[R] conversion of data structure between R and Perl
Dear R users,
I am trying to call a Perl subroutine from R . The subroutine returns an
arrray contaning three elements wihch are all strings. But the calling in R
return an integer which is 0. I have no idea how this could happen. Maybe
becasue I shouldn't use system() in R or I should load a particular package
for my R in windows. Please help
---
the perl subroutine in presentPerformance.pl
sub findAccuracy{
while(defined($filename=glob("*.log"))){
open(WORDLIST , $filename)||die("can't open the file!");
while($line=){
if ($line=~m/accuracy/){
$line=~s/-accuracy://;
@temp=split(" ",$line);
$temp[0]=~s/\%//;
$temp[2]=~s/\%//;
@accInfoList=($temp[0],$temp[2],$filename);
}
}
}
return(@accInfoList)
}
findAccuracy();
The R code
> class(system("perl presentPerformance.pl"))
[1] "integer"
regard,
Shu-Kai Chang
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[R] locate substring in the string it belong to
Hi R users, I am trying generate the indices for locating a in the string it come from. Given the length of the string, it will take too long using the combn() for further comparison. I am wondering if R has any built-in function for this purpose. To make it concrete: this.substring="cc" this.string="ccc" start.location=1,2 end.location=2,3 Thanks in advance, Kevin -- View this message in context: http://www.nabble.com/locate-substring-in-the-string-it-belong-to-tp24565937p24565937.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.
[R] combine venn diagram and pie chart
Hi R users, I am wondering if it there is R's function that can help integrate venn diagram and pie chart to compare two related datasets. I know the package limma has something built-in for making venn diagram, but I guess it would be very painful to use line and text to specify the proportions in the fashion of pie chart . Thanks in advance, Kevin Chang -- View this message in context: http://www.nabble.com/combine-venn-diagram-and--pie-chart-tp24784565p24784565.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.
[R] layout of igraph
Dear R users, I am trying to draw a network using igraph package. I intend to place the hub nodes (the ones with the relatively more connection with other nodes) in the center of the graph. Also, the graph need to be in the fashion that the higher the correlation between two nodes is , the closer the two nodes will be. Is there any layout that can help or any other way to do this? Thanks in advance. Shukai -- View this message in context: http://www.nabble.com/layout-of-igraph-tp6348p6348.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] layout of igraph
Thanks Gabor's fast reply. In my research, every node has it's own vector of scores. So I can compute correlation between every pair of nodes. I used the width and color of the edge for this purpose. But visualizing the correlations by distance may be clearer. Best, Shukai Gábor Csárdi-2 wrote: > > Shukai, > > the force based layout algorithms (layout.drl, > layout.fruchterman.reingold, layout.graphopt, layout.kamada.kawai) are > likely to do this; although they are not explicitly required to place > hubs in the center, usually they do. > > I am not sure what is the "correlation between two nodes". You mean > that the graph is weighted? > > If you have a small graph, then you can refine the layout > interactively by using 'tkplot'. > > Gabor > > On Thu, Feb 26, 2009 at 4:20 PM, kevinchang wrote: >> >> Dear R users, >> >> I am trying to draw a network using igraph package. I intend to place the >> hub nodes (the ones with the relatively more connection with other nodes) >> in >> the center of the graph. Also, the graph need to be in the fashion that >> the >> higher the correlation between two nodes is , the closer the two nodes >> will >> be. Is there any layout that can help or any other way to do this? >> >> Thanks in advance. >> Shukai >> -- >> View this message in context: >> http://www.nabble.com/layout-of-igraph-tp6348p6348.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. >> > > > > -- > Gabor Csardi UNIL DGM > > __ > 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. > > -- View this message in context: http://www.nabble.com/layout-of-igraph-tp6348p6854.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.
[R] save the layout using igraph
Hi R users, I am using built-in functions in igraph package to draw networks . I need to compare several network with exactly the same structure but with edge hightlighted differently. I am wondering if there is a way to save the layout so that every graph will look the same as each other except for the colors of edges. Or is there any parameter I can set for this purpose?? Thanks in advance, Shukai -- View this message in context: http://www.nabble.com/save-the-layout-using-igraph-tp22316155p22316155.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.
[R] function for special matrix design
Hi All, I am trying to make a matrix with a particular value for all the elements above and including diagonal and another particular value for all the elements below diagonal. Obviously , Matrix function in Matrix package does not work since it only allow filling by either row or column. So I am wondering if there is a built-in function allowing me to do this ? please help. Thanks -- View this message in context: http://www.nabble.com/function-for-special-matrix-design-tf4549437.html#a12982709 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.
[R] inverse of matrix made by low.tri function
Hi all, I am using R trying to get a inverse matrix of (X^T)X , but I keep getting the error message like: no b argument and no default value for sprintf(gettext(fmt, domain = domain), ...) . # my code X<-Matrix(rep(1,500),100,5) X[lower.tri(X)]<-1-10^-7 XtX<- t(X)%*% X XtXu<-lu(XtX) InverseXtX<-solve(XtXu) - The cause suggested for this error is that the lower.tri function returns a matrix of logicals. If so, is trying to fix this by using sprintf function a good idea ? Or is there is any alternative way to get the inverse matrix? Please help. Thanks -- View this message in context: http://www.nabble.com/inverse-of-matrix-made-by-low.tri-function-tf4562543.html#a13021480 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.
[R] Newton method iteration problem
Hi all,
I am coding for finding the root of f(x)= phi(x) -alpha where phi(x) is the
cumulative density function and alpha is constant . The problem right now is
I can't get the "initialX" representing the root out of the while loop when
ending , it seems to me it disappear when the loop ends accroding to the
error message. I need help . Please suggest the cause or solution to this
problem. Thanks.
# code
#generate target function (phi(x)-alpha) (allow input x and alpha)
target<-function(x,alpha){
pnorm(x)-alpha
}
#generate the first derivative of the of the target function
firstDerivative<-function(x){
exp(-(x^2)/2)/sqrt(2*pi)
}
# Finding the root by Newton method
rootFinding<-function(initialX,setAlpha){
while(target(initialX,setAlpha)!=0){
initialX<-initialX-(target(initialX,setAlpha)/firstfirstDerivative(initialX)
}
initialX
}
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Re: [R] Newton method iteration problem
Thanks Chales for pointing out the errors.
I fixed an errorr and R accepted my "rootFinding" code.
But the problem right now is that my code will work only if the intialX
value is close enough to the solution.
Otherwise, R says there is missing true/false value in the codition test of
while loop. I can't figure out what happens. Some advice , please??
#generate target function (phi(x)-alpha) (allow input x and alpha)
target<-function(x,alpha){
pnorm(x)-alpha
}
#generate the first derivative of the of the target function
firstDerivative<-function(x){
exp(-(x^2)/2)/sqrt(2*pi)
}
# Finding the root by Newton method
rootFinding<-function(initialX,setAlpha,maxIter){
while((target(initialX,setAlpha)!=0) && maxIter>0){
initialX<-initialX-(target(initialX,setAlpha)/firstDerivative(initialX))
maxIter<-maxIter-1
}
initialX
}
Charles C. Berry wrote:
>
> On Fri, 26 Oct 2007, kevinchang wrote:
>
>>
>> Hi all,
>>
>> I am coding for finding the root of f(x)= phi(x) -alpha where phi(x) is
>> the
>> cumulative density function and alpha is constant . The problem right now
>> is
>> I can't get the "initialX" representing the root out of the while loop
>> when
>> ending , it seems to me it disappear when the loop ends accroding to the
>> error message. I need help . Please suggest the cause or solution to
>> this
>> problem. Thanks.
>
> Learn to type without making errors? Learn to format (space and indent)
> your code so errors will be more obvious to you??
>
> Your code worked for me once I corrected the typos and syntax errors.
>
> It even agrees with qnorm( setAlpha ).
>
> If all you want is root finding capability, I suggest you see
>
> ?uniroot
>
> and friends.
>
> HTH,
>
> Chuck
>
>>
>> # code
>>
>> #generate target function (phi(x)-alpha) (allow input x and alpha)
>> target<-function(x,alpha){
>> pnorm(x)-alpha
>> }
>>
>>
>> #generate the first derivative of the of the target function
>> firstDerivative<-function(x){
>> exp(-(x^2)/2)/sqrt(2*pi)
>> }
>>
>> # Finding the root by Newton method
>> rootFinding<-function(initialX,setAlpha){
>> while(target(initialX,setAlpha)!=0){
>> initialX<-initialX-(target(initialX,setAlpha)/firstfirstDerivative(initialX)
>> }
>> initialX
>> }
>>
>>
>> --
>> View this message in context:
>> http://www.nabble.com/Newton-method-iteration-problem-tf4701085.html#a13439031
>> 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.
>>
>
> Charles C. Berry(858) 534-2098
> Dept of Family/Preventive
> Medicine
> E mailto:[EMAIL PROTECTED]UC San Diego
> http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
>
> __
> 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.
>
>
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[R] flops calculation
Hi all, Since proc.time return three different kind of times (user, system and elapsed) , I am wondering which one is right for calculating flops. In New S Language (Becker et. al. ) , it seems to be the user because " the user time measures the processor time used in S and the system time measures the operating system in response to S's request". But in R Help , system time sounds better as " The first two entries(referred to user and system time respectively) are the total user and system CPU times of the current R process and any child processes on which it has waited". Please help . Thanks. -- View this message in context: http://www.nabble.com/flops-calculation-tf4708965.html#a13459745 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.
[R] alternative way to loop
I heard that if-loop may result in errors if we are going to loop for a lot of times. And sum() can be the alternative way to do this kind of hugbe looping. But I haven't figure out how . Can someone please give me an concrete example of using sum() for this purpose? -- View this message in context: http://www.nabble.com/alternative-way-to-loop-tf4422299.html#a12613696 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.
[R] rearrange problem
Hi All, I am trying to rearrange alphabetically each element in a character vector. ex: say the first element in the vector is "cba", and my goal is to turn it into "abc". The suggested function to use is sort(). But it turns out that sort doesn't work at the level of element. So I am wondering that if there is an alternative function for this purpose. Please help me out . Thanks. -- View this message in context: http://www.nabble.com/rearrange-problem-tf4434906.html#a12652394 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.
[R] locate word in vector
Hey All, I am wondering if there is a built-in function allowing us to locate a particular word in a character vector. ex: vector a a [1] "superman" "xamn" "spiderman" "superman" "superman" "xman" [7] "spiderman" Is there any built-in function that can show "superman" are the first, fourth and fifith element in "a"? Please help me out. Thanks. -- View this message in context: http://www.nabble.com/locate-word-in-vector-tf4445881.html#a12685567 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.
[R] starting with a capital letter
Hi everyone, I am wondering if there is any built-in funcion that can determine whether words in a character vector start with a captial letter or not. Help, please. Thanks. -- View this message in context: http://www.nabble.com/starting-with-a-capital-letter-tf4447302.html#a12689105 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.
[R] naming columns of data frame
Hey, I am trying to make a data frame and the name of a column is composed of a number, a dot, and a word, such as "1.whatever". But I always get this error message:"syntax error, unexpected SYMBOL, expecting ',' in:" while printing data frame out . When I rename the column with purely letter, everything works fine. Some suggestion about the cause/ solution ?? Thanks. -- View this message in context: http://www.nabble.com/naming-columns-of-data-frame-tf4449324.html#a12694795 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.
[R] stalled loop
Hi, The loop I wrote executes correctly but is stalled seriously. Is there a way to hasten execution without coming up with a brand new algorithm ? please help. Thanks. -- View this message in context: http://www.nabble.com/stalled-loop-tf4451301.html#a12699524 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.
[R] stalled loop
Hey everyone,
The code I wrote executes correctly but is stalled seriously. Is there a
way to hasten execution without coming up with a brand new algorithm
?please help. Thanks a lot for your time.
#a simplified version of the code
a<-c("superman" , "xman" , "spiderman" ,"wolfman" ,"mansuper","manspider" )
b<-sapply(a,function(.srt){paste(sort(strsplit(.srt,'')[[1]]),
collapse="")})
c<-NA
for(i in 1:length(b)) {
if(length(which(b==b[i]))>1)
c[i]<-b[i]
}
c<-c[!is.na(c)]
# But if my get the volumne of "a" up to about 15 words , the loop will
work incredibly slowly.
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