[R] cluster non-diet, diet example.
Suppose, we have 3 people called: Francis, Cedric and Nina. Base on what they have eaten, we want to cluster people by diet, non-diet. # original data file, named as filename food.csv. Francis|potato Francis|chocolate Francis|chocolate Francis|milk Cedric|vegetable Cedric|vegetable Cedric|potato Nina|potato Nina|chocolate Nina|chocolate Nina|potato # Step 1: I plan to reform the food.csv file into following frame: FrancisCedricNina potato112 chocolate202 milk1000 fish0100 vegetable020 But, I have problem to reform the original file into that way I want. Basically, I have only tried: org-read.table(food.csv,col.name=c(name,food_list), sep=|) # import file to R x-data.frame(Francis=rep(0,times=5))# set up the frame of file rownames(x)-org$food_list here I failed, and don't know how to continue. Please help me out with the proper R command. # Step 2: I want to draw 3 overlapped barplot with x-axis(5 food name list), y-axis(the occurence value of each food by each person). # Step 3: By comparing the barplots, I should be able to draw the conclusion: Francis and Nina are in the group of non-diet, and Cedric is in the group of diet. Well, that's my simple strategy of clustering, if any of you have better suggestion, I really appreciate it. Thanks! [[alternative HTML version deleted]] __ 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] merge files after cor.test
Dear All, Suppose I have 2 files: # first one : testid.csv A B C D E (id- read.table (testid.csv,col.name=c(id))) id 1 A 2 B 3 C 4 D 5 E # second file is the result file I calculate from cor.text, which shows the correlation coefficient. cor.value.t 1 2 3 4 5 1 1.000 0.2156213 0.31000492 0.22282154 0.1822277 2 0.2156213 1.000 -0.31183893 0.42681488 0.3421535 3 0.3100049 -0.3118389 1. -0.02801885 -0.1307732 4 0.2228215 0.4268149 -0.02801885 1. 0.1454049 5 0.1822277 0.3421535 -0.13077317 0.14540493 1.000 # I tried to merge these two files together. # what I expected is like this: A 1.000 0.2156213 0.31000492 0.22282154 0.1822277 B 0.2156213 1.000 -0.31183893 0.42681488 0.3421535 C 0.3100049 -0.3118389 1. -0.02801885 -0.1307732 D 0.2228215 0.4268149 -0.02801885 1. 0.1454049 E 0.1822277 0.3421535 -0.13077317 0.14540493 1.000 # but after I used (output-merge(id,cor.value.t)), which shows 25 lines (below): id 1 2 3 4 5 1 A 1.000 0.2156213 0.31000492 0.22282154 0.1822277 2 B 1.000 0.2156213 0.31000492 0.22282154 0.1822277 3 C 1.000 0.2156213 0.31000492 0.22282154 0.1822277 4 D 1.000 0.2156213 0.31000492 0.22282154 0.1822277 5 E 1.000 0.2156213 0.31000492 0.22282154 0.1822277 6 A 0.2156213 1.000 -0.31183893 0.42681488 0.3421535 7 B 0.2156213 1.000 -0.31183893 0.42681488 0.3421535 8 C 0.2156213 1.000 -0.31183893 0.42681488 0.3421535 9 D 0.2156213 1.000 -0.31183893 0.42681488 0.3421535 10 E 0.2156213 1.000 -0.31183893 0.42681488 0.3421535 11 A 0.3100049 -0.3118389 1. -0.02801885 -0.1307732 12 B 0.3100049 -0.3118389 1. -0.02801885 -0.1307732 13 C 0.3100049 -0.3118389 1. -0.02801885 -0.1307732 14 D 0.3100049 -0.3118389 1. -0.02801885 -0.1307732 15 E 0.3100049 -0.3118389 1. -0.02801885 -0.1307732 16 A 0.2228215 0.4268149 -0.02801885 1. 0.1454049 17 B 0.2228215 0.4268149 -0.02801885 1. 0.1454049 18 C 0.2228215 0.4268149 -0.02801885 1. 0.1454049 19 D 0.2228215 0.4268149 -0.02801885 1. 0.1454049 20 E 0.2228215 0.4268149 -0.02801885 1. 0.1454049 21 A 0.1822277 0.3421535 -0.13077317 0.14540493 1.000 22 B 0.1822277 0.3421535 -0.13077317 0.14540493 1.000 23 C 0.1822277 0.3421535 -0.13077317 0.14540493 1.000 24 D 0.1822277 0.3421535 -0.13077317 0.14540493 1.000 25 E 0.1822277 0.3421535 -0.13077317 0.14540493 1.000 Is anybody know why it outputs 5 times? Thanks a lot! Nina [[alternative HTML version deleted]] __ 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 can i see all the .Rdata files within R
For example, I saved several .Rdata files with different names: a.Rdata, b.Rdata ... But, if I forget the specific file name, how can I get all files list? One more question about .R file: source(~/Desktop/allchapters.R,local=FALSE) Error in parse(file, n = -1, NULL, ?) : syntax error at 135: names(airquality) 136: [ why? Nina __ 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
Re: [R] how can i see all the .Rdata files within R
On 3/17/06, jia ding [EMAIL PROTECTED] wrote: For example, I saved several .Rdata files with different names: a.Rdata, b.Rdata ... But, if I forget the specific file name, how can I get all files list? One more question about .R file: source(~/Desktop/allchapters.R,local=FALSE) Error in parse(file, n = -1, NULL, ?) : syntax error at 135: names(airquality) 136: [ And I tried: load(~/Desktop/allchapters.R) Error: bad restore file magic number (file may be corrupted) -- no data loaded another error msg, I can not find explaination. why? Nina __ 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
Re: [R] Question about 'lables' ect.
Thanks Marc Liaw! On 3/15/06, Marc Schwartz (via MN) [EMAIL PROTECTED] wrote: On Wed, 2006-03-15 at 17:54 +0100, jia ding wrote: Hi, I have a file named: test_R.txt aaa 2 bbb 5 ccc 7 sss 3 xxx 8 I want to have a plot: test-read.table(test_R.txt,col.name=c(Name,Score)) par(mfrow=c(1,2)) It's not clear what the purpose is here, at least in this example. Do you plan on creating a second plot? Yes, I want to plot the second one. e.g. the second file is : test2_R.txt zszs 2 gjie 4 gjai 5 opwn 6 jgio 3 gjwn 8 owln 6 aonl 1 gols 7 I post the complete command here: test-read.table(/vol/fpsearch/jiading/berman/single/test_R.txt,col.name=c (Name,Score)) #single-single[order(-single$Weights),] #decreastest_R.txt,col.name=c(Name,Score)) test2-read.table(/vol/fpsearch/jiading/berman/single/test2_R.txt, col.name=c(Name,Score)) par(mfrow=c(2,1)) t-barplot(test$Score,space=0.5) axis(1,at=t,labels=as.character (test$Name)) t2-barplot(test2$Score,space=0.5) axis(1,at=t2,labels=as.character(test2$Name)) P1; The problem is, even I set each plot with space=0.5, the bar's width are different. The first plot's bars are lot wider than the second plot's. What I want is, to make 2 plots same width. barplot(test$Score) name-test$Name axis(1,at=1:length(test$Name),labels=paste(name)) Q1, if you try the script above,you will get 5 bars, the axis only shows aaa, ccc,xxx, but where are bbbsss? The easiest way to do this is to use the ' names.arg' argument in barplot(): barplot(test$Score, names.arg = as.character(test$Name)) P2: if I made 2 barplot next to each other by: par(mfrow=c(1,2)). It seems names.arg doesn't work for the second plot ( test2_R.txt), as it automatically hides some of the labels. Of course, in order to draw everything, I can try to rotate the labels e.g. par(las=2). While, I am thinking, it should have some solution to solve this problem without turning labels. P3: if I typed pdf(test.pdf) Suppose the plot has lots of bars. Sometimes,there is not enough space for pdf to draw everything. Which means it's not a complete file. Do you have any suggestion about it? PS: do you know, if there is the website which provides all the questions people are asking now? I mean, when I have problems I send email to r-help@stat.math.ethz.ch, and then some nice people will have a look of my problems and send me back their solutions. I am puzzled, except daily R-help-request mail, how can I get other people's r-help mail simultaneous? I remember I do subscribe to the mail group. Thanks! Nina Note that the 'Name' column in the 'test' data frame will be a factor by default, so you need to convert it to a character vector here. Q2, pls have a look this x-axis again, you will find the middle of the bars are not pointing to the x-axes. Note that in the Value section of ?barplot, it indicates that barplot() returns the bar midpoints, which are not at integer values along the x axis. You would need to do something like: mp - barplot(test$Score) axis(1, at = mp, labels = as.character(test$Name)) Q3, how can i change the width of the bars? I feel they are too fat. You can use the 'space' argument: barplot(test$Score, names.arg = as.character(test$Name), space = 0.5) See the descriptions of the 'width' and 'space' arguments in ?barplot for some of the subtleties here. See ?barplot for more information and further examples. HTH, Marc Schwartz [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Question about 'lables' ect.
Hi, I have a file named: test_R.txt aaa 2 bbb 5 ccc 7 sss 3 xxx 8 I want to have a plot: test-read.table(test_R.txt,col.name=c(Name,Score)) par(mfrow=c(1,2)) barplot(test$Score) name-test$Name axis(1,at=1:length(test$Name),labels=paste(name)) Q1, if you try the script above,you will get 5 bars, the axis only shows aaa, ccc,xxx, but where are bbbsss? Q2, pls have a look this x-axis again, you will find the middle of the bars are not pointing to the x-axes. Q3, how can i change the width of the bars? I feel they are too fat. Thanks! Nina [[alternative HTML version deleted]] __ 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
Re: [R] 2 barplots in the same graph
Thanks All! I combine your answers and post the code here again, if later somebody need it. Actually, what I want is: x1 [1] 1 2 10 x2 [1] -3 5 -8 barplot(x1,col=white,border=red) barplot(x2,col=white,border=green,add=T) So that, the two plots even share the same x-axis. But, It comes another question: barplot(x2,col=white,border=green,add=T), because there are 2 numbers are negative, some part of the bar is missing. Is there any automatic function to make the axes fit very well for both bars? And, suppose I want to add another command: axis(1, 0:20) to draw x-axis. I notice it increase like: 0,1,2,3,...20; how can I make it 0,5,15,20? Thanks! On 2/22/06, Gabor Grothendieck [EMAIL PROTECTED] wrote: The barplot solution already presented is probably what you want but just in case here is a zoo solution: library(zoo) z - merge(zoo(x2), zoo(x1, seq(x1)+.5)) plot(z, type = h, plot.type = single, col = 1:2, lwd = 5) Or a similar solution without zoo: plot(c(x1, x2) ~ c(seq(x1)+.5, seq(x2)), col = c(1+0*x1, 2+0*x2), type = h, lwd = 5) On 2/22/06, jia ding [EMAIL PROTECTED] wrote: Hello, I have a very simple question about 2 barplots in the same graph. It seems quite easy, but I searched google for long time, haven't find solution. For example, I want one graph like: x1=seq(0,2,by=0.3) x2=seq(3,0,by=-0.1) barplot(x1,col=red) barplot(x2,col=green) It means if it's on the same graph, some bars are overlaped. So if the bars are hollow, instead of filled with color, it will be better. Actually, I think it's something similar with matlab's hold on command. Thanks! Nina [[alternative HTML version deleted]] __ 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 [[alternative HTML version deleted]] __ 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
Re: [R] 2 barplots in the same graph
Hi, Would you pls try these? x1-c(1,2,10) x2-c(-3,5,-8) barplot(x1,col=white,border=red,ylim=range(c(x1,x2))) barplot(x2,col=white,border=green,ylim=range(c(x1,x2)),add=T) axis(1, 0:3) box() Q1, on x-axis 1,2,3 is not shown at the middle position of the bars. e.gfor first bar, 1 is tend to right ; while third bar, 3 is tend to left. Q2, once box(), then bars are cut again. Q3, when y-axis is 0, I want to draw a parallel line to x-axis: I tried lines(c(0,5),c(0,0)) ; is there any other way to do it? Thanks. Nina On 2/24/06, Romain Francois [EMAIL PROTECTED] wrote: Le 24.02.2006 11:17, jia ding a écrit : Thanks All! I combine your answers and post the code here again, if later somebody need it. Actually, what I want is: x1 [1] 1 2 10 x2 [1] -3 5 -8 barplot(x1,col=white,border=red) barplot(x2,col=white,border=green,add=T) So that, the two plots even share the same x-axis. But, It comes another question: barplot(x2,col=white,border=green,add=T), because there are 2 numbers are negative, some part of the bar is missing. Is there any automatic function to make the axes fit very well for both bars? R barplot(x1,col=white,border=red, ylim=range(c(x1,x2))) And, suppose I want to add another command: axis(1, 0:20) to draw x-axis. I notice it increase like: 0,1,2,3,...20; how can I make it 0,5,15,20? before doing axis(1, 0:20) have you tried to do R 0:20 So, R axis(1, (0:4)*5) or R axis(1, c(0,5, 10, 15, 20)) or R axis(1, seq(0,20, by=5)) it's up to you. There are probably other solutions as well Thanks! You're welcome Romain -- visit the R Graph Gallery : http://addictedtor.free.fr/graphiques Discover the R Movies Gallery : http://addictedtor.free.fr/movies +---+ | Romain FRANCOIS - http://francoisromain.free.fr | | Doctorant INRIA Futurs / EDF | +---+ [[alternative HTML version deleted]] __ 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] 2 barplots in the same graph
Hello, I have a very simple question about 2 barplots in the same graph. It seems quite easy, but I searched google for long time, haven't find solution. For example, I want one graph like: x1=seq(0,2,by=0.3) x2=seq(3,0,by=-0.1) barplot(x1,col=red) barplot(x2,col=green) It means if it's on the same graph, some bars are overlaped. So if the bars are hollow, instead of filled with color, it will be better. Actually, I think it's something similar with matlab's hold on command. Thanks! Nina [[alternative HTML version deleted]] __ 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] help-ERROR: unknown GUI none from Statistics::R
Hi, I download Statistics::R from http://search.cpan.org/~gmpassos/Statistics-R-0.02/ I am going to combine R with perl. but it keeps give the error msg: ERROR: unknown GUI none stop running script. I feel very strange, because previously it works. my perl version is 5.8.6 my R version is Version 2.2.1 Is there anybody know about it? Thanks a lot. Nina [[alternative HTML version deleted]] __ 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] histogram error: 'x' must be numeric
Hi All,
I have problem to plot histogram.
What I did is:
export a .csv file from PSQL database's table.
so, inside this .csv file it looks like:
31.845
24.598
29.1223
24.715
23.1847
24.2321
25.2995
23.4261
30.7873
..
Then, I use command:
score- read.csv('file.csv', header = FALSE,sep = ,)
hist(score, main = score)
it gives error msg:
Error in hist.default(score, main = score) :
'x' must be numeric
Can any of you know about it explain me why?
Thanks a lot.
Nina
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[R] library(lattice)
I first try these command, it works quite well. library(lattice) data(cuckoos) levnam - strsplit(levels(cuckoos$species), \\.) BUT, i want to try : levnam - strsplit(levels(cuckoos$species), .) to see the difference. They maybe I modified the data file, because when I try again, it says: data(cuckoos) Warning message: data set 'cuckoos' not found in: data(cuckoos) would you please tell me how to deal with this problem? I have already tried update.packages() it doesn't help. Thanks. DJ [[alternative HTML version deleted]] __ 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] accident modified dataset. How can I recovery it?!
I first try these command, it works quite well. library(lattice) data(cuckoos) levnam - strsplit(levels(cuckoos$species), \\.) BUT, i want to try : levnam - strsplit(levels(cuckoos$species), .) to see the difference. They maybe I modified the data file, because when I try again, it says: data(cuckoos) Warning message: data set 'cuckoos' not found in: data(cuckoos) would you please tell me how to deal with this problem? I have already tried update.packages() it doesn't help. Thanks. DJ [[alternative HTML version deleted]] __ 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
Re: [R] accident modified dataset. How can I recovery it?!
I tried to reinstall the package. but my R version is too old. [EMAIL PROTECTED]:~$ sudo R CMD INSTALL -l /usr/lib/R/library /home/dj/Desktop/lattice_0.12-11.tar.gz Password: ERROR: This R is version 2.1.1 package 'lattice' needs R = 2.2.0 So, *my question being, how do I upgrade from R version *R = 2.2.0 * to R *2.1.1* and keep all of my libraries intact? * On 11/9/05, jia ding [EMAIL PROTECTED] wrote: I first try these command, it works quite well. library(lattice) data(cuckoos) levnam - strsplit(levels(cuckoos$species), \\.) BUT, i want to try : levnam - strsplit(levels(cuckoos$species), .) to see the difference. They maybe I modified the data file, because when I try again, it says: data(cuckoos) Warning message: data set 'cuckoos' not found in: data(cuckoos) would you please tell me how to deal with this problem? I have already tried update.packages() it doesn't help. Thanks. DJ [[alternative HTML version deleted]] __ 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] question about R graphics-example plot attached
-- Forwarded message -- From: jia ding [EMAIL PROTECTED] Date: Nov 2, 2005 4:03 PM Subject: question about R graphics-example plot attached To: [EMAIL PROTECTED] Suppose I have the data set like this: A 1 3 7 10 B 5 9 13 The numbers here actually is A or B's occurence positions.So it means, position 1,3,7,10 is A;position 5,9,13 is B's occurence. I want the plot is a line with a little dot (or bar) at the position 1(A-show red), position 3(A-red),position 5(B-blue),7(A-red),10(A-red),13(B-blue) I am not sure, If I explained very clearly about my question. What a pity google group not support to attach a file. Otherwise,I can provide an example. Thanks for the help! Thanks Marc. DJ output.png Description: PNG image __ 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
