Re: [R] Get bearing for cartesian coordinates
I think all you need is bearing - function(x, y) atan2(y, x)*180/pi This gives the bearing in degrees from the origin. If you wanted the bearing from some other point, just take the differences: bearing - function(x, y, origin = c(x=0,y=0)) atan2(y-origin[y], x-origin[x])*180/pi Bill Venables http://www.cmis.csiro.au/bill.venables/ -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of pecardoso Sent: Tuesday, 28 July 2009 9:40 AM To: r-help@r-project.org Subject: [R] Get bearing for cartesian coordinates Is it possible to get bearing in degrees from Cartesian (not lat long) coordinates? [[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. __ 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] Making a sub data.frame
Suppose DF is the data frame and someIDs is the vector subDF - subset(DF, ID %in% someIDs) Bill Venables http://www.cmis.csiro.au/bill.venables/ -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of desper Sent: Tuesday, 28 July 2009 6:41 AM To: r-help@r-project.org Subject: [R] Making a sub data.frame Dear all, I have a data.frame like this ID VAR1 11 blaaal 121 blalda 121 adada 234baada 231 ddaaa 231 baada ... ... and I have another vector of ID, say, c(121,234,231) How could I collect all the observations start with ID from c(121,234,231) ? Thanks All the Best, Desper -- View this message in context: http://www.nabble.com/Making-a-sub-data.frame-tp24687873p24687873.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-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] Splitting matrix into several small matrices
I take it you want to split the matrix into sub-matrices for which some collection of columns is constant. In your case this is the last four columns. Here's an idea: z - matrix(c(13,1,1,1,1,12,0,0,0,0,8,1,0,1,1,8,0,1,0,0, + 10,1,1,1,1,3,0,1,0,0,3,1,0,1,1,6,1,1,1,1),8,5,byrow = T) z [,1] [,2] [,3] [,4] [,5] [1,] 131111 [2,] 120000 [3,]81011 [4,]80100 [5,] 101111 [6,]30100 [7,]31011 [8,]61111 ind - do.call(paste, data.frame(z[, 2:5])) split(data.frame(z), ind) $`0 0 0 0` X1 X2 X3 X4 X5 2 12 0 0 0 0 $`0 1 0 0` X1 X2 X3 X4 X5 4 8 0 1 0 0 6 3 0 1 0 0 $`1 0 1 1` X1 X2 X3 X4 X5 3 8 1 0 1 1 7 3 1 0 1 1 $`1 1 1 1` X1 X2 X3 X4 X5 1 13 1 1 1 1 5 10 1 1 1 1 8 6 1 1 1 1 Bill Venables http://www.cmis.csiro.au/bill.venables/ -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of kathie Sent: Tuesday, 28 July 2009 8:47 AM To: r-help@r-project.org Subject: [R] Splitting matrix into several small matrices Dear R users... I need to split this matrix(or dataframe), for example, z - matrix(c(13,1,1,1,1,12,0,0,0,0,8,1,0,1,1,8,0,1,0,0, 10,1,1,1,1,3,0,1,0,0,3,1,0,1,1,6,1,1,1,1),8,5,byrow = T) z [,1] [,2] [,3] [,4] [,5] [1,] 131111 [2,] 120000 [3,]81011 [4,]90100 [5,] 101111 [6,]30100 [7,]31011 [8,]61111 (actually, z matrix is big, about 1000*15 matrix) to 4 matrices like this way, #- 1st matrix-- 131111 101111 61111 #- 2nd matrix-- 120000 #- 3rd matrix-- 81011 31011 #- 4th matrix-- 90100 30100 Any comments will be greatly appreciated. Kathryn Lord -- View this message in context: http://www.nabble.com/Splitting-matrix-into-several-small-matrices-tp24689585p24689585.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-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] Split rownames into factors
?substring Bill Venables http://www.cmis.csiro.au/bill.venables/ -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of jimdare Sent: Tuesday, 28 July 2009 8:10 AM To: r-help@r-project.org Subject: [R] Split rownames into factors Hi Guys, I was wondering how you would go about solving the following problem: I have a list where the grouping information is in the row names. Rowname [,1] X1Jan08 324 X1Jun08 65 X1Dec08 543 X2Jan08 23 X2Jun08 54 X2Dec08 8765 X3Jan08 213 X3Jun08 43 X3Dec08 65 How can I create the following dataframe: ValueDateGroup [1,] 324 Jan 08X1 [2,] 65 Jun 08X1 [3,] 543 Dec 08X1 etc. Thanks for your help! James -- View this message in context: http://www.nabble.com/Split-rownames-into-factors-tp24689181p24689181.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-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] storing output in html or pdf table format.
Hello, On 7/28/09, Albert EINstEIN sateeshvar...@gmail.com wrote: clarification on output in R. I have generated summary statistics output for dataset (E.g. sales) in output window. Now i want to store that output in a html or pdf in a table format. if possible can any one provide code for this one. http://www.rseek.org/?cx=010923144343702598753%3Aboaz1reyxd4q=html+outputsa=Searchcof=FORID%3A11 There is also html() in Hmisc. There are others: do an in-line search for HTML on CRAN [1]. Liviu [1] http://cran.r-project.org/web/packages/ __ 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] Sort a dataframe on the column Date
Dear Users I have a dataframe called mydata4 of the following order with the first column as a date and the rest of the columns are numeric with rate. Column 1 Rate1 : Rate 20 (PxMid) 01/01/2003 07/01/2001 -- I wish to sort this dataframe on the first col in ascending order. I tried to do the following mydata4-mydata4[,order(mydata4$PxMid)] This give an error. Please help. Regards Meenu [[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] calculating p-values from t-values for a Bonferroni adjustment
NativeBuff2003 wrote: Sorry I'm new to the list and not great with R. My advisor performed several for me but I am getting a different output when I try to reproduce it. 2*(1-pt(-3.59,598)) 0.000358 -his answer [1] 1.999642 -my answer I was working with a different data set in the following but the answer doesn't fit. 2*(1-pt(-5.542,389)) [1] 2 - my answer I assume that his answer was generated not by the same code, but from what (s)he looked up in the table. Note that your result = 2-her result, and compare the output from the code below. Dieter 2*(pt(abs(-3.59),598,lower.tail=TRUE)) 2*(pt(-3.59,598,lower.tail=TRUE)) 2*(pt(abs(-3.59),598,lower.tail=FALSE)) 2*(pt(-3.59,598,lower.tail=FALSE)) -- View this message in context: http://www.nabble.com/calculating-p-values-from-t-values-for-a-Bonferroni-adjustment-tp24689680p24693461.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] computing the radius of an arc
Nair, Murlidharan T mnair at iusb.edu writes: Alex Brenning, the developer of the RSAGA package told me that and I quote the RSAGA package (which uses functions from the free geographical information system [GIS] SAGA GIS) has a curvature function that is designed to calculate the curvature of surfaces, in particular raster (i.e. gridded) digital elevation models. I am not aware of a function in SAGA GIS or other GIS that would calculate curvatures along a line, especially not in 3D I have difficulties seeing how you would go about to do this. A surface locally is characterized by two main curvatures --- this is Gauss' theorem for 2-dim geometry. The sphere has the same curvature, 1/r, in both directions. So maybe you can approximate the surface by an ellipsoid, but a strange one as the main directions may not be orthogonal. I am not sure this is what you wanted to achieve. As a side remark: The circle approximating a curve in three dimensions is not uniquely determined. Regards Hans Werner I shall try to develop it and if I am successful I shall make it available. Cheers../Murli __ 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] Cumulative row sums, row differences
I tried searching but I couldn't quite find what I was looking for. Here's a dummy data matrix (with row and column labels): y 0 1 2 3 4 21 3 4 8 5 5 22 3 6 8 6 NA 23 4 5 11 4 3 24 4 2 1 4 6 25 6 4 4 6 6 I can get cumulative row sums as follows: cy-t(apply(y,1,cumsum)) cy 0 1 2 3 4 21 3 7 15 20 25 22 3 9 17 23 NA 23 4 9 20 24 27 24 4 6 7 11 17 25 6 10 14 20 26 Which works, but this seems rather clumsy, especially the need for t(). Is there a better way? One that still retains row and/or column labels? (that will also work for data frames, if possible - though of course one can always as.data.frame() ) Row differences present a different problem. Here's one way to get back the original data: cbind(cy[,1],cy[,-1]-cy[,-nrow(cy)]) 1 2 3 4 21 3 4 8 5 5 22 3 6 8 6 NA 23 4 5 11 4 3 24 4 2 1 4 6 25 6 4 4 6 6 However, if I use that I lose the first column label. Is there a way to do something like this without losing that label? (again, if possible, that also works for data frames?) thanks! Glen_B. -- View this message in context: http://www.nabble.com/Cumulative-row-sums%2C-row-differences-tp24692986p24692986.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] Draw plot.table axis on right hand side
Sean Carmody wrote: With an ordinary plot, to customise the axis it is possible to suppress drawing the axis and then call Axis. I have been trying to change the location of the y-axis on a plot.table plot to the right hand side, but cannot even work out how to suppress drawing the labels. Thanks for the nice example. plot calls mosaicplot, and looking at the code it seems that the labels are rather hard-wired. Even dirty tricks like setting the margins do not help, and data$a - c(, , , , )[data$x] neither. So I would recommend to use package vcd instead, which has very detailed detail handling. Dieter -- View this message in context: http://www.nabble.com/Draw-plot.table-axis-on-right-hand-side-tp24689766p24693737.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] probability on a barplot
Erin Hodgess-2 wrote: I have a barplot created from a table. What is the best way to set up the barplot such that is shows probability rather totals, please? Maybe histogram or densityplot in lattice? Dieter -- View this message in context: http://www.nabble.com/probability-on-a-barplot-tp24685060p24693842.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] pairs plot
Hi Greg I saw, read, the TeachingDemos you suggesttef but when run pairs2 function on my R module says Can´t find function pairs2 How can I load the module or function pairs2? Thanks in advance for your help. You are the best. 2009/7/27, Greg Snow greg.s...@imail.org: Look at the pairs2 function in the TeachingDemos package. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Jose Narillos de Santos Sent: Monday, July 27, 2009 9:02 AM To: r-help@r-project.org Subject: [R] pairs plot Hi all, I want to plot trough pairs() plot a matrix with 4 columns. I want to make a trhee plot in a graph. Plotting pairs colum 2,3,4 on y axis and 1 on X axis. You mean (a plot with three graphs) ommitting the first pair with itself. And only the pairs with colum 1 with the other not all pairs. I. e. this matrix 4177 289390 8740 17220 3907 301510 8530 17550 3975 316970 8640 17650 3651 364220 9360 21420 3031 387390 9960 23410 2912 430180 11040 25820 3018 499930 12240 27620 2685 595010 13800 31670 2884 661870 14760 37170 Thanks in advance. [[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.
[R] R Excel
Hi, whenever am trying to start R from excel, or by clicking the[ RExcel2007 with RCommander] icon., i got the following messages boxes : SCTools not available then: there seems to be no R process connected to excel though both r and excel starts after I click the Icon!! Please help Hassan [[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] creating and populating an environment
I have looked a bit more at this issue. Using new.env() I am able to put
new vars into the new environment by using the env$... syntax. This
allows to eliminate all variables in one step with rm(env), thus
fixing problem 2) in my original mail. Problem 1) though is unsolved, or
even worsened, since now I need to prepend the environment name to each
variable whenever I use one. Even doing attach(env) does not help,
since the global environment has higher priority than the local one.
Does anyone have a suggestion? Ideally, I would like to have a separate
environment like I have inside a user-defined function.
Thanks
Christian Prinoth
-Original Message-
From: Christian Prinoth
Sent: 27 July, 2009 13:33
To: 'r-help@r-project.org'
Subject: creating and populating an environment
Hi, I often work with R by writing long(ish) Excel-VBA macros
interspersed with calls to R via RExcel. A typical example of
this would be:
Sub VBAMacro()
'fetch some data from an excel sheet
'do some basic stuff on said data
'transfer data from vba to R
'run some R statements
'get data back to vba
'show results on the excel sheet
'clean R by deleting all vars that were created: rrun
rm(a,b,c,)
end sub
This has two obvious disadvantages, as I have to make sure:
1) not to use R variable names which may already exist
2) to remove all variables (garbage collection)
In order to overcome these issues I was wondering if I should
execute all R statements inside the R macro in a separate
namespace. I have looked at new.env() but am not really sure
how it is supposed to be used. If I type temp-new.env(),
how do I make sure that all variables declared from then on
end up in the temp environment? Once I am done, is
rm(temp) sufficient to get rid of all its content?
Basically, I would like to replace the above example with:
Sub VBAMacro()
rrun A-new.env()
'fetch some data from an excel sheet
'do some basic stuff on said data
'transfer data from vba to R
'run some R statements
'get data back to vba
'show results on the excel sheet
rrun rm(A)
end sub
Thanks
Christian Prinoth
DISCLAIMER:\ L'utilizzo non autorizzato del presente mes...{{dropped:16}}
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[R] Odp: Cumulative row sums, row differences
Hi r-help-boun...@r-project.org napsal dne 28.07.2009 09:18:43: I tried searching but I couldn't quite find what I was looking for. Here's a dummy data matrix (with row and column labels): y 0 1 2 3 4 21 3 4 8 5 5 22 3 6 8 6 NA 23 4 5 11 4 3 24 4 2 1 4 6 25 6 4 4 6 6 I can get cumulative row sums as follows: cy-t(apply(y,1,cumsum)) cy 0 1 2 3 4 21 3 7 15 20 25 22 3 9 17 23 NA 23 4 9 20 24 27 24 4 6 7 11 17 25 6 10 14 20 26 Which works, but this seems rather clumsy, especially the need for t(). Is there a better way? One that still retains row and/or column labels? (that will also work for data frames, if possible - though of course one can always as.data.frame() ) Row differences present a different problem. Here's one way to get back the original data: cbind(cy[,1],cy[,-1]-cy[,-nrow(cy)]) 1 2 3 4 21 3 4 8 5 5 22 3 6 8 6 NA 23 4 5 11 4 3 24 4 2 1 4 6 25 6 4 4 6 6 However, if I use that I lose the first column label. Is there a way to do something like this without losing that label? (again, if possible, that also works for data frames?) You can use apply approach with diff cbind(vvv[,1, drop=F],t(apply(vvv,1, diff))) or your construction cbind(cy[,1, drop=F],cy[,-1]-cy[,-nrow(cy)]) Do not forget drop argument which prevents losing label!!! Regards Petr And with data frames do not forget they need not have only numeric columns, even if they look like numeric. thanks! Glen_B. -- View this message in context: http://www.nabble.com/Cumulative-row-sums%2C- row-differences-tp24692986p24692986.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-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] pairs plot
Hi r-help-boun...@r-project.org napsal dne 28.07.2009 09:55:11: Hi Greg I saw, read, the TeachingDemos you suggesttef but when run pairs2 function on my R module says Can´t find function pairs2 How can I load the module or function pairs2? Did you do library(TeachingDemos)? Regards Petr Thanks in advance for your help. You are the best. 2009/7/27, Greg Snow greg.s...@imail.org: Look at the pairs2 function in the TeachingDemos package. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Jose Narillos de Santos Sent: Monday, July 27, 2009 9:02 AM To: r-help@r-project.org Subject: [R] pairs plot Hi all, I want to plot trough pairs() plot a matrix with 4 columns. I want to make a trhee plot in a graph. Plotting pairs colum 2,3,4 on y axis and 1 on X axis. You mean (a plot with three graphs) ommitting the first pair with itself. And only the pairs with colum 1 with the other not all pairs. I. e. this matrix 4177 289390 8740 17220 3907 301510 8530 17550 3975 316970 8640 17650 3651 364220 9360 21420 3031 387390 9960 23410 2912 430180 11040 25820 3018 499930 12240 27620 2685 595010 13800 31670 2884 661870 14760 37170 Thanks in advance. [[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. __ 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] storing output in html or pdf table format.
Have a look at Sweave (in the utils package) or the R2HTML package. HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens Albert EINstEIN Verzonden: dinsdag 28 juli 2009 6:56 Aan: r-help@r-project.org Onderwerp: [R] storing output in html or pdf table format. Hi every one, Thanks for every one who are all supporting to us. we want some clarification on output in R. I have generated summary statistics output for dataset (E.g. sales) in output window. Now i want to store that output in a html or pdf in a table format. if possible can any one provide code for this one. Thanks in advance. -- View this message in context: http://www.nabble.com/storing-output-in-html-or-pdf-table-format.-tp2469 2508p24692508.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. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ 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] Searching for specific values in a matrix
BertG == Bert Gunter gunter.ber...@gene.com
on Mon, 27 Jul 2009 15:30:08 -0700 writes:
BertG Nothing wrong with rolling your own, but see
BertG ?all.equal for R's built-in almost.equal version.
Yes, indeed! Note that that needs a little extra care, as it
either returns TRUE or a character vector.
In sum, I'd strongly suggest you use
%~% - function(x,y) isTRUE(all.equal(x,y))
Martin Maechler, ETH Zurich and R Core Team
BertG Bert Gunter Genentech Nonclinical Biostatistics
BertG -Original Message- From:
BertG r-help-boun...@r-project.org
BertG [mailto:r-help-boun...@r-project.org] On Behalf Of
BertG Steve Lianoglou Sent: Monday, July 27, 2009 3:17 PM
BertG To: Mehdi Khan Cc: r-help@r-project.org Subject: Re:
BertG [R] Searching for specific values in a matrix
BertG Ahh ..
BertG On Jul 27, 2009, at 6:01 PM, Mehdi Khan wrote:
Even when choosing a value from the first few rows, it
doesn't work. okay here it goes:
rearranged[1:10, 1:5] x y band1 VSCAT.001 soiltype 1
-124.3949 40.42468 NA NA CD 2 -124.3463 40.27358 NA NA CD
3 -124.3357 40.25226 NA NA CD 4 -124.3663 40.40241 NA NA
CD 5 -124.3674 40.49810 NA NA CD 6 -124.3083 40.24744 NA
464 NA 7 -124.3017 40.31295 NA NA D 8 -124.3375
40.47557 NA 464 NA 9 -124.2511 40.11697 1 NA NA 10
-124.2532 40.12640 1 NA NA
query- rearranged$y== 40.42468 rearranged[query,]
[1] x y band1 VSCAT.001 soiltype 0 rows (or 0-length
row.names)
BertG This isn't working because the numbers you see for y
BertG (40.42468) isn't precisely what that number is. As I
BertG mentioned before you should use an almost.equals
BertG type of search for this scenario. My %~% function
BertG isn't working in your session because that is a
BertG function I've defined myself. You can of course use
BertG it, you just have to define it in your
BertG workspace. Paste these lines into your workspace (or
BertG save them to a file and source that file into your
BertG workspace).
BertG ## === almost.equal functions
BertG almost.equal - function(x, y,
BertG tolerance=.Machine$double.eps^0.5) { abs(x - y)
BertG tolerance }
BertG %~% - function(x, y) almost.equal(x, y)
BertG ## === end paste ==
BertG Now you can use %~% once that's in. Let's use the
BertG almost.equal function now because I don't know if the
BertG default tolerance here is too strict (I suspect
BertG showing the value for rearranged$y[1] will show you
BertG more significant digits than you're seeing in the
BertG table(?))
BertG query - almost.equal(rearranged$y, 40.42468,
BertG tolerance=0.0001) rearranged[query,]
BertG This will get you something.
query- rearranged$ VSCAT.001== 464 except it's a huge
table (I guess I have to get rid of all rows with NA).
BertG Yes, I believe I mentioned earlier that you have to
BertG axe the NA matches manually:
BertG query - rearranged$VSCAT.001 == 464
BertG !is.na(rearranged$VSCAT.001) rearranged[query,]
BertG Will get you what you want.
I tried using the %~% but R doesn't recognize it. So
maybe it has to do with the rounding errors?
BertG Rounding errors won't happen with integer comparisons
BertG (and it looks like the VSCAT.001 columns is integers,
BertG no?).
BertG -steve
BertG -- Steve Lianoglou Graduate Student: Computational
BertG Systems Biology | Memorial Sloan-Kettering Cancer
BertG Center | Weill Medical College of Cornell University
BertG Contact Info: http://cbio.mskcc.org/~lianos/contact
BertG __
BertG R-help@r-project.org mailing list
BertG https://stat.ethz.ch/mailman/listinfo/r-help PLEASE
BertG do read the posting guide
BertG http://www.R-project.org/posting-guide.html and
BertG provide commented, minimal, self-contained,
BertG reproducible code.
BertG __
BertG R-help@r-project.org mailing list
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BertG http://www.R-project.org/posting-guide.html and
BertG provide commented, minimal, self-contained,
BertG reproducible code.
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[R] Fwd: randomized block design analysis in R
-- Forwarded message -- From: alis villiyam aalisi...@gmail.com Date: Mon, Jul 27, 2009 at 9:47 AM Subject: randomized block design analysis in R To: bol...@zoology.ufl.edu Dear All user Hello, I'm a student and I have some trouble with the experimental (columns-experiments) design of my project. I use a randomized block design with 4 treatments including a control. For each treatment, I use 3 replicates and 3 blocks. The treatments are: -T1 = COD (300 mg/Lit) COD=chemical oxygen demand -T2 = COD (200 mg/Lit) -T3 = COD (100 mg/Lit) -T4 = COD (0 mg/Lit) as a control The experiment is conducted during three months and a sample is taken each Week in every experimental unit. At the first, I irrigated all soil columns (12 columns) with demonize water for 1 week. Then during 8 weeks, I irrigated all columns with waste water with different concentration. Then, gain, I irrigated all columns with demonize water for 4 weeks. Now I want to know how I can analyses the results in R. For example, I want to detect the Effect of waste water on some physical properties of soil, before, during use waste water and after use waste water (Is there any significant change in properties of soil.) Time is also important, so I want to know the interaction between time and some physical properties of soil, like water content .first comprises between Treatments and then comprise between weeks). Questions to be answered: 1) Theta (water content), before (1 week) and after the COD; is there a difference? 2) Theta, during, before and after the COD; is there a difference? 3) Is there a trend in Theta, during COD (8 weeks)? 4) Is there a difference in Theta, during COD between the treatments? I hope somebody can help me to find correct statistical analyses in R. Kind regards, Alisia __ 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] vary the parameters for a function
How I can vary the parameters for a function? I have a function with 5 parameters I want to turn the function for a range of numbers for one of these parameters!! i want to have in the end the value of the function in the different cas of one of the paramter (the others paramters are fixes!!) thank you for your help [[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.
[R] Odp: vary the parameters for a function
Hi maybe outer? Regards Petr r-help-boun...@r-project.org napsal dne 28.07.2009 11:36:10: How I can vary the parameters for a function? I have a function with 5 parameters I want to turn the function for a range of numbers for one of these parameters!! i want to have in the end the value of the function in the different cas of one of the paramter (the others paramters are fixes!!) thank you for your help [[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. __ 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] storing output in html or pdf table format.
Or you can have a look to ascii package (examples here http://eusebe.github.com/ascii/or herehttp://www.ncfaculty.net/dogle/fishR/bookex/AIFFD/AIFFD.html ). david 2009/7/28 ONKELINX, Thierry thierry.onkel...@inbo.be Have a look at Sweave (in the utils package) or the R2HTML package. HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens Albert EINstEIN Verzonden: dinsdag 28 juli 2009 6:56 Aan: r-help@r-project.org Onderwerp: [R] storing output in html or pdf table format. Hi every one, Thanks for every one who are all supporting to us. we want some clarification on output in R. I have generated summary statistics output for dataset (E.g. sales) in output window. Now i want to store that output in a html or pdf in a table format. if possible can any one provide code for this one. Thanks in advance. -- View this message in context: http://www.nabble.com/storing-output-in-html-or-pdf-table-format.-tp2469 2508p24692508.htmlhttp://www.nabble.com/storing-output-in-html-or-pdf-table-format.-tp2469%0A2508p24692508.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. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ 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.
[R] vary paramter of a function
i have a function who depends of many parameters and i want to have at the end the result givien by this function for a different value of only one parameter the others parameters are fixed. thank you i didn't understand your answer peter can you explain me? thank you [[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.
[R] How to do poisson distribution test like this?
Dear R-listers, I want to reperfrom a poisson distribution test that presented in a recent-published biological research paper (Plant Physiology 2008, vol 148, pp. 1189-1200). That test is about the occurrence number of a kind of gene in separate chromosomes. For instance: The observed gene number in chromosome A is 36. The expected gene number in chromosome A is 30. Then, the authors got a probability 0.137 by distribution test on this trial. In this test, a Poisson distribution was used to determine the significance of the gene distribution. Questions: How can I reperform this test in R? Thank you in advance. Mao Jian-Feng Institue of Botany, CAS, China [[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.
[R] Sort a column in a dataframe
Dear Users This is my dataset called mydata4. I want to sort the dataframe on the first column PxMid which is basically a column with dates. I've tried mydata4-mydata4[order(mydata4$PxMid),] but it doesnt work. Could it be because these are dates? Please help I'm really stuck !! Thank you for your time. Regards Meenu PxMid EU0006MIndex.x DMSW1Curncy.x DMSW2Curncy.x DMSW3Curncy.x 1 01/01/20032.801132.70702.89203.1720 2 01/01/20073.853504.07604.12504.1230 3 01/02/20023.415633.63854.08104.3587 4 01/02/20062.72.95453.16723.2792 5 01/05/20023.498633.79404.23004.4920 6 01/05/20063.035883.32543.59503.7380 DMSW4Curncy.x DMSW5Curncy.x DMSW6Curncy.x DMSW7Curncy.x DMSW8Curncy.x 13.43603.66403.86404.03604.1790 24.12304.12504.13504.14604.1620 34.54874.69884.83134.93385.0138 43.36273.43423.48993.54373.5941 54.76504.86755.05505.16005.2400 63.82903.90503.96904.02404.0750 DMSW9Curncy.x DMSW10Curncy.x DMSW12Curncy.x DMSW15Curncy.x DMSW20Curncy.x 14.2990 4.4000 4.5575 4.7175 4.8600 24.1800 4.2000 4.2330 4.2750 4.3120 35.0788 5.1263 5.2100 5.2887 5.3562 43.6457 3.6913 3.7725 3.8669 3.9410 55.3050 5.3575 5.4450 5.5425 5.6300 64.1230 4.1650 4.2360 4.3170 4.3960 DMSW30Curncy.x EUSA40Curncy.x EUSA50Curncy.x spread.x level.x State1 State2 1 4.8925 4.8400 4.7975 2.0005 4.006772 NA NA 2 4.2890 4.2460 4.2040 0.1640 4.165147 NA NA 3 5.3412 5.2913 5.2638 1.2602 4.792737 NA NA 4 3.9840 3.9760 3.9560 0.8168 3.550524 NA NA 5 5.6275 5.5775 5.5375 1.3975 5.007331 NA NA 6 4.4290 4.4190 4.3980 0.8340 3.998781 NA NA State3 State4 State5 State6 State7 State8 State9 1 NA NA NA 6 NA NA NA 2 NA NA 5 NA NA NA NA 3 NA NA NA NA NA NA 9 4 NA NA NA 6 NA NA NA 5 NA NA NA NA NA NA 9 6 NA NA NA 6 NA NA NA [[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 do poisson distribution test like this?
On 28-Jul-09 10:03:41, Mao Jianfeng wrote: Dear R-listers, I want to reperfrom a poisson distribution test that presented in a recent-published biological research paper (Plant Physiology 2008, vol 148, pp. 1189-1200). That test is about the occurrence number of a kind of gene in separate chromosomes. For instance: The observed gene number in chromosome A is 36. The expected gene number in chromosome A is 30. Then, the authors got a probability 0.137 by distribution test on this trial. In this test, a Poisson distribution was used to determine the significance of the gene distribution. Questions: How can I reperform this test in R? Thank you in advance. Mao Jian-Feng Institue of Botany, CAS, China Since it is not clear what test procedure they used, I have done a couple of numerical experiments in R: 1. Compare the upper-tail probability of the POisson distribution with mean mu = 30 of the event that at least 36 are observed: 1-ppois(36,30) # [1] 0.1196266 Not quite the 0.137 that they got. 2. A similar comparison, using a Normal approximation to the Poisson (mean mu = 30, SD = sqrt(mu)): 1 - pnorm(6/sqrt(30)) # [1] 0.1366608 which, after rounding, is exactly the 0.137 that they got. So it seems they have used an upper-tail test based on the Normal approximation to the Poisson distribution. Method 1 (using the exact Poisson distribution) is preferable, since it is accurate (given the assumption of Poisson distribution). So that would, in principle, be the best way to do it in R (as illustrated). Possibly their adoption of Method 2 is based on a naive acceptance of the rule-of-thumb from some textbook; or maybe their available software does not offer ready access to the exact Poisson distribution (which wouldn't happen if they used R -- see Method 1). As stated, it is inaacurate compared with Method 1, so is not to be preferred. However, if you need to reproduce their method (regardless of merit), then use Method 2. Hoping this helps, Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 28-Jul-09 Time: 11:42:08 -- XFMail -- __ 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] Draw plot.table axis on right hand side
Dieter Menne wrote: With an ordinary plot, to customise the axis it is possible to suppress drawing the axis and then call Axis. I have been trying to change the location of the y-axis on a plot.table plot to the right hand side, but cannot even work out how to suppress drawing the labels. Thanks for the nice example. plot calls mosaicplot, and looking at the code it seems that the labels are rather hard-wired. Even dirty tricks like setting the margins do not help, and data$a - c(, , , , )[data$x] neither. So I would recommend to use package vcd instead, which has very detailed detail handling. Dieter Thanks Dieter. I see vcd had a detailed vignette. That should help me get to grips with mosaic, which does appear to be extremely flexible. -- Sean Carmody The Stubborn Mule http://www.stubbornmule.net http://twitter.com/seancarmody [[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] local regression using loess
cindy Guo wrote: Hi, All, I have a dataset with binary response ( 0 and 1) and some numerical covariates. I know I can use logistic regression to fit the data. But I want to consider more locally. So I am wondering how can I fit the data with 'loess' function in R? And what will be the response: 0/1 or the probability in either group like in logistic regression? Thank you, Cindy [[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. Why don't you fit a GAM with a logistic link function and binomial distirbution? Alain - Dr. Alain F. Zuur First author of: 1. Analysing Ecological Data (2007). Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p. 2. Mixed effects models and extensions in ecology with R. (2009). Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer. 3. A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer Statistical consultancy, courses, data analysis and software Highland Statistics Ltd. 6 Laverock road UK - AB41 6FN Newburgh Email: highs...@highstat.com URL: www.highstat.com -- View this message in context: http://www.nabble.com/local-regression-using-loess-tp24689834p24696908.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] creating and populating an environment
prepending with env$ seems not so terrible.
Another form is:
with(e, ...stmt...) or
with(e, { ...stmt...; ...stmt...; ... })
where e is your environment.
On Tue, Jul 28, 2009 at 3:59 AM, Christian
Prinothchristian.prin...@epsilonsgr.it wrote:
I have looked a bit more at this issue. Using new.env() I am able to put
new vars into the new environment by using the env$... syntax. This
allows to eliminate all variables in one step with rm(env), thus
fixing problem 2) in my original mail. Problem 1) though is unsolved, or
even worsened, since now I need to prepend the environment name to each
variable whenever I use one. Even doing attach(env) does not help,
since the global environment has higher priority than the local one.
Does anyone have a suggestion? Ideally, I would like to have a separate
environment like I have inside a user-defined function.
Thanks
Christian Prinoth
-Original Message-
From: Christian Prinoth
Sent: 27 July, 2009 13:33
To: 'r-help@r-project.org'
Subject: creating and populating an environment
Hi, I often work with R by writing long(ish) Excel-VBA macros
interspersed with calls to R via RExcel. A typical example of
this would be:
Sub VBAMacro()
'fetch some data from an excel sheet
'do some basic stuff on said data
'transfer data from vba to R
'run some R statements
'get data back to vba
'show results on the excel sheet
'clean R by deleting all vars that were created: rrun
rm(a,b,c,)
end sub
This has two obvious disadvantages, as I have to make sure:
1) not to use R variable names which may already exist
2) to remove all variables (garbage collection)
In order to overcome these issues I was wondering if I should
execute all R statements inside the R macro in a separate
namespace. I have looked at new.env() but am not really sure
how it is supposed to be used. If I type temp-new.env(),
how do I make sure that all variables declared from then on
end up in the temp environment? Once I am done, is
rm(temp) sufficient to get rid of all its content?
Basically, I would like to replace the above example with:
Sub VBAMacro()
rrun A-new.env()
'fetch some data from an excel sheet
'do some basic stuff on said data
'transfer data from vba to R
'run some R statements
'get data back to vba
'show results on the excel sheet
rrun rm(A)
end sub
Thanks
Christian Prinoth
DISCLAIMER:\ L'utilizzo non autorizzato del presente mes...{{dropped:16}}
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Re: [R] Multiple graphs
Data Analytics Corp. wrote: Hi, I wrote a simple master function, run(), that has inside six qplot functions. The goal is to type run() and have all six graphs appear as separate windows so that I can copy them into PowerPoint for a client. When I type run(), only the last graph appears, the first five apparently being overwritten. How do I get all six in separate windows, ready for copying? By the way, is the a way to create a PowerPoint deck directly in R the way you can in S-Plus? Thanks, Walt -- Walter R. Paczkowski, Ph.D. Data Analytics Corp. 44 Hamilton Lane Plainsboro, NJ 08536 (V) 609-936-8999 (F) 609-936-3733 dataanalyt...@earthlink.net www.dataanalyticscorp.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. There is an example in our A Beginner's Guide to R that exports the graphs automatically to jpg files (from a loop inside a function)...which you could then import into powerpoint. But as you can see from the other post, it can even be done automatically. Alain - Dr. Alain F. Zuur First author of: 1. Analysing Ecological Data (2007). Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p. 2. Mixed effects models and extensions in ecology with R. (2009). Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer. 3. A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer Statistical consultancy, courses, data analysis and software Highland Statistics Ltd. 6 Laverock road UK - AB41 6FN Newburgh Email: highs...@highstat.com URL: www.highstat.com -- View this message in context: http://www.nabble.com/Multiple-graphs-tp24690227p24697026.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] check for new files in a given directory
I am trying to continuously evaluate online created data files using R-algorithms. Is there any simple way to let R iteratively check for new files in a given directory, load them and process them? Any help would be highly appreciated. Best, A. [[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.
[R] Problem runnin rSymPy
Hi all,
I'm having major difficulty using the rSymPy package this week, but I have
used it without problems before now. Here is an example of what's happening:
library(rSymPy)
Loading required package: rJava
sympy(var('a b c d'))
Error in .jcheck() : No running detected. Maybe .jinit() would help.
And I have no idea how to fix it. I Have tried re-installing but that
doesn't seem to work either. Any help would be great, thanks!
--
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http://www.nabble.com/Problem-runnin-rSymPy-tp24697166p24697166.html
Sent from the R help mailing list archive at Nabble.com.
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Re: [R] Problem runnin rSymPy
Try reviewing the Troubleshooting section on the rSymPy home page:
http://rsympy.googlecode.com/#Troubleshooting
On Tue, Jul 28, 2009 at 7:12 AM,
stenortsten...@merchantsconnected.org.uk wrote:
Hi all,
I'm having major difficulty using the rSymPy package this week, but I have
used it without problems before now. Here is an example of what's happening:
library(rSymPy)
Loading required package: rJava
sympy(var('a b c d'))
Error in .jcheck() : No running detected. Maybe .jinit() would help.
And I have no idea how to fix it. I Have tried re-installing but that
doesn't seem to work either. Any help would be great, thanks!
--
View this message in context:
http://www.nabble.com/Problem-runnin-rSymPy-tp24697166p24697166.html
Sent from the R help mailing list archive at Nabble.com.
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and provide commented, minimal, self-contained, reproducible code.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] check for new files in a given directory
On Tue, Jul 28, 2009 at 12:04 PM, Andreas Poschandreas.po...@tugraz.at wrote: I am trying to continuously evaluate online created data files using R-algorithms. Is there any simple way to let R iteratively check for new files in a given directory, load them and process them? Any help would be highly appreciated. list.files(dir) will tell you what files are in a directory. file.info(filepath) will tell you things about a file (modification time etc). Sys.sleep(n) will put R to sleep for n seconds so you don't have a tight loop checking the directory every millisecond. That's probably all the functionality you need, except maybe to keep track of what files you consider 'new', and some way of deciding if something has already been processed. But that's a bit application-specific! Barry __ 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] check for new files in a given directory
I am trying to continuously evaluate online created data files using R-algorithms. Is there any simple way to let R iteratively check for new files in a given directory, load them and process them? I am using R on Windows XP. Any help would be highly appreciated. Best, A. [[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] check for new files in a given directory
On 28-Jul-09 11:04:39, Andreas Posch wrote: I am trying to continuously evaluate online created data files using R-algorithms. Is there any simple way to let R iteratively check for new files in a given directory, load them and process them? Any help would be highly appreciated. Best, A. If in Linux/Unix, the following sort of thing will work: LastList - system(ls,intern=TRUE) then, later, NewList - system(ls,intern=TRUE) and then NewList[!(NewList %in% LastList)] is a character vector of the names in NewList which are not in LastList (i.e. the ones which have come in since LastList was created). Then you can do what you like with these names. Finally: LastList - NewList means you can repeat the check on the same basis. Don't ask me how to do this in Windows ... Hpoing this helps, Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 28-Jul-09 Time: 12:24:42 -- XFMail -- __ 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] check for new files in a given directory
On 28-Jul-09 11:23:21, Barry Rowlingson wrote: On Tue, Jul 28, 2009 at 12:04 PM, Andreas Poschandreas.po...@tugraz.at wrote: I am trying to continuously evaluate online created data files using R-algorithms. Is there any simple way to let R iteratively check for new files in a given directory, load them and process them? Any help would be highly appreciated. list.files(dir) will tell you what files are in a directory. file.info(filepath) will tell you things about a file (modification time etc). Sys.sleep(n) will put R to sleep for n seconds so you don't have a tight loop checking the directory every millisecond. That's probably all the functionality you need, except maybe to keep track of what files you consider 'new', and some way of deciding if something has already been processed. But that's a bit application-specific! Barry Snap, Baz! (Except that we played different cards -- and in view of Andreas's follow-up, yours would be the solution for him). However, this got me looking into '?list.files, and I see there (R version 2.9.0 (2009-04-17)): recursive: logical. Should the listing recurse into directories? But: Directories are included only if 'recursive = FALSE'. Surely the latter is the wrong way round, and should be Directories are included only if 'recursive = TRUE'. (that's how it worked when I just tried it). Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 28-Jul-09 Time: 12:36:45 -- XFMail -- __ 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] Odp: Sort a column in a dataframe
Hi r-help-boun...@r-project.org napsal dne 28.07.2009 12:40:59: Dear Users This is my dataset called mydata4. I want to sort the dataframe on the first column PxMid which is basically a column with dates. I've tried mydata4-mydata4[order(mydata4$PxMid),] but it doesnt work. Could it be because these are dates? How do you know these are dates? I suspect str(mydata4) will have factor at PxMid and not date. If this is true, you need to transform it to dates by as.Date, strptime or other suitable time/date function e.g. fro chron package. Regards Petr Please help I'm really stuck !! Thank you for your time. Regards Meenu PxMid EU0006MIndex.x DMSW1Curncy.x DMSW2Curncy.x DMSW3Curncy.x 1 01/01/20032.801132.70702.89203.1720 2 01/01/20073.853504.07604.12504.1230 3 01/02/20023.415633.63854.08104.3587 4 01/02/20062.72.95453.16723.2792 5 01/05/20023.498633.79404.23004.4920 6 01/05/20063.035883.32543.59503.7380 DMSW4Curncy.x DMSW5Curncy.x DMSW6Curncy.x DMSW7Curncy.x DMSW8Curncy.x 13.43603.66403.86404.03604.1790 24.12304.12504.13504.14604.1620 34.54874.69884.83134.93385.0138 43.36273.43423.48993.54373.5941 54.76504.86755.05505.16005.2400 63.82903.90503.96904.02404.0750 DMSW9Curncy.x DMSW10Curncy.x DMSW12Curncy.x DMSW15Curncy.x DMSW20Curncy.x 14.2990 4.4000 4.5575 4.7175 4.8600 24.1800 4.2000 4.2330 4.2750 4.3120 35.0788 5.1263 5.2100 5.2887 5.3562 43.6457 3.6913 3.7725 3.8669 3.9410 55.3050 5.3575 5.4450 5.5425 5.6300 64.1230 4.1650 4.2360 4.3170 4.3960 DMSW30Curncy.x EUSA40Curncy.x EUSA50Curncy.x spread.x level.x State1 State2 1 4.8925 4.8400 4.7975 2.0005 4.006772 NA NA 2 4.2890 4.2460 4.2040 0.1640 4.165147 NA NA 3 5.3412 5.2913 5.2638 1.2602 4.792737 NA NA 4 3.9840 3.9760 3.9560 0.8168 3.550524 NA NA 5 5.6275 5.5775 5.5375 1.3975 5.007331 NA NA 6 4.4290 4.4190 4.3980 0.8340 3.998781 NA NA State3 State4 State5 State6 State7 State8 State9 1 NA NA NA 6 NA NA NA 2 NA NA 5 NA NA NA NA 3 NA NA NA NA NA NA 9 4 NA NA NA 6 NA NA NA 5 NA NA NA NA NA NA 9 6 NA NA NA 6 NA NA NA [[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. __ 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] Looking for example of usage of function unz
I would greatly appreciate some example of correct usage of function unz. I have to download and uncompress the following web compressef file: ftp://ftp.sanger.ac.uk/pub/mirbase/targets/v5/arch.v5.txt.homo_sapiens.zip I tried the following command that does not work: Targets.rec - readLines(zz - unz(ftp://ftp.sanger.ac.uk/pub/mirbase/targets/v5/arch.v5.txt.homo_sapiens.zip;)) Thank you in advance, Maura tutti i telefonini TIM! [[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.
[R] reading jpeg images?
Can someone advise me what the most sensible way is to read jpeg images? For our work with image analysis and eye-tracking we have been using the rimage package, on both Macs and Windows PCs. But while setting up a new Windows machine yesterday, I see that rimage is regarded as orphaned, and no Windows binary is available. I eventually found an old zip file for the package, so I am not stuck, but I wonder what the right way is to go forward. I did find the readimages package, but it also seemed problematic to install on both Windows on Mac, requiring extra software that it was itself unclear how to install. Is there some simpler solution I should be looking at? Are jpeg files so probematic I should be converting them to some other format and using a different package to read that? Thanks Robert Biddle __ 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] pairs plot
Hi, I tried to load typing library(TeachingDemos) But the message can´t find package TeachingDemos) occurs. I use versión R 2.9 on windows. Can you please guide me? Sorry¡¡¡ 2009/7/28, Petr PIKAL petr.pi...@precheza.cz: Hi r-help-boun...@r-project.org napsal dne 28.07.2009 09:55:11: Hi Greg I saw, read, the TeachingDemos you suggesttef but when run pairs2 function on my R module says Can´t find function pairs2 How can I load the module or function pairs2? Did you do library(TeachingDemos)? Regards Petr Thanks in advance for your help. You are the best. 2009/7/27, Greg Snow greg.s...@imail.org: Look at the pairs2 function in the TeachingDemos package. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Jose Narillos de Santos Sent: Monday, July 27, 2009 9:02 AM To: r-help@r-project.org Subject: [R] pairs plot Hi all, I want to plot trough pairs() plot a matrix with 4 columns. I want to make a trhee plot in a graph. Plotting pairs colum 2,3,4 on y axis and 1 on X axis. You mean (a plot with three graphs) ommitting the first pair with itself. And only the pairs with colum 1 with the other not all pairs. I. e. this matrix 4177 289390 8740 17220 3907 301510 8530 17550 3975 316970 8640 17650 3651 364220 9360 21420 3031 387390 9960 23410 2912 430180 11040 25820 3018 499930 12240 27620 2685 595010 13800 31670 2884 661870 14760 37170 Thanks in advance. [[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. [[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.
[R] Fwd: Forecasting Inflation
-- Forwarded message -- From: Dilip Bayas agrikonnect.dilipba...@gmail.com Date: Mon, Jul 27, 2009 at 4:51 PM Subject: Forecasting Inflation To: r-help@r-project.org Dear All, I wanted to forecast Inflation for Indian Economy. please send what techniques to be used after the variable selection. WPI, CPI, Money supply, IIP, Interest rate and so on..How i can use R for the same [[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] Looking for example of usage of function unz
On 28-Jul-09 12:15:33, mau...@alice.it wrote: I would greatly appreciate some example of correct usage of function unz. I have to download and uncompress the following web compressef file: ftp://ftp.sanger.ac.uk/pub/mirbase/targets/v5/arch.v5.txt.homo_sapiens.z ip I tried the following command that does not work: Targets.rec - readLines(zz - unz(ftp://ftp.sanger.ac.uk/pub/mirbase/targets/v5/arch.v5.txt.homo_sapi ens.zip)) Thank you in advance, Maura Maura, unz() is insisting that you give the filename argument, which, according to '?unz', is: filename: a filename within a zip file. This means that you would first need to know the name[s] of the file[s] archived in the .zip file, as far as I can see. So, in that case, a first step would be to download the .zip file anyway, to your local system, and then, in whatever way is appropriate for your system (unzip -l in Linux), find out what the files in it are called. But once you have got that far, you may prefer to handle the .zip file outside of R ... Hoping this helps, Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 28-Jul-09 Time: 13:50:45 -- XFMail -- __ 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] storing output in html or pdf table format.
Hi Albert. I also came across this: http://cran.r-project.org/web/packages/hwriter/index.html Which is very nice (although I still didn't play with it as much as I wanted) On Tue, Jul 28, 2009 at 7:56 AM, Albert EINstEIN sateeshvar...@gmail.comwrote: Hi every one, Thanks for every one who are all supporting to us. we want some clarification on output in R. I have generated summary statistics output for dataset (E.g. sales) in output window. Now i want to store that output in a html or pdf in a table format. if possible can any one provide code for this one. Thanks in advance. -- View this message in context: http://www.nabble.com/storing-output-in-html-or-pdf-table-format.-tp24692508p24692508.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. -- -- My contact information: Tal Galili Phone number: 972-50-3373767 FaceBook: Tal Galili My Blogs: http://www.r-statistics.com/ http://www.talgalili.com http://www.biostatistics.co.il [[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] Sort a dataframe on the column Date
On Mon, Jul 27, 2009 at 11:46 PM, Meenu Sahimeenus...@gmail.com wrote: Dear Users I have a dataframe called mydata4 of the following order with the first column as a date and the rest of the columns are numeric with rate. Column 1 Rate1 : Rate 20 (PxMid) 01/01/2003 07/01/2001 -- I wish to sort this dataframe on the first col in ascending order. I tried to do the following mydata4-mydata4[,order(mydata4$PxMid)] This give an error. Please help. Regards Meenu Try mydata4-mydata4[order(mydata4$PxMid), ] Cheers, Mark __ 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] Fwd: randomized block design analysis in R
Dear Alisia, These are not very easy questions to answer without detailed knowledge on your design. That's probably why you did not get any responses so far (I've seen your mail pop-up several times). I would recommend that you seek guidance with your supervisor or with the local statistician. Have a look at the posting guide (http://www.r-project.org/posting-guide.html). It states: Questions about statistics: The R mailing lists are primarily intended for questions and discussion about the R software. However, questions about statistical methodology are sometimes posted. If the question is well-asked and of interest to someone on the list, it may elicit an informative up-to-date answer. See also the Usenet groups sci.stat.consult (applied statistics and consulting) and sci.stat.math (mathematical stat and probability). HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens alis villiyam Verzonden: dinsdag 28 juli 2009 11:28 Aan: r-help@r-project.org Onderwerp: [R] Fwd: randomized block design analysis in R -- Forwarded message -- From: alis villiyam aalisi...@gmail.com Date: Mon, Jul 27, 2009 at 9:47 AM Subject: randomized block design analysis in R To: bol...@zoology.ufl.edu Dear All user Hello, I'm a student and I have some trouble with the experimental (columns-experiments) design of my project. I use a randomized block design with 4 treatments including a control. For each treatment, I use 3 replicates and 3 blocks. The treatments are: -T1 = COD (300 mg/Lit) COD=chemical oxygen demand -T2 = COD (200 mg/Lit) -T3 = COD (100 mg/Lit) -T4 = COD (0 mg/Lit) as a control The experiment is conducted during three months and a sample is taken each Week in every experimental unit. At the first, I irrigated all soil columns (12 columns) with demonize water for 1 week. Then during 8 weeks, I irrigated all columns with waste water with different concentration. Then, gain, I irrigated all columns with demonize water for 4 weeks. Now I want to know how I can analyses the results in R. For example, I want to detect the Effect of waste water on some physical properties of soil, before, during use waste water and after use waste water (Is there any significant change in properties of soil.) Time is also important, so I want to know the interaction between time and some physical properties of soil, like water content .first comprises between Treatments and then comprise between weeks). Questions to be answered: 1) Theta (water content), before (1 week) and after the COD; is there a difference? 2) Theta, during, before and after the COD; is there a difference? 3) Is there a trend in Theta, during COD (8 weeks)? 4) Is there a difference in Theta, during COD between the treatments? I hope somebody can help me to find correct statistical analyses in R. Kind regards, Alisia Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ 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] Looking for example of usage of function unz
Also see ?zip.unpack On Tue, Jul 28, 2009 at 8:15 AM, mau...@alice.it wrote: I would greatly appreciate some example of correct usage of function unz. I have to download and uncompress the following web compressef file: ftp://ftp.sanger.ac.uk/pub/mirbase/targets/v5/arch.v5.txt.homo_sapiens.zip I tried the following command that does not work: Targets.rec - readLines(zz - unz(ftp://ftp.sanger.ac.uk/pub/mirbase/targets/v5/arch.v5.txt.homo_sapiens.zip;)) Thank you in advance, Maura tutti i telefonini TIM! [[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. __ 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] check for new files in a given directory
Andreas Posch wrote: I am trying to continuously evaluate online created data files using R-algorithms. Is there any simple way to let R iteratively check for new files in a given directory, load them and process them? I am using R on Windows XP. See ?list.files and ?setdiff Uwe Ligges Any help would be highly appreciated. Best, A. [[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. __ 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] xyplot, panel.abline, from, to
All,
I'm trying to truncate some lines that are added to an xyplot via
panel.abline to allow additional space for inserted text. According to
?panel.abline it seems like from and to will do the trick but it does
not work for the sample code below. Any hints much appreciated.
Cheers,
David
x = seq(1,8)
y.1 = .6*x + 3.5 + rnorm(8, 0, .5); y.2 = .4*x + 1 + rnorm(8,0, .5)
data.ex = data.frame( x.var = c(x,x), y.var = c(y.1, y.2), id = c(rep(y1,
8), rep(y2, 8)))
xyplot( y.var ~ x.var, data = data.ex, groups = id, pch = 16, panel =
function(...) {
panel.abline(a = 2, b = .5, lty = 1, from = 1, to = 8)
panel.abline(a = 3.5, b = .6, lty = 3, from = 1, to = 8)
panel.abline(a = 1, b = .4, lty = 4, from = 1, to = 8)
panel.xyplot(...)
}, scales = list(y = list(limits = c(0,10)), x = list(limits =
c(0,12)) ))
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Re: [R] Superscripts and rounding
ehux wrote:
I am new to the world of R/programming so this may be a really easy question.
I thank you for your patience and help in advance
I would like the characters km^2 to be displayed on the plot subtitle as km
squared - two as a superscript.
I would also like to have the numbers from the data set for longitude and
latitude to be rounded to four decimal places.
Thank you.
plot (
decade[['date']],
decade[['value']],
type = 'l',
col = 'lightsteelblue4',
ylab = 'Discharge [cms]',
main = sprintf('%s [%s]', stn[['metadata']][['name']],
stn[['metadata']][['id']]),
km^2 - expression
sub = sprintf('Seasonal station with natural streamflow - Lat: %s Lon: %s
Gross Area %s km^2 - Effective Area %s km^2',
stn[['metadata']][['latitude']],
stn[['metadata']][['longitude']],stn[['metadata']][['grossarea']],
stn[['metadata']][['effectivearea']]),
cex.sub = 1, font.sub = 3, col.sub = black
)
Since I do not have the data I can only guess:
sub = substitute('Seasonal station with natural streamflow - Lat:' * a *
' Lon:' * b * ' Gross Area ' * c * km^2 * ' - Effective Area ' * d * km^2',
list(a = stn[['metadata']][['latitude']],
b = stn[['metadata']][['longitude']],
c = stn[['metadata']][['grossarea']],
d = stn[['metadata']][['effectivearea']]))
Uwe Ligges
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[R] Skew-Normal Linear Mixed Model (SNLMM)
Dear ALL, In the Normal Linear Mixed Model (NLMM) we make the assumption that the random effects are normally distributed. Is it possible to fit a linear mixed model in R where the random effects are assumed to have a Skew-Normal distribution? I am trying to reproduce the results in the paper referenced below. Can anyone help? Tsung I. Lin, Jack C. Lee. Estimation and prediction in linear mixed models with skew-normal random effects for longitudinal data. Statistics in Medicine 2008; 27 (9):1490–1507 Regards, Raphael -- Raphael A. Fraser, MSc Lecturer in Biostatistics Tropical Medicine Research Institute Faculty of Medical Sciences University of the West Indies Mona Campus Kingston, JAMAICA Tel: (876) 927-2471; 977-6151 Mobile: (876) 410-4699 Fax: (876) 927-2984 e-mail: raphael.fra...@uwimona.edu.jm __ 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] check for new files in a given directory
On Tue, Jul 28, 2009 at 12:36 PM, Ted Hardingted.hard...@manchester.ac.uk wrote: However, this got me looking into '?list.files, and I see there (R version 2.9.0 (2009-04-17)): recursive: logical. Should the listing recurse into directories? But: Directories are included only if 'recursive = FALSE'. Surely the latter is the wrong way round, and should be Directories are included only if 'recursive = TRUE'. by 'included' it means 'returned'. If you do 'recursive=TRUE' it scans recursively for files and only files. If you do recursive=FALSE it returns files and directories in the specified directory. Makes it tricky to figure out a complete directory tree since empty directories won't appear at all if recursive=TRUE. You'd have to implement your own recursive search based on list.files(d,recursive=FALSE) and then testing for directoriness Sucky, unless there's a better way... Barry __ 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] R freezes all the time.
Hi from Brazil, I have installed the latest version of R in my system (WinXP SP3) but R is constantly freezing. Sometimes it happens after loading a module, sometimes it happens when I switch to an othe opened program, sometimes after loading or saving a workspace or after viewing a plot and sometimes it just happens while I am just visualizing R screen. I have reinstalled R and also my video driver but that freezing keeps happening. Any ideas? Thanks! Harerton __ 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] Graphing Significant difference
I am new to R and would appreciate help in dealing with this problem. I worked on a some African grasses and have a matrix based on TukeyHSD test showing how the species differ from each other. A value of 1 means they DON't differ significantly from each other, whiles 0 means they differ significantly from each other. I want to assign letters to these combination and show them on a histogram. How to I go about this. I attach the file to the mail and look forward to hearing for you http://www.nabble.com/file/p24697164/R-request-Bright.xls R-request-Bright.xls . Bright -- View this message in context: http://www.nabble.com/Graphing-Significant-difference-tp24697164p24697164.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] pairs plot
Have you installed it first? First: install.packages(TeachingDemos) Then: library(TeachingDemos) --- On Tue, 7/28/09, Jose Narillos de Santos narillosdesan...@gmail.com wrote: From: Jose Narillos de Santos narillosdesan...@gmail.com Subject: Re: [R] pairs plot To: Petr PIKAL petr.pi...@precheza.cz, r-help@r-project.org, greg.s...@imail.org Received: Tuesday, July 28, 2009, 8:24 AM Hi, I tried to load typing library(TeachingDemos) But the message can´t find package TeachingDemos) occurs. I use versión R 2.9 on windows. Can you please guide me? Sorry¡¡¡ 2009/7/28, Petr PIKAL petr.pi...@precheza.cz: Hi r-help-boun...@r-project.org napsal dne 28.07.2009 09:55:11: Hi Greg I saw, read, the TeachingDemos you suggesttef but when run pairs2 function on my R module says Can´t find function pairs2 How can I load the module or function pairs2? Did you do library(TeachingDemos)? Regards Petr Thanks in advance for your help. You are the best. 2009/7/27, Greg Snow greg.s...@imail.org: Look at the pairs2 function in the TeachingDemos package. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Jose Narillos de Santos Sent: Monday, July 27, 2009 9:02 AM To: r-help@r-project.org Subject: [R] pairs plot Hi all, I want to plot trough pairs() plot a matrix with 4 columns. I want to make a trhee plot in a graph. Plotting pairs colum 2,3,4 on y axis and 1 on X axis. You mean (a plot with three graphs) ommitting the first pair with itself. And only the pairs with colum 1 with the other not all pairs. I. e. this matrix 4177 289390 8740 17220 3907 301510 8530 17550 3975 316970 8640 17650 3651 364220 9360 21420 3031 387390 9960 23410 2912 430180 11040 25820 3018 499930 12240 27620 2685 595010 13800 31670 2884 661870 14760 37170 Thanks in advance. [[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. [[alternative HTML version deleted]] -Inline Attachment Follows- __ 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. __ Yahoo! Canada Toolbar: Search from anywhere on the web, and bookmark your favourite sites. Download it now http://ca.toolbar.yahoo.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] R package for Hierarchical Modelling of Multinomial Logistic Regression
Hello, I need to implement a hierarchical model for Bayesian multinomial logistic regression (also known as polytomous logistic regression). I plan to use Gaussian priors. I have about 800 variables which are mostly dichotomous. Some are integer valued. What R package would you recommend? thanks, Nick -- View this message in context: http://www.nabble.com/R-package-for-Hierarchical-Modelling-of-Multinomial-Logistic-Regression-tp24694202p24694202.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] create dataset permanently in package (i.e. default or our own package)
Hi, Thanks for your support. we are not getting any thing from your code. i.e. we are unable to creating new package and adding dataset to that new package. so can you help me out in other way i.e. how to add a new dataset to default R distributions like cars and datasets. these two are default distributions (i.e. packages). so please help us in this aspect. Thanks in advance. -- View this message in context: http://www.nabble.com/create-dataset-permanently-in-package-%28i.e.-default-or-our-own-package%29-tp24679076p24694060.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] Downloaded file is larger than the starting file
I'm running R for windows 2.9.1. When I use a script to download a file from the internet, the file is 1,496 bytes larger than the reported file size in the download process. It doesn't give the correct answer when I process it but it doesn't appear to be completely corrupt as the processing script runs. I can download the file from Firefox and the size of the downloaded file is correct. I tried starting with the internet2 flag set and it didn't help. The url of the file is: http://iup.physik.uni-bremen.de:8084/amsredata/asi_daygrid_swath/l1a/n6250/2009/jun/asi-n6250-20090603-v5.hdf . Is this a bug or do I have some configuration problem with my computer? Thanks, DeWitt Payne __ 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] how to add a new dataset to default R distributions
Hi, Thanks for your support. we are not getting any thing from your code. i.e. we are unable to creating new package and adding dataset to that new package. so can you help me out in other way i.e. how to add a new dataset to default R distributions like cars and datasets. these two are default distributions (i.e. packages). so please help us in this aspect. Thanks in advance. -- View this message in context: http://www.nabble.com/how-to-add-a-new-dataset-to-default-R-distributions-tp24696796p24696796.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] useR! 2010
We are happy to announce that the R user conference useR! 2010 is scheduled for July 21-23, 2010, and will take place at the campus of the National Institute of Standards and Technology (NIST) in Gaithersburg, Maryland, USA. As for the predecessor conferences, the program will consist of two parts: invited lectures and user-contributed sessions (abstract submission will be available online starting from October 2009). Prior to the conference, there will be tutorials on R (proposals for tutorials should be sent before 2009-11-01). INVITED LECTURES Invited speakers will include Mark Handcock, Frank Harrell Jr, Friedrich Leisch, Michael Meyer, Richard Stallman, Luke Tierney, Diethelm Wuertz. USER-CONTRIBUTED SESSIONS The sessions will be a platform to bring together R users, contributors, package maintainers and developers in the S spirit that `users are developers'. People from different fields will show us how they solve problems with R in fascinating applications. The sessions are organized by members of the program committee, including Dirk Eddelbuettel, John Fox, Virgilio Gomez-Rubio, Richard Heiberger, Torsten Hothorn, Aaron King, Jan de Leeuw, Nicholas Lewin-Koh, Andy Liaw, Uwe Ligges, Martin Maechler, Katharine Mullen, Heather Turner, Ravi Varadhan, H. D. Vinod, John Verzani, Alan Zaslavsky, Achim Zeileis. The program will cover topics such as * Applied Statistics Biostatistics * Bayesian Statistics * Bioinformatics * Chemometrics and Computational Physics * Data Mining * Econometrics Finance * Environmetrics Ecological Modeling * High Performance Computing * Machine Learning * Marketing Business Analytics * Psychometrics * Robust Statistics * Social network analysis * Spatial Statistics * Statistics in the Social and Political Sciences * Teaching * Visualization Graphics * and many more. PRE-CONFERENCE TUTORIALS Before the official program, half-day tutorials will be offered on Tuesday, July 20th. We invite R users to submit proposals for three hour tutorials on special topics on R. The proposals should give a brief description of the tutorial, including goals, detailed outline, justification why the tutorial is important, background knowledge required and potential attendees. The proposals should be sent before 2009-11-01 to useR-2010 at R-project.org. CONFERENCE WEBPAGE A webpage offering more information is available at http://www.R-project.org/useR-2010 IMPORTANT DATES 2009-10-01 open submission of abstracts 2009-10-01 open registration 2009-11-01 tutorial submission deadline 2010-03-01 early registration deadline 2010-03-01 submission deadline for abstracts Before 2010-03-15notification of acceptance 2010-06-20 registration deadline (later registration NOT possible on site) 2010-07-20 tutorials 2010-07-21 conference start 2010-07-23 conference end We hope to meet you in Gaithersburg! The organizing committee: Nathan Dodder, William Guthrie, Walter Liggett, John Lu, Katharine Mullen, Jonathon Phillips, Antonio Possolo, Ravi Varadhan. ___ r-annou...@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-announce __ 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] Reg: Creation of own Package and Permanent Dataset in R
Hi, This is Raj from ClinAsia and we have a small query with respect to R Statistical Package. Our Query: Actually while opening R console and R commander we see some packages like car and datasets. In these packages we have default datasets. For example: Women and Prestige so on. Now we created a Sales dataset importing either from excel, xml or text file. Now we are trying to store that dataset permanently in any one of the packages mentioned above (car or datasets). I am able to create them temporarily untill that pirticular session. But once we close the session and try to log into R Console and R Commander. We are not able to find the earlier created datasets Sales in the packages (Car and Datasets). Kindly suggest how to create permanent datasets in packages and also suggest how to create our own packages. If possible please send us the code it will be very helpful for us. Thanks and Regards, Raj ClinAsia 91-40-20010112 [[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.
[R] help
How I can vary the parameters for a function? I have a function with 5 parameters I want to turn the function for a range of numbers for one of these parameters!! i want to have in the end the value of the function in the different cas of one of the paramter (the others paramters are fixes!!) thank you for your help [[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] xyplot, panel.abline, from, to
On Tue, Jul 28, 2009 at 09:23:58AM -0400, Afshartous, David wrote: All, I'm trying to truncate some lines that are added to an xyplot via panel.abline to allow additional space for inserted text. According to ?panel.abline it seems like from and to will do the trick but it does not work for the sample code below. Any hints much appreciated. As far as I understand, 'from' and 'to' are not parameters of panel.abline. Have a look at panel.segements for arbitrary lines (altough you will not be able to use intercept and slope in that case). cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://webclu.bio.wzw.tum.de/~pagel/ __ 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] R freezes all the time.
How much RAM do you have on the machine? On Tue, Jul 28, 2009 at 8:42 AM, Harerton Douradoharer...@terra.com.br wrote: Hi from Brazil, I have installed the latest version of R in my system (WinXP SP3) but R is constantly freezing. Sometimes it happens after loading a module, sometimes it happens when I switch to an othe opened program, sometimes after loading or saving a workspace or after viewing a plot and sometimes it just happens while I am just visualizing R screen. I have reinstalled R and also my video driver but that freezing keeps happening. Any ideas? Thanks! Harerton __ 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. -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ 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] Determine the dimension-names of an element in an array in R
Hey,
I think I have a solution for your problem:
Correl-apply(DataArray_1,1:3, function(d1)
apply(DataArray_2,c(2,1,3), function(d) cor(d1,d))
)
Correl-Correl[1:4,,,]
dimnames(Correl)[[1]]-c
Correl-aperm(Correl,c(2,3,1,4))
This one should work. :-)
Best Regards,
Christian
Sauvik De schrieb:
Hi there,
Thanks again for your reply. I know for-loop is always a solution to
my problem and I had already coded using for-loop. But the number of
levels for each dimension is large enough in actual problem and hence
it was time-consuming.
So, I was just wondering if there are any other alternative way-outs
to solving my problem. That's why I tried with apply functions
(sapply)assuming that this might work out faster even fractionally as
compared to for-loop.
Cheers,
Sauvik
On Mon, Jul 27, 2009 at 12:28 AM, Poersching poerschin...@web.de
mailto:poerschin...@web.de wrote:
Sauvik De schrieb:
Hi:
Lots of thanks for your valuable time!
But I am not sure how you would like to use the function in this
situation.
As I had mentioned that the first element of my output array
should be like:
cor(DataArray_1[dimnames(Correl)[[1]][1],dimnames(Correl)[[2]][1],dimnames(Correl)[[4]][1],],DataArray_2[dimnames(Correl)[[1]][1],dimnames(Correl)[[3]][1],dimnames(Correl)[[4]][1],],use=pairwise.complete.obs)
in my below code.
and
the output array of correlation I wish to get using sapply as
follows:
Correl = sapply(Correl,function(d)
cor(DataArray_1[...],DataArray_2[...],
use=pairwise.complete.obs))
So it would be of great help if you could kindly specify how to
utilise your function findIndex in ...
Apologies for all this!
Thanks Regards,
Sauvik
Hey,
sorry, I haven't understood your problem last time, but now this
solution should solve your problem, so I hope. :-)
It's only a for to loop, but an apply function may work too. I
will think about this, but for now... ;-)
la-length(a)
lb-length(b)
lc-length(c)
ld-length(d)
for (ia in 1:la) {
for (ib in 1:lb) {
for (ic in 1:lc) {
for (id in 1:ld) {
Correl[ia,ib,ic,id]-cor(
DataArray_1[dimnames(Correl)[[1]][ia],
dimnames(Correl)[[2]][ib],
dimnames(Correl)[[4]][id],]
,
DataArray_2[dimnames(Correl)[[1]][ia],
dimnames(Correl)[[3]][ic],
dimnames(Correl)[[4]][id],]
,
use=pairwise.complete.obs)
}
}
}
}
## with function findIndex you can find the dimensions with
## i.e. cor values greater 0.5 or smaller -0.5, like:
findIndex(Correl,Correl[Correl0.5])
findIndex(Correl,Correl[Correl(-0.5)])
I have changed the code of the function findIndex in line which
contents: el[j]-which(is.element(data,element[j]))
Rigards,
Christian
On Sun, Jul 26, 2009 at 3:54 PM, Poerschingpoerschin...@web.de
mailto:poerschin...@web.de wrote:
Sauvik De schrieb:
Hi Gabor:
Many thanks for your prompt reply!
The code is fine. But I need it in more general form as I had
mentioned that
I need to input any 0 to find its dimension-names.
Actually, I was using sapply to calculate correlation and
this idea was
required in the middle of correlation calculation.
I am providing the way I tried my calculation.
a= c(A1,A2,A3,A4,A5)
b= c(B1,B2,B3)
c= c(C1,C2,C3,C4)
d= c(D1,D2)
e= c(E1,E2,E3,E4,E5,E6,E7,E8)
DataArray_1 = array(c(rnorm(240)),dim=c(length(a),length(b),
length(d),length(e)),dimnames=list(a,b,d,e))
DataArray_2 = array(c(rnorm(320)), dim=c(length(a),length(c),
length(d),length(e)),dimnames=list(a,c,d,e))
#Defining an empty array which will contain the correlation
values (output
array)
Correl = array(NA, dim=c(length(a),length(b),
length(c),length(d)),dimnames=list(a,b,c,d))
#Calculating Correlation between attributes b c over values of e
Correl = sapply(Correl,function(d)
cor(DataArray_1[...],DataArray_2[...],
use=pairwise.complete.obs))
This is where I get stuck.
In the above, d is acting as an element in the Correl array.
Hence I need
to get the dimension-names for d.
#The first element of Correl will be:
cor(DataArray_1[dimnames(Correl)[[1]][1],dimnames(Correl)[[2]][1],dimnames(Correl)[[4]][1],],DataArray_2[dimnames(Correl)[[1]][1],dimnames(Correl)[[3]][1],dimnames(Correl)[[4]][1],],use=pairwise.complete.obs)
So my problem boils down to extracting the dim-names in terms
of element(d)
and not in terms of Correl (that I have mentioned as ... in
the above
code)
My sincere thanks for your valuable time
Re: [R] How to deal with this random variable?
Thank you for your replay Bert. You are right, is complicated to get a good response when people do not know how the experiment was conducted, etc. The main problem, maybe, is that this experiment has a wrong design being complicated to get some good conclusion from it. I read this forum frequently and I found a lot of useful information on it. For that reason I decided to ask to the forum; maybe someone can help us. Thank you again for your response Bert. Bert Gunter wrote: This sounds way too complicated for this forum, which is designed to provide help to users on the use of the R language, not remote statistical consulting. While you may receive replies, I would argue that you would do better to find a local statistical expert with whom to work -- not least because they should probably have a deep understanding of how your experiment was conducted, data gathered, measurements made, etc. to be able to give you worthwhile advice. Long distance consulting based on incomplete understanding is very risky. Caveat emptor! Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Manuel Ramon Sent: Monday, July 27, 2009 9:54 AM To: r-help@r-project.org Subject: [R] How to deal with this random variable? Hello to everybody, I have a data frame with 100 measures of quality for 3 variables: A, B and C. These quality variables are measured in diferent times along the productive process. My data comes from 5 experiments (5 replicates with 20 measures for replicate). I also have a final measure (Z) but just one measure for each unit, that is, for the 20 units that are measured on each replica. My objetive is to study the relationships between the 3 quality parameters with the last measure, that is: lm(Z ~ A+B+C, data=mydata) I have found significant differences between replicas for each qualite parameters (A, B and C) and I would like to include the replica effect as a random effect: lme(Z ~ A+B+C, data=mydata, random=~1|replica) And here is my problem. I know that there are signifficant diferences between replicas but since the final measure, Z, is the same for each replica I do not know how to deal with. Can you help me? How could I take into account the variability due to the replica when I want to study the effects of variables A, B and C on the final result of a productive process? Thank you in advance. - Manuel Ramón Fernández Group of Reproductive Biology (GBR) University of Castilla-La Mancha (Spain) mra...@jccm.es -- View this message in context: http://www.nabble.com/How-to-deal-with-this-random-variable--tp24684341p2468 4341.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-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. - Manuel Ramón Fernández Group of Reproductive Biology (GBR) University of Castilla-La Mancha (Spain) mra...@jccm.es -- View this message in context: http://www.nabble.com/How-to-deal-with-this-random-variable--tp24684341p24695050.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] xyplot, panel.abline, from, to
David,
?panel.abline does not indicate that 'from/to' are arguments to
that function. If you read the help page carefully, you'll see
that 'from/to' apply to panel.curve(). Perhaps you thought that
the '...' argument can take 'from/to'; again the help page makes
it clear that those are to be *graphical* parameters.
One quick fix would be to use panel.curve with, e.g. expr set to
a + b*x:
panel.curve(2 + .5*x, ...)
Peter Ehlers
Afshartous, David wrote:
All,
I'm trying to truncate some lines that are added to an xyplot via
panel.abline to allow additional space for inserted text. According to
?panel.abline it seems like from and to will do the trick but it does
not work for the sample code below. Any hints much appreciated.
Cheers,
David
x = seq(1,8)
y.1 = .6*x + 3.5 + rnorm(8, 0, .5); y.2 = .4*x + 1 + rnorm(8,0, .5)
data.ex = data.frame( x.var = c(x,x), y.var = c(y.1, y.2), id = c(rep(y1,
8), rep(y2, 8)))
xyplot( y.var ~ x.var, data = data.ex, groups = id, pch = 16, panel =
function(...) {
panel.abline(a = 2, b = .5, lty = 1, from = 1, to = 8)
panel.abline(a = 3.5, b = .6, lty = 3, from = 1, to = 8)
panel.abline(a = 1, b = .4, lty = 4, from = 1, to = 8)
panel.xyplot(...)
}, scales = list(y = list(limits = c(0,10)), x = list(limits =
c(0,12)) ))
__
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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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Kernlab - Splinedot Kernel
Hi, I am trying to use the splinedot kernel as part of the kernlab package, but I get the following error: Error in votematrix[i, ret 0] - votematrix[i, ret 0] + 1 : NAs are not allowed in subscripted assignments The parameters that I have used to build the model are: SVMmodel - ksvm(Classification~., data=dsTrain, type=C-svc, kernel=splinedot, C=1) My training set does not contain NAs and all of the values range between 0 to 1. I am using R version 2.7.0. If anyone has used ksvm with the splinedot kernel, any tips would be greatfully accepted. Mark -- Mark McDowall __ 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 add a new dataset to default R distributions
On Tue, 2009-07-28 at 04:54 -0700, Albert EINstEIN wrote: Hi, Thanks for your support. we are not getting any thing from your code. i.e. we are unable to creating new package and adding dataset to that new package. so can you help me out in other way i.e. how to add a new dataset to default R distributions like cars and datasets. these two are default distributions (i.e. packages). so please help us in this aspect. Thanks in advance. Highly likely that that won't happen as you are asking R Core to maintain your data sets. You should use a package for this - hundreds of other useRs have done so! Given that creating your own package is easy once you've read R Exts manual: http://cran.r-project.org/doc/manuals/R-exts.html despite seeming a bit daunting at first if you are new to this kind of thing. And creating a data set is as easy as getting the data into R and formatting it as required and then, if the data are in object 'foo' doing: save(foo, file = foo.rda) Then move the foo.rda file to the data directory in your package structure (see ?package.skeleton to do even this bit for you). Then write an Rd help page to describe the data, and that data set is included. You can store your data in other formats (csv say) and there you don't even need to get it into R first, just drop the csv file in the ./data directory. Given that you completely fail to provide *any* of the requested information mentioned in the posting guide, how can we help you? You don't tell us what didn't work. Given the evidence of this and other posts, I suspect lack of effort on your part yet you seem to be requesting more and more help from the rest of us. Read the posting guide and form an appropriate posting and then maybe people on the list can sort out what is not working for you. G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ 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] check for new files in a given directory
On 28-Jul-09 13:40:31, Barry Rowlingson wrote: On Tue, Jul 28, 2009 at 12:36 PM, Ted Hardingted.hard...@manchester.ac.uk wrote: However, this got me looking into '?list.files, and I see there (R version 2.9.0 (2009-04-17)): _recursive: logical. Should the listing recurse into directories? But: _Directories are included only if 'recursive = FALSE'. Surely the latter is the wrong way round, and should be _Directories are included only if 'recursive = TRUE'. by 'included' it means 'returned'. If you do 'recursive=TRUE' it scans recursively for files and only files. If you do recursive=FALSE it returns files and directories in the specified directory. Makes it tricky to figure out a complete directory tree since empty directories won't appear at all if recursive=TRUE. You'd have to implement your own recursive search based on list.files(d,recursive=FALSE) and then testing for directoriness Sucky, unless there's a better way... Barry Thanks for the clarification, Barry! I hadn't appreciated all that (I think the wording of ?list.files is misleading here). I agree that it can leave you falling between two stools in the sort of situation you describe. Which, as it happens, leads me back to the use of system(...) in Unix/Linux systems. For example, to list all the directories (without their files) in the current directory you could do: system(find . -type d -print) which finds (recursively) everything in and under the current directory (.) which is of type directory (d). Likewise, the 'ls' command with suitable options (perhaps combined with judicious 'grep'ping) can enable you to select what you want. For example, if something is planting data files with extension .dat from time to time, system(ls -tr *.dat) would list all files with extension .dat in time (-t) order reversed (r) (most recent last). Again, find could be useful. Suppose the last one of such files you accessed was lastfile.dat; then: system(find -maxdepth 0 -newer lastfile.dat -name '*.dat' -print) would find, in the current directory only (-depth 0) all files with extension .dat (-name '*.dat') which are newer than the given file lastfile.dat. It is for reasons of flexibility like this that I use system() for this kind of thing anyway (with 'intern=TRUE' if the results are to be saved in a variable), so I hadn't looked into list.files() before! Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 28-Jul-09 Time: 15:24:09 -- XFMail -- __ 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] formatting in r
Hello, I have output that I want to print out. I am having a few issues. 1] output u to power is really nothing more than a 2 x 11 set of values formed using cbind function and printed out as a data frame How can I get it to output over several lines such as seen here? 2] Critical Z etc. were added by hand. I need an example of how I can mix alphanumeric and numeric data on output. Can you assist? R is proving to be a really fine computational language that is easy to use. Thank you. Sincerely, Mary A. Marion u xbar alpha zcrit zcrit2 zstatpvalue 140 150.05 1.64491.96 4 6.334248e-05 LB95 UB95LB90UB90 145.1 154.9 145.888 154.112 Beta Power 0.021 0.979 Critical Z = 1.645 Zstatistic = 4 Empirical Mean 150[ 135.1, 144.9 ) = Ao(µo) Population Mean 140[ 145.1, 154.9 ] = C(x) Pvalue .0001 __ 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] help
On 28-Jul-09 08:28:22, Inchallah Yarab wrote:
How I can vary the parameters for a function?
I have a function with 5 parameters I want to turn the function for a
range of numbers for one of these parameters!! i want to have in the
end the value of the function in the different cas of one of the
paramter (the others paramters are fixes!!) thank you for your help
It depends on the internals of the function. In R, most functions
(including what you write yourself, if written in the right way)
allow you to give a vector of numbers to a numerical parameter.
The calculations are then vectorised in a single pass, and the
results for each value are returned as a vector.
For example, the pnorm() function for several different standard
deviations:
SD = c(1,1.5,2,2.5,3)
cbind(SD,pnorm(q=0.5, mean=0, sd=SD))
# [1,] 1.0 0.6914625
# [2,] 1.5 0.6305587
# [3,] 2.0 0.5987063
# [4,] 2.5 0.5792597
# [5,] 3.0 0.5661838
Likewise, if your function is
my.fun - function(par1,par2,par3,par4,par5){
(par1 + par2*par3 + (par3^2)*(par4 + par5))
}
then you could have
par1 - 1.1 ; par2 - 1.2 ; par4 - 1.4; par5 - 1.5
par3 - SD # (as above)
cbind(SD,my.fun(par1,par2,par3,par4,par5))
# SD
# [1,] 1.0 5.200
# [2,] 1.5 9.425
# [3,] 2.0 15.100
# [4,] 2.5 22.225
# [5,] 3.0 30.800
Hoping this helps!
Ted.
E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 28-Jul-09 Time: 15:39:27
-- XFMail --
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Re: [R] re ading jpeg images?
I found the 'biOps' package for Image and data analysis quite helpful. (I did some astronomical investigations with it --- counting galaxies in a Hubble picture---and I do recommend this package.) Under Windows you have to unpack the 'libjpeg' and 'libtiff' libraries beforehand somewhere in your path. See finzi.psych.upenn.edu/Rhelp08/2009-April/194630.html for a link to download all necessary libraries as a zip-file. If this link to RapidShare does not work anymore, I think I still have that file somewhere and could send it to you by e-mail. Regards Hans Werner Robert Biddle wrote: Can someone advise me what the most sensible way is to read jpeg images? For our work with image analysis and eye-tracking we have been using the rimage package, on both Macs and Windows PCs. But while setting up a new Windows machine yesterday, I see that rimage is regarded as orphaned, and no Windows binary is available. I eventually found an old zip file for the package, so I am not stuck, but I wonder what the right way is to go forward. I did find the readimages package, but it also seemed problematic to install on both Windows on Mac, requiring extra software that it was itself unclear how to install. Is there some simpler solution I should be looking at? Are jpeg files so probematic I should be converting them to some other format and using a different package to read that? Thanks Robert Biddle __ 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/reading-jpeg-images--tp24698332p24700340.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] Downloaded file is larger than the starting file
We cannot know without seeing your script. Uwe Ligges DeWitt Payne wrote: I'm running R for windows 2.9.1. When I use a script to download a file from the internet, the file is 1,496 bytes larger than the reported file size in the download process. It doesn't give the correct answer when I process it but it doesn't appear to be completely corrupt as the processing script runs. I can download the file from Firefox and the size of the downloaded file is correct. I tried starting with the internet2 flag set and it didn't help. The url of the file is: http://iup.physik.uni-bremen.de:8084/amsredata/asi_daygrid_swath/l1a/n6250/2009/jun/asi-n6250-20090603-v5.hdf . Is this a bug or do I have some configuration problem with my computer? Thanks, DeWitt Payne __ 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-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] create dataset permanently in package (i.e. default or our own package)
Hi If you want to use brute force without much knowledge about packages make your own directory in librarary directory select any package in your library directory and copy it to directory you just made leave only INDEX and DESCRIPTION files and R and Data directorires change DESCRIPTION file according your wish, leave INDEX as is. in R directory put any text file which will contain any of your custom functions in Data directory put any text file which will contain your data in etc directory change Rprofile.site and add something like library(fun) data(modely) data(stand) it may work, however if you want to be serious with your own package(s) you shall follow advice in R-exts.html manual as was advised earlier. Regards Petr r-help-boun...@r-project.org napsal dne 28.07.2009 11:40:06: Hi, Thanks for your support. we are not getting any thing from your code. i.e. we are unable to creating new package and adding dataset to that new package. so can you help me out in other way i.e. how to add a new dataset to default R distributions like cars and datasets. these two are default distributions (i.e. packages). so please help us in this aspect. Thanks in advance. -- View this message in context: http://www.nabble.com/create-dataset- permanently-in-package-%28i.e.-default-or-our-own-package%29-tp24679076p24694060.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-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] xyplot, panel.abline, from, to
On Tue, Jul 28, 2009 at 6:58 AM, Peter Ehlersehl...@ucalgary.ca wrote: David, ?panel.abline does not indicate that 'from/to' are arguments to that function. If you read the help page carefully, you'll see that 'from/to' apply to panel.curve(). Perhaps you thought that the '...' argument can take 'from/to'; again the help page makes it clear that those are to be *graphical* parameters. One quick fix would be to use panel.curve with, e.g. expr set to a + b*x: panel.curve(2 + .5*x, ...) Yes, that would be my suggestion too, or using panel.segments fab - function(x) a + b * x panel.segments(from, fab(from), to, fab(to)) -Deepayan __ 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] pairs plot
r-help-boun...@r-project.org napsal dne 28.07.2009 15:39:03: Have you installed it first? First: install.packages(TeachingDemos) Or if you have problems with correct setting through corporate network rules (like myself) you can download a zip (for Windows) version and unzip it to library subdirectory. Then: library(TeachingDemos) shall be executed without problem Regards Petr --- On Tue, 7/28/09, Jose Narillos de Santos narillosdesan...@gmail.com wrote: From: Jose Narillos de Santos narillosdesan...@gmail.com Subject: Re: [R] pairs plot To: Petr PIKAL petr.pi...@precheza.cz, r-help@r-project.org, greg.s...@imail.org Received: Tuesday, July 28, 2009, 8:24 AM Hi, I tried to load typing library(TeachingDemos) But the message can´t find package TeachingDemos) occurs. I use versión R 2.9 on windows. Can you please guide me? Sorry¡¡¡ 2009/7/28, Petr PIKAL petr.pi...@precheza.cz: Hi r-help-boun...@r-project.org napsal dne 28.07.2009 09:55:11: Hi Greg I saw, read, the TeachingDemos you suggesttef but when run pairs2 function on my R module says Can´t find function pairs2 How can I load the module or function pairs2? Did you do library(TeachingDemos)? Regards Petr Thanks in advance for your help. You are the best. 2009/7/27, Greg Snow greg.s...@imail.org: Look at the pairs2 function in the TeachingDemos package. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Jose Narillos de Santos Sent: Monday, July 27, 2009 9:02 AM To: r-help@r-project.org Subject: [R] pairs plot Hi all, I want to plot trough pairs() plot a matrix with 4 columns. I want to make a trhee plot in a graph. Plotting pairs colum 2,3,4 on y axis and 1 on X axis. You mean (a plot with three graphs) ommitting the first pair with itself. And only the pairs with colum 1 with the other not all pairs. I. e. this matrix 4177 289390 8740 17220 3907 301510 8530 17550 3975 316970 8640 17650 3651 364220 9360 21420 3031 387390 9960 23410 2912 430180 11040 25820 3018 499930 12240 27620 2685 595010 13800 31670 2884 661870 14760 37170 Thanks in advance. [[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. [[alternative HTML version deleted]] -Inline Attachment Follows- __ 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. __ Yahoo! Canada Toolbar: Search from anywhere on the web, and bookmark your favourite sites. Download it now http://ca.toolbar.yahoo.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-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] Superscripts and rounding
sub = sprintf('Seasonal station with natural streamflow - Lat: %s Lon: %s
Gross Area %s km^2 - Effective Area %s km^2',
stn[['metadata']][['latitude']],
stn[['metadata']][['longitude']],stn[['metadata']][['grossarea']],
stn[['metadata']][['effectivearea']]),
I tried your code and a few variations, but was able to make it work - Uwe
(but thank you!!)
I am having no problem with retrieving the data for the above code. i would
just like the sub-title to display the units after the data correctly (aka
km suberscript 2 - instead of km^2). In addition i want the numbers being
pulled from the database to round to four decimal places as currently the
lat and lon come in as huge numbers. I have tried a to use the round command
but it always just shows up as text in my title
--
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Re: [R] local regression using loess
Actually, loess is much more than an interpolant. I wouldn't even call it that. It is a local regression technique that comes with all the equipment you get in classical regression. But it is meant for normal-like errors, which is not what you have. -- This is misleading. The local smoother part makes a big difference. For example df (and standard tests, consequently)are not defined as in conventional multiple regression (though the enp argument gives you something like df). Also, it was specifically designed for _non_-normal errors -- specifically, long-tailed distributions -- via use of the symmetric family argument which fits via a re-descending M-estimator not Gaussian likelihood = least squares. But you are certainly free to characterize it as you think appropriate if you do not think interpolant is reasonable... -- Bert I would recommend that you take a look at the locfit package. It fits local likelihood models. I've never tried it with binary data, but if y is your 0/1 response and x is a covariate, you might try something like: locfit(y ~ x, ..., family=binomial) If you have a good library at your disposal, try picking up Loader's book Local Regression and Likelihood. __ 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-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] Help with significance. T-test?
mik07 wrote: Hi, this is more a general statistics question I think. I am working on a system which automatically answers user questions (such systems are commonly called Question Answering systems). I evaluated different versions of the same system on a publicly available test set. This set contains 500 question. Naturally, for each question the answer can be wrong or right, which is coded as 0 (wrong) or 1 (correct). By adding up all values, and dividing them by the number of questions in the test set (that's 500), one gets a measure for how well the system performs, commonly called accuracy. As mentioned I evaluated two different versions of the system, and received two different accuracy values. Now I want to know whether the difference is statistically significant. ?prop.test -- View this message in context: http://www.nabble.com/Help-with-significance.-T-test--tp24699690p24701848.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] Help with significance. T-test?
Hi, this is more a general statistics question I think. I am working on a system which automatically answers user questions (such systems are commonly called Question Answering systems). I evaluated different versions of the same system on a publicly available test set. This set contains 500 question. Naturally, for each question the answer can be wrong or right, which is coded as 0 (wrong) or 1 (correct). By adding up all values, and dividing them by the number of questions in the test set (that's 500), one gets a measure for how well the system performs, commonly called accuracy. As mentioned I evaluated two different versions of the system, and received two different accuracy values. Now I want to know whether the difference is statistically significant. Can I use a t-test? I know it has certain requirements, for example a somewhat normal distribution. That's difficult of course when the values in question are only 0 and 1... Has anybody any ideas? Thanks a lot, Mika PS: The data I have looks something like this (of course I actually have 500 values, not only 10): results1: 0,1,1,1,0,1,1,0,1,0accuracy: 0.6 results2: 0,0,1,1,0,0,1,1,1,0accuracy: 0.5 -- View this message in context: http://www.nabble.com/Help-with-significance.-T-test--tp24699690p24699690.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] spherical wavelets package
Hello to all, I am trying to use the spherical wavelets package on my altimetry data. I am having some problems now and then. Currently I am having an error of error in matrix(0,KK,JJ) : too many elements specified there is a thread of possibly same error (https://stat.ethz.ch/pipermail/r-help/2005-January/064308.html) but it seems like it doesnt really help me. More specifically i am trying the following command. ssha is a vector of 1038240 observations, latlon1 a matrix 1038240x2, net a list of 1038240 points. out.ls-sbf(obs=ssha, latlon=latlon1, netlab=net, eta=eta, method=ls, approx=TRUE,grid.size=c(100,200)) I would be highly grateful if anybody could help in any way. Best regards Konstantina Konstantina Rizopoulou MRes in Ocean Remote Sensing Konstantina Rizopoulou MRes in Ocean Remote Sensing National Oceanography Centre Southampton, UK +44 (0) 7772156968 (uk) +30 6975205837 (greece) _ re.aspx?tab=1 [[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.
[R] Reading Excel files in Linux
Hi, I'm using the RODBC package to read Excel files in Windows. I would like to do it in Linux. What´s the best way to read Excel files in Linux? Thanks in advance, Srpd _ y-edit.aspx [[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] local regression using loess
Are X1 and X2 both numeric? You might want to get them on equivalent scales, and also play around with the smoothing parameter. Try something like: fit - locfit(Y ~ lp(X1, X2, nn=___, scale=TRUE), family=binomial) and see what happens for different values of nn (try values between 0 and 1 and then some larger than one). I can't be much more help without data. On Jul 27, 2009, at 9:41 PM, cindy Guo wrote: Hi, Ryan, Thank you for the information. I tried it. But there are some error messages. When I use fit - locfit(Y~X1*X2,family='binomial'), the error message is error lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, : compparcomp: parameters out of bounds And when I use fit - locfit(Y~X1*X2), the error message is error lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, : newsplit: out of vertex space This happens sometimes, not every time for different data. Do you know what's the reason? Thank you, Cindy On Mon, Jul 27, 2009 at 5:25 PM, Ryan rha...@purdue.edu wrote: Hi, All, I have a dataset with binary response ( 0 and 1) and some numerical covariates. I know I can use logistic regression to fit the data. But I want to consider more locally. So I am wondering how can I fit the data with 'loess' function in R? And what will be the response: 0/1 or the probability in either group like in logistic regression? -- Neither. Loess is an algorithm that smoothly interpolates the data. It makes no claim of modeling the probability for a binary response variable. -- Bert Gunter Genentech Nonclinical Statistics Thank you, Cindy [[alternative HTML version deleted]] Actually, loess is much more than an interpolant. I wouldn't even call it that. It is a local regression technique that comes with all the equipment you get in classical regression. But it is meant for normal-like errors, which is not what you have. I would recommend that you take a look at the locfit package. It fits local likelihood models. I've never tried it with binary data, but if y is your 0/1 response and x is a covariate, you might try something like: locfit(y ~ x, ..., family=binomial) If you have a good library at your disposal, try picking up Loader's book Local Regression and Likelihood. __ 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.
[R] aggregating strings
I am currently summarising a data set by collapsing data based on common
identifiers in a column. I am using the 'aggregate' function to summarise
numeric columns, i.e. aggregate(dat[,3], list(dat$gene), mean). I also wish
to summarise text columns e.g. by concatenating values in a comma separated
list, but the aggregate function can only return scalar values and so something
like aggregate(dat[,3], list(dat$gene), cat) will not work. Is there a
simple function like aggregate that works for strings in R?
--
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Re: [R] Reading Excel files in Linux
The read.xls function in the gdata package can read Excel 2003 files on all platforms. On Tue, Jul 28, 2009 at 10:11 AM, srpd TCLTKsrpd2...@hotmail.com wrote: Hi, I'm using the RODBC package to read Excel files in Windows. I would like to do it in Linux. What´s the best way to read Excel files in Linux? Thanks in advance, Srpd _ y-edit.aspx [[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. __ 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] Odp: aggregating strings
Hi
r-help-boun...@r-project.org napsal dne 28.07.2009 17:34:35:
I am currently summarising a data set by collapsing data based on common
identifiers in a column. I am using the 'aggregate' function to
summarise
numeric columns, i.e. aggregate(dat[,3], list(dat$gene), mean). I
also wish
to summarise text columns e.g. by concatenating values in a comma
separated
list, but the aggregate function can only return scalar values and so
something like aggregate(dat[,3], list(dat$gene), cat) will not work.
Is
there a simple function like aggregate that works for strings in R?
Try
aggregate(dat[,3], list(dat$gene), paste, collapse=,)
Regards
Petr
--
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Engl...{{dropped:21}}
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http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: [R] skip plot/blank plot on purpose (multi-plot question)
Just to expand a little. Your original question also asked if there is a way to specify which figure to plot in next. If you use par(mfrow=c()) (or mfcol), then you can use par(mfg=c()) to specify which figure to plot next. There is also the split.screen approach where you can split the device into several screens and use the screen function to specify which to plot to. This probably gives the most control, but I have usually found layout to be sufficient and easier to use. As has also been mentioned, lattice allows for multiple panels in a plot, but sometimes lattice is more complicated than base graphs for doing these things (and for other cases it is much simpler). For your task, layout and plot.new is probably the most straight forward. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Greg Snow Sent: Monday, July 27, 2009 5:42 PM To: Mark Knecht; Bert Gunter Cc: r-help Subject: Re: [R] skip plot/blank plot on purpose (multi-plot question) Also look at the frame and plot.new functions. -Original Message- From: Mark Knecht markkne...@gmail.com To: Bert Gunter gunter.ber...@gene.com Cc: r-help r-help@r-project.org Sent: 7/27/09 1:56 PM Subject: Re: [R] skip plot/blank plot on purpose (multi-plot question) On Mon, Jul 27, 2009 at 12:21 PM, Bert Guntergunter.ber...@gene.com wrote: Well, all of this can be done quite nicely with lattice graphics: ?xyplot (See, e.g. the skip argument) 1) Is there some generic way to call plot and have it plot, but it plots nothing so I don't see anything at all in position 12? This could be a blank plot function I call when I notice the data set is empty. -- But if you do not wish to learn lattice, please at least read the docs on standard graphics: ?plot (the type argument) ?plot.default (the axes argument) Thank you. It was the ?plot.default/axis argument that I was looking for. I knew type=n. Cheers, Mark -- Bert Gunter Genentech, Inc. 2) Is there some generic way to specify the position number I want the next plot to use so that I'd not plot 12 but would specify 13? Thanks, Mark __ 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-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-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-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] check for new files in a given directory
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Barry Rowlingson
Sent: Tuesday, July 28, 2009 6:41 AM
To: ted.hard...@manchester.ac.uk
Cc: r-help@r-project.org; Andreas Posch
Subject: Re: [R] check for new files in a given directory
On Tue, Jul 28, 2009 at 12:36 PM, Ted
Hardingted.hard...@manchester.ac.uk wrote:
However, this got me looking into '?list.files, and I see there
(R version 2.9.0 (2009-04-17)):
recursive: logical. Should the listing recurse into directories?
But:
Directories are included only if 'recursive = FALSE'.
Surely the latter is the wrong way round, and should be
Directories are included only if 'recursive = TRUE'.
by 'included' it means 'returned'. If you do 'recursive=TRUE' it
scans recursively for files and only files. If you do
recursive=FALSE it returns files and directories in the specified
directory.
Makes it tricky to figure out a complete directory tree since empty
directories won't appear at all if recursive=TRUE. You'd have to
implement your own recursive search based on
list.files(d,recursive=FALSE) and then testing for directoriness
Sucky, unless there's a better way...
Barry
S+'s dir() and list.files() functions have an extra argument called type
that let you say if you are interested in only files (non-directories) or
directories or want all directory entries listed in the output. Its default
value
is set to match the R behavior
function(...,
recursive=FALSE,
type = if(recursive) c(files, directories, all) else c(all,
files, directories))
{
type - match.arg(type)
...
}
I put it in when I was looking for all directories named 'R' in a collection of
packages and bundles and I didn't want to use the platform-dependent
system() function. Should this argument be added to R's dir() and
list.files() functions?
Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com
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Re: [R] local regression using loess
Bert Gunter gunter.berton at gene.com writes: Actually, loess is much more than an interpolant. I wouldn't even call it that. It is a local regression technique that comes with all the equipment you get in classical regression. But it is meant for normal-like errors, which is not what you have. Bert - when I hear interpolate, I think of connecting the data points, like using something like divided differences or hermite interpolation, so I thought that's what you meant. Sorry for the misunderstanding. True that loess was designed to be robust, but when I said it is meant for normal-like errors, I was referring to loess with statistical procedures analagous to the classical regression setting, such as confidence intervals, anova, etc. (see Locally Weighted Regression: An Approach to Regression Analysis by Local Fitting, 1988). __ 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] some QCA questions
Dear Adrian Dusa, others, I've recently started to learn R in order to use the QCA package because i think it might offer what other QCA packages don't: possibilities for quite a few conditions and large n. However, can someone tell me approx. how much RAM i need to run QCA on set of +/- 400.000 cases and +/- 15 conditions? (or differently: how much time will it take with RAM of a certain size?) Also I'm very keen on hearing any news on the fuzzy and multivalue options for R...How's that comming along? Thanks a lot for any information you can provide! And of course major thanks for all the information you've already provided for me in existing manuals, R-fora etc. Great work! Greetings, Suzan van der Post [[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] aggregating strings
You are probably going to get tons of answers, as there are many ways -- and
packages -- to do this (e.g. see packages reshape and plyr). However, you
might want to take a look at ?tapply, for which aggregate() is a wrapper,
for the basic core R approach.
Bert Gunter
Genentech Nonclinical Biostatistics
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Dry, Jonathan R
Sent: Tuesday, July 28, 2009 8:35 AM
To: r-help@r-project.org
Subject: [R] aggregating strings
I am currently summarising a data set by collapsing data based on common
identifiers in a column. I am using the 'aggregate' function to summarise
numeric columns, i.e. aggregate(dat[,3], list(dat$gene), mean). I also
wish to summarise text columns e.g. by concatenating values in a comma
separated list, but the aggregate function can only return scalar values and
so something like aggregate(dat[,3], list(dat$gene), cat) will not work.
Is there a simple function like aggregate that works for strings in R?
--
AstraZeneca UK Limited is a company incorporated in Engl...{{dropped:8}}
__
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] vary the parameters for a function
If you want to have a gui that allows you to change parameter values using buttons/sliders/etc. and see what the effects are, then look at the tkexamp function in the TeachingDemos package (see the examples on the help page). If you have a predetermined set of values for the parameter of interest and want to run the function multiple times with those values (and other set values), then try mapply. Here is an example using the power.t.test function to find the power for different sample sizes (and a fixed delta of 0.3, everything else at its default): tmp - mapply(power.t.test, n=c(10,20,30,50), MoreArgs=list(delta=0.3)) unlist(tmp['power',]) [1] 0.09271619 0.15031255 0.20689369 0.31751712 Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Inchallah Yarab Sent: Tuesday, July 28, 2009 3:36 AM To: r-help@r-project.org Subject: [R] vary the parameters for a function How I can vary the parameters for a function? I have a function with 5 parameters I want to turn the function for a range of numbers for one of these parameters!! i want to have in the end the value of the function in the different cas of one of the paramter (the others paramters are fixes!!) thank you for your help [[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. __ 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] Density plot in ggplot2
Hi all, I was trying to draw a stacked density plot like that : library(ggplot2); library(plyr) dat - cbind(rnorm(300), rep(c(1,2), each=150)) ggplot() + geom_density(aes(x=dat[,1], fill=factor(dat[,2]), position=stack)) + xlab() + ylab() + scale_colour_manual(name = Pallet, labels = c(X, Y)) Here everything is ok, except few points : 1. I want to remove the name of y-axis, which is by default density. Here I put ylab(), however although for x-axis it is working, for y-axis it is not. Is there any specific formula for that? 2. I want to rename the color plot, as well as the title of the color. The function scale_colour_manual() seems not working. Can anyone please suggest me how to achieve desired thing? Thanks -- View this message in context: http://www.nabble.com/Density-plot-in-ggplot2-tp24702858p24702858.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] Skew-Normal Linear Mixed Model (SNLMM)
Dear ALL, In the Normal Linear Mixed Model (NLMM) we make the assumption that the random effects are normally distributed. Is it possible to fit a linear mixed model in R where the random effects are assumed to have a Skew-Normal distribution? I am trying to reproduce the results in the paper referenced below. Can anyone help? Tsung I. Lin, Jack C. Lee. Estimation and prediction in linear mixed models with skew-normal random effects for longitudinal data. Statistics in Medicine 2008; 27 (9):1490–1507 Regards, Raphael -- Raphael A. Fraser, MSc Lecturer in Biostatistics Tropical Medicine Research Institute Faculty of Medical Sciences University of the West Indies Mona Campus Kingston, JAMAICA Tel: (876) 927-2471; 977-6151 Mobile: (876) 410-4699 Fax: (876) 927-2984 e-mail: raphael.fra...@uwimona.edu.jm __ 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] Help with significance. T-test?
Look up the McNemar test. That sounds right... Daniel - cuncta stricte discussurus - -Ursprüngliche Nachricht- Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Im Auftrag von mik07 Gesendet: Tuesday, July 28, 2009 10:49 AM An: r-help@r-project.org Betreff: [R] Help with significance. T-test? Hi, this is more a general statistics question I think. I am working on a system which automatically answers user questions (such systems are commonly called Question Answering systems). I evaluated different versions of the same system on a publicly available test set. This set contains 500 question. Naturally, for each question the answer can be wrong or right, which is coded as 0 (wrong) or 1 (correct). By adding up all values, and dividing them by the number of questions in the test set (that's 500), one gets a measure for how well the system performs, commonly called accuracy. As mentioned I evaluated two different versions of the system, and received two different accuracy values. Now I want to know whether the difference is statistically significant. Can I use a t-test? I know it has certain requirements, for example a somewhat normal distribution. That's difficult of course when the values in question are only 0 and 1... Has anybody any ideas? Thanks a lot, Mika PS: The data I have looks something like this (of course I actually have 500 values, not only 10): results1: 0,1,1,1,0,1,1,0,1,0accuracy: 0.6 results2: 0,0,1,1,0,0,1,1,1,0accuracy: 0.5 -- View this message in context: http://www.nabble.com/Help-with-significance.-T-test--tp24699690p24699690.ht ml 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-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] Help with significance. T-test?
Mika Are you familiar with item response theory? You might consider functions in ltm or MiscPsycho for dealing with binary response data. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of mik07 Sent: Tuesday, July 28, 2009 10:49 AM To: r-help@r-project.org Subject: [R] Help with significance. T-test? Hi, this is more a general statistics question I think. I am working on a system which automatically answers user questions (such systems are commonly called Question Answering systems). I evaluated different versions of the same system on a publicly available test set. This set contains 500 question. Naturally, for each question the answer can be wrong or right, which is coded as 0 (wrong) or 1 (correct). By adding up all values, and dividing them by the number of questions in the test set (that's 500), one gets a measure for how well the system performs, commonly called accuracy. As mentioned I evaluated two different versions of the system, and received two different accuracy values. Now I want to know whether the difference is statistically significant. Can I use a t-test? I know it has certain requirements, for example a somewhat normal distribution. That's difficult of course when the values in question are only 0 and 1... Has anybody any ideas? Thanks a lot, Mika PS: The data I have looks something like this (of course I actually have 500 values, not only 10): results1: 0,1,1,1,0,1,1,0,1,0accuracy: 0.6 results2: 0,0,1,1,0,0,1,1,1,0accuracy: 0.5 -- View this message in context: http://www.nabble.com/Help-with-significance.-T-test--tp246996 90p24699690.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-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] Searching for specific values in a matrix
quick question, i am trying to get an interval of values now with this code by toggling the tolerance limit. is there any way i can modify this code to find values which are within limits of BOTH latitude and longitude? currently i have to pick one or the other. It's not really clear where your data is lat/long .. is this x/y? Anyway, you can two query vectors to get the data that's between both. For instance: rearranged[1:10, 1:5] xy band1 VSCAT.001 soiltype 1 -124.3949 40.42468NANA CD 2 -124.3463 40.27358NANA CD 3 -124.3357 40.25226NANA CD 4 -124.3663 40.40241NANA CD 5 -124.3674 40.49810NANA CD 6 -124.3083 40.24744NA 464 NA 7 -124.3017 40.31295NANAD 8 -124.3375 40.47557NA 464 NA 9 -124.2511 40.11697 1NA NA 10 -124.2532 40.12640 1NA NA Assume you want a range constrained by x and y: good.x - rearranged$x 124.3 rearranged$x 125 good.y - rearranged$y 40.5 rearranged$y 41 rearranged[good.x good.y,] Like that? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ 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] Density plot in ggplot2
Hi Ron, I'm not sure why ylab doesn't work. Maybe a bug. I note the label doesn't get removed with labs() either. However using scale_y_continuous(name=) does remove the label. For the legend, you are using a fill scale, not a colour scale i.e. fill=factor(dat[,2]), not colour=factor(dat[,2]) use scale_fill_hue(name = Pallet, labels = c(X, Y)) instead. Regards, Paul RON70 wrote: Hi all, I was trying to draw a stacked density plot like that : library(ggplot2); library(plyr) dat - cbind(rnorm(300), rep(c(1,2), each=150)) ggplot() + geom_density(aes(x=dat[,1], fill=factor(dat[,2]), position=stack)) + xlab() + ylab() + scale_colour_manual(name = Pallet, labels = c(X, Y)) Here everything is ok, except few points : 1. I want to remove the name of y-axis, which is by default density. Here I put ylab(), however although for x-axis it is working, for y-axis it is not. Is there any specific formula for that? 2. I want to rename the color plot, as well as the title of the color. The function scale_colour_manual() seems not working. Can anyone please suggest me how to achieve desired thing? Thanks __ 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] character vector - numeric matrix ??
Dear R users... I'd like to change this character vector, zz, zz - c(12,56,89) to the following numeric matrix. [,1] [,2] [1,]12 [2,]56 [3,]89 Actually, zz vector has a long length. Any comments will be greatly appreciated. Kathryn Lord -- View this message in context: http://www.nabble.com/character-vector--%3E-numeric-matrixtp24703927p24703927.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.
