Cole 00 0 0
0 0 0 0 0
Patrick Hunt 00 0 0
0 0 0 0 0
Andrei Savu 00 0 0
0 0 0 0 0
Bruno Dumon 00 0 0
0 0 0 0 0
Edward J. Yoon00 0 0
0 0 0 0 0
Eugene Koontz 00 0 0
0 0 0 0 0
Jakob Homan 00 0 0
0 0 0 0 0
Kelvin Kakugawa
Re: [R] Script to count unique values from two linked matricies
We can have something like this;
*Data1-data.frame(Site1=c(5,NA,4),Site2=c(3,2,4),Site3=c(NA,5,NA))
Data2-data.frame(TraitType1=c(1,2,3),TraitType2=c(2,4,2),TraitType3=c(5,1,1))
*
*rownames(Data1)-paste(Species,1:3)*
*rownames(Data2)-paste(Species,1:3)*
*User_Defined=function(dat1,dat2){c1=ncol(dat1)*
*out=NULL*
*dummy=lapply(1:c1,function(x){step1=dat1[,x]*
*step2=dat2[which(is.na(step1)==F),]*
*step3=length(unlist(apply(step2,2,unique)))*
*out-c(out,step3)*
*})*
*Final-data.frame(TraitRichness=out)*
*rownames(Final)-paste('Site',1:3)*
*Final_Table-Final*
*}*
*User_Defined(Data1,Data2)*
*Final_Table*
I hope this is what you need.
Best,
Heramb
On Tue, Sep 25, 2012 at 1:41 PM, Benjamin Gillespie gy...@leeds.ac.ukwrote:
Hi,
Thanks for helping me with this one.
To save you time, the following is the code for the tables I uploaded as
jpegs that you may not have received:
dat1-data.frame(Species=paste(Species,1:3),Site1=c(5,NA,4),Site2=c(3,2,4),Site3=c(NA,5,NA))
dat2-data.frame(Species=paste(Species,1:3),TraitType1=c(1,2,3),TraitType2=c(2,4,2),TraitType3=c(5,1,1))
dat3-data.frame(Site=paste(Site,1:3),Trait_Richness=c(5,7,3))
So,
I have two matricies, dat1 and dat2.
Dat1 is a species abundance matrix. Dat2 is a species trait matrix.
I want to create dat3 through use of a script.
Dat 3 is a count of unique traits observed at each site. i.e. at site 1,
species 1 and 3 are present (ass seen in dat1). Species 1 has traits: 1, 2
and 5 for trait types 1, 2 and 3 respectively. Species 3 has traits: 3, 2
and 1 for trait types 1, 2 and 3 respectively.
So, at site 1:
For trait type 1, 2 unique traits were observed. For trait type 2, 1
unique trait was observed (both species 1 and 3 were classed as 1) and
for trait type 3, 2 unique traits (trait richness) were observed; thus,
2+1+2=5.
and so on... so at site 2, all three species were observed...
For trait type 1, 3 unique traits were observed (1, 2, 3), for trait type
2, 2 unique traits were observed (2, 4, 2) and for trait type 3, 2 unique
traits were observed (5, 1, 1). So, for site 2, trait richness is 7 (3+2+2)
traits.
I hope this helps to explain, please let me know if you need any further
information,
Ben Gillespie
Research Postgraduate
School of Geography
University of Leeds
Leeds
LS2 9JT
Tel: +44(0)113 34 33345
Mob: +44(0)770 868 7641
http://www.geog.leeds.ac.uk/
From: arun [smartpink...@yahoo.com]
Sent: 24 September 2012 19:36
To: Benjamin Gillespie
Subject: Re: [R] Script to count unique values from two linked matricies
HI Ben,
Sorry,I couldn't understand how you counted the trait richness. Could you
elaborate?
A.K.
- Original Message -
From: benrgillespie gy...@leeds.ac.uk
To: r-help@r-project.org
Cc:
Sent: Monday, September 24, 2012 7:47 AM
Subject: [R] Script to count unique values from two linked matricies
I hope you can help with this one.
I have two matricies:
1. A species abundance matrix:
http://r.789695.n4.nabble.com/file/n4643979/2species_matrix.jpg
2. A species trait score matrix:
http://r.789695.n4.nabble.com/file/n4643979/2trait_matrix.jpg
The trait matrix lists trait scores for each species as listed in the
species abundance matrix.
I would like to create a script that would effectively count the unique
traits (trait richness) for each site and produce an output like this:
http://r.789695.n4.nabble.com/file/n4643979/trait_richness.jpg
Firstly, is this possible in R? Secondly, if so, how would you go about
writing a script to achieve my aim?
Many thanks in advance, please let me know if you need further information.
Ben Gillespie (Research Postgraduate)
--
View this message in context:
http://r.789695.n4.nabble.com/Script-to-count-unique-values-from-two-linked-matricies-tp4643979.html
Sent from the R help mailing list archive at Nabble.com.
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[[alternative HTML version deleted]]
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Re: [R] scraping with session cookies
This may be because connection to the site via R is taking a lot of time. I
too faced this problem for the site Social-Mention.
I tried very primitive approach. I put the 'if' condition in the loop.
if(length(output)==0){getURL(site)
}else{continue with the code}
It might help you.
Best,
Heramb
On Fri, Sep 21, 2012 at 8:45 PM, CPV ceal...@gmail.com wrote:
Thanks for your suggestion,
The issue was resolved by Duncan's recommendation.
Now I am trying to obtain data from different pages from the same site
through a loop, however, the getURLContent keeps timing out, the odd part
is that I can access to the link through a browser with no issues at all!!
Any ideas why it keeps timing out? Also how can I keep the loop running
after this error?
Thanks again for your help!
On Wed, Sep 19, 2012 at 11:36 PM, Heramb Gadgil
heramb.gad...@gmail.comwrote:
Try this,
library(RCurl)
library(XML)
site-
http://www.wateroffice.ec.gc.ca/graph/graph_e.html?mode=textstn=05ND012prm1=3syr=2012smo=09sday=15eyr=2012emo=09eday=18
URL-getURL(site)
Text=htmlParse(URL,asText=T)
This will give you all the web dat in an HTML-Text format.
You can use getNodeSet function to extract whatever links or texts that
you want from that page.
I hope this helps.
Best,
Heramb
On Wed, Sep 19, 2012 at 10:26 PM, CPV ceal...@gmail.com wrote:
Thanks again,
I run the script with the postForm(site, disclaimer_action=I Agree) and
it does not seem to do anything,
the webpage is still the disclaimer page thus I am getting the error
below
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function readHTMLTable, for
signature NULL
I also downloaded the latest version of RHTMLForms
(omegahat-RHTMLForms-251743f.zip)
and it does not seem to install correctly.. I used the code
install.packages(C:/Users/cess/Downloads/omegahat-RHTMLForms-251743f.zip,
type=win.binary, repos=NULL)
Any suggestion of what could be causing these problems?
On Wed, Sep 19, 2012 at 9:49 AM, Duncan Temple Lang
dtemplel...@ucdavis.edu
wrote:
You don't need to use the getHTMLFormDescription() and
createFunction().
Instead, you can use the postForm() call. However,
getHTMLFormDescription(),
etc. is more general. But you need the very latest version of the
package
to deal with degenerate forms that have no inputs (other than button
clicks).
You can get the latest version of the RHTMLForms package
from github
git clone g...@github.com:omegahat/RHTMLForms.git
and that has the fixes for handling the degenerate forms with
no arguments.
D.
On 9/19/12 7:51 AM, CPV wrote:
Thank you for your help Duncan,
I have been trying what you suggested however I am getting an error
when
trying to create the function fun- createFunction(forms[[1]])
it says Error in isHidden I hasDefault :
operations are possible only for numeric, logical or complex types
On Wed, Sep 19, 2012 at 12:15 AM, Duncan Temple Lang
dtemplel...@ucdavis.edu wrote:
Hi ?
The key is that you want to use the same curl handle
for both the postForm() and for getting the data document.
site = u =
http://www.wateroffice.ec.gc.ca/graph/graph_e.html?mode=textstn=05ND012prm1=3syr=2012smo=09sday=15eyr=2012emo=09eday=18
library(RCurl)
curl = getCurlHandle(cookiefile = , verbose = TRUE)
postForm(site, disclaimer_action=I Agree)
Now we have the cookie in the curl handle so we can use that same
curl
handle
to request the data document:
txt = getURLContent(u, curl = curl)
Now we can use readHTMLTable() on the local document content:
library(XML)
tt = readHTMLTable(txt, asText = TRUE, which = 1, stringsAsFactors =
FALSE)
Rather than knowing how to post the form, I like to read
the form programmatically and generate an R function to do the
submission
for me. The RHTMLForms package can do this.
library(RHTMLForms)
forms = getHTMLFormDescription(u, FALSE)
fun = createFunction(forms[[1]])
Then we can use
fun(.curl = curl)
instead of
postForm(site, disclaimer_action=I Agree)
This helps to abstract the details of the form.
D.
On 9/18/12 5:57 PM, CPV wrote:
Hi, I am starting coding in r and one of the things that i want to
do
is
to
scrape some data from the web.
The problem that I am having is that I cannot get passed the
disclaimer
page (which produces a session cookie). I have been able to collect
some
ideas and combine them in the code below but I dont get passed the
disclaimer page.
I am trying to agree the disclaimer with the postForm and write the
cookie
to a file, but I cannot do it succesfully
The webpage cookies are written to the file but the value is
FALSE...
So
any ideas of what I should do or what I am doing wrong with?
Thank you for your help
Re: [R] (no subject)
Hi,
Another way of doing may be like this;
a - c(d, d, j, f, e, g, f, f, i, g)
b - c(a, g, d, f, g, a, f, a, b, g)
ta - table(a)
tb - table(b)
Function-function(Tab1,Tab2){elements=sort(unique(c(names(ta),names(tb
OP=lapply(1:length(elements),FUN=function(x){a=which(elements[x]==names(Tab1))
b=which(elements[x]==names(Tab2))
if(length(a)0length(b)0){Tab1[a]+Tab2[b]
}else if (length(a)0){Tab1[a]
}else{Tab2[b]}
})
return(unlist(OP))
}
Function(ta,tb)
Best,
Heramb
On Thu, Sep 20, 2012 at 10:40 PM, arun smartpink...@yahoo.com wrote:
HI Stefan,
Thanks for the solutions.
Just to add 1 more:
f.a-table(a); f.b-table(b)
c(f.a[!names(f.a)%in%names(f.b)],f.b[!names(f.b)%in%names(f.a)],xtabs(f.a[names(f.a)%in%names(f.b)]+f.b[names(f.b)%in%names(f.a)]~
names(f.a[names(f.a)%in%names(f.b)])))
#e i j a b d f g
#1 1 1 3 1 3 5 5
A.K.
- Original Message -
From: Stefan Th. Gries stgr...@gmail.com
To: mce...@lightminersystems.com
Cc: r-help@r-project.org
Sent: Thursday, September 20, 2012 10:57 AM
Subject: [R] (no subject)
From my book on corpus linguistics with R:
# (10) Imagine you have two vectors a and b such that
a-c(d, d, j, f, e, g, f, f, i, g)
b-c(a, g, d, f, g, a, f, a, b, g)
# Of these vectors, you can create frequency lists by writing
freq.list.a-table(a); freq.list.b-table(b)
rm(a); rm(b)
# How do you merge these two frequency lists without merging the two
vectors first? More specifically, if I delete a and b from your
memory,
rm(a); rm(b)
# how do you generate the following table only from freq.list.a and
freq.list.b, i.e., without any reference to a and b themselves? Before
you complain about this question as being unrealistic, consider the
possibility that you generated the frequency lists of two corpora
(here, a and b) that are so large that you cannot combine them into
one (a.and.b-c(a, b)) and generate a frequency list of that combined
vector (table(a.and.b)) ...
joint.freqs
a b d e f g i j
3 1 3 1 5 5 1 1
joint.freqs-vector(length=length(sort(unique(c(names(freq.list.a),
names(freq.list.b)) # You generate an empty vector joint.freqs (i)
that is as long as there are different types in both a and b (but note
that, as requested, this information is not taken from a or b, but
from their frequency lists) ...
names(joint.freqs)-sort(unique(c(names(freq.list.a),
names(freq.list.b # ... and (ii) whose elements have these
different types as names.
joint.freqs[names(freq.list.a)]-freq.list.a # The elements of the new
vector joint.freqs that have the same names as the frequencies in the
first frequency list are assigned the respective frequencies.
joint.freqs[names(freq.list.b)]-joint.freqs[names(freq.list.b)]+freq.list.b
# The elements of the new vector joint.freqs that have the same names
as the frequencies in the second frequency list are assigned the sum
of the values they already have (either the ones from the first
frequency list or just zeroes) and the respective frequencies.
joint.freqs # look at the result
# Another shorter and more elegant solution was proposed by Claire
Crawford (but uses a function which will only be introduced later in
the book)
freq.list.a.b-c(freq.list.a, freq.list.b) # first the two frequency
lists are merged into a single vector ...
joint.freqs-as.table(tapply(freq.list.a.b, names(freq.list.a.b),
sum)) # ... and then the sums of all numbers that share the same names
are computed
joint.freqs # look at the result
# The shortest, but certainly not memory-efficient way to do this
involves just using the frequency lists to create one big vector with
all elements and tabulate that.
table(c(rep(names(freq.list.a), freq.list.a), rep(names(freq.list.b),
freq.list.b))) # kind of cheating but possible with short vectors ...
HTH,
STG
--
Stefan Th. Gries
---
University of California, Santa Barbara
http://www.linguistics.ucsb.edu/faculty/stgries
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Re: [R] SQL query with Multicore option on R -linux
This is what I think; Hive internally distributes the data. If you have set up Hive on single core it will fetch the query results from that core. If you have multi-core system on which you have setup the Hive, it will search all the cores for the query submitted and results would be compiled together for final output. The query would remain the same no matter whther you have a single core or multiple cores or a cluster of machines. Please correct me if I am going the wrong way. Best, Heramb On Thu, Sep 20, 2012 at 11:34 PM, Madana_Babu madana_b...@infosys.comwrote: Hi all, I have the following sql query that I am executing on a machine with single core. I want to know how can I execute the same sqery on a maching that is running with 4 cores. Please provide me the code. NEW_TABLE - rhive.query(SELECT A, B, COUNT(C) FROM TABLE_A WHERE A='01-01-2012') Also let me know how can I leverage only 2 / 3 cores of the machine. Regards, Madana -- View this message in context: http://r.789695.n4.nabble.com/SQL-query-with-Multicore-option-on-R-linux-tp4643771.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. [[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] VarBrul in R
I do not know about the packages that you mentioned. I am trying to answer your query based on the term socio-linguistic analytics. There are packages like OpenNLP,OpenNLP.en,tm (Text Mining) that might be of your interest. Best, Heramb On Fri, Sep 21, 2012 at 1:04 AM, Trevor Jenkins bslwann...@gmail.comwrote: Several years ago there were R implementations of a socio-linguistics analysis method called Variable Rule Analysis namely rbrul and r-varb. Both neither of the sites listed (in the method's WikiPedia page http://en.wikipedia.org/wiki/Variable_rules_analysis ) appear to be online any more (one was at UPenn and the other at Indiana). Does anyone know a) whether the code for either or both of these implementations survives out there and b) is anyone maintaining these implementations? There are no listings for either of them at R Forge. And no listing for varbrul, which is the name for the original Fortran program. (Even that Fortran source can't be found online anymore.) Regards, Trevor. Re: deemed! [[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. [[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] issue accessing help files
Try this; help(anova) I have used this in R-2.14.1 It has worked fine for me. Hope it works for you as well. Best, Heramb On Thu, Sep 20, 2012 at 1:40 AM, Rui Barradas ruipbarra...@sapo.pt wrote: Hello, I had a problem seeing the help pages with R 2.14.(0 or 1? I don't remember) on Windows 7. Then I realized that after a command like print, Rgui would first display an error message saying that the temp directory used by help didn't exist. The solution I've found was to manually create it whenever this happened. And to issue a print statement after a missed ?function one. Apparently the error message was waiting to be displayed somewhere. The problem was corrected with R 2.15.0 so I recommened you update your installation of R. Hope this helps, Rui Barradas Em 19-09-2012 19:19, Basil Iannone escreveu: Dear R-help community, I am unable to access help files when using the typical ?function.of.interest command. For example, if I type ?anova, Internet Explorer opens, but I am never connected to the usual page describing the nuances of the anova function. This is a new problem (just started occurring a few days ago). I am currently using R 2.14.1 on a Windows XP machine. As suggested by someone else on another list serve I have placed the session info below for a brief session where this occurred. NOTE: I am not trying to access any functions for libraries that are not active (for example, anova is in the default Stats package). Any suggestions on how to resolve this issue or any insights on why this may be occurring are greatly appreciated. Thanks in advance for your help. sessionInfo() R version 2.14.1 (2011-12-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.14.1 __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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] Importing a CSV file
Hi All, I have used windows R. We can also write like this: A - read.csv(C:/Users/Anthi/Desktop/R/A.csv,header=TRUE) On Wed, Sep 19, 2012 at 8:09 PM, Marc Schwartz marc_schwa...@me.com wrote: On Sep 19, 2012, at 9:26 AM, Rui Barradas ruipbarra...@sapo.pt wrote: Em 19-09-2012 15:01, Sarah Goslee escreveu: On Wed, Sep 19, 2012 at 9:53 AM, Frans Marcelissen frans.marcelis...@digipsy.nl wrote: Hi, Should'nt it be A - read.csv(C:Users\\Anthi\\Desktop\\R\\A.csv, header=TRUE) (c:\\ becomes c:\ In general I think it is better to use / and //) Frans No idea; I was copying the original poster's version. In this case, it would definitely be better to take advice on path construction from someone who uses Windows! I use Windows and the answer is no, the four backslashes don't make sense, because like Frans said, c:\\ becomes c:\ (There is no such thing as c: --- c:\\). Rui Barradas Ahoy Mateys, Not to mention, creating file paths on Windows is an A FAQ: http://cran.r-project.org/bin/windows/base/rw-FAQ.html#R-can_0027t-find-my-file Savvy? Marc Schwartz P.S. It's International Talk Like a Pirate Day, which of course fits with a certain language we all hold dear. Somebody had to do it... ;-) Sarah -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org ] Namens Sarah Goslee Verzonden: woensdag 19 september 2012 15:44 Aan: Anthi Oikonomou CC: r-h...@stat.math.ethz.ch Onderwerp: Re: [R] Importing a CSV file Hi, load() is for R's binary data files. You need to use read.csv(), as you tried, but probably with the complete path. A - read.csv(C:\\Users\\Anthi\\Desktop\\R\\A.csv, header=TRUE) Sarah On Wed, Sep 19, 2012 at 4:54 AM, Anthi Oikonomou anthi.oi...@gmail.com wrote: Hi, I am trying to import csv file in R console I have saved my data in a file on the desktop named R and here is my problematic script load(C:\\Users\\Anthi\\Desktop\\R\\A.csv) Error: bad restore file magic number (file may be corrupted) -- no data loaded In addition: Warning message: file 'A.csv' has magic number ';Abra' Use of save versions prior to 2 is deprecated when I don t load and I ask to read here is the answer A -read.csv(A.csv,header=TRUE) Error in file(file, rt) : cannot open the connection In addition: Warning message: In file(file, rt) : cannot open file 'A.csv': No such file or directory Do you know what should I do? Thank you in advance __ 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. [[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] scraping with session cookies
Try this,
library(RCurl)
library(XML)
site-
http://www.wateroffice.ec.gc.ca/graph/graph_e.html?mode=textstn=05ND012prm1=3syr=2012smo=09sday=15eyr=2012emo=09eday=18
URL-getURL(site)
Text=htmlParse(URL,asText=T)
This will give you all the web dat in an HTML-Text format.
You can use getNodeSet function to extract whatever links or texts that
you want from that page.
I hope this helps.
Best,
Heramb
On Wed, Sep 19, 2012 at 10:26 PM, CPV ceal...@gmail.com wrote:
Thanks again,
I run the script with the postForm(site, disclaimer_action=I Agree) and
it does not seem to do anything,
the webpage is still the disclaimer page thus I am getting the error below
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function readHTMLTable, for
signature NULL
I also downloaded the latest version of RHTMLForms
(omegahat-RHTMLForms-251743f.zip)
and it does not seem to install correctly.. I used the code
install.packages(C:/Users/cess/Downloads/omegahat-RHTMLForms-251743f.zip,
type=win.binary, repos=NULL)
Any suggestion of what could be causing these problems?
On Wed, Sep 19, 2012 at 9:49 AM, Duncan Temple Lang
dtemplel...@ucdavis.edu
wrote:
You don't need to use the getHTMLFormDescription() and
createFunction().
Instead, you can use the postForm() call. However,
getHTMLFormDescription(),
etc. is more general. But you need the very latest version of the package
to deal with degenerate forms that have no inputs (other than button
clicks).
You can get the latest version of the RHTMLForms package
from github
git clone g...@github.com:omegahat/RHTMLForms.git
and that has the fixes for handling the degenerate forms with
no arguments.
D.
On 9/19/12 7:51 AM, CPV wrote:
Thank you for your help Duncan,
I have been trying what you suggested however I am getting an error
when
trying to create the function fun- createFunction(forms[[1]])
it says Error in isHidden I hasDefault :
operations are possible only for numeric, logical or complex types
On Wed, Sep 19, 2012 at 12:15 AM, Duncan Temple Lang
dtemplel...@ucdavis.edu wrote:
Hi ?
The key is that you want to use the same curl handle
for both the postForm() and for getting the data document.
site = u =
http://www.wateroffice.ec.gc.ca/graph/graph_e.html?mode=textstn=05ND012prm1=3syr=2012smo=09sday=15eyr=2012emo=09eday=18
library(RCurl)
curl = getCurlHandle(cookiefile = , verbose = TRUE)
postForm(site, disclaimer_action=I Agree)
Now we have the cookie in the curl handle so we can use that same curl
handle
to request the data document:
txt = getURLContent(u, curl = curl)
Now we can use readHTMLTable() on the local document content:
library(XML)
tt = readHTMLTable(txt, asText = TRUE, which = 1, stringsAsFactors =
FALSE)
Rather than knowing how to post the form, I like to read
the form programmatically and generate an R function to do the
submission
for me. The RHTMLForms package can do this.
library(RHTMLForms)
forms = getHTMLFormDescription(u, FALSE)
fun = createFunction(forms[[1]])
Then we can use
fun(.curl = curl)
instead of
postForm(site, disclaimer_action=I Agree)
This helps to abstract the details of the form.
D.
On 9/18/12 5:57 PM, CPV wrote:
Hi, I am starting coding in r and one of the things that i want to do
is
to
scrape some data from the web.
The problem that I am having is that I cannot get passed the
disclaimer
page (which produces a session cookie). I have been able to collect
some
ideas and combine them in the code below but I dont get passed the
disclaimer page.
I am trying to agree the disclaimer with the postForm and write the
cookie
to a file, but I cannot do it succesfully
The webpage cookies are written to the file but the value is FALSE...
So
any ideas of what I should do or what I am doing wrong with?
Thank you for your help,
library(RCurl)
library(XML)
site -
http://www.wateroffice.ec.gc.ca/graph/graph_e.html?mode=textstn=05ND012prm1=3syr=2012smo=09sday=15eyr=2012emo=09eday=18
postForm(site, disclaimer_action=I Agree)
cf - cookies.txt
no_cookie - function() {
curlHandle - getCurlHandle(cookiefile=cf, cookiejar=cf)
getURL(site, curl=curlHandle)
rm(curlHandle)
gc()
}
if ( file.exists(cf) == TRUE ) {
file.create(cf)
no_cookie()
}
allTables - readHTMLTable(site)
allTables
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Re: [R] eval(parse(...)) only once in a function
If you have a data frame df with a column JT
Try this one:
str - df$JT == 12
fun-function(str){b-eval(parse(text=str))
return(b)}
fun(str)
On Mon, Sep 17, 2012 at 11:57 AM, Christof Kluß ckl...@email.uni-kiel.dewrote:
Hi
I would like to have something like
str - df$JT == 12
fun - function(df) {
b - eval(parse(str))
return(b)
}
but for performance eval(parse(a)) should not be evaluated at each
function call, but should work as
fun - function(df) {
b - df$JT == 12
return(b)
}
Do you have an idea how I can implement this?
Thx
Christof
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Re: [R] I want to send the vector a into the Object A.......
A- get(a)
This will work fine
Best,
Heramb
On Mon, Sep 17, 2012 at 5:43 PM, Sri krishna Devarayalu Balanagu
balanagudevaray...@gvkbio.com wrote:
a=c(1,2,3)
b=c(23, 24, 25)
x=c(a, b)
#if (length(x[1]) == 0) {cat(x[1] is having 3 elements)}
Suppose I want to send the vector a into the Object A,
um getting only a as the ouput for Object A but not getting required
output as the vector with the elements 1, 2, 3 with the following code
A- x[1]
How to code it?
Can anyone help?
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