[R] Can a hyperlink be placed, thorugh R programming, on a graph?
Hi, If I use x-1:10 y-rnorm(10,0,1) ### pdf(file=c:\\aldi\\test.pdf) plot(x,y) segments(x,y,x+2,y+2) segments(x,y,x+0.5,y+0.5,col=3) ### dev.off() ### q() Is there a way that I can imbed in the graph plot for each point defined by x to x+0.5 and y to y+0.5 (and colored in green) a different hyperlink? For example point one (together with the green tail) will have the hyperlink: www.r-project.org; point 2 with the link www.google.com; point 3 with the link www.yahoo.com etc. So in general, can the graph be manupulated within R? TIA, Aldi __ R-help@stat.math.ethz.ch 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] Can a hyperlink be placed, thorugh R programming, on a graph?
Ok, Here is a simple solution: One can apply the text step (within a loop) for any other points and the hyperlinks are functional in the pdf format, and not viewable unless the mouse is over the link. If you have a better solution, let me know. x-1:10 y-rnorm(10,0,1) pdf(file=c:\\aldi\\test.pdf) plot(x,y) segments(x,y,x+2,y+2) text(x[3],y[3],c(http://www.r-project.org;),cex=0.1,col=white) segments(x,y,x+0.5,y+0.5,col=3) dev.off() Thanks, Aldi Aldi Kraja wrote: Hi, If I use x-1:10 y-rnorm(10,0,1) ### pdf(file=c:\\aldi\\test.pdf) plot(x,y) segments(x,y,x+2,y+2) segments(x,y,x+0.5,y+0.5,col=3) ### dev.off() ### q() Is there a way that I can imbed in the graph plot for each point defined by x to x+0.5 and y to y+0.5 (and colored in green) a different hyperlink? For example point one (together with the green tail) will have the hyperlink: www.r-project.org; point 2 with the link www.google.com; point 3 with the link www.yahoo.com etc. So in general, can the graph be manupulated within R? TIA, Aldi __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Plotting a broken line?
Hi, Is there a smart way in the R graphs to create a line that is broken in intervals based on the indicator given below. following is a small test graph Location,indicator,otherinfo 1.2,1,2.2 2.5,1,2.5 3.7,1,2.3 20.1,2,4.3 22.5,2,5.2 25.0,2,3.4 27.3,2,2.2 35.1,3,3.4 37.0,3,7.2 38.0,3,6.1 40.1,3,5.4 52.9,3,3.3 Right now in the plot the line is continuous, but I would like to have it broken based on the indicator. If the line of the plot reaches the last observation of indicator=1 then the line needs to stop; the next line will start at location 22.5 and continue up top 27.3; the next line goes from 35.1 up to 52.9. x-read.table(file='c:\\aldi\\testgraph.csv',sep=',',header=T) x Location indicator otherinfo 1 1.2 1 2.2 2 2.5 1 2.5 3 3.7 1 2.3 4 20.1 2 4.3 5 22.5 2 5.2 6 25.0 2 3.4 7 27.3 2 2.2 8 35.1 3 3.4 9 37.0 3 7.2 10 38.0 3 6.1 11 40.1 3 5.4 12 52.9 3 3.3 plot(x$Location,x$indicator,type='l',xlim=c(0,max(x$Location)),ylim=c(0,max(x$indicator,x$otherinfo))) points(x$Location,x$otherinfo) TIA, Aldi -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plotting a broken line?
Hi Greg, Thank you for your response and a previous posting about Macros in R. Thank you also to Ken Knoblouch (Ken had the same idea as Greg's and Peter Pikal (who proposed the use of segments function). There is only a technical specific that when applying max function to find the limit of y one has to use it with max(x$indicator, na.rm =TRUE)) It worked!!! x Location indicator otherinfo 1 1.2 1 2.2 2 2.5 1 2.5 3 3.7 1 2.3 4 3.7NANA 5 20.1 2 4.3 6 22.5 2 5.2 7 25.0 2 3.4 8 27.3 2 2.2 9 27.3NANA 10 35.1 3 3.4 11 37.0 3 7.2 12 38.0 3 6.1 13 40.1 3 5.4 14 52.9 3 3.3 Aldi Greg Snow wrote: If you insert an NA (or row of NA's) into the data at each place you want a break (after indicator increases), then the regular plot with type='l' will break the line for you. Is this what you want? -- __ R-help@stat.math.ethz.ch 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 protect two jobs running on the same directory at the same time not to corrupt each other results:
Hi, I have a large group of jobs, some of them are running on the same directory. All of them in batch mode. What are the best ways to protect from corrupting the results two or more jobs running on the same directory. One, I would think can be to run each job in a separate directory, collect the results and after remove the directories. But I have thousands of jobs that will run in parallel and I have placed about 100 of them in each directory. They all do the same process, but on different variables, replications etc. Is there any other solution better than creating separate directories in R? I am thinking if there is any option in R to create a unique id which has its own unique .Rdata, although in the same directory? SAS for example to each batch job it assigns a different ID and a separate temp space, and does not mix it with another job running in parallel. Thanks, Aldi -- __ R-help@stat.math.ethz.ch 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] Error: cannot take a sample larger than the population
Hi, In Splus7 this statement xlrmN1 - sample(c(0,1,2),400 ,prob=c(0.02 ,0.93 ,0.05 )) worked fine, but in R the interpreter reports that the length of the vector to chose c(0,1,2) is shorter than the size of many times I want to be selected from the vector c(0,1,2). Any good reason? See below the error. xlrmN1 - sample(c(0,1,2),400 ,prob=c(0.02 ,0.93 ,0.05 )) Error in sample(length(x), size, replace, prob) : cannot take a sample larger than the population when 'replace = FALSE' Execution halted TIA, Aldi -- __ R-help@stat.math.ethz.ch 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] Error: cannot take a sample larger than the population
Partial Summary and discussion: = Thank you to Chao Gai, Chuck Cleland, and Jim Lemon for their suggestion to use replace=T in R. There is a problem though (see below) In the Splus7, sample is defined as - sample(x, size = n, replace = F, prob = NULL, n = NULL, ...) where replace=F In Splus7 xlrmN1 - sample(c(0,1,2),400 ,prob=c(0.02 ,0.93 ,0.05 )) and the table(xlrmN1)/400 012 0.02 0.93 0.05 show that sample is working exactly as expected based on the prob vector. When sample is used in Splus7 with replacement we see the following result: xlrmN1 - sample(c(0,1,2),400 ,replace=T,prob=c(0.02 ,0.93 ,0.05 )) table(xlrmN1)/400 0 1 2 0.0125 0.925 0.0625 which I think is working again as expected. In the R, sample is defined as - sample(x, size, replace = FALSE, prob = NULL) So the above statement with replace=F did not work (reported error) but with replace=T produced, table(xlrmN1)/400 xlrmN1 0 1 2 0.0200 0.9225 0.0575 which is not exactly the sample with the probabilities provided (0.02,0.93,0.05) Now let's return to the concept of replace=F and replace=T. When I ask sample to select a sample of 400 from a vector of 3 with NO replacement, I would think the following a). create a very large sample from 0, 1, and 2. b). From this large sample, based on the prob vector select without replacement. c). As result I expect the probability of selected sample to be exactly the same with the prob vector (As in Splus7) When I ask sample to select a sample of 400 from a vector of 3 with replacement, I would think the following a). create a very large sample from 0, 1, and 2. b). From this large sample, based on the prob vector select with replacement, which means some of the previous selected 0, 1, 2 can be selected again. c). As result I expect the probability of selected sample to be NOT exactly the same with the prob vector (As in Splus7 and R). So there are two conclusions: sample in R is not working correct, OR I am missing some precision as a rounding error to produce prob=c(0.02 ,0.93 ,0.05 ). Am I misunderstanding the sample function in R? Any suggestions are appreciated. TIA, Aldi Aldi Kraja wrote: Hi, In Splus7 this statement xlrmN1 - sample(c(0,1,2),400 ,prob=c(0.02 ,0.93 ,0.05 )) worked fine, but in R the interpreter reports that the length of the vector to chose c(0,1,2) is shorter than the size of many times I want to be selected from the vector c(0,1,2). Any good reason? See below the error. xlrmN1 - sample(c(0,1,2),400 ,prob=c(0.02 ,0.93 ,0.05 )) Error in sample(length(x), size, replace, prob) : cannot take a sample larger than the population when 'replace = FALSE' Execution halted TIA, Aldi -- -- __ R-help@stat.math.ethz.ch 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] var-covar matrices comparison:
Thank you Patrick for your thoughts. I was expecting someone had written a function that does maybe a hierarchical comparison of var-covar matrices using the flury hierarchy as proposed by Philips and Arnold in Evolution 53(5), 1999;1506-1515. But your email has an interesting idea, so I will try to test it. Thank you, Aldi Patrick Burns wrote: My first thought is to use a random permutation test. In this setting the main question you need to ask is what distance measure do you want to use between variance matrices -- there are lots of choices. One that I've found useful is the absolute value of the maximum eigenvalue of the difference of the matrices. If you have a hypothesis about how the variances may differ, then you should be able to come up with a more powerful statistic. Patrick Burns [EMAIL PROTECTED] +44 (0)20 8525 0696 http://www.burns-stat.com (home of S Poetry and A Guide for the Unwilling S User) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] var-covar matrices comparison:
Hi, Using package gclus in R, I have created some graphs that show the trends within subgroups of data and correlations among 9 variables (v1-v9). Being interested for more details on these data I have produced also the var-covar matrices. Question: From a pair of two subsets of data (with 9 variables each, I have two var-covar matrices for each subgroup, that differ for a treatment on one group (treatment A) vs (non-Treatment A). Is there a software that can compare if two var-covar matrices are statistically the same? Below are a pair of two matrices, from several others. Thank you in advance for any input. Aldi First group var-covar matrix (the data were under treatment a) v1v2 v3 v4 v5 v6 v7v8 v9 v1 730.87 3.406 -283.41-74.68 107.57 -1355.13 -112.46 14.000 5.776 v2 3.41 24.950 105.45 -121.31 -307.68 -285.4029.65 -2.500 -7.796 v3 -283.41 105.451 6292.19 -2676.46 -970.80 29296.23 10715.29 3.156 -66.313 v4 -74.68-121.307 -2676.46 124492.30 -2289.47 -20377.34 -409.71 183.500 563.102 v5 107.57-307.681 -970.80 -2289.47 7045.62 12118.09 954.51 38.258 96.355 v6 -1355.13-285.404 29296.23 -20377.34 12118.09 218555.93 70126.71 137.000-130.667 v7 -112.46 29.645 10715.29 -409.71 954.51 70126.71 28239.57 67.989 -26.370 v814.00 -2.500 3.16183.50 38.26137.0067.99 24.500 9.000 v9 5.78 -7.796 -66.31563.10 96.35 -130.67 -26.37 9.000 22.776 Second group var-covar matrix (the data were NOT under treatment a) v1v2 v3 v4 v5 v6 v7v8 v9 v1 2696.25 27.05 201.06 2745.54 -344.39540.48654.20 34.363 7.623 v227.05 86.37 -96.89 -497.28 -1185.10 -3108.71 -910.38 -4.254 -9.115 v3 201.06 -96.89 10647.26 8378.07 595.81 66122.43 26237.21 -65.093 -51.998 v4 2745.54 -497.28 8378.07 408391.25 -3887.28 40477.40 30652.01 450.539 50.311 v5 -344.39-1185.10 595.81 -3887.28 29204.00 65320.00 15238.41 -98.237 102.975 v6 540.48-3108.71 66122.43 40477.40 65320.00 549955.14 194691.90-555.552 -95.210 v7 654.20 -910.38 26237.21 30652.01 15238.41 194691.90 82698.88 -70.417 -75.585 v834.36 -4.25 -65.09450.54 -98.24 -555.55-70.42 79.689 8.164 v9 7.62 -9.11 -52.00 50.31 102.97-95.21-75.58 8.164 30.492 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] text miner:
Hi, Does a text miner exist in R-language similar to Splus miner or SAS text miner? I would appreciate any information. TIA, Aldi -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How to install a package that needs to see oher pkg dependencies:
Hi, I am trying to install the genetics package on a server with Linux, Fedora. I installed it in a PC and worked fine. In a server since I am not used with R, I am not sure what do I need to change so genetics pkg can see some package dependencies: Any suggestion is appreciated, Aldi Note: genetics expects gregmisc and mvtnorm to be installed already. gregmisc creates gdata etc dependencies. So here is what I have done: Retrieved the base R and installed and compiled it with make under : /users/genetics/aldi/r/R/R-2.0.0 Under it directories: /mvtnorm /gregmisc /genetics are created. Installed mvtnorm and gregmisc with no problem, but genetics is not recognizing the location of /gregmisc/gdata The command I am using to install genetics package is the following: ../bin/R CMD ../bin/INSTALL genetics_1.1.0.tar.gz Here is the problem: [EMAIL PROTECTED]:/users/genetics/aldi/r/R-2.0.0/genetics% ../bin/R CMD ../bin/INSTALL -l . genetics_1.1.0.tar.gz * Installing *source* package 'genetics' ... ** R ** data ** inst ** preparing package for lazy loading Error in loadNamespace(i[[1]], c(lib.loc, .libPaths()), keep.source) : There is no package called 'gdata' Execution halted ERROR: lazy loading failed for package 'genetics' [EMAIL PROTECTED]:/users/genetics/aldi/r/R-2.0.0/genetics% __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
