Re: [R] Error: unexpected '' in when modifying existing functions

2012-01-14 Thread Rui Esteves
Thank you both. 1) As Duncan said, if I leave environment: namespace:stats out, it will not work since it is using .C and .Fortran functions that kmeans calls. I 2) don`t know how to use the as.environment() (I did not understood by reading the help). 3) Setting environment(kmeansnew) -

Re: [R] Problems with plotCI

2012-01-14 Thread Martin Maechler
JL == Jim Lemon j...@bitwrit.com.au on Sat, 14 Jan 2012 18:52:50 +1100 writes: JL On 01/14/2012 06:35 PM, Jim Lemon wrote: On 01/13/2012 11:09 PM, Lasse DSR-mail wrote: Got problems with plotCI (plotrix) ... JL Whoops - looks like the R help list doesn't accept R JL

Re: [R] plotting regression line in with lattice

2012-01-14 Thread matteo dossena
Weidong, thanks for the suggestion, but i also need to show to which trt each point belongs to. I had my problem solved by the way. I've been told to add a group subscript object within the panel function, and than use panel.points to plot the original data as data points and panel.lines to

Re: [R] Problems with plotCI

2012-01-14 Thread Jim Lemon
On 01/14/2012 09:22 PM, Martin Maechler wrote: JL == Jim Lemonj...@bitwrit.com.au on Sat, 14 Jan 2012 18:52:50 +1100 writes: JL On 01/14/2012 06:35 PM, Jim Lemon wrote: On 01/13/2012 11:09 PM, Lasse DSR-mail wrote: Got problems with plotCI (plotrix) ... JL

Re: [R] Converting .Rout file to pdf via Sweave automatically

2012-01-14 Thread Duncan Murdoch
On 12-01-13 10:21 PM, Parag Magunia wrote: The R documentation mentions to create a PDF or DVI file from an Rnw template, the Sweave command can be used used. However, is there any way to go from a .Rout file straight to pdf with an Rnw template ? What I'm trying to avoid is adding the

[R] Determining if an object name does not exist

2012-01-14 Thread Ajay Askoolum
Is there a way to tell whether an object name 1. is valid 2. is not going to cause a collision with an existing object by the same name? Thanks. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

Re: [R] Error: unexpected '' in when modifying existing functions

2012-01-14 Thread Duncan Murdoch
On 12-01-14 3:58 AM, Rui Esteves wrote: Thank you both. 1) As Duncan said, if I leaveenvironment: namespace:stats out, it will not work since it is using .C and .Fortran functions that kmeans calls. I 2) don`t know how to use the as.environment() (I did not understood by reading the help). 3)

Re: [R] Determining if an object name does not exist

2012-01-14 Thread Duncan Murdoch
On 12-01-14 5:47 AM, Ajay Askoolum wrote: Is there a way to tell whether an object name 1. is valid 2. is not going to cause a collision with an existing object by the same name? For 1, you could put your names in a character vector x, then check whether x and make.names(x) are identical; if

Re: [R] Error: unexpected '' in when modifying existing functions

2012-01-14 Thread Rui Esteves
All of these tries leave to the same result: 1) First I defined kmeansnew with the content of kmeans, but leaving the environment: namespace:stats out. Then I run environment(kmeansnew)- environment(stats::kmeans) at the command line. 2) kmeansnew - kmeans() { environment(kmeansnew)-

Re: [R] multidimensional array calculation

2012-01-14 Thread Johannes Radinger
Dear Jean, Thank you, expand.grid was the function I needed. /johannes See ?expand.grid For example, df - expand.grid(L=L, AR=AR, SO=SO, T=T) df$y - fun(df$L, df$AR, df$SO, df$T) Jean Johannes Radinger wrote on 01/13/2012 12:28:46 PM: Hello,

Re: [R] fUtilities removed -- use fBasics

2012-01-14 Thread Martin Maechler
David Winsemius dwinsem...@comcast.net on Fri, 13 Jan 2012 13:52:57 -0500 writes: On Jan 13, 2012, at 12:33 PM, Dominic Comtois wrote: When setting up my new machine, I had the surprise to see that Package 'fUtilities' was removed from the CRAN repository.

Re: [R] Error: unexpected '' in when modifying existing functions

2012-01-14 Thread Duncan Murdoch
On 12-01-14 6:08 AM, Rui Esteves wrote: All of these tries leave to the same result: 1) First I defined kmeansnew with the content of kmeans, but leaving theenvironment: namespace:stats out. Then I run environment(kmeansnew)- environment(stats::kmeans) at the command line. 2) kmeansnew-

[R] Date/time

2012-01-14 Thread claire5
Hey guys, I have been trying for some time to nicely plot some of my data, I have around 1800 values for some light intensity, taken every hour of the day over almost 2 months. My data file looks like: DateTime. GMT.02.00 Intensity 106.10.11 11:00:00AM x 206.10.11

Re: [R] The Future of R | API to Public Databases

2012-01-14 Thread Benjamin Weber
Spencer I highly appreciate your input. What we need is a standard for statistics. That may reinvent the way how we see data. The recent crisis is the best proof that we are lost in our own generated information overload. The traditional approach is not working anymore. Finding the right members

Re: [R] tm package, custom reader

2012-01-14 Thread Milan Bouchet-Valat
Le vendredi 13 janvier 2012 à 09:00 -0800, pl.r...@gmail.com a écrit : I need help with creating custom xml reader for use with the tm package. The objective is to crate a corpus for analysis. Files that I'm working with come from solr and are in a funky XML format never the less I'm able to

Re: [R] Date/time

2012-01-14 Thread R. Michael Weylandt
What exactly is your problem? People quite like the zoo package for handling and plotting time series: perhaps that will work for you? Michael On Sat, Jan 14, 2012 at 4:35 AM, claire5 claire.moran...@free.fr wrote: Hey guys, I have been trying for some time to nicely plot some of my data, I

Re: [R] Date/time

2012-01-14 Thread claire5
Well, I am not sure how to use the zoo package to be honest. I am trying to plot all 1800 data in the same graph but of course it looks super messy. And R does not really recognize the time data input. so i just want to plot the time series kind of. The problem is that the x value is date and time

Re: [R] The Future of R | API to Public Databases

2012-01-14 Thread Jason Edgecombe
Web services are only part of the problem. In essence, there are at least two facets: 1. downloading the data using some protocol 2. mapping the data to a common model Having #1 makes the import/download easier, but it really becomes useful when both are included. I think #2 is the harder

Re: [R] Date/time

2012-01-14 Thread Gabor Grothendieck
On Sat, Jan 14, 2012 at 4:35 AM, claire5 claire.moran...@free.fr wrote: I have been trying for some time to nicely plot some of my data, I have around 1800 values for some light intensity, taken every hour of the day over almost 2 months. My data file looks like:     Date    Time. GMT.02.00

[R] HOW To CHANGE THE TYPE OF NUMBER IN THE X-Y AXIS in the (barplot) GRAPH?

2012-01-14 Thread Yakamu Yakamu
Dear all, I have troubles where i have to make all the fonts in my grpahs into TImes New Roman, I know now how to change fonts for the x-axis-y-axis labels (from http://www.statmethods.net/advgraphs/parameters.html )   but HOW CAN I ALSO CHANGE THE TYPE OF FONT FOR THE NUMBER INTO Times New

Re: [R] Change state names to abbreviations in an irregular list of names, abbreviations, null values, and foreign provinces

2012-01-14 Thread Ben Bolker
David Kikuchi dkikuchi at email.unc.edu writes: I'm trying to create maps of reptile abundance in different states counties using data from Herp.net, which provides lists of specimens with the places that they were found. First I would like to parse the list by state using 2-letter

Re: [R] Quantiles in boxplot‏

2012-01-14 Thread peter dalgaard
On Jan 14, 2012, at 16:07 , René Brinkhuis wrote: Based on your information I created a custom function for calculating the first and third quartile according to the 'boxplot logic'. A more compact (though not as readable) version is afforded by stats:::fivenum. A convenient description

Re: [R] The Future of R | API to Public Databases

2012-01-14 Thread Mike Marchywka
LOL, I remember posting about this in the past. The US gov agencies vary but mostare quite good. The big problem appears to be people who push proprietary orcommercial standards for which only one effective source exists. Some formats,like Excel and PDF come to mind and there is a

Re: [R] Averaging within a range of values

2012-01-14 Thread Gabor Grothendieck
On Fri, Jan 13, 2012 at 6:34 AM, doggysaywhat chwh...@ucsd.edu wrote: Hello all. I have two data frames. Group       Start          End G1                     200               700 G2                     500               1000 G3                     2000        3000 G4                    

Re: [R] The Future of R | API to Public Databases

2012-01-14 Thread Benjamin Weber
Mike We see that the publishers are aware of the problem. They don't think that the raw data is the usable for the user. Consequently they recognizing this fact with the proprietary formats. Yes, they resign in the information overload. That's pathetic. It is not a question of *which* data

Re: [R] The Future of R | API to Public Databases

2012-01-14 Thread Joshua Wiley
I have been following this thread, but there are many aspects of it which are unclear to me. Who are the publishers? Who are the users? What is the problem? I have a vauge sense for some of these, but it seems to me like one valuable starting place would be creating a document that clarifies

[R] How can I change font type in graph (including all the text in lagend, and the number in x-y axis)

2012-01-14 Thread Yakamu Yakamu
Dear all, I would like to make a survival analysis graph line with all fonts in Times New Roman, Including all the numbers in x-y axis and the legend explanation. I know how to change fonts for the x-y axis labels (from http://www.statmethods.net/advgraphs/parameters.html )  and this is what

Re: [R] fUtilities removed -- use fBasics

2012-01-14 Thread Dominic Comtois
Thank you for your prompt and useful replies. I will be using fBasics from now on. Regards, Dominic Comtois, Montréal -Message d'origine- De : Martin Maechler [mailto:maech...@stat.math.ethz.ch] Envoyé : 14 janvier 2012 06:39 À : David Winsemius Cc : Dominic Comtois;

[R] metafor: weights computation in Mantel-Haenszel method

2012-01-14 Thread Ignacio López De Ullibarri Galparsoro
Dear R users, In metafor 1.6-0, the Mantel-Haenszel method is implemented by the rma.mh() function. I have observed that the sum of the weights computed by weights(x) doesn't add to 100% when x is an object of class rma.mh. The consequences of this fact can be clearly seen when a forest

Re: [R] Nabble? Was Re: function to replace values doesn't work on vectors

2012-01-14 Thread Duncan Murdoch
On 12-01-13 11:48 AM, Sarah Goslee wrote: ... I hope that it was a momentary glitch; greater disagreement between Nabble and the email list will cause all sorts of fun. If the interface, whatever it is, starts stripping out code? I'll have to quit answering Nabble queries entirely. You know,

Re: [R] tm package, custom reader

2012-01-14 Thread Andy Adamiec
On Sat, Jan 14, 2012 at 12:41 PM, Milan Bouchet-Valat nalimi...@club.frwrote: Le samedi 14 janvier 2012 à 12:24 -0600, Andy Adamiec a écrit : Hi Milan, The xml solr files are not in a typical format, here is an example http://www.omegahat.org/RSXML/solr.xml I'm not sure how to parse

Re: [R] tm package, custom reader

2012-01-14 Thread Andy Adamiec
On Sat, Jan 14, 2012 at 12:41 PM, Milan Bouchet-Valat nalimi...@club.frwrote: Le samedi 14 janvier 2012 à 12:24 -0600, Andy Adamiec a écrit : Hi Milan, The xml solr files are not in a typical format, here is an example http://www.omegahat.org/RSXML/solr.xml I'm not sure how to parse

Re: [R] How can I change font type in graph (including all the text in lagend, and the number in x-y axis)

2012-01-14 Thread David Winsemius
On Jan 14, 2012, at 2:19 PM, Yakamu Yakamu wrote: Dear all, I would like to make a survival analysis graph line with all fonts in Times New Roman, Including all the numbers in x-y axis and the legend explanation. I know how to change fonts for the x-y axis labels (from

Re: [R] The Future of R | API to Public Databases

2012-01-14 Thread Paul Gilbert
The situation for this kind of interface is much more advanced (for economic time series data) than has been suggested in other postings. Several of the organizations you mention support SDMX and I believe there is a working R interface to SDMX which has not yet been made public. A more

Re: [R] HOW To CHANGE THE TYPE OF NUMBER IN THE X-Y AXIS in the (barplot) GRAPH?

2012-01-14 Thread Jim Lemon
On 01/15/2012 02:16 AM, Yakamu Yakamu wrote: Dear all, I have troubles where i have to make all the fonts in my grpahs into TImes New Roman, I know now how to change fonts for the x-axis-y-axis labels (from http://www.statmethods.net/advgraphs/parameters.html ) but HOW CAN I ALSO CHANGE THE

Re: [R] simulating stable VAR process

2012-01-14 Thread John C Frain
Mark, statquant2 As I understand the question it is not to test if a VAR is stable but how to construct a VAR that is stable and automatically satisfies the condition Mark has taken from Lutkohl. The algorithm that I have set out will automatically satisfy that condition.The matrix that should be

Re: [R] par.plot() for repeated measurements

2012-01-14 Thread Jonas Stein
I am using the package gamlss in R to plot repeated measurements. The command I am using is par.plot(). It works great except one thing about the label of the axises. I tried to label both x and y axises using ylab and xlab options. But the plot only gives variable variables. The labels did

Re: [R] The Future of R | API to Public Databases

2012-01-14 Thread Jason Edgecombe
HI, Happy to oblidge: Background: All data is dirty to some degree. A large portion of the time spent in doing data analysis is spent doing data cleaning (removing invalid data, transforming data columns into something useful). When data from multiple sources are used, then some time must be

Re: [R] simulating stable VAR process

2012-01-14 Thread John C Frain
Mark This should be reasonably straightforward. In the simplest case you wih to draw a random complex number in the unit circle. This is best done in polar coordinates. If r is a random mumber on (0,1) and theta a random number on (0, 2 Pi) then if x=r cos(theta) and y= r sin(theta), x + i y is

Re: [R] simulating stable VAR process

2012-01-14 Thread Mark Leeds
gotcha john. thanks. On Sat, Jan 14, 2012 at 9:28 PM, John C Frain fra...@gmail.com wrote: Mark This should be reasonably straightforward. In the simplest case you wih to draw a random complex number in the unit circle. This is best done in polar coordinates. If r is a random mumber on

[R] GUI preferences are not saved

2012-01-14 Thread Phillip Feldman
I'm running R version 2.14.1 (2011-12-22) on a 32-bit Windows machine. I've edited the GUI preferences to increase the font size, saving my preferences after doing so, but the next time I start an R session, my changes to the GUI preferences are lost. Is there a way to make the GUI preference

Re: [R] Averaging within a range of values

2012-01-14 Thread cberry
doggysaywhat chwh...@ucsd.edu writes: My apologies for the context problem. I'll explain. df1 is a matrix of genes labeled g1 through g5 with start positions in the START column and end positions in the END column. df2 is a matrix of chromatin modification values at positions along the

[R] add column with values found in another data frame

2012-01-14 Thread jdog76
I am positive this problem has a very simple solution, but I have been unable to find it, so I am asking for your help. I need to know how to look something up in one data frame and add it as a column in another. If I have a data frame that looks like this: frame1 ID score test age 1 Guy1

[R] Estimate the average abundance using Poisson regression with a log link.

2012-01-14 Thread frankthetank
Hello, please excuse the simplicity of this question as I am not very good with stats. I am taking a class, using R which I am learning at the same time, and the questions asks us to Estimate the average abundance using Poisson regression with a log link. I can estimate the abundance from x, but I

[R] How can I doing Quality adjusted survival analysis in R?

2012-01-14 Thread Pedro Mota Veiga
Hi R users I need to estimate, with kaplan Meier methodology, a Quality adjusted survival analysis. It is possible doing this at R? Thanks in advance. Best Regards Pedro Mota Veiga -- View this message in context:

Re: [R] Estimate the average abundance using Poisson regression with a log link.

2012-01-14 Thread Rui Barradas
P.S. I don't understand what you mean by log link but if it's the use of a log-normal to get improved confidence intervals, package 'SPECIES' implements it, unlike 'Rcapture' that only gives point estimates. Rui Barradas -- View this message in context:

Re: [R] Estimate the average abundance using Poisson regression with a log link.

2012-01-14 Thread Rui Barradas
There is a no homework rule, but: 1. abundance + poisson seems to be an animal species abundance problem in a capture-recapture framework. 2. If so, check out packages 'Rcapture' and 'SPECIES'. They both implement several estimators, such as Burnham and Overton's jacknife or Chao's estimators.

Re: [R] add column with values found in another data frame

2012-01-14 Thread Jorge I Velez
Hi Jeremy, Try frame1 - structure(list(ID = structure(c(1L, 1L, 2L, 2L), .Label = c(Guy1, Guy2), class = factor), score = c(10L, 13L, 9L, 11L), test = c(1L, 2L, 1L, 2L), age = c(20L, 20L, 33L, 33L)), .Names = c(ID, score, test, age), class = data.frame, row.names = c(1, 2, 3, 4)) frame2 -

Re: [R] add column with values found in another data frame

2012-01-14 Thread Pete Brecknock
jdog76 wrote I am positive this problem has a very simple solution, but I have been unable to find it, so I am asking for your help. I need to know how to look something up in one data frame and add it as a column in another. If I have a data frame that looks like this: frame1 ID

Re: [R] Coloring counties on a full US map based on a certain criterion

2012-01-14 Thread Ray Brownrigg
On 14/01/2012 10:33 a.m., Dimitri Liakhovitski wrote: Somewhat related question out of curiousity: Does anyone know how often the list of the counties and county names is updated in this package? Or is it done centrally for all packages that deal with US counties? Thanks! Dimitri Well, I would

Re: [R] The Future of R | API to Public Databases

2012-01-14 Thread Prof Brian Ripley
On 14/01/2012 18:51, Joshua Wiley wrote: I have been following this thread, but there are many aspects of it which are unclear to me. Who are the publishers? Who are the users? What is the problem? I have a vauge sense for some of these, but it seems to me like one valuable starting place

Re: [R] GUI preferences are not saved

2012-01-14 Thread Prof Brian Ripley
On 15/01/2012 01:57, Phillip Feldman wrote: I'm running R version 2.14.1 (2011-12-22) on a 32-bit Windows machine. I've edited the GUI preferences to increase the font size, saving my preferences after doing so, but the next time I start an R session, my changes to the GUI preferences are