[R] Combined grouped and stacked bargraph

2012-05-02 Thread Nicola Van Wilgen
Dear R-list I am having some trouble drawing a bar-graph with two groups, both of which are stacked. Here are my data in the dput format: cs.not.log.bp - ( structure(c(168, 69, 16, 69, 41, 6, 148, 6, 5, 4, 7, 4, 4, 2, 7, 2, 4, 2, 4, 2, 1, 0, 2, 0), .Dim = c(4L, 6L), .Dimnames = list(

[R] How can I read the text or character string from a txt file?

2012-05-02 Thread jpm miao
Hello, I have a large number of time series, which needs to be transformed by log or difference. Some of them are just processed by level (LV) without any transformation. For that purpose, I produce a text file (.csv or .xls) as follows: DLN DLNDLN LV LV LV... How can I read the

[R] Hmisc's latex: na.blank and grouping not working as expected

2012-05-02 Thread Marius Hofert
Dear expeRts, Why does na.blank=TRUE not replace the NA's in the following LaTeX table? x - matrix(1:72, ncol=4, nrow=8) colnames(x) - c(gr1.sgr1, gr1.sgr2, gr2.sgr1, gr2.sgr2) rn - apply(expand.grid(beta=c(0.25, 0.75), n=c(100, 500), d=c(10, 100))[, 3:1], 2, rmNames) x - cbind(rn, x) # append

Re: [R] Define lower-upper bound for parameters in Optim using Nelder-Mead method

2012-05-02 Thread Hans W Borchers
Ben Bolker bbolker at gmail.com writes: Ted.Harding at wlandres.net writes: In addition to these options, there is also a derivative-free box-constrained optimizer (bobyqa) in the 'minqa' package (and in an optim-like wrapper via the optimx package), and a box-constrained Nelder-Mead

[R] Help in poLCA

2012-05-02 Thread arunkumar1111
Hi My data looks like this dat= X1 X2 Group 84 44 1 86 29 1 94 77 1 78 87 2 94 78 2 60 31 2 I use the formula form = cbind(X1,X2) ~ Group poLCA(form,dat) But i'm getting error stating that ALERT: some manifest variables

[R] calibration of Garch models to historical data

2012-05-02 Thread Ivette
I have done the usual estimation of GARCH models, applied to my historical dataset (commodities futures) with a maximum likelihood function and selected the best model on the basis of information criteria such as Akaike and Bayes. Can somebody explain me please the calibration scheme for a GARCH

Re: [R] How to read ANOVA output

2012-05-02 Thread aRghhhhhh
Hey all who have responded to this post. I am a newbie to ANOVA analysis in R, and let me tell you- resources for us learners are scant, horrible, unclear, imprecise.. in other words.. the worst ever. So advice like go look it up in your classical textbook or on google is not helpful at all. I am

[R] DepmixS4

2012-05-02 Thread deepakw
Hi I am trying to use depmixS4 package. Based on the documentation, it seems that depmix allows one to fit an HMM model based on a training data with time-varying co-variates. However, I did not find any routines which can help test the accuracy on the fitted HMM model on out-of-sample data. Can

[R] Tutorial for ff package

2012-05-02 Thread Indrajit Sengupta
Is anybody planning to write an extensive tutorial on the ff package? I am finding the web links highly inadequate.   Regards, Indrajit [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

[R] Referencing factors through their equivalent numeric level

2012-05-02 Thread Kaushik Krishnan
Hey folks I'm sorry for bringing what must be a very simple question to R-help, but after some research I haven't been able to find a solution to my problem. Suppose I create a simple factor: [code] x-c(A,B,B,C,A) x [1] A B B C A x - as.factor(x) x [1] A B B C A Levels: A B C [/code] Now,

[R] list objects calculation

2012-05-02 Thread jiangxijixzy
I have two kinds of list, for example, one is like t[[1]]= 1 6 2 7 3 8 4 9 5 10 ... t[[731]] the other is k[[1]]= 9 10 ... k[[731]] I want to have a new list,like x x[[1]]= (1-9)/9(6-10)/10 (2-9)/9(7-10)/10 (3-9)/9(8-10)/10 (4-9)/9(9-10)/10 (5-9)/9(10-10)/10 ... x[[731]] How

[R] Extracting results from a median polish

2012-05-02 Thread Martin Raymond Lefebvre
Quick question from a new user to R, How do I extract my solution of a median polish matrix from R to a spreadsheet file such as .csv? From my reading of my guide book (R for SPSS and SAS users version 2), I deduce that exporting a file to .csv would look like the following:

Re: [R] Numeric data not numeric in .csv file

2012-05-02 Thread Jim Lemon
On 05/02/2012 10:47 AM, Eve Proper wrote: I am a raw novice to R, playing around with a mini .csv dataset created in Excel. I can read it in and the data looks OK in Excel and upon initial inspection in R: hikes- read.csv(/Users/eproper/Desktop/hikes.csv, header=TRUE) print(hikes) does exactly

[R] How to plot stacked histogram in R?

2012-05-02 Thread Manish Gupta
Hi, I am working on data analysis. I need to plot stacked histogram for two Files. File1: 1 2 3 3 4 4 File2: 4 5 6 6 7 7 7 How can i plot them on same graph? Thanks -- View this message in context: http://r.789695.n4.nabble.com/How-to-plot-stacked-histogram-in-R-tp4602369.html Sent from

Re: [R] Batch importing data

2012-05-02 Thread jiangxijixzy
Thank you very much. -- View this message in context: http://r.789695.n4.nabble.com/Batch-importing-data-tp4592997p4602378.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list

Re: [R] Combined grouped and stacked bargraph

2012-05-02 Thread Jim Lemon
On 05/02/2012 04:18 PM, Nicola Van Wilgen wrote: Dear R-list I am having some trouble drawing a bar-graph with two groups, both of which are stacked. Here are my data in the dput format: cs.not.log.bp- ( structure(c(168, 69, 16, 69, 41, 6, 148, 6, 5, 4, 7, 4, 4, 2, 7, 2, 4, 2, 4, 2, 1,

Re: [R] How to plot stacked histogram in R?

2012-05-02 Thread Jim Lemon
On 05/02/2012 02:58 PM, Manish Gupta wrote: Hi, I am working on data analysis. I need to plot stacked histogram for two Files. File1: 1 2 3 3 4 4 File2: 4 5 6 6 7 7 7 How can i plot them on same graph? Hi Manish, Have a look at the third example for the barp function (plotrix). Jim

[R] Two ecdf with log-scales

2012-05-02 Thread Johannes Radinger
Hi, i want to plot empirical cumulative density functions for two variables in one plot. For better visualizing the differences in the two cumulative curves I'd like to log-scale the axis. So far I found 3 possible functions to plot ecdf: 1) ecdf() from the package 'stats'. I don't know how to

Re: [R] How can I read the text or character string from a txt file?

2012-05-02 Thread Jim Holtman
If the symbols are separated by spaces, try: scan(yourFile, what = '') Sent from my iPad On May 2, 2012, at 2:36, jpm miao miao...@gmail.com wrote: Hello, I have a large number of time series, which needs to be transformed by log or difference. Some of them are just processed by level

Re: [R] How to read ANOVA output

2012-05-02 Thread Ista Zahn
My experience is the opposite -- the web is filled with introductory statistics material, some of it quite good. If you google for introduction to anova textbook the first hit seems to give exactly what you are asking for. The fifth one down the list also looks good

Re: [R] Referencing factors through their equivalent numeric level

2012-05-02 Thread Berend Hasselman
On 02-05-2012, at 07:22, Kaushik Krishnan wrote: Hey folks I'm sorry for bringing what must be a very simple question to R-help, but after some research I haven't been able to find a solution to my problem. Suppose I create a simple factor: [code] x-c(A,B,B,C,A) x [1] A B B C A x -

Re: [R] Clustering analysis with ordination plots

2012-05-02 Thread Gavin Simpson
Please read the posting guide for future questions. I presume you mean using the vegan package? If so, then see this blog post of mine which shows how to do something similar: http://wp.me/pZRQ9-73 If you post more details and an example I will help further if the blog post is not sufficient

Re: [R] VarCorr procedure from lme4

2012-05-02 Thread Nutter, Benjamin
I've run into this situation and have been able to prevent problems by using lme4::VarCor(...)   Benjamin Nutter |  Biostatistician   |  Quantitative Health Sciences   Cleveland Clinic  |  9500 Euclid Ave.  |  Cleveland, OH 44195  | (216) 445-1365 -Original Message- From:

Re: [R] Define lower-upper bound for parameters in Optim using Nelder-Mead method

2012-05-02 Thread Arnaud Mosnier
Thanks for this good idea ! Arnaud 2012/5/1 Ted Harding ted.hard...@wlandres.net On 01-May-2012 19:58:41 Arnaud Mosnier wrote: Dear UseRs, Is there a way to define the lower-upper bounds for parameters fitted by optim using the Nelder-Mead method ? Thanks, Arnaud The

Re: [R] error in La.svd Lapack routine 'dgesdd'

2012-05-02 Thread Philipp Grueber
Dear R Users, I have an unbalanced panel with (on average) approx. 100 individuals over 1370 time intervals (with individual time series of different lengths, varying between 60 and 1370 time intervals). I use the following model: res1-plm(x~c+d+e,data=pdata_frame, effect=twoways,

Re: [R] Hypothesis Testing using Wald Criterion for two regression models with dummy variables

2012-05-02 Thread peter dalgaard
On May 1, 2012, at 22:01 , meredith wrote: I have two models, controlled by dummy variables to see if the models can be combined into one model with similar intercepts and slopes. Has anyone tried to conduct this type of test in R. I am utilizing the econometric idea of hypothesis testing

[R] 2nd call for chapters: book Data Mining Applications with R; due by 31 May 2012

2012-05-02 Thread Yanchang Zhao
Book title: Data Mining Applications with R Publisher: Elsevier URL: http://www.rdatamining.com/books/book2 Due date: 2nd round of chapter proposals due by 31 May 2012 Potential authors are expected to submit a 1-2 page manuscript proposal clearly explaining the mission and concerns of the

[R] PLS validation value

2012-05-02 Thread Charles Determan Jr
Greetings R users, My interest in the Q2cum score comes my endeavor to replicate SIMCAP PLS-DA analysis in R. I use the exact same dataset. After doing the analysis in R, I can get the exact same R2Ycum. However, the Q2cum is significantly off. Adding the Q2cum of the 1st and 2nd component

Re: [R] list objects calculation

2012-05-02 Thread Petr PIKAL
Hi you maybe can use mapply If you have 2 lists xl-list(x, x+5) xl [[1]] [1] 1 2 3 4 5 [[2]] [1] 6 7 8 9 10 yl-list(9,10) yl [[1]] [1] 9 [[2]] [1] 10 and this function fff- function(xl,yl) (xl-yl)/yl mapply(fff, xl, yl) [,1] [,2] [1,] -0.889 -0.4 [2,] -0.778

[R] Formal test for proportional subdistribution hazards assumption

2012-05-02 Thread Kruijsdijk, R.C.M. van
L.s. I want to test the proportional subdistribution hazards assumption for several competing risk regression models I fitted using the crr()-function (cmprsk-package). I am able to plot the Schoenfeld-type residuals against failure time, but in some cases I doubt whether the assumption holds

[R] date and time conversion

2012-05-02 Thread mpostje
Hi I've been trying to convert numbers from an online temperature database into dates and time that R recognizes. the problem is that the database has put a T between the numbers and R will not accept any conversions. this is the format that it's in now 1981-01-02T08:00 can anyone help?

[R] convert numbers into dates and time

2012-05-02 Thread mpostje
Hi I've been trying to convert numbers from an online temperature database into dates and time that R recognizes. the problem is that the database has put a T between the numbers and R will not accept any conversions. this is the format that it's in now 1981-01-02T08:00 can anyone help?

[R] factor conversion to date/time

2012-05-02 Thread marjolein post
Hi, I've been trying to convert numbers from an online temperature database into dates and time that R recognizes. I've tried as.Date, as.POSIXlt and strptime the problem is that the database has put a T between the numbers and R will not accept any conversions. currently it sees the date

[R] scanning a data set for strings

2012-05-02 Thread Daniel_55
Hello, I'm looking for what I'm sure is a quick answer. I'm working with a data set that looks like this: Week Game.ID VTm VPts HTm HPts Differential HomeWin 11 NFL_20050908_OAK@NE OAK 20 NE 30 10 FALSE 21

Re: [R] How to read ANOVA output

2012-05-02 Thread John Kane
Or look for A handbook of Statistical Analyses using R. (Everitt and Holhorn) available on line in pdf format. John Kane Kingston ON Canada -Original Message- From: istaz...@gmail.com Sent: Wed, 2 May 2012 07:01:22 -0400 To: sydney.ver...@gmail.com Subject: Re: [R] How to read

[R] Multiple plots

2012-05-02 Thread alcesgabbo
I have a variable : *sim.var[,1] * Object of class SpatialPixelsDataFrame Object of class SpatialPixels Grid topology: cellcentre.offset cellsize cells.dim Xloc 0.3 0.0597 Yloc 0.1 0.05 117 SpatialPoints: Xloc Yloc [1,] 0.30 1.70

Re: [R] DepmixS4

2012-05-02 Thread Ingmar Visser
Deepak, On Wed, May 2, 2012 at 7:53 AM, deepakw deepakwarr...@gmail.com wrote: Hi I am trying to use depmixS4 package. Based on the documentation, it seems that depmix allows one to fit an HMM model based on a training data with time-varying co-variates. However, I did not find any routines

Re: [R] Hypothesis Testing using Wald Criterion for two regression models with dummy variables

2012-05-02 Thread Bert Gunter
Meredith: You are clearly out of your depth. Get local help. R-help is, err, an R help list, not a resource for remote statistical consulting. Although, I admit, there is often some overlap. -- Bert On Wed, May 2, 2012 at 5:58 AM, peter dalgaard pda...@gmail.com wrote: On May 1, 2012, at

Re: [R] factor conversion to date/time

2012-05-02 Thread Duncan Murdoch
On 02/05/2012 8:08 AM, marjolein post wrote: Hi, I've been trying to convert numbers from an online temperature database into dates and time that R recognizes. I've tried as.Date, as.POSIXlt and strptime the problem is that the database has put a T between the numbers and R will not accept

Re: [R] Numeric data not numeric in .csv file

2012-05-02 Thread R. Michael Weylandt
On Wed, May 2, 2012 at 4:34 AM, Jim Lemon j...@bitwrit.com.au wrote: On 05/02/2012 10:47 AM, Eve Proper wrote: I am a raw novice to R, playing around with a mini .csv dataset created in Excel. I can read it in and the data looks OK in Excel and upon initial inspection in R: hikes-

Re: [R] scanning a data set for strings

2012-05-02 Thread R. Michael Weylandt
I think you are looking for something like aggregate(cbind(VPts, HPts) ~ VTm + HTm, data = NFL, sum) but you should look at the examples for ?aggregate to tweak it to what you need. Michael On Wed, May 2, 2012 at 7:45 AM, Daniel_55 serna.da...@gmail.com wrote: Hello, I'm looking for what

Re: [R] date and time conversion

2012-05-02 Thread R. Michael Weylandt
Quick and dirty solution is to use sub() to change the T to a space and then use as.POSIXct as usual. x - 1981-01-02T08:00 as.POSIXct(sub(T, , x), format = %Y-%m-%d %H:%M) but it does look to me like R can work around the T if you give a good format argument: as.POSIXct(x, format =

Re: [R] factor conversion to date/time

2012-05-02 Thread R. Michael Weylandt
Please don't triple post. Michael On Wed, May 2, 2012 at 8:08 AM, marjolein post mayo_j...@hotmail.com wrote: Hi, I've been trying to convert numbers from an online temperature database into dates and time that R recognizes. I've tried as.Date, as.POSIXlt and strptime  the problem is

Re: [R] Hypothesis Testing using Wald Criterion for two regression models with dummy variables

2012-05-02 Thread meredith
Peter- Maybe I have not articulately my problem clearly, I have had local help with the statistical part just trying to figure out how to correctly program this test. For clarity's sake, I have months worth of data, I want to potentially combine those months into four, shall we say seasons,

Re: [R] Numeric data not numeric in .csv file

2012-05-02 Thread David Winsemius
On May 1, 2012, at 8:47 PM, Eve Proper wrote: I am a raw novice to R, playing around with a mini .csv dataset created in Excel. I can read it in and the data looks OK in Excel and upon initial inspection in R: hikes - read.csv(/Users/eproper/Desktop/hikes.csv, header=TRUE) print(hikes)

Re: [R] calibration of Garch models to historical data

2012-05-02 Thread R. Michael Weylandt
This might be more of a question for R-SIG-Finance and followup should probably be there, but you might get a start with the rugarch package. Michael On Wed, May 2, 2012 at 4:13 AM, Ivette iva_mihayl...@mail.ru wrote: I have done the usual estimation of GARCH models, applied to my historical

Re: [R] Arules and different item columns with same item labelsŠ.

2012-05-02 Thread John Kane
It is not clear what you mean. Can you supply some sample data? Have a look at ?dput for a handy way to supply data. John Kane Kingston ON Canada -Original Message- From: lterle...@anadolu.edu.tr Sent: Tue, 1 May 2012 17:55:25 + To: r-help@r-project.org Subject: [R] Arules

Re: [R] coxph reference hazard rate

2012-05-02 Thread David Winsemius
As has been answered several times on rhelp ... the baseline hazard is for a case with the mean value. It's not a meaningful case with all factor variables. There can be no cases where fidelity3 has a fractional value. You should be using predict() and survfit() to display estimates for

Re: [R] Extracting results from a median polish

2012-05-02 Thread R. Michael Weylandt
write.csv() is definitely the right way to go so you're on track What is str(medpolish)? From the error message, it sounds like it's a functionIf it is, are you sure you don't mean write.csv(medpolish( xx )) ? Michael On Wed, May 2, 2012 at 12:39 AM, Martin Raymond Lefebvre mlefe...@uwo.ca

Re: [R] Two ecdf with log-scales

2012-05-02 Thread David Winsemius
On May 2, 2012, at 6:14 AM, Johannes Radinger wrote: Hi, i want to plot empirical cumulative density functions for two variables in one plot. For better visualizing the differences in the two cumulative curves I'd like to log-scale the axis. So far I found 3 possible functions to plot

Re: [R] factor conversion to date/time

2012-05-02 Thread John Kane
Try something like this. Convert the vector to character and grab the first 10 characters then convert to a date. aa - as.factor(1981-01-02T08:00I) aa - as.character(aa) aa - substr(aa, 1, 10) class(b) John Kane Kingston ON Canada -Original Message- From: mayo_j...@hotmail.com

Re: [R] Hypothesis Testing using Wald Criterion for two regression models with dummy variables

2012-05-02 Thread peter dalgaard
On May 2, 2012, at 15:48 , meredith wrote: Peter- Maybe I have not articulately my problem clearly, I have had local help with the statistical part just trying to figure out how to correctly program this test. For clarity's sake, I have months worth of data, I want to potentially combine

[R] selection by two unique variables

2012-05-02 Thread Ayyappa Chaturvedula
Dear Group, I am working with a large dataset where I need to select for each unique id the the unique lastpk row. Here is a sample subject: id wtdt wt lastpk 64050256 2010-09-18 275 2010-09-16 64050256 2010-09-19 277 2010-09-18 64050256

[R] rgl.Sweave not producing transparency in pdf plots with alpha

2012-05-02 Thread Alexander Shenkin
Hi Folks, I'm trying to get rgl.Sweave to produce plots with transparency. However, it just seems to produce opaque plots when pdf is the output type. Perhaps this is a known issue? I'll just use .png in the meantime, but wanted to see about this, as I didn't see it in the documentation (though

Re: [R] selection by two unique variables

2012-05-02 Thread Bert Gunter
?tapply ?with is also useful here as in (untested) with(yourdataframe, tapply(lastpk, id, unique)) -- Bert On Wed, May 2, 2012 at 7:58 AM, Ayyappa Chaturvedula ayyapp...@gmail.com wrote: Dear Group, I am working with a large dataset where I need to select for each unique id the the unique

[R] strange differences in vector operation versus manual calculation

2012-05-02 Thread Rajarshi Guha
Hi, I'm running a calculation in two ways. The first way is to employ vectors and evaluate a function in one go. The second way is to break down the function into pieces and combine the pieces to the final answer. Algebraically, they should give me the same result. But the final vector differs

Re: [R] error bars for a barchart

2012-05-02 Thread Beatriz De Francisco
Walmes, Thank you so much!!! I am still trying to understand all of your code but it works. I have changed it a bit so that I get upper and lower limits for the error bar, and that the origin starts at 0 so the negative values are plotted correctly. barchart(Change~fTreat,groups=Process,change,

Re: [R] strange differences in vector operation versus manual calculation

2012-05-02 Thread William Dunlap
Your multistep approach corresponds to the following, which has one more set of parentheses than you used yy - params[4] + (params[3] - params[4])/((1 + 10^(params[1]-xx))^params[2]) In R lingo, both of your approaches are vectorized and you probably won't find a huge difference in speed

[R] interactive loop

2012-05-02 Thread Ondřej Mikula
Dear R-helpers, I have a number of point configurations representing skull shapes, but some of them contain superfluous points. I want to write a loop in which each configuration is plotted and I am asked to write the numbers of points that are superfluous. However, I don't know how to introduce

Re: [R] interactive loop

2012-05-02 Thread R. Michael Weylandt michael.weyla...@gmail.com
I think readline() will do what you want. It can display a message and take user input, assigning it to a character value so you might need as.numeric() Michael On May 2, 2012, at 12:08 PM, Ondřej Mikula onmik...@gmail.com wrote: Dear R-helpers, I have a number of point configurations

Re: [R] rgl.Sweave not producing transparency in pdf plots with alpha

2012-05-02 Thread Duncan Murdoch
On 02/05/2012 11:00 AM, Alexander Shenkin wrote: Hi Folks, I'm trying to get rgl.Sweave to produce plots with transparency. However, it just seems to produce opaque plots when pdf is the output type. Perhaps this is a known issue? I'll just use .png in the meantime, but wanted to see about

Re: [R] interactive loop

2012-05-02 Thread Sarah Goslee
You might start with par(ask=TRUE) and identify(). A reproducible example might get you actual code. Also, how do you know they're superfluous? Perhaps that knowledge can be used to automate identification. Sarah On Wed, May 2, 2012 at 12:08 PM, Ondřej Mikula onmik...@gmail.com wrote: Dear

[R] Statistical test for predictor selection

2012-05-02 Thread jing tang
Hi, In a data I have two predictors and one response variable. The response variable is categorical and fixed. Now I want to choose which predictor would better predict the response variable. Is there a statistical test for that? Best, Jing -- Jing Tang, PhD Senior Researcher

Re: [R] Problems accessing environment() in function

2012-05-02 Thread Uwe Ligges
On 01.05.2012 19:57, Heiko Neuhaus wrote: Hi all, I am trying to create a list of all variable/value combinations in environment(). When a function with unset arguments is called, the method I have been using fails with a missing argument error. However it should be possible to simply skip

Re: [R] interactive loop

2012-05-02 Thread Sarah Goslee
And now we have two entirely different interpretations of the question. I think Ondřej needs to provide a more detailed explanation of the problem and intended result. Sarah On Wed, May 2, 2012 at 12:23 PM, R. Michael Weylandt michael.weyla...@gmail.com michael.weyla...@gmail.com wrote: I

Re: [R] rgl.Sweave not producing transparency in pdf plots with alpha

2012-05-02 Thread Duncan Murdoch
On 02/05/2012 12:26 PM, Duncan Murdoch wrote: On 02/05/2012 11:00 AM, Alexander Shenkin wrote: Hi Folks, I'm trying to get rgl.Sweave to produce plots with transparency. However, it just seems to produce opaque plots when pdf is the output type. Perhaps this is a known issue? I'll

Re: [R] rgl.Sweave not producing transparency in pdf plots with alpha

2012-05-02 Thread Alexander Shenkin
On 5/2/2012 11:40 AM, Duncan Murdoch wrote: On 02/05/2012 12:26 PM, Duncan Murdoch wrote: On 02/05/2012 11:00 AM, Alexander Shenkin wrote: Hi Folks, I'm trying to get rgl.Sweave to produce plots with transparency. However, it just seems to produce opaque plots when pdf is the output

Re: [R] please help me

2012-05-02 Thread Uwe Ligges
On 02.05.2012 02:55, Ulfa Hasanah wrote: hi all,can you help me? index moran is very difficut for me, i have data n neighbor as enclosure: please help me to make the program for find index moran value each variabel,...thank very much Which translates to: please help me, and note that -

Re: [R] convert numbers into dates and time

2012-05-02 Thread Uwe Ligges
On 02.05.2012 11:19, mpostje wrote: Hi I've been trying to convert numbers from an online temperature database into dates and time that R recognizes. the problem is that the database has put a T between the numbers and R will not accept any conversions. this is the format that it's in now

Re: [R] selection by two unique variables

2012-05-02 Thread jim holtman
try this: x - read.table(text = id wtdt wt lastpk + + 64050256 2010-09-18 275 2010-09-16 + + 64050256 2010-09-19 277 2010-09-18 + + 64050256 2010-09-20 272 2010-09-18 + + 64050256 2010-09-21 277 2010-09-18, as.is = TRUE, header = TRUE) first -

Re: [R] Problems accessing environment() in function

2012-05-02 Thread Heiko Neuhaus
Thanks a lot for your answer! -- test1 - function(a, b, c) { x - as.list(environment()) print (hi from test1!) test2(a = a, b = b, c = c) You are rying to pass a, b, c here and hence R tries to insert those into the environment of test2 once it is called, you have

Re: [R] strange differences in vector operation versus manual calculation

2012-05-02 Thread Petr Savicky
On Wed, May 02, 2012 at 11:42:27AM -0400, Rajarshi Guha wrote: Hi, I'm running a calculation in two ways. The first way is to employ vectors and evaluate a function in one go. The second way is to break down the function into pieces and combine the pieces to the final answer. Algebraically,

[R] Forestplot question

2012-05-02 Thread Ben Ganzfried
Hi, I'm trying to build a Forest Plot using the second and fourth columns in the table (test.csv) below. My code is the following: curated - data.frame(test.csv) tmp - curated$coef tmp1 - curated$se_coef plt - metaplot(tmp, tmp1, xlim = c(-.45, .45)) I keep getting the following error at the

Re: [R] Problems accessing environment() in function

2012-05-02 Thread Duncan Murdoch
On 02/05/2012 12:59 PM, Heiko Neuhaus wrote: Thanks a lot for your answer! -- test1- function(a, b, c) { x- as.list(environment()) print (hi from test1!) test2(a = a, b = b, c = c) You are rying to pass a, b, c here and hence R tries to insert those

[R] adding a caption to a mosaic plot?

2012-05-02 Thread Simon Kiss
Dear all: Is there a way to add text to the margins or outer margins of a mosaic plot using the vcd package? I understand the margins argument to mosaic, but I don't know how to add text to that. I'd like to add a caption to a plot. If possible, I'd like to know how to set the font and size

[R] Problem with 'nls' fitting logistic model (5PL)

2012-05-02 Thread Michal Figurski
Dear R-Helpers, I'm working with immunoassay data and 5PL logistic model. I wanted to experiment with different forms of weighting and parameter selection, which is not possible in instrument software, so I turned to R. I am using R 2.14.2 under Win7 64bit, and the 'nls' library to fit the

Re: [R] Problem with 'nls' fitting logistic model (5PL)

2012-05-02 Thread Bert Gunter
Plot the data. You're clearly overfitting. (If you don't know what this means or why it causes the problems you see, try a statistical help list or consult your local statistician). -- Bert On Wed, May 2, 2012 at 12:32 PM, Michal Figurski figur...@mail.med.upenn.edu wrote: Dear R-Helpers,

Re: [R] Problems accessing environment() in function

2012-05-02 Thread Heiko Neuhaus
Thank you very much for your suggestion. f - function(a,b,c) { names - ls(environment()) # get all the names result - list() for (n in names) { if (!do.call(missing, list(as.name(n result[n] - get(n) } result } I have already figured out a very similar solution using for/eval that

[R] Quickest way to make a large empty file on disk?

2012-05-02 Thread Jonathan Greenberg
R-helpers: What would be the absolute fastest way to make a large empty file (e.g. filled with all zeroes) on disk, given a byte size and a given number number of empty values. I know I can use writeBin, but the object in this case may be far too large to store in main memory. I'm asking

Re: [R] [R-sig-hpc] Quickest way to make a large empty file on disk?

2012-05-02 Thread Jeff Ryan
Look at the man page for dd (assuming you are on *nix) A quick google will get you a command to try. I'm not at my desk or I would as well. Jeff Jeffrey Ryan|Founder|jeffrey.r...@lemnica.com www.lemnica.com On May 2, 2012, at 5:23 PM, Jonathan Greenberg j...@illinois.edu

Re: [R] Quickest way to make a large empty file on disk?

2012-05-02 Thread Henrik Bengtsson
An R solution is: allocateFile - function(pathname, nbrOfBytes) { con - file(pathname, open=wb); on.exit(close(con)); seek(con, where=nbrOfBytes-1L, origin=start, rw=write); writeBin(as.raw(0), con=con); invisible(pathname); } # allocateFile() allocateFile(foo.bin, nbrOfBytes=985403)

Re: [R] Problems accessing environment() in function

2012-05-02 Thread Duncan Murdoch
On 12-05-02 5:20 PM, Heiko Neuhaus wrote: Thank you very much for your suggestion. f- function(a,b,c) { names- ls(environment()) # get all the names result- list() for (n in names) { if (!do.call(missing, list(as.name(n result[n]- get(n) } result } I have already figured out a very

Re: [R] [R-sig-hpc] Quickest way to make a large empty file on disk?

2012-05-02 Thread Jeff Ryan
Something like: http://markus.revti.com/2007/06/creating-empty-file-with-specified-size/ Is one way I know of. Jeff Jeffrey Ryan|Founder|jeffrey.r...@lemnica.com www.lemnica.com On May 2, 2012, at 5:23 PM, Jonathan Greenberg j...@illinois.edu wrote: R-helpers: What

Re: [R] Forestplot question

2012-05-02 Thread Thomas Lumley
It works for me with your data: dat-read.table(/tmp/foo.txt,header=TRUE) metaplot(a$coef,a$se_coef) It has boxes of size zero for the point estimates, but that's because you give the standard error as zero for the second estimate, which implies all the other boxes should be infinitely smaller.

Re: [R] error in La.svd Lapack routine 'dgesdd'

2012-05-02 Thread Philipp Grueber
Addendum to my first post: Since I wish to understand what plm does to my data, I tried to manually calculate the demeaned values and use OLS. See below how far I got with the Grunfeld data; formula's are based on Greene's Econometric Analysis. Obviously, I am missing at least one important

Re: [R] Numeric data not numeric in .csv file

2012-05-02 Thread Eve Proper
Thanks everyone for your helpful responses. I looked at the csv file in a text editor and saw no spaces or non-numerical characters (other than periods as decimals) outside of the header. str() says me that the variables are either num or int. David was spot-on; I was trying storage.mode(~miles)

[R] is there a way of identifying batch mode running?

2012-05-02 Thread Paul.Rustomji
Hello list Is there a way of identifying from within R whether a script has been source(d) from Rgui.exe or via Rscript.exe in batch mode? For the code I have I use the commandArgs() function to pick up command line args when running in batch mode via Rscript.exe However I like to get the code

Re: [R] is there a way of identifying batch mode running?

2012-05-02 Thread William Dunlap
interactive() does not do exactly what you ask for, but may be close enough. It returns FALSE when run from Rscript and TRUE from R when you have not redirected standard input. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From:

Re: [R] [R-sig-hpc] Quickest way to make a large empty file on disk?

2012-05-02 Thread Simon Urbanek
On May 2, 2012, at 6:23 PM, Jonathan Greenberg wrote: R-helpers: What would be the absolute fastest way to make a large empty file (e.g. filled with all zeroes) on disk, given a byte size and a given number number of empty values. I know I can use writeBin, but the object in this case

Re: [R] [R-sig-hpc] Quickest way to make a large empty file on disk?

2012-05-02 Thread Jeff Newmiller
On most UNIX systems this will leave a large unallocated virtual hole in the file. If you are not bothered by spreading the allocation task out over the program execution interval, this won't matter and will probably give the best performance. However, if you wanted to benchmark your

Re: [R] scanning a data set for strings

2012-05-02 Thread Daniel_55
Worked like a charm. Thanks for the help! It's really appreciated. -- View this message in context: http://r.789695.n4.nabble.com/scanning-a-data-set-for-strings-tp4602953p4603410.html Sent from the R help mailing list archive at Nabble.com. __

[R] error fitting coxph model

2012-05-02 Thread Jessica Myers
Hi, I am using coxph from the survival package to fit a large model (100,000 observations, ~35 covariates) using both ridge regression (on binary covariates) and penalized splines (for continuous covariates). In fitting, I get a strange error: Error in if (abs((y[nx] - target)/(y[nx - 1]

[R] How can a function in R handle different types of input?

2012-05-02 Thread stella
Hi, How can a function in R handle different types of input? I have written a function, which should calculate the slope from several 3-time-point measurements by linear regression 4 three-time-point-measurements: x-cbind(c(1,2,3,4),c(2,3,4,5),c(3,4,5,6)) time points: time-c(1,3,9) function

[R] pick up the values

2012-05-02 Thread jiangxijixzy
Hi, I have a list of data, e.g. r[[i]] r[[1]]= 1 2 1 6 5 5 5.5 3 r[[2]]= 46 35 78 35 … r[[500]]. In the first column, the selected values should like this: (the later value)-(the former value)=1 In the second column, the selected values should like this: (the

Re: [R] date and time conversion

2012-05-02 Thread Rui Barradas
Hello, mpostje wrote Hi I've been trying to convert numbers from an online temperature database into dates and time that R recognizes. the problem is that the database has put a T between the numbers and R will not accept any conversions. this is the format that it's in now

Re: [R] strange differences in vector operation versus manual calculation

2012-05-02 Thread Rui Barradas
Hello, I must be missing something very obvious, but I just cannot see it. The hardest to find errors. Wrong manual calculation in t1, powers have precedence right to left and before additions. t1b - 10^(params[1]-xx)^params[2] t3b - 1 + t1b t4b - t2/t3b t5b - params[4] + t4b all.equal(yy,

[R] Binary logistic regression with binary predictors

2012-05-02 Thread F.j. Berg
Ey R-people Trying to do a binary logistic regression with only categorical(age,ballot) and binary predictors for a binary response variable. I can model them at least at least i treat the binary predictors as categorical with the use of as.factor(etc) and use glm with binomial distribution

[R] Multiple correlation

2012-05-02 Thread Silvia Molteni
I'm looking for a function for the multiple correlation among three variables. I have created three vectors (x, y and z) and I want to find a correlation coefficient and evaluate its significance. Can anyone help me?   Thanks in advance. [[alternative HTML version deleted]]

[R] output Shapiro-Wild results to a table

2012-05-02 Thread Mary Ann Middleton
Hello, I have applied the Shapiro test to a matrix with 26.925 rows of data using the following F1.norm-apply(F1.n.mat,1,shapiro.test) I would now like to view and export a table of the p and W values from the Shapiro test, but I am not sure how to approach this. I have tried the

Re: [R] Referencing factors through their equivalent numeric level

2012-05-02 Thread Kaushik Krishnan
That did it! Thanks very much Berend. On Wed, May 2, 2012 at 4:19 AM, Berend Hasselman b...@xs4all.nl wrote: On 02-05-2012, at 07:22, Kaushik Krishnan wrote: Hey folks I'm sorry for bringing what must be a very simple question to R-help, but after some research I haven't been able to find

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