Re: [R] Controlling size of boxplot when it is added in a plot
Charilaos Skiadas wrote: Greetings, I am trying to add a boxplot to the bottom of a histogram, right between the histogram bars and the x axis. Here is the code I am using at the moment (the par line is probably not relevant for our discussion): hs - hist(x, breaks = 20, plot = F) par(mar = c(3,3,2,1)) hist(x, breaks = 20, main = NULL, ylim = c(-2, max(hs$counts))) boxplot(x, horizontal = T, axes = T, add = T, at = -1) The problem is the following. As it is, the boxplot restricts itself to the -1 line. I would like it to occupy both the -1 and the -2 lines ( I guess more generally I would like to control how much vertical space the embedded boxplot occupies). I tried to set the width parameter in the boxplot, but that seemed to have no effect at all. Try setting the boxwex argument instead: par(mfrow=c(1,2)) set.seed(54321) x - rnorm(100) hs - hist(x, breaks = 20, plot = F) hist(x, breaks = 20, main = NULL, ylim = c(-2, max(hs$counts))) boxplot(x, horizontal = T, axes = T, add = T, at = -1, boxwex = 1) hist(x, breaks = 20, main = NULL, ylim = c(-2, max(hs$counts))) boxplot(x, horizontal = T, axes = T, add = T, at = -1, boxwex = 3) On an OT note, I haven't seen this way of combining a histogram with a boxplot (perhaps I haven't looked really hard). I thought it would be useful for my students to see them next to each other, to develop a feeling for what histograms might correspond to what boxplots. Is there perhaps some reason why I should avoid showing those graphs to them like that, that I am not aware of? Or just a reason why I haven't seen them combined like this much? TIA Charilaos Skiadas Department of Mathematics Hanover College P.O.Box 108 Hanover, IN 47243 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ks.test not working?
Hi, I am trying the following: library(ismev) library(evd) fit - gev.fit(x,show=FALSE) ks.test(x,pgev,fit$mle[1],fit$mle[2],fit$mle[3]) but I am getting: Warning message: cannot compute correct p-values with ties in: ks.test(x, pgev, fit$mle[1], fit$mle[2], fit$mle[3]) where x is: [1] 239 381 43 22159 15619 156 253 1006 [18]5 100 10 103 25512 118 68 13 154 67 125 15 [35]5 130 47 143 176 573 592 213 54 10 179 198 293 77 11 44 [52]6 222 10812 164 70 1247 134 41 5158 [69] 200 1692 13 49 218 48 34 74 19 44 1286 96 238 17 167 [86] 308 204 416 32 77 14 62 103642 1114 [103] 22 15 13 12 34 14 1331122 52 3469 31 [120] 342 34827 52 39 795 88 238 40 294 69 878 7516 [137]5 381 58 84 588 345 161 12936 403 516 161 1112 54 3812 [154] 526 38 17 20 17 800 1891 57 90 92 16 17 31 114 17 [171] 129 10 46 14 23111 313 Can anyone tell me why that could be? Thank you very much, Benjamin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ks.test not working?
Benjamin Dickgiesser wrote: Hi, I am trying the following: library(ismev) library(evd) fit - gev.fit(x,show=FALSE) ks.test(x,pgev,fit$mle[1],fit$mle[2],fit$mle[3]) 1. The test *is* working. It simply warns (and does not report an error) that you have ties in your data and the assumption for calculating p-values do not hold. 2. The KS tests tends to be very conservative given you specify estimated parameters of the distribution. Uwe Ligges but I am getting: Warning message: cannot compute correct p-values with ties in: ks.test(x, pgev, fit$mle[1], fit$mle[2], fit$mle[3]) where x is: [1] 239 381 43 22159 15619 156 253 1006 [18]5 100 10 103 25512 118 68 13 154 67 125 15 [35]5 130 47 143 176 573 592 213 54 10 179 198 293 77 11 44 [52]6 222 10812 164 70 1247 134 41 5158 [69] 200 1692 13 49 218 48 34 74 19 44 1286 96 238 17 167 [86] 308 204 416 32 77 14 62 103642 1114 [103] 22 15 13 12 34 14 1331122 52 3469 31 [120] 342 34827 52 39 795 88 238 40 294 69 878 7516 [137]5 381 58 84 588 345 161 12936 403 516 161 1112 54 3812 [154] 526 38 17 20 17 800 1891 57 90 92 16 17 31 114 17 [171] 129 10 46 14 23111 313 Can anyone tell me why that could be? Thank you very much, Benjamin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] PCA (prcomp) details info.
Francesco Savorani wrote: I'm handling a matrix dataset composed by a number of variables much higher than the objects (900 vs 100) and performing a prcomp (centered and scaled) PCA on it. What I get is a Loadings (rotation) matrix limited by my lower number of objects and thus 900x100 instead of 900x900. If I try to manually calculate the matrix scores multiplying the original variables (centered and scaled) for such a loadings matrix I cannot obtain the same values calculated by R and stored on the prcomp$x matrix (100x100). This works for me: M - matrix(rnorm(900*100), ncol = 900) pca - prcomp(M, scale = TRUE) S - scale(M) %*% pca$rotation all.equal(S, pca$x) ## = TRUE -- Bjørn-Helge Mevik __ 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] merging two lists but get indexes
Suppose I have two columns of entries, how can I get the union of the two columns? Please note: I input my columns through excel. These entries have text format in excel. Also, out of curiosity, how can I find out the data type of a data frame ? a - read.csv(book1.csv) a n1 n2 1 apple soda 2 orange apple 3 soda green 4red yellow 5 white blue 6 white union(a$n1,a$n2) [1] 2 3 5 4 6 1 I want the actual names instead of the indexes. __ 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] merging two lists but get indexes
Teng Sun wrote: Suppose I have two columns of entries, how can I get the union of the two columns? Please note: I input my columns through excel. These entries have text format in excel. Also, out of curiosity, how can I find out the data type of a data frame ? df - data.frame(n1 = c(apple,orange,soda,red,white,), n2 = c(soda,apple,green,yellow,blue,white), x = rnorm(6)) str(df) 'data.frame': 6 obs. of 3 variables: $ n1: Factor w/ 6 levels ,apple,orange,..: 2 3 5 4 6 1 $ n2: Factor w/ 6 levels apple,blue,..: 4 1 3 6 2 5 $ x : num -0.0932 -2.0714 -0.9539 0.7249 -0.7039 ... lapply(df, class) $n1 [1] factor $n2 [1] factor $x [1] numeric a - read.csv(book1.csv) a n1 n2 1 apple soda 2 orange apple 3 soda green 4red yellow 5 white blue 6 white union(a$n1,a$n2) [1] 2 3 5 4 6 1 I want the actual names instead of the indexes. You are getting the union of factor levels rather than the union of the strings. Try this: union(as.character(df$n1), as.character(df$n2)) [1] apple orange soda [4] redwhite [7] green yellow blue __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] merging two lists but get indexes
Try: a - read.csv(book1.csv, as.is = TRUE) to read the columns in as character class rather than the default of factor . See ?read.csv On 1/14/07, Teng Sun [EMAIL PROTECTED] wrote: Suppose I have two columns of entries, how can I get the union of the two columns? Please note: I input my columns through excel. These entries have text format in excel. Also, out of curiosity, how can I find out the data type of a data frame ? a - read.csv(book1.csv) a n1 n2 1 apple soda 2 orange apple 3 soda green 4red yellow 5 white blue 6 white union(a$n1,a$n2) [1] 2 3 5 4 6 1 I want the actual names instead of the indexes. __ 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] changes in the structure of mer objects?
Dear all, I try to run the example of lmer and get the following error message. library(lme4) example(lmer) lmer (fm1 - lmer(Reaction ~ Days + (Days | Subject), sleepstudy)) [[1]] Error in get(x, envir, mode, inherits) : variable as.dpoMatrix was not found This error message is similar to what I get with other models. It looks like the mer class has a slightly different structure. Anybody an idea how to solve this? I am using R 2.4.1 under linux and the latest releases of lme4 and Matrix lme4_0.9975-10 Matrix_0.9975-8 version _ platform x86_64-unknown-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 4.1 year 2006 month 12 day18 svn rev40228 language R version.string R version 2.4.1 (2006-12-18) Thanks Joris De Wolf Phone: +32 9 2429155, E-Mail: [EMAIL PROTECTED] Postal Address: CropDesign N.V. Technologiepark 3, 9052 Gent Belgium __ 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] extracting data into different subsets
y Slide Block ID 441068 -0.020464103 1 15 GFASKTPANQA 448844 0.061400545 1 41 GFASKTPANQA 456620 -0.031026896 10 15 GFASKTPANQA 464396 -0.033166864 10 41 GFASKTPANQA 472172 -0.108148804 11 15 GFASKTPANQA 479948 -0.397759508 11 41 GFASKTPANQA 4167 -0.67283526 1 13 ALPAFSPPAQA 11943 -0.23982701 1 37 ALPAFSPPAQA 19719 -0.10169540 10 13 ALPAFSPPAQA 27495 0.70043972 10 37 ALPAFSPPAQA 35271 -0.18807235 11 13 ALPAFSPPAQA 43047 -0.17982104 11 37 ALPAFSPPAQA 5264 -0.011681805 1 17 ATQAAGAGAVA 13040 -0.073063462 1 41 ATQAAGAGAVA 20816 -0.017996429 10 17 ATQAAGAGAVA 28592 0.010159866 10 41 ATQAAGAGAVA 36368 -0.056034035 11 17 ATQAAGAGAVA 44144 -0.346175641 11 41 ATQAAGAGAVA 5612 -0.7121977 1 18 GFASKTPANQA 13388 -0.4076580 1 42 GFASKTPANQA 21164 -0.1864131 10 18 GFASKTPANQA 28940 -0.1140163 10 42 GFASKTPANQA 36716 -0.3246222 11 18 GFASKTPANQA 44492 -0.4355016 11 42 GFASKTPANQA where there are 4 different IDs and each ID appears twice in two blocks for each of 3 slides. I want to extract the data in such a way that every ID that appears the first time will be grouped to group 1, and the second time to group 2. For the data above, it means that the IDs with response y that are in blocks 15,13,17,18 for each slide will be in group 1 and the rest are in group 2. How can I do this in R ? Thanks for your help, Jenny - [[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.
Re: [R] extracting data into different subsets
try this: input -y Slide Block ID + 441068 -0.020464103 1 15 GFASKTPANQA + 448844 0.061400545 1 41 GFASKTPANQA + 456620 -0.031026896 10 15 GFASKTPANQA + 464396 -0.033166864 10 41 GFASKTPANQA + 472172 -0.108148804 11 15 GFASKTPANQA + 479948 -0.397759508 11 41 GFASKTPANQA + 4167 -0.67283526 1 13 ALPAFSPPAQA + 11943 -0.23982701 1 37 ALPAFSPPAQA + 19719 -0.10169540 10 13 ALPAFSPPAQA + 27495 0.70043972 10 37 ALPAFSPPAQA + 35271 -0.18807235 11 13 ALPAFSPPAQA + 43047 -0.17982104 11 37 ALPAFSPPAQA + 5264 -0.011681805 1 17 ATQAAGAGAVA + 13040 -0.073063462 1 41 ATQAAGAGAVA + 20816 -0.017996429 10 17 ATQAAGAGAVA + 28592 0.010159866 10 41 ATQAAGAGAVA + 36368 -0.056034035 11 17 ATQAAGAGAVA + 44144 -0.346175641 11 41 ATQAAGAGAVA + 5612 -0.7121977 1 18 GFASKTPANQA + 13388 -0.4076580 1 42 GFASKTPANQA + 21164 -0.1864131 10 18 GFASKTPANQA + 28940 -0.1140163 10 42 GFASKTPANQA + 36716 -0.3246222 11 18 GFASKTPANQA + 44492 -0.4355016 11 42 GFASKTPANQA + x - read.table(textConnection(input), header=TRUE) # find the breaks in the ID ID.breaks - c(TRUE, diff(as.numeric(x$ID)) != 0) group.1 - x[ID.breaks,] group.2 - x[!ID.breaks,] group.1 y Slide Block ID 441068 -0.02046410 115 GFASKTPANQA 4167 -0.67283526 113 ALPAFSPPAQA 5264 -0.01168180 117 ATQAAGAGAVA 5612 -0.71219770 118 GFASKTPANQA group.2 y Slide Block ID 448844 0.06140055 141 GFASKTPANQA 456620 -0.031026901015 GFASKTPANQA 464396 -0.033166861041 GFASKTPANQA 472172 -0.108148801115 GFASKTPANQA 479948 -0.397759511141 GFASKTPANQA 11943 -0.23982701 137 ALPAFSPPAQA 19719 -0.101695401013 ALPAFSPPAQA 27495 0.700439721037 ALPAFSPPAQA 35271 -0.188072351113 ALPAFSPPAQA 43047 -0.179821041137 ALPAFSPPAQA 13040 -0.07306346 141 ATQAAGAGAVA 20816 -0.017996431017 ATQAAGAGAVA 28592 0.010159871041 ATQAAGAGAVA 36368 -0.056034041117 ATQAAGAGAVA 44144 -0.346175641141 ATQAAGAGAVA 13388 -0.40765800 142 GFASKTPANQA 21164 -0.186413101018 GFASKTPANQA 28940 -0.114016301042 GFASKTPANQA 36716 -0.324622201118 GFASKTPANQA 44492 -0.435501601142 GFASKTPANQA On 1/14/07, Jenny persson [EMAIL PROTECTED] wrote: y Slide Block ID 441068 -0.020464103 1 15 GFASKTPANQA 448844 0.061400545 1 41 GFASKTPANQA 456620 -0.031026896 10 15 GFASKTPANQA 464396 -0.033166864 10 41 GFASKTPANQA 472172 -0.108148804 11 15 GFASKTPANQA 479948 -0.397759508 11 41 GFASKTPANQA 4167 -0.67283526 1 13 ALPAFSPPAQA 11943 -0.23982701 1 37 ALPAFSPPAQA 19719 -0.10169540 10 13 ALPAFSPPAQA 27495 0.70043972 10 37 ALPAFSPPAQA 35271 -0.18807235 11 13 ALPAFSPPAQA 43047 -0.17982104 11 37 ALPAFSPPAQA 5264 -0.011681805 1 17 ATQAAGAGAVA 13040 -0.073063462 1 41 ATQAAGAGAVA 20816 -0.017996429 10 17 ATQAAGAGAVA 28592 0.010159866 10 41 ATQAAGAGAVA 36368 -0.056034035 11 17 ATQAAGAGAVA 44144 -0.346175641 11 41 ATQAAGAGAVA 5612 -0.7121977 1 18 GFASKTPANQA 13388 -0.4076580 1 42 GFASKTPANQA 21164 -0.1864131 10 18 GFASKTPANQA 28940 -0.1140163 10 42 GFASKTPANQA 36716 -0.3246222 11 18 GFASKTPANQA 44492 -0.4355016 11 42 GFASKTPANQA where there are 4 different IDs and each ID appears twice in two blocks for each of 3 slides. I want to extract the data in such a way that every ID that appears the first time will be grouped to group 1, and the second time to group 2. For the data above, it means that the IDs with response y that are in blocks 15,13,17,18 for each slide will be in group 1 and the rest are in group 2. How can I do this in R ? Thanks for your help, Jenny - [[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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? [[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.
Re: [R] Controlling size of boxplot when it is added in a plot
Sorry, meant to send this to the list.
On Jan 14, 2007, at 4:28 PM, Charilaos Skiadas wrote:
On Jan 14, 2007, at 5:50 AM, Chuck Cleland wrote:
Try setting the boxwex argument instead:
Thanks Chuck, that does indeed seem to work pretty well. I'm not
quite sure what the best way to determine an appropriate size for
the boxplot would be, but the following kind of works, at least for
the cases I tried. Though I'm not entirely happy with it. And I'm
sure I've made a bunch of errors along the way, that someone more
experienced in R could spot easily. Feel free to criticize the
code. the boxwex default I guess is probably terribly named. One
over it is supposed to be the size of the boxplot over the size of
the histogram.
force.odd - function(x) {
x + 1 - x %% 2;
}
boxhist - function(x, boxwex = 8, ...) {
hs - hist(x, breaks = 20, plot = F)
space - force.odd(max(floor(hs$counts / boxwex), 1))
plot(hs, main = NULL, ylim = c(-space, max(hs$counts)), ...)
boxplot(x, horizontal = T, axes = T, add = T, at = -space/2,
boxwex = space)
}
x - rweibull(300,1,1); boxhist(x)
Haris
Haris
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[R] [R-pkgs] spatstat 1.11-0
spatstat 1.11-0 Version 1.11-0 of package 'spatstat' is now available. Spatstat is a package for the analysis of spatial data, mostly point pattern data. See www.spatstat.org Important changes in version 1.11-0: New format for ppm objects (objects in old format are still handled). More stringent checking of function arguments. Improved handling of pixellation effects. Extensions to variance-covariance calculations for fitted models. Adrian Baddeley and Rolf Turner ___ R-packages mailing list R-packages@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-packages __ 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 detect if R is running on Mac OS X?
This question is probably trivial, but I don't find the answer. I have code that is different for Windows, Unix/Linux and Mac OSX. The man page of .Platform tells that .Platform$OS.type is the right way to test for it... but it also tels that it returns either windows or unix. Is Mac OS X reported as unix? If yes, how do I make the difference? Thanks, Philippe Grosjean __ 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.
