[R] Error in solve.default(inf, tol = tol.solve) :

2011-02-04 Thread Marie-Line Glaesener
Hello, I'm trying to run a lagsarlm (maximum likelihood estimation of a spatial lag model) in the spdep library ; but R gives following error message: Error in solve.default(inf, tol = tol.solve) : system is computationally singular: reciprocal condition number = 4.20137e-12 I get

Re: [R] Applying multiple functions to one object

2011-02-04 Thread Karl Ove Hufthammer
Eik Vettorazzi wrote: ... and so the following is from scratch, not from memory. fun-function(x,...){ mthd-list(...) lapply(mthd,function(m) do.call(m,list(x))) } fun(3.14, mode, typeof, class) there is no error-catching for non-existing functions, no naming of results and so on, but

Re: [R] rgenoud for multiple chips: does a more recent special version of snow exist?

2011-02-04 Thread Uwe Ligges
On 03.02.2011 22:06, Dimitri Liakhovitski wrote: Just a small correction: the package snow does install. But once I try to load it: library(snow), I get an error: Error: package 'snow' was built before R 2.10.0: please re-install it Dimitri On Thu, Feb 3, 2011 at 3:57 PM, Dimitri Liakhovitski

Re: [R] Can an xyplot() plus legend be saved as an Enhanced Windows Metafile (EMF)?

2011-02-04 Thread Dennis Murphy
Hi: This is FAQ 7.22 (Why do lattice/trellis graphics not work?) You need to print() the plot, as in print(xyplot(a ~ b)) This problem also extends to ggplot2 graphics. (BTW, the legend statement after xyplot() won't work because the legend() function is meant for use in base graphics. Lattice

Re: [R] hubers function in R MASS library : problem and solution

2011-02-04 Thread Martin Maechler
Feiming Chen feimingc...@yahoo.com on Thu, 3 Feb 2011 12:03:05 -0800 (PST) writes: Hello: I found the hubers function in MASS library is NOT working on the following data: a -

Re: [R] how to learn more from R

2011-02-04 Thread Toby Marthews
Hi Jie Tang, You could try my Friendly Beginners' R Course. Online resource at: http://www.R-project.org/ → Documentation/Other (left-hand panel) → Contributed Documentation (middle of screen) → (scroll down a little) which is a quick intro to what R can do in 14 pages with lots of links for

[R] least significant difference error bars

2011-02-04 Thread Asan Ramzan
Hello R Currently I am using the sciplot function to draw error bars on my bar charts, but this uses standard error of a mean SEM, is there an alternative variant that will allow me to draw error bars using least significant difference.   Than you. [[alternative HTML version

Re: [R] least significant difference error bars

2011-02-04 Thread Jim Lemon
On 02/04/2011 07:14 PM, Asan Ramzan wrote: Hello R Currently I am using the sciplot function to draw error bars on my bar charts, but this uses standard error of a mean SEM, is there an alternative variant that will allow me to draw error bars using least significant difference. Hi Asan, The

Re: [R] how to learn more from R

2011-02-04 Thread Karl Ove Hufthammer
Jie TANG wrote: Now I want to know how much R can do .where can i get some examples or demo resource to study advanced function of R ? Not really what you were thinking of, I guess, but don’t overlook the ‘demo’ function. For example, try ‘demo(graphics)’. Type ‘demo()’ for a list of demos,

[R] Adding axes label to image

2011-02-04 Thread ogbos okike
Dear all, Using the code I got from the link ( http://www.phaget4.org/R/image_matrix.html), I obtained a nice plot that suits me. However, adding axes labels proved difficult for me . I have succeeded in adding a few things to the plot function so as to get what a better plot. Other things work

[R] cancel hclust at bottom of dendrogram plot

2011-02-04 Thread james.foadi
Dear R community, I can't find the way to eliminate the hclust() print at the bottom of the dendrogram plot (plclust). Can this be done? J Dr James Foadi PhD Membrane Protein Laboratory (MPL) Diamond Light Source Ltd Diamond House Harewell Science and Innovation Campus Chilton, Didcot

Re: [R] Finding non-normal distributions per row of data frame?

2011-02-04 Thread Patrizio Frederic
Hi Danny, it sounds to much easer than that. Try y - data.frame(matrix(rnorm(100),10)) nr - ncol(y) test - lapply(y, shapiro.test) sapply(test,function(x)c(x$statistic, x$p.value)) it should perform the required task. Cheers, P On Fri, Feb 4, 2011 at 4:52 AM, DB1984 dannyb...@gmail.com

Re: [R] Adding axes label to image

2011-02-04 Thread Jim Lemon
On 02/04/2011 09:14 PM, ogbos okike wrote: Dear all, Using the code I got from the link ( http://www.phaget4.org/R/image_matrix.html), I obtained a nice plot that suits me. However, adding axes labels proved difficult for me . I have succeeded in adding a few things to the plot function so as to

Re: [R] cancel hclust at bottom of dendrogram plot

2011-02-04 Thread Sarah Goslee
It isn't immediately obvious. but that's the subtitle. You can use plclust(myclusters, sub=Something else) to change it, including plclust(myclusters, sub=) to get rid of it. Sarah On Fri, Feb 4, 2011 at 5:42 AM, james.fo...@diamond.ac.uk wrote: Dear R community, I can't find the way to

[R] GAM quasipoisson in MuMIn

2011-02-04 Thread Karen Moore
Hi, I have a GAM quasipoisson that I'd like to run through MuMIn package - dredge - gettop.models - model.avg However, I'm having no luck with script from an example in MuMIn help file. In MuMIn help they advise include only models with smooth OR linear term (but not both) for each

[R] recode according to specific sequence of characters within a string variable

2011-02-04 Thread D. Alain
Dear R-List, I have a dataframe with one column name.of.report containing character values, e.g. df$name.of.report jeff_2001_teamx teamy_jeff_2002 robert_2002_teamz mary_2002_teamz 2003_mary_teamy ... (i.e. the bit of interest is not always at same position) Now I want to recode the column

Re: [R] GAM quasipoisson in MuMIn

2011-02-04 Thread Gavin Simpson
On Fri, 2011-02-04 at 12:31 +, Karen Moore wrote: Hi, snip / My formula is GAM-gam(Species richness (count) ~ Categorical + Continous + Continous + * s*(Continous ) + Continous : Continous + Continous : Continous, family=quasipoisson, data =) Ok, I'm reasonably certain that that is

[R] shade between two curves

2011-02-04 Thread David Bickel
Is there a function that can shade the region between two arbitrary curves? For example, how can I fill in the area between these two plotted curves? x - 1:10 y - x + rnorm(10) z - x + 10 + rnorm(10) plot(x, y, type = l, ylim = c(0,20)) lines(x, z) I would appreciate any help. David

[R] shade between two curves

2011-02-04 Thread David Bickel
Is there a function that can shade the region between two arbitrary curves? For example, how can I fill in the area between these two plotted curves? x - 1:10 y - x + rnorm(10) z - x + 10 + rnorm(10) plot(x, y, type = l, ylim = c(0,20)) lines(x, z) I would appreciate any help. David

[R] shade between two curves

2011-02-04 Thread David Bickel
Is there a function that can shade the region between two arbitrary curves? For example, how can I fill in the area between these two plotted lines? x - 1:10 y - x + rnorm(10) z - x + 10 + rnorm(10) plot(x, y, type = l, ylim = c(0,20)) lines(x, z) I would appreciate any help. David

[R] Rexcel for mac

2011-02-04 Thread Clayton Coffman
Is there anything out there which replicates the functionality of RExcel on a mac? I have Excel for mac, and would just like something which makes its easy to put sheets into R as a dataframe etc. __ R-help@r-project.org mailing list

[R] uniroot

2011-02-04 Thread dpender
Hi, I am using the uniroot function in order to carry out a bivariate Monte Carlo simulation using the logistics model. I have defined the function as: BV.FV - function(x,y,a,A) (((x^(-a^-1)+y^(-a^-1))^(a-1))*(y^(a-1/a))*(exp(-((1^(-a^-1)+y^(-a^-1))^a)+y^-1)))-A and the procedure is as

[R] Multiple line-plots from one data file using factor

2011-02-04 Thread jonathan byrne
Hi, I'm processing a data file with the following structure: #index time distance 1 10 500 1 15 300 1 23 215 1 34 200 2 5400 2 13 340 2 15 210 3 10 200 3 12 150 3 16 30 etc My intention was to generate line plots for the datapoints using their index to group the elements.

[R] customizing names in an ordination biplot

2011-02-04 Thread swertie
Hello, I would like to change the names of the sites in an ordination biplot (resulting from the function rda in vegan). Can somebody give me some trick? Thank you very much -- View this message in context:

Re: [R] shade between two curves

2011-02-04 Thread Sarah Goslee
polygon() will do it. That's a frequently-discussed topic on this list, so there are plenty of examples in the archives, and also some on the R Graph Gallery. Sarah On Fri, Feb 4, 2011 at 8:03 AM, David Bickel davidbickel.com+rh...@gmail.com wrote: Is there a function that can shade the region

[R] multivariate regression

2011-02-04 Thread Deniz SIGIRLI
How can I run multivariate linear regression in R (I have got 3 dependent variables and only 1 independent variable)? I tried lm function, but it gave different R2 and p values for every dependent variable. I need one R2 and p value for the model.

Re: [R] recode according to specific sequence of characters within a string variable

2011-02-04 Thread Marc Schwartz
On Feb 4, 2011, at 6:32 AM, D. Alain wrote: Dear R-List, I have a dataframe with one column name.of.report containing character values, e.g. df$name.of.report jeff_2001_teamx teamy_jeff_2002 robert_2002_teamz mary_2002_teamz 2003_mary_teamy ... (i.e. the bit of interest is

Re: [R] shade between two curves

2011-02-04 Thread Dirk Eddelbuettel
On 4 February 2011 at 07:55, David Bickel wrote: | Is there a function that can shade the region between two arbitrary | curves? For example, how can I fill in the area between these two | plotted curves? | | x - 1:10 | y - x + rnorm(10) | z - x + 10 + rnorm(10) | plot(x, y, type = l, ylim =

Re: [R] Multiple line-plots from one data file using factor

2011-02-04 Thread baptiste auguie
Hi, It's a piece of cake with ggplot, d - read.table(textConnection(id x y 1 10 500 1 15 300 1 23 215 1 34 200 2 5400 2 13 340 2 15 210 3 10 200 3 12 150 3 16 30), head=TRUE) str(d) library(ggplot2) p - ggplot(d) + geom_path(aes(x,y, group=id)) p ## grouping

Re: [R] Please stop all e-mail

2011-02-04 Thread Gavin Simpson
On Fri, 2011-02-04 at 13:06 +0800, cahyo kristiono wrote: Dear r-help I don't want to receive againevery e-mail about [R] in my address e-mail (cahyo_kristi...@yahoo.com), because it is cause my inbox so full quickly. So I need your help to stop every e-mail about [R] in my address.

Re: [R] multivariate regression

2011-02-04 Thread John Sorkin
Please help us help you. Follow the posting rules and send us a copy of your code and output. John John Sorkin Chief Biostatistics and Informatics Univ. of Maryland School of Medicine Division of Gerontology and Geriatric Medicine jsor...@grecc.umaryland.edu -Original Message- From:

Re: [R] Rexcel for mac

2011-02-04 Thread Marc Schwartz
On Feb 4, 2011, at 4:36 AM, Clayton Coffman wrote: Is there anything out there which replicates the functionality of RExcel on a mac? I have Excel for mac, and would just like something which makes its easy to put sheets into R as a dataframe etc. On OSX, I believe that the two primary

Re: [R] GAM quasipoisson in MuMIn

2011-02-04 Thread Karen Moore
Thanks for that Gavin - yeah you're right that was not my actual model, which is: GAMV2c-gam(VASCSR~ROTATION+ CANCOV +LAreaoldwood+ + s(SOILPH) + CANCOV:LAreaoldwood + CANCOV:SOILPH,family=quasipoisson, data =HIGHBRYOSR) For MMI the script I use, and have used successfully with *exactly* same

Re: [R] Rexcel for mac

2011-02-04 Thread Gabor Grothendieck
On Fri, Feb 4, 2011 at 5:36 AM, Clayton Coffman clayton.coff...@gmail.com wrote: Is there anything out there which replicates the functionality of RExcel on a mac?  I have Excel for mac, and would just like something which makes its easy to put sheets into R as a dataframe etc. See:

Re: [R] recode according to specific sequence of characters within a string variable

2011-02-04 Thread Marc Schwartz
Do you mean something like: with(DF.new, paste(person, year, paste(team, team, sep = ), sep = _)) [1] jeff_2001_teamx jeff_2002_teamy robert_2002_teamz [4] mary_2002_teamz mary_2003_teamy ? See ?paste and ?with for more information, if so. HTH, Marc On Feb 4, 2011, at 7:26 AM, Denis

Re: [R] coxph fails to survfit

2011-02-04 Thread Terry Therneau
I have a model with quant vars only and the error message does not make sense: Could you tell us what version of S and of the survival package you are using? You can get this with sessionInfo(), see the posting guide for details. This would help me identify the issue. I was planning to

Re: [R] get caller's name

2011-02-04 Thread Duncan Murdoch
On 03/02/2011 10:27 AM, Ernest Adrogué wrote: Hi, Suppose a function that checks an object: stop.if.dims- function(x) { if (! is.null(dim(x))) { stop(cannot handle dimensional data) } } This would be used by other functions that can only work with dimensionless objects. The problem

[R] vegan and sweave using xtable

2011-02-04 Thread Olga Lyashevska
Dear all, Using: library(vegan) data(BCI) mod - radfit(BCI[1,]) mod RAD models, family poisson No. of species 93, total abundance 448 par1 par2 par3Deviance AIC BIC Null 39.5261 315.4362 315.4362 Preemption 0.042797

Re: [R] recode according to specific sequence of characters within a string variable

2011-02-04 Thread Denis Kazakiewicz
Dear R people Could you please help I have similar but opposite question How to reshape data from DF.new to DF from example, Mark kindly provided? Thank you Denis On Пят, 2011-02-04 at 07:09 -0600, Marc Schwartz wrote: On Feb 4, 2011, at 6:32 AM, D. Alain wrote: Dear R-List, I have

[R] sensitivity analysis with external simulation model - decoupling in package sensitivity or alternative?

2011-02-04 Thread Rainer M Krug
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi I hava a simulation model, of which I want to do a sensitivity analysis. I have identified a number of input variables and my response variable. What I hava done so far: 1) I created a Latin Hypercube with the lhs package (10.000 simulations) 2)

[R] Adding axes label to image:Fixed

2011-02-04 Thread ogbos okike
Dear Jim, One touch!! Thank you very much Best regards Ogbos On 4 February 2011 13:47, Jim Lemon j...@bitwrit.com.au wrote: On 02/04/2011 09:14 PM, ogbos okike wrote: Dear all, Using the code I got from the link ( http://www.phaget4.org/R/image_matrix.html), I obtained a nice plot

Re: [R] Applying multiple functions to one object

2011-02-04 Thread jctoll
On Wed, Feb 2, 2011 at 7:59 AM, Karl Ove Hufthammer k...@huftis.org wrote: Dear list members, I recall seeing a convenience function for applying multiple functions to one object (i.e., almost the opposite of 'mapply’) somewhere. Example: If the function was named ’fun’ the output of  

[R] Importing dates from SPSS file

2011-02-04 Thread dunner
Hello all, kind regards, I have imported a data.frame from SPSS using foreign:read.spss but unfortunately it is reading dates in a way neither R nor myself can understand. book$DATE [1] 13502246400 13443321600 13477795200 13472956800 13501728000 13445395200 13501382400 13502851200 13444185600

Re: [R] Importing dates from SPSS file

2011-02-04 Thread jim holtman
What do the dates look like in the original file? On Fri, Feb 4, 2011 at 9:47 AM, dunner ross.du...@tcd.ie wrote: Hello all, kind regards, I have imported a data.frame from SPSS using foreign:read.spss but unfortunately it is reading dates in a way neither R nor myself can understand.

Re: [R] coxph fails to survfit

2011-02-04 Thread Bond, Stephen
Responding to T. Therneau: sessionInfo() R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United

Re: [R] Importing dates from SPSS file

2011-02-04 Thread Gabor Grothendieck
On Fri, Feb 4, 2011 at 9:47 AM, dunner ross.du...@tcd.ie wrote: Hello all, kind regards, I have imported a data.frame from SPSS using foreign:read.spss but unfortunately it is reading dates in a way neither R nor myself can understand. book$DATE  [1] 13502246400 13443321600 13477795200

Re: [R] Importing dates from SPSS file

2011-02-04 Thread dunner
as.POSIXlt(book$DATE, origin=1582/10/14) works. The Gregorian calendar was the kicker, thanks to ggrothendieck at gmail.com Ross -- View this message in context: http://r.789695.n4.nabble.com/Importing-dates-from-SPSS-file-tp3260293p3260329.html Sent from the R help mailing list archive at

Re: [R] vegan and sweave using xtable

2011-02-04 Thread Ista Zahn
Hi Olga, Here is how I would approach this problem. I hope it is instructive. library(vegan) data(BCI) mod - radfit(BCI[1,]) class(mod) #find out what mod is methods(class=radfit) #find out what methods are available for objects of this class. Nothing looks promising, so define a summary method

Re: [R] vegan and sweave using xtable

2011-02-04 Thread Olga Lyashevska
Thanks Ista, Very instructive and works like a charm! Cheers! Olga __ 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] GAM quasipoisson in MuMIn - SOLVED

2011-02-04 Thread Karen Moore
Hi, Got my issues sorted. Error message solved: I heard from the guy who developed MuMIn and his suggestion worked. As for the error you get, it seems you are running an old version of MuMIn. Please update the package first. I did (I was only 1 version behind in both R and in MuMIn) and error

[R] Layout control from RCytoscape

2011-02-04 Thread Fahim M
Hi I have a list of nodes and edges. I want to draw a graph from two different direction left and right. I am drawing the required graph which is growing from left. Similar will be the case that will grow from right. the one that grows from right may have few nodes present in left subtree.

Re: [R] Estimation and Forecast of Seasonal Component

2011-02-04 Thread Giovanni Petris
I would probably use a Dynamic Linear Model, combining seasonal component and regression. See package dlm and its vignette for examples. HTH, Giovanni On Tue, 2011-02-01 at 11:01 +, Paolo Rossi wrote: Hi list, I would like to estimate and forecast the seasonal component of a series.

Re: [R] My own distribution in survreg function

2011-02-04 Thread Terry Therneau
--- begin included message I'm trying to do some analysis using survreg function. I need to implement there my own distribution with density: lambda*exp(-lambda*y), where y = a1/(1+exp(-a2*x)). a1, a2 are unknown parameters and x 0. --- end inclusion -- The survreg

[R] lapply, strsplit, and list elements

2011-02-04 Thread Dick Harray
Hi there, I have a problem about lapply, strsplit, and accessing list elements, which I don't understand or cannot solve: I have e.g. a character vector with three elements: x = c(349/077,349/074,349/100,349/117, 340/384.2,340/513,367/139,455/128,D13/168,

Re: [R] recode according to specific sequence of characters within a string variable

2011-02-04 Thread David Winsemius
On Feb 4, 2011, at 8:26 AM, Denis Kazakiewicz wrote: Dear R people Could you please help I have similar but opposite question How to reshape data from DF.new to DF from example, Mark kindly provided? Well, I don't think you want a random order, right? If what you are asking is for a

[R] environment: 0x000000000734f888 in object of class formula

2011-02-04 Thread Aviad Klein
# Hi all, # I've made a function to make a formula out of a data.frame without columns which contain a constant value. # The function which.constant returns the indices of colums with constant values: which.constant - function(data.frame) { # counts the number of columns in a data.frame which

Re: [R] lapply, strsplit, and list elements

2011-02-04 Thread William Dunlap
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Dick Harray Sent: Friday, February 04, 2011 7:37 AM To: r-help@r-project.org Subject: [R] lapply, strsplit, and list elements Hi there, I have a problem about lapply,

Re: [R] uniroot

2011-02-04 Thread Berend Hasselman
dpender wrote: Hi, I am using the uniroot function in order to carry out a bivariate Monte Carlo simulation using the logistics model. I have defined the function as: BV.FV - function(x,y,a,A) (((x^(-a^-1)+y^(-a^-1))^(a-1))*(y^(a-1/a))*(exp(-((1^(-a^-1)+y^(-a^-1))^a)+y^-1)))-A

Re: [R] get caller's name

2011-02-04 Thread William Dunlap
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Duncan Murdoch Sent: Friday, February 04, 2011 6:03 AM To: Ernest Adrogué Cc: r-h...@stat.math.ethz.ch Subject: Re: [R] get caller's name On 03/02/2011 10:27 AM, Ernest

Re: [R] environment: 0x000000000734f888 in object of class formula

2011-02-04 Thread Prof Brian Ripley
Did you look at the help? ?formula has a whole section about why formulas have environments and what they do. On Fri, 4 Feb 2011, Aviad Klein wrote: # Hi all, # I've made a function to make a formula out of a data.frame without columns which contain a constant value. # The function

[R] (no subject)

2011-02-04 Thread Yan Jiao
Dear R users? I want to know how to use strata in survival analysis, I want to combine multiple dataset: Coxph(Surv(merged.time.v, merged.event.v)~merged.score+ strata(dataset.v)) So merged.time.v and merged.event.v are from multiple datasets. How should I define dataset.v here?

Re: [R] Finding non-normal distributions per row of data frame?

2011-02-04 Thread Greg Snow
I get a different set of errors than you do (what version of R are you using?). Patrizio showed one way to do what you want. But, what is it that you are really trying to accomplish? What do you think the result of 20,000 normality tests (each of which may not be answering the real question

[R] How to get the variables used in stepwise logistic regression?

2011-02-04 Thread Soyeon Kim
Dear All, I used glm and then used step function for stepwise regression. Now, I want to store the variables used in the stepwise regression. The code is the following. m_logistic - glm(y ~ . + M1:T + M2:T + M3:T+ M4:T +M5:T, family=binomial(logit), data = data) step_glm - step(m_logistic)

Re: [R] How to get the variables used in stepwise logistic regression?

2011-02-04 Thread David Winsemius
On Feb 4, 2011, at 11:56 AM, Soyeon Kim wrote: Dear All, I used glm and then used step function for stepwise regression. Now, I want to store the variables used in the stepwise regression. I am not sure that what you ask here is actually what you eventually ask and will limit my answer to

Re: [R] How to get the variables used in stepwise logistic regression?

2011-02-04 Thread Soyeon Kim
Thank you. This is what I want. I need to study about attr :). Soyeon On Fri, Feb 4, 2011 at 11:07 AM, David Winsemius dwinsem...@comcast.net wrote: On Feb 4, 2011, at 11:56 AM, Soyeon Kim wrote: Dear All, I used glm and then used step function for stepwise regression. Now, I want to

Re: [R] recode according to specific sequence of characters within a string variable

2011-02-04 Thread Greg Snow
So you want to combine multiple columns back into a single column with the strings pasted together? If that is correct then look at the paste and sprintf functions (use one or the other, not both). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare

Re: [R] recode according to specific sequence of characters within a string variable

2011-02-04 Thread Greg Snow
You can do this with regular expressions, since you want to extract specific values from the string I would suggest learning about the gsubfn package, it is a bit easier with gsubfn than with the other matching tools. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain

[R] dataframes from a function

2011-02-04 Thread chris20
Hi, I'm trying to create a function to return three dataframes for later use in a graphic so I want the return from the function to give me dataframes and with unique names relating to the variable they are based on. For example. sub-c(6-1a,6-1a,6-1a,9-2b,9-2b,9-2b,7c,7c,7c)

Re: [R] exact logistic regression

2011-02-04 Thread Denis Kazakiewicz
Dear Łukasz Thank you very much for information Dear R people could you please help please with following questions Sorry for my silly questions, because I am not a mathematician. 1. Is elrm() works similar as exact regression in SAS or Stata? After double check in Stata and R some results from

[R] Apply parameters to a function from a list

2011-02-04 Thread Florian Burkart
Hey, this may be a simple question, but I am struggling to apply a list of parameters to a function. Say I have the following function: test-function(a=1,b=2,c=3,d=4){a+b+c+d} And the following list: point-list(a=3,d=2) Is there a way I can evaluate function test at point? (Apart from

[R] RODBC : how to avoid truncatig big integer when using sqlsave

2011-02-04 Thread PtitBleu
Hello, I'm still trying to modify my script in order to use RODBC instead of RMySQL (no more ready-to-use package for windows). My new problem is the following one (not seen with RMySQL): I'd like to copy a data.frame to a mysql table. One column is a numeric one with big integer like :

Re: [R] Applying multiple functions to one object

2011-02-04 Thread Den
'Aggregate multiple functions into a single function. Combine multiple functions to a single function returning a named vector of outputs' This is a short description of each() function from plyr package Here is an example from help each(min, max)(1:10) Hope this helps Regards Denis У

Re: [R] Finding non-normal distributions per row of data frame?

2011-02-04 Thread DB1984
Thanks for the feedback Patrizio - but your function is performing the shapiro.test on columns instead of rows... I tried: nt-data.frame(#a dataframe with 6 columns and 9 rows) nr - nrow(nt) test - apply(nt, nt[1:nr,], shapiro.test) Error in ds[-MARGIN] : invalid subscript type 'list'

[R] MSBVAR and hc.forecast

2011-02-04 Thread david ostrowski
attempting to do multivariate modelling in R with known future conditions (in this case variable 'b') using MSBVAR and hc.forecast. The sample code (a paired down representation) does not give anywhere near the expected results - I am assuming that a forecast 8 steps out would approximate 'a' as

[R] exact logistic regression

2011-02-04 Thread Den
Hate to say that, but it looks like Stata is way above R, considering exact logistic regression. To use elrm() I have to aggregate my data,which is really time consuming when I look for the way out through many variables. But the worst thing is that I am not not sure if I can trust to p-values in

Re: [R] always about positive definite matrix

2011-02-04 Thread Mike Miller
I'm also not an expert on this topic. I just wanted to list a couple of ways that non-PD matrices might arise. I'll just add now a couple of pointers: First, I believe the term semipositive definite is considered ambiguous because in some literature it means that the matrix the smallest

Re: [R] get caller's name

2011-02-04 Thread Luke Tierney
The options showWarnCalls and showErrorCalls may also help -- they can be use do enable automatic printing of a call stack summary. From ?options: ‘showWarnCalls’, ‘showErrorCalls’: a logical. Should warning and error messages show a summary of the call stack? By default

Re: [R] pass nrow(x) to dots in function(x){plot(x,...)}

2011-02-04 Thread rex.dwyer
Hi Marianne, The quick-and-dirty solution is to add one character and make ns global: ns - nrow(x) Poor practice, but OK temporarily if you're just debugging. This is an issue of scope. You are assuming dynamic scope, whereas R uses static scope. 'ns' was not defined when you said

Re: [R] always about positive definite matrix

2011-02-04 Thread spencerg
1. Martin Maechler's comments should be taken as replacements for anything I wrote where appropriate. Any apparent conflict is a result of his superior knowledge. 2. 'eigen' returns the eigenvalue decomposition assuming the matrix is symmetric, ignoring anything in

Re: [R] Finding non-normal distributions per row of data frame?

2011-02-04 Thread David Winsemius
On Feb 4, 2011, at 10:48 AM, DB1984 wrote: Thanks for the feedback Patrizio - but your function is performing the shapiro.test on columns instead of rows... I tried: nt-data.frame(#a dataframe with 6 columns and 9 rows) nr - nrow(nt) test - apply(nt, nt[1:nr,], shapiro.test) Error in

Re: [R] always about positive definite matrix

2011-02-04 Thread Spencer Graves
1. Martin Maechler's comments should be taken as replacements for anything I wrote where appropriate. Any apparent conflict is a result of his superior knowledge. 2. 'eigen' returns the eigenvalue decomposition assuming the matrix is symmetric, ignoring anything in

Re: [R] always about positive definite matrix

2011-02-04 Thread Mike Miller
(Apologies to the cc-list: I'm resending from a different address because I didn't realize it was going to r-help.) I'm also not an expert on this topic. I just wanted to list a couple of ways that non-PD matrices might arise. I'll just add now a couple of pointers: First, I believe the

[R] Suppress only Z axis tick marks and numbers in wireframe statement

2011-02-04 Thread Matthew A. H. Walters
I actually have several questions revolving around the generation of wireframe plots. The most pressing is that which is described by the subject line. I am trying to produce a figure with x, y, and z labels, but only tick marks on the x, and y axes. I have supplied sample code below

[R] spatial autocorrelation for data that are temporally pseudoreplicated

2011-02-04 Thread Gagic, Vasna
Dear all, I collected my data from the different agricultural fields every week over a period of a month. how can I test for spatial autocorrelation in R with data that are temporally pseudoreplicated? I used lme with correlation=corCompSymm(form=~Date) to model temporal pseudoreplication.

Re: [R] Apply parameters to a function from a list

2011-02-04 Thread Henrique Dallazuanna
Try this: do.call(test, point) On Fri, Feb 4, 2011 at 12:35 PM, Florian Burkart florian.burk...@whu.eduwrote: Hey, this may be a simple question, but I am struggling to apply a list of parameters to a function. Say I have the following function: test-function(a=1,b=2,c=3,d=4){a+b+c+d}

Re: [R] dataframes from a function

2011-02-04 Thread Phil Spector
Chris - You can solve your problem by removing the print statements and replacing them with answer = list(org.plot[org.plot$sub %in% ex.plot,], new.pl[new.pl$yar %in% 1991,], new.pl[new.pl$yar %in% 1993,]) prefix = sub('-','.',ex.plot) names(answer) =

Re: [R] lapply, strsplit, and list elements

2011-02-04 Thread Greg Snow
Try this: x - c(349/077,349/074,349/100,349/117, + 340/384.2,340/513,367/139,455/128,D13/168, + 600/437,128/903,128/904) library(gsubfn) out - strapply(x, '([0-9]+)(?=/)') out [[1]] [1] 349 349 349 349 [[2]] [1] 340 340 367 455 13 [[3]] [1] 600 128 128 The strapply

Re: [R] Apply parameters to a function from a list

2011-02-04 Thread Greg Snow
Try: do.call(test,point) -- 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-bounces@r- project.org] On Behalf Of Florian Burkart Sent: Friday,

Re: [R] Apply parameters to a function from a list

2011-02-04 Thread Florian Burkart
Of course. Thanks. On 04/02/2011 18:32, Greg Snow wrote: Try: do.call(test,point) __ 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

[R] switching y-axis to x-axis for qqmath

2011-02-04 Thread Anderson, Chris
This is the qqmath example from the lattice package. I added the scales to the example. I would like to switch the axis and not sure how? Meaning I would like the height on the x-axis and the probability on the y-axis. Will you show me the correct syntax for this switch thanks. qqmath(~

Re: [R] Finding non-normal distributions per row of data frame?

2011-02-04 Thread DB1984
Thanks David - but '1' (if I understood correctly) returns the same value for each row, which I took to be an error. nt V1V2V3V4V5V6 1 24.71 23.56 24.71 23.56 24.71 23.56 2 25.64 25.06 25.64 25.06 25.64 25.06 3 21.29 20.87 21.29 20.87 21.29 20.87 4 25.92 26.92 25.92

Re: [R] lapply, strsplit, and list elements

2011-02-04 Thread Henrique Dallazuanna
Try this: strsplit(x, /\\d+\\.\\d+,|/\\d+,|/\\d+) On Fri, Feb 4, 2011 at 1:37 PM, Dick Harray tomdhar...@gmail.com wrote: Hi there, I have a problem about lapply, strsplit, and accessing list elements, which I don't understand or cannot solve: I have e.g. a character vector with three

Re: [R] Finding non-normal distributions per row of data frame?

2011-02-04 Thread David Winsemius
On Feb 4, 2011, at 1:41 PM, DB1984 wrote: Thanks David - but '1' (if I understood correctly) returns the same value for each row, which I took to be an error. And exactly what were you expecting with that data? nt V1V2V3V4V5V6 1 24.71 23.56 24.71 23.56 24.71

Re: [R] Finding non-normal distributions per row of data frame?

2011-02-04 Thread DB1984
Hi Greg, In addition to the reply above, to address your questions - I fully appreciate that my understanding of the code is basic - this is my first attempt at putting this together... My starting point is a data frame with numeric and text columns, but I can cut columns to make a fully

[R] Avoiding two loops

2011-02-04 Thread sudhir cr
Hello, I have a R code for doing convolution of two functions: convolveSlow - function(x, y) { nx - length(x); ny - length(y) xy - numeric(nx + ny - 1) for(i in seq(length = nx)) { xi - x[[i]] for(j in seq(length = ny)) { ij - i+j-1 xy[[ij]] -

Re: [R] Avoiding two loops

2011-02-04 Thread Dirk Eddelbuettel
On 4 February 2011 at 14:03, sudhir cr wrote: | Hello, | | I have a R code for doing convolution of two functions: | | convolveSlow - function(x, y) { | nx - length(x); ny - length(y) | xy - numeric(nx + ny - 1) | for(i in seq(length = nx)) { | xi - x[[i]] | for(j in

[R] GWAF package: lme.batch.imputed(): object 'kmat' not found

2011-02-04 Thread Jim Moon
Hello, All, GWAF 1.2 R.Version() is below. system(lme.batch.imputed( phenfile = 'phenfile.csv', genfile = 'CARe_imputed_release.0.fhsR.gz', pedfile='pedfile.csv', phen='phen1', covar=c('covar1','covar2'), kinmat='imputed_fhs.kinship.RData', outfile='imputed.FHS.IBC.GWAF.LME.output.0.txt' ))

Re: [R] lapply, strsplit, and list elements

2011-02-04 Thread Gabor Grothendieck
On Fri, Feb 4, 2011 at 1:27 PM, Greg Snow greg.s...@imail.org wrote: Try this: x - c(349/077,349/074,349/100,349/117, +          340/384.2,340/513,367/139,455/128,D13/168, +          600/437,128/903,128/904) library(gsubfn) out - strapply(x, '([0-9]+)(?=/)') out [[1]] [1] 349 349 349

Re: [R] Finding non-normal distributions per row of data frame?

2011-02-04 Thread Peter Ehlers
On 2011-02-04 11:00, DB1984 wrote: Hi Greg, In addition to the reply above, to address your questions - I fully appreciate that my understanding of the code is basic - this is my first attempt at putting this together... My starting point is a data frame with numeric and text columns, but I

Re: [R] Finding non-normal distributions per row of data frame?

2011-02-04 Thread DB1984
Yes, that was dumb - I got that... -- View this message in context: http://r.789695.n4.nabble.com/Finding-non-normal-distributions-per-row-of-data-frame-tp3259439p3260843.html Sent from the R help mailing list archive at Nabble.com. __

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