[R] How to write the log function in R

2008-09-01 Thread toh
Hi, I need help to write the following log-likelihood function in R: log(L) = sum [(y_k - y_k-1).log(m(t_k) - m(t_k-1)) - (m(t_k) - m(t_k-1)) - log((y_k -y_k-1)!)] I need to write this log-likelihood function in order to find the parameters by MLE method. Appreciate the help. -- View this m

Re: [R] correlation with boot

2008-09-01 Thread ctu
Hi Professor Ripley, (Thank you very much)^infinite for your response. I still have few questions 1. R shows that I have two column in nlaw data. ncol(nlaw) [1] 2 corr(nlaw) [1] 0.7763745 2. Why can't I use boot::corr? I check corr in boot package and it seems to be used for computing correl

Re: [R] qcc help

2008-09-01 Thread Jorge Ivan Velez
Dear Renata, In your particular case, something like this should do the job: res=qcc(MDI, type = "xbar.one") names(res) res$limits A general approach (using the example in ?qcc) could be: require(qcc) data(pistonrings) attach(pistonrings) diameter <- qcc.groups(diameter, sample) ex = qcc(diamet

Re: [R] Help with stl

2008-09-01 Thread Ryan
charter.net> writes: > > I just realized after some tips and a little digging that what I was trying to do "manually" has already been > done. I was trying to fit my data using 'lm' then taking the "residual" data and trying to do a spectral > estimate (for seasonality) usiing fft and then pass

Re: [R] intercept of 3D line? (Orthogonal regression)

2008-09-01 Thread Moshe Olshansky
I do not see why you can not use regression even in this case. To make things more simple suppose that the exact model is: y = a + b*x, i.e. y1 = a + b*x1 ... yn = a + b*xn But you can not observe y and x. Instead you observe ui = xi + ei (i=1,...,n) and vi = yi + di (i=1,...,n) Now you have

Re: [R] How to disable character escaping ?

2008-09-01 Thread Prof Brian Ripley
On Tue, 2 Sep 2008, Leon Yee wrote: Dear all, I have a string (a file path in windows system) contains several "\"s. When I copy and paste it into R for assignment to an variable, the "\"s are always interpreted as escaping characters. How can I keep it intact? By reading from a file or co

Re: [R] correlation with boot

2008-09-01 Thread Prof Brian Ripley
Please look at the help for boot, in particular what it says the form of 'statistic' should be. Possibly what you want is corr.t <- function(data, ind) cor(data[ind,])[1,2] nlaw appears to be a single-column matrix: that will not work either. On Mon, 1 Sep 2008, [EMAIL PROTECTED] wrote: Hi

[R] How to disable character escaping ?

2008-09-01 Thread Leon Yee
Dear all, I have a string (a file path in windows system) contains several "\"s. When I copy and paste it into R for assignment to an variable, the "\"s are always interpreted as escaping characters. How can I keep it intact? Thanks. Regards, Leon __

Re: [R] Help with stl

2008-09-01 Thread stephen sefick
if your two points are valid and you would be willing to run a least spuares regression on then you should be fairly comfortable with using na.approx in the zoo package. If interpolating values is going to give you an erroneous result then maybe this is not the correct path. But have a look. On

[R] correlation with boot

2008-09-01 Thread ctu
Hi R users, I have one simple question but I really don't know why I can't get it work. The data was adopted from Efron's An introduction to the bootstrap book. nlaw LSAT GPA [1,] 576 3.39 [2,] 635 3.30 [3,] 558 2.81 [4,] 578 3.03 [5,] 666 3.44 [6,] 580 3.07 [7,] 555 3.00 [

Re: [R] Upgrade 'R'

2008-09-01 Thread Leon Yee
Hello, Kevin You can get some hints by browsing in this mailist with the subject of " Upgrading R means I lose my packages", which were posted several days ago. HTH Leon [EMAIL PROTECTED] wrote: More and more I am getting warnings from packages that I install that the package was buil

[R] Upgrade 'R'

2008-09-01 Thread rkevinburton
More and more I am getting warnings from packages that I install that the package was built with 2.7.2 (I am running 2.7.1). I would like to upgrade but don't want to loose all of the packages that I have installed and the settings. Is there a way to just "upgrade" without uninstalling and reins

[R] How is the binding for a super assignment made visible?

2008-09-01 Thread morphwj
The statement Globals <<- list() in the body of a function in a package was intended to write an empty list to the R workspace to collect results during the computations of the function. A package name space has not been specified. The package appears to function correctly, but during the R CM

Re: [R] qcc help

2008-09-01 Thread Cleber Nogueira Borges
Renata Mara Schneckenberg Wowk wrote: Hi Gents, I need to get the control limits from qcc function. As follows: qcc(MDI, type = "xbar.one") Call: qcc(data = MDI, type = "xbar.one") xbar.one chart for MDI Summary of group statistics: Min. 1st Qu. MedianMean

Re: [R] programming

2008-09-01 Thread Gabor Grothendieck
Check out: http://www.sciviews.org/_rgui/projects/Editors.html On Mon, Sep 1, 2008 at 8:52 PM, Yuan Jian <[EMAIL PROTECTED]> wrote: > Hi, > > I am looking for R editor. does anyone know good editor? which tells you > syntax error and it has function to beautify format (insert TAB etc.). > > Yu > >

[R] qcc help

2008-09-01 Thread Renata Mara Schneckenberg Wowk
Hi Gents, I need to get the control limits from qcc function. As follows: qcc(MDI, type = "xbar.one") Call: qcc(data = MDI, type = "xbar.one") xbar.one chart for MDI Summary of group statistics: Min. 1st Qu. MedianMean 3rd Qu.Max. 0.3266 0.4249 0.4371 0.

[R] programming

2008-09-01 Thread Yuan Jian
Hi,   I am looking for R editor. does anyone know good editor? which tells you syntax error and it has function to beautify format (insert TAB etc.).   Yu   [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https:

[R] multinomial estimation output stat question - not R question

2008-09-01 Thread markleeds
I am estimating a multinomial model with two quantitative predictors, X1 and X2, and 3 responses. The responses are called neutral, positive and negative with neutral being the baseline. There are actually many models being estimated because I estimate the model over time and also for various

[R] Exporting frequency distributions

2008-09-01 Thread Luz Milena Zea Fernandez
Dear support, we are trying to export a frequency distributions obtanined by stament freq(x,variable.labels=NULL,display.na=TRUE,levels=NULL) of prettyR. How can I do it? Thanks in advance __ R-help@r-project.org mailing list https://stat.ethz.ch/mailm

Re: [R] LDA predictions

2008-09-01 Thread Bill.Venables
I don't really understand this. You seem willing only to reveal the bit of the process where you are convinced the problem is. This may not be helpful if the problem lies elsewhere. I take it you are using the lda() function from MASS, though you don't say. Let's look at a little example: re

[R] LDA predictions

2008-09-01 Thread Gareth Campbell
I've made an LDA model on some data from one source. I have some new data that I want to see if I can "place" to the sources in the LDA model. I used the predict function as follows: predict(wak.insitu.ld, wak.alr.alluvial) where wak.insitu.ld is an LDA model generated from some data and wak.

Re: [R] Interpolation Problems

2008-09-01 Thread Duncan Murdoch
On 01/09/2008 6:17 PM, Steve Murray wrote: Dear all, I'm trying to interpolate a dataset to give it twice as many values (I'm giving the dataset a finer resolution by interpolating from 1 degree to 0.5 degrees) to match that of a corresponding dataset. I have the data in both a data frame for

Re: [R] opening an external file

2008-09-01 Thread Applejus
Thank you prof, Answered by the author of the function in question! :) Who could ask for more? Imad. Prof Brian Ripley wrote: > > On Mon, 1 Sep 2008, Henrique Dallazuanna wrote: > >> See ?browseURL > > Or more generally on Windows, ?shell.exec (which is what browseURL does by > default on

[R] Interpolation Problems

2008-09-01 Thread Steve Murray
Dear all, I'm trying to interpolate a dataset to give it twice as many values (I'm giving the dataset a finer resolution by interpolating from 1 degree to 0.5 degrees) to match that of a corresponding dataset. I have the data in both a data frame format (longitude column header values along t

Re: [R] RCurl: authentication when posting forms

2008-09-01 Thread Valerie Obenchain
Hi Duncan, Yes, unfortunately my filter must have eaten your first response to my parseHTTPHeader question. Thanks for responding to it again here on the list and for the more efficient paste tip. Below is a getURI call that returns a "not found" message. It is a publicly available web site

Re: [R] Question about type conversion in read.table with columns that contain "+" and "-" in R > 2.7

2008-09-01 Thread Prof Brian Ripley
On Mon, 1 Sep 2008, Tim Beissbarth wrote: Somewhere in between the R-Versions 2.6 and 2.7 the behaviour of the function type.convert and therefore also read.table, read.csv, etc. has changed (see below): In 2.6 and before: type.convert(c("+", "-", "+")) [1] + - + Levels: + - In 2.7 and lat

Re: [R] opening an external file

2008-09-01 Thread Prof Brian Ripley
On Mon, 1 Sep 2008, Henrique Dallazuanna wrote: See ?browseURL Or more generally on Windows, ?shell.exec (which is what browseURL does by default on Windows). On Mon, Sep 1, 2008 at 5:06 PM, Applejus <[EMAIL PROTECTED]> wrote: Hi, Is there a way to launch a file from an R command? To

Re: [R] email just sent

2008-09-01 Thread Duncan Murdoch
ivo welch wrote: please ignore part 1. of course, the cat works. my mistake. I just need to learn how to step up frames, please. parent.frame() will give you the frame of the caller. For example, in the browser, caller <- parent.frame() ls(caller) caller$foo etc. parent.frame() has

Re: [R] how to read multiple lines per case

2008-09-01 Thread Duncan Murdoch
Michael Friendly wrote: How can I read a space-delimited file, where the data values for each case are folded before column 80, and so appear on two lines for each case? The first few cases look like this loc type bio H2S sal Eh7 pH buf P K Ca Mg Na Mn Zn Cu NH4 OI DVEG 676 -610 33 -290 5.00 2.

[R] Question about type conversion in read.table with columns that contain "+" and "-" in R > 2.7

2008-09-01 Thread Tim Beissbarth
Somewhere in between the R-Versions 2.6 and 2.7 the behaviour of the function type.convert and therefore also read.table, read.csv, etc. has changed (see below): In 2.6 and before: > type.convert(c("+", "-", "+")) [1] + - + Levels: + - In 2.7 and later: > type.convert(c("+", "-", "+")) [1] 0 0

[R] [Fwd: Re: how to read multiple lines per case]

2008-09-01 Thread Peter Dalgaard
Hum, looks like I forgot to copy r-help on this. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED])

Re: [R] opening an external file

2008-09-01 Thread Henrique Dallazuanna
See ?browseURL On Mon, Sep 1, 2008 at 5:06 PM, Applejus <[EMAIL PROTECTED]> wrote: > > Hi, > > Is there a way to launch a file from an R command? > To be more precise: I am using windows, and I have an html file in the > working directory of R, and I would like my code in R to automatically > lau

[R] difficulties in pvclust package

2008-09-01 Thread ram basnet
Hi I am a new user of R, and doing clustering analysis (dendrogram). I am quite interested in pvclust package because of facility of AU probability of each cluster. Now, i have a problem when handling large data set. I have data set of 183 rows and 5546 columns, and interested to make clusterin

Re: [R] SQL Primer for R

2008-09-01 Thread Duncan Murdoch
ivo welch wrote: stumped again by SQL... If I have a table named "main" in an SQLite data base, how do I get the names of all its columns? (I have a mysql book that claims the SHOW command does this sort of thing, but it does not seem to work on SQLite.) If you are using RSQLite, then a lot

Re: [R] Text

2008-09-01 Thread Patrick Connolly
On Mon, 01-Sep-2008 at 07:32PM +0200, Dani Valverde wrote: > I've thought about it, but the position should be always the same, > locator() should return me the same value. Here's a function I wrote for this type of job many years ago. The xp and yp paramaters are very similar to ncp units in g

[R] opening an external file

2008-09-01 Thread Applejus
Hi, Is there a way to launch a file from an R command? To be more precise: I am using windows, and I have an html file in the working directory of R, and I would like my code in R to automatically launch the html file in the browser (that is, open the file). Basically, i would like to simulate a

[R] Polychoric and tetrachoric correlation

2008-09-01 Thread Andy Fugard
Hi there, Am I correct to believe that tetrachoric correlation is a special case of polychoric correlation when there are only two levels to the ordered factor? Thus it should be okay to use hetcor from the polycor package to build a matrix of correlations for binary variables? If this is t

Re: [R] how to pass additional parameters to a function called in tapply?

2008-09-01 Thread jim holtman
try: tapply(data,factor-vectors,avg.f, part) On Mon, Sep 1, 2008 at 1:41 PM, Wolfgang Waser <[EMAIL PROTECTED]> wrote: > Hi all, > > the following problem is still beyond my R-knowledge: > > I have one data vector containing the signal from 4 channels that are measured > subsequently and in repea

[R] intercept of 3D line? (Orthogonal regression)

2008-09-01 Thread William Simpson
I posted before recently about fitting 3D data x, y, z where all have error attached. I want to predict z from x and y; something like z = b0 + b1*x + b2*y But multiple regression is not suitable because all of x, y, and z have errors. I have plotted a 3D scatterplot of some data using rgl. I see

[R] email just sent

2008-09-01 Thread ivo welch
please ignore part 1. of course, the cat works. my mistake. I just need to learn how to step up frames, please. regards, /iaw __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://w

[R] debugging

2008-09-01 Thread ivo welch
dear R wizards---I am not sure at what point I owe pennance for asking so many questions. I am now wrangling debugging. I want to write a function assert = function( condition, ... ) { if (!condition) { cat(...); cat("\n"); browser(); } stopifnot(condition); } assert( nrow(ds)==12,

Re: [R] how to read multiple lines per case

2008-09-01 Thread Spencer Graves
Dear Michael: There are doubtless better ways to do this, but the I just got the following ugly hack to work for me: rawDat <- readLines('linthall.dat') (N <- length(rawDat)) N2 <- ((N-1)/2) outDat <- character(N2+1) outDat[1] <- rawDat[1] for(i in 1:N2) outDat[i+1] <- paste(rawDat[(2*

[R] how to pass additional parameters to a function called in tapply?

2008-09-01 Thread Wolfgang Waser
Hi all, the following problem is still beyond my R-knowledge: I have one data vector containing the signal from 4 channels that are measured subsequently and in repeating cycles (with one factor vector for cycle and one for channel identification). To extract the mean of each channel during ea

Re: [R] npc to native coordinates for xyplot

2008-09-01 Thread Deepayan Sarkar
On 9/1/08, Jason Pare <[EMAIL PROTECTED]> wrote: > Hello, > > I am having trouble adding symbols to grid graphics. I am able to > create a lattice scatterplot using xyplot, which has a range from > -15:15 in both the X and Y directions. However, when I try to add > circles and text to this grap

Re: [R] Text

2008-09-01 Thread Dani Valverde
I've thought about it, but the position should be always the same, locator() should return me the same value. Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Cen

Re: [R] Text

2008-09-01 Thread Peter Dalgaard
Dani Valverde wrote: > Hello, > I would like to place some text that should appear in the same > position of the graphic device, preferably outside the plotting area, > regardless the x and y axes limits. How can I do this? I think you can use title() with an adj= argument. Otherwise, try mtext()

[R] Text

2008-09-01 Thread Dani Valverde
Hello, I would like to place some text that should appear in the same position of the graphic device, preferably outside the plotting area, regardless the x and y axes limits. How can I do this? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària

Re: [R] how to read multiple lines per case

2008-09-01 Thread Henrique Dallazuanna
Try this: lines <- read.table(" http://www.math.yorku.ca/SCS/viscollin/data/linthall.dat";, fill = TRUE, header = TRUE) DF <- do.call(rbind, lapply(split(lines, rep(1:(nrow(lines)/2), each = 2)), function(x)cbind(x[1, 1:13], x[2, 1:4]))) names(DF) <- names(lines) On

[R] Transformation of nls() to nlme()

2008-09-01 Thread Dong-hyun Oh
Dear useRs, I would like to transform nls() to nlme(). The script for my estimation with nls() is the following: - R> sapply(demeaned, class) idyrclckgp sic

[R] npc to native coordinates for xyplot

2008-09-01 Thread Jason Pare
Hello, I am having trouble adding symbols to grid graphics. I am able to create a lattice scatterplot using xyplot, which has a range from -15:15 in both the X and Y directions. However, when I try to add circles and text to this graph using grid.circle() and grid.text(), they are offset using the

Re: [R] give all combinations

2008-09-01 Thread Carl Witthoft
I seem to be missing something here: given a set X:{a,b,c,whatever...} the mathematical definition of 'permutation' is the set of all possible sequences of the elements of X. The definition of 'combination' is all elements of 'permutation' which cannot be re-ordered to become a different elemen

[R] how to read multiple lines per case

2008-09-01 Thread Michael Friendly
How can I read a space-delimited file, where the data values for each case are folded before column 80, and so appear on two lines for each case? The first few cases look like this loc type bio H2S sal Eh7 pH buf P K Ca Mg Na Mn Zn Cu NH4 OI DVEG 676 -610 33 -290 5.00 2.34 20.238 1441.67 2150.00

[R] ordered factor and table

2008-09-01 Thread Troels Ring
dear friends - I have an ordered factor, ID, in a data.frame, labs, and make a table, aa <- with(labs,table(val >150,ID)) - and now the order in the table is according to the alphabetic order in ID, and not as I want it. I have tried adding [order(unique(labs$ID)] but it doesn't help. I have R

[R] How remove the small outline around R plots in LaTeX?

2008-09-01 Thread Kenneth Benoit
Dear R List, I noticed something odd when I started saving R graphs in pdf format and including them in LaTeX documents using (e.g.) \includegraphics{mygraphic.pdf}. A very thin dotted border is included in the LaTeX document around the graphic, and I cannot seem to make it go away. I s

Re: [R] linebreak in mathematical anotation?

2008-09-01 Thread Rainer M Krug
On Mon, Sep 1, 2008 at 5:26 PM, Rainer M Krug <[EMAIL PROTECTED]> wrote: > On Mon, Sep 1, 2008 at 5:22 PM, Henrique Dallazuanna <[EMAIL PROTECTED]> > wrote: >> If I understand: >> >> tt <- c(expression(italic('First\nset')), expression(italic('Second\nset')), >> expression(italic('third\nset'))) >

Re: [R] linebreak in mathematical anotation?

2008-09-01 Thread Rainer M Krug
On Mon, Sep 1, 2008 at 5:22 PM, Henrique Dallazuanna <[EMAIL PROTECTED]> wrote: > If I understand: > > tt <- c(expression(italic('First\nset')), expression(italic('Second\nset')), > expression(italic('third\nset'))) > barplot(1:3, names.arg=tt) Thanks a lot - that is exactly what I was looking for

Re: [R] linebreak in mathematical anotation?

2008-09-01 Thread Henrique Dallazuanna
If I understand: tt <- c(expression(italic('First\nset')), expression(italic('Second\nset')), expression(italic('third\nset'))) barplot(1:3, names.arg=tt) On Mon, Sep 1, 2008 at 12:17 PM, Rainer M Krug <[EMAIL PROTECTED]> wrote: > Hi > > I am using mathematical anotation to make the labels in a

[R] linebreak in mathematical anotation?

2008-09-01 Thread Rainer M Krug
Hi I am using mathematical anotation to make the labels in a barplot in italics. as an example (adapted from http://finzi.psych.upenn.edu/R/Rhelp02a/archive/129808.html): tt <- c("italic(First~~set)", "italic(Second~~set)", "italic(third~~set") barplot(1:3, names.arg=parse(text=tt)) But I would

Re: [R] ordered factor and table

2008-09-01 Thread Peter Dalgaard
Troels Ring wrote: > dear friends - I have an ordered factor, ID, in a data.frame, labs, > and make a table, > aa <- with(labs,table(val >150,ID)) - and now the order in the table > is according to the alphabetic order in ID, and not as I want it. I > have tried adding > [order(unique(labs$ID)] but

Re: [R] SQL Primer for R

2008-09-01 Thread ivo welch
wow! the answer seems to be "pragma table_info(main);" thanks, Gabor. __ 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,

Re: [R] another histogram question

2008-09-01 Thread Antje
Henrique Dallazuanna schrieb: You can do this: hh <- lapply(h, head, mh) hh$breaks <- head(h$breaks, mh + 1) class(hh) <- "histogram" plot(hh) Thanks a lot, that's exactly what I need :-) (I did not consider the class...) Putting an xlim could also be an solution but I think this is much more

[R] confidence interval

2008-09-01 Thread Sudheer Joseph
I am a new user of R package and I needed a help regarding plotting confidence limits for FFT ( chisquare based) and spectrum using the monte carlo simulations of background red noise . How do I do it in R can any one help in this issue? sudheer --

Re: [R] another histogram question

2008-09-01 Thread Marianne Promberger
> I tried to shorten my histogram (because the distribution is quite skewed > and I simply don't want to see the long tail but still use the histogram > plot). How can I do something like this? (The example does not work but I > don't know why...) > > data <- rnorm(100) # as example, of course t

Re: [R] another histogram question

2008-09-01 Thread Henrique Dallazuanna
You can do this: hh <- lapply(h, head, mh) hh$breaks <- head(h$breaks, mh + 1) class(hh) <- "histogram" plot(hh) On Mon, Sep 1, 2008 at 10:44 AM, Antje <[EMAIL PROTECTED]> wrote: > Hi there, > > I hope this question is not as stupid as the one before ... > I tried to shorten my histogram (becaus

Re: [R] another histogram question

2008-09-01 Thread ONKELINX, Thierry
Antje, Have a look at ?hist. It seems like you want this: data <- rnorm(100) hist(data, xlim = c(0,6)) HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and F

[R] another histogram question

2008-09-01 Thread Antje
Hi there, I hope this question is not as stupid as the one before ... I tried to shorten my histogram (because the distribution is quite skewed and I simply don't want to see the long tail but still use the histogram plot). How can I do something like this? (The example does not work but I don'

Re: [R] SQL Primer for R

2008-09-01 Thread Steve Revilak
Date: Sun, 31 Aug 2008 21:29:38 -0400 From: "ivo welch" Subject: Re: [R] SQL Primer for R stumped again by SQL... If I have a table named "main" in an SQLite data base, how do I get the names of all its columns? (I have a mysql book that claims the SHOW command does this sort of thing, but it

Re: [R] warning with hist

2008-09-01 Thread Antje
[EMAIL PROTECTED] schrieb: I don't understand the warning I get when executing the following code: x <- rnorm(100) h <- hist(x, plot= FALSE, freq = FALSE) The warning is "Warning message: In hist.default(x, plot = FALSE, freq = FALSE) : argument ‘freq’ is not made use of" The explanation is

[R] Plotting significance level

2008-09-01 Thread Sudheer Joseph
I am a new user of R package and I needed a help regarding plotting confidence limits for FFT ( chisquare based) and spectrum using the monte carlo simulations of background red noise . How do I do it in R can any one help in this issue? sudheer º¤ø,¸¸,ø¤º°`°º¤ø,¸¸,ø¤º°`°º¤ø,¸¸,ø

Re: [R] convenient way to calculate specificity, sensitivity and accuracy from raw data

2008-09-01 Thread Gabor Grothendieck
Some junk got in at the beginning. It should be: Lines <- "video 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Re: [R] convenient way to calculate specificity, sensitivity and accuracy from raw data

2008-09-01 Thread Gabor Grothendieck
Try this: pairs <- data.frame(pred = unlist(DF[2:21]), lab = DF[,22]) library(caret) pred <- factor(pairs$pred) lab <- factor(pairs$lab) table(pred, lab) sensitivity(pred, lab) specificity(pred, lab) Lines <- "video 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 1 1 0 0 0 0 0 0 0 0

Re: [R] play3d() translation

2008-09-01 Thread Duncan Murdoch
On 01/09/2008 7:11 AM, Chibisi Chima-Okereke wrote: Hi All, I would like to be able to use play3d() to translate the view along a surface, and zoom in and out. All the examples in play3d() function description are of rotations. I would also like to know if there is a method of creating a legend

[R] play3d() translation

2008-09-01 Thread Chibisi Chima-Okereke
Hi All, I would like to be able to use play3d() to translate the view along a surface, and zoom in and out. All the examples in play3d() function description are of rotations. I would also like to know if there is a method of creating a legend of for the 3d surface using rgl package. Thanks in a

Re: [R] warning with hist

2008-09-01 Thread Richard . Cotton
> I don't understand the warning I get when executing the following code: > > x <- rnorm(100) > h <- hist(x, plot= FALSE, freq = FALSE) The warning is "Warning message: In hist.default(x, plot = FALSE, freq = FALSE) : argument ‘freq’ is not made use of" The explanation is pretty simple. freq

Re: [R] Avoiding factors and levels in data frames

2008-09-01 Thread Prof Brian Ripley
It's a problem in read.fwf. It should not set a default for as.is, and in R-devel will not. On Mon, 1 Sep 2008, [EMAIL PROTECTED] wrote: On 01-Sep-08 08:20:25, ONKELINX, Thierry wrote: Try to add options(stringsAsFactors = FALSE) in your Rprofile.site (in the etc directory). Using as.is = T

Re: [R] convenient way to calculate specificity, sensitivity and accuracy from raw data

2008-09-01 Thread bartjoosen
Dear Felix, I have no idea about the calculation of your accuracy, sensitivity, etc, but the sums: dat <- read.table(file="clipboard") #read in your data as dataframe dat dat$comp <- apply(dat,1,function(x) sum(x[-c(1,22)]==as.numeric(x[22]))) Good luck Bart drflxms wrote: > > Dear R-collea

Re: [R] convenient way to calculate specificity, sensitivity and accuracy from raw data

2008-09-01 Thread Dimitris Rizopoulos
try something like this: dat <- read.table(textConnection("video 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Re: [R] Avoiding factors and levels in data frames

2008-09-01 Thread Ted Harding
Hi Thierry, On 01-Sep-08 09:45:27, ONKELINX, Thierry wrote: > > Dear Ted, > > I noticed that as.is was set by default in read.fwf. So if the > user sets stringsAsFactor it is passed through ... to read.table. > But I'm not sure how as.is is passed to read.table when onlye > stringsAsFactors is s

Re: [R] Avoiding factors and levels in data frames

2008-09-01 Thread ONKELINX, Thierry
Dear Ted, I noticed that as.is was set by default in read.fwf. So if the user sets stringsAsFactor it is passed through ... to read.table. But I'm not sure how as.is is passed to read.table when onlye stringsAsFactors is set. If it's the default (FALSE) then it might be conflicting with stringsAs

[R] convenient way to calculate specificity, sensitivity and accuracy from raw data

2008-09-01 Thread drflxms
Dear R-colleagues, this is a question from a R-newbie medical doctor: I am evaluating data on inter-observer-reliability in endoscopy. 20 medical doctors judged 42 videos filling out a multiple choice survey for each video. The overall-data is organized in a classical way: observations (items fro

Re: [R] Avoiding factors and levels in data frames

2008-09-01 Thread Ted Harding
On 01-Sep-08 08:20:25, ONKELINX, Thierry wrote: > > Try to add options(stringsAsFactors = FALSE) in your Rprofile.site > (in the etc directory). Using as.is = TRUE seems safer than > stringsAsFactors = FALSE in the read.fwf function. Because as.is > is set to FALSE by default and stringsAsFactors

[R] warning with hist

2008-09-01 Thread Antje
Hello everybody, I don't understand the warning I get when executing the following code: x <- rnorm(100) h <- hist(x, plot= FALSE, freq = FALSE) If I don't use the plot-argument, I don't get a warning... Any explanations for me? Antje __ R-help@r-p

Re: [R] give all combinations

2008-09-01 Thread Robin Hankin
Hi Yuan, Lucien, List. try this: f <- function (...) { args <- list(...) if(length(args)==0){ return(NULL) } if (length(args) == 1) { return(args[[1]]) } if (length(args) > 2) { jj <- do.call("Recall", c(args[-1])) return(do.call("Recall", c(list(ar

Re: [R] tryCatch

2008-09-01 Thread Richard . Cotton
> I am trying to debug a program, and I think tryCatch will help. The > functions involved > process through so many times before I encounter the error, things > are a bit slow to > use debug and browser(). > > I've read the help file and postings on conditions, and am still > having trouble.

Re: [R] Avoiding factors and levels in data frames

2008-09-01 Thread ONKELINX, Thierry
Try to add options(stringsAsFactors = FALSE) in your Rprofile.site (in the etc directory). Using as.is = TRUE seems safer than stringsAsFactors = FALSE in the read.fwf function. Because as.is is set to FALSE by default and stringsAsFactors is not set. HTH, Thierry -

Re: [R] give all combinations

2008-09-01 Thread ONKELINX, Thierry
A more generic solution is allComb <- expand.grid(rep(list(letters[1:5]), 7)) whichComb <- sapply(seq_len(ncol(allComb) - 1), x = allComb, function(i, x){ whichCombination <- sapply(seq(i + 1, ncol(x)), y = x, function(j, y){ as.numeric(y[, i]) <= as.numeric(y[, j]) }) apply(w