Re: [R] Rms package - problems with fit.mult.impute

2011-07-06 Thread Lina Hellström
Thank you Frank! Now it works perfectly fine. Regards Lina Message: 73 Date: Thu, 23 Jun 2011 14:13:06 -0700 (PDT) From: Frank Harrell To: r-help@r-project.org Subject: Message-ID: <1308863586428-3621045.p...@n4.nabble.com> Content-Type: text/plain; charset=UTF-8 There is a problem passing x in

Re: [R] loop in optim

2011-07-06 Thread Joshua Wiley
I don't know what else to say. Your code looks right to me, and it all runs. I would check the value of a at each loop: for (i in 1:4) { a <- afull[seq(20 * (i - 1) +1, 20 * i), ] print(a) # so you can see what it is out[i, ] <- optim(llik, par = start.par, method = "Nelder-Mead")[[1]] }

Re: [R] Substring a column vector

2011-07-06 Thread Dennis Murphy
Hi: Here's one take: shalve <- function(x) { nc <- sapply(x, nchar) ns <- nc %/% 2 cbind(a1 = substring(x, 1, ns), a2 = substring(x, ns + 1, nc)) } > shalve(a) a1a2 [1,] "1" "1" [2,] "1" "2" [3,] "12" "34" [4,] "12" "45" [5,] "124" "567" [6,] "126" "786" [7,] "14

Re: [R] loop in optim

2011-07-06 Thread EdBo
I have one last theoretical question, I did not adjust my code prior so that it maximise the likehood function. I googled that to make optim maximise you multiply fn by -1. In my code, would that be the same as saying "-sum" on the "sum" part of my code (see below)? llik = function(x) {

Re: [R] loop in optim

2011-07-06 Thread EdBo
I am sorry if I sound stupid but I am not able to correct the error even after running this code. > afull=read.table("D:/hope.txt",header=T) > llik = function(x) + { +al_j=x[1]; au_j=x[2]; sigma_j=x[3]; b_j=x[4] +sum(na.rm=T, +ifelse(a$R_j< 0, log(1/(2*pi*(sigma_j^2)))- +

[R] CAPdiscrim error in BiodiversityR

2011-07-06 Thread Sparsons
Hello, I having trouble running the CAPdiscrim function located in biodiversityR. My data tables are as follows: community data frame (called "spdata") Species1... Speciesn site1.. site2.. siten with abundance data as values. Site names are row names. and environmental data (ca

Re: [R] Substring a column vector

2011-07-06 Thread Peter Maclean
How to substring the following vector (in data frame b) >b a 11 12 1234 1245 124567 126786 145769 such that: a1    a2 1 1 1 2 12    23 12    34 124   567 126   787 145   769   I tried logical commands with substr() did not work out. __ R-help@r

Re: [R] How to Execute A Query Stored In Access 2007

2011-07-06 Thread Steven Kennedy
You should just be able to use the sqlQuery function to execute the query something like this: con<-odbcConnect(...) sqlQuery(con,"EXEC ") On Thu, Jul 7, 2011 at 11:40 AM, Alex Zhang wrote: > Steven - I use RODBC. Thx, > - Alex > > From: Steven Kennedy > To: A

Re: [R] Simulating from the null distribution of a 2 x 3 table

2011-07-06 Thread Thomas Lumley
On Thu, Jul 7, 2011 at 12:58 PM, Jim Silverton wrote: > Dear all, > > I want to simulate from the null distribution of the following 2 x 3 table, > > 2   5  10 > 4   8   5 > > I am using  a chi-squared test. > Anyone has any idea how to do this? The r2dtable() function will simulate tables with a

Re: [R] identifying a 'run' in a vector

2011-07-06 Thread B77S
Yes Gabor, you definition (a sequence of numbers which each increase by 1 over the prior number) is what I meant. Sorry it that was not clear and I thank you and Joshua for your time and your explanation. This should work fine. Gabor Grothendieck wrote: > > On Wed, Jul 6, 2011 at 7:32 PM, B

Re: [R] Simulating from the null distribution of a 2 x 3 table

2011-07-06 Thread Bert Gunter
Homework? If not, context? -- Bert On Wed, Jul 6, 2011 at 5:58 PM, Jim Silverton wrote: > Dear all, > > I want to simulate from the null distribution of the following 2 x 3 table, > > 2   5  10 > 4   8   5 > > I am using  a chi-squared test. > Anyone has any idea how to do this? > > -- > Thanks

Re: [R] How to Execute A Query Stored In Access 2007

2011-07-06 Thread Alex Zhang
Steven - I use RODBC. Thx, - Alex From: Steven Kennedy To: Alex Zhang Cc: "r-help@R-project.org" Sent: Wednesday, July 6, 2011 7:18 PM Subject: Re: [R] How to Execute A Query Stored In Access 2007 What package are you using to connect to the Access database?

Re: [R] Subset creates row_names column when exported to MYSQL

2011-07-06 Thread Thiago Clark
Hi, Steven i just solved it. the problem was with RMYSQL, not with the subset. > dbWriteTable(..., row.names=FALSE) solved my problem... thanks, sorry for the inconvenience. 2011/7/6 Steven Kennedy > What function are you using to export your data.frame to MySQL? > > > > On Wed, Jul 6, 2011

Re: [R] identifying a 'run' in a vector

2011-07-06 Thread Gabor Grothendieck
On Wed, Jul 6, 2011 at 7:32 PM, B77S wrote: > Hi, > > How can I discern which elements in x (see below) are in 'order', but more > specifically.. only the 1st 'ordered run'? > I would like for it to return elements 1:8... there may be ordered values > after 1:8, but those are not of interest. > >

Re: [R] Simulating from the null distribution of a 2 x 3 table

2011-07-06 Thread David Winsemius
On Jul 6, 2011, at 8:58 PM, Jim Silverton wrote: Dear all, I want to simulate from the null distribution of the following 2 x 3 table, 2 5 10 4 8 5 I am using a chi-squared test. Yeah. Right. A "chi-squared test". That certainly narrows it down ... to maybe one quarter of all

Re: [R] Simulating from the null distribution of a 2 x 3 table

2011-07-06 Thread Jim Silverton
Dear all, I want to simulate from the null distribution of the following 2 x 3 table, 2 5 10 4 8 5 I am using a chi-squared test. Anyone has any idea how to do this? -- Thanks, Jim. [[alternative HTML version deleted]] __ R-help@r-p

Re: [R] identifying a 'run' in a vector

2011-07-06 Thread Joshua Wiley
I seem to recall seeing this done in one or two elegant lines, but run <- function(x, type = 1) { index <- rle(diff(c(NA, x))) i <- cumsum(index$lengths) j <- match(type, index$values) x[seq.int(i[j - 1], i[j])] } run(c(1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 45)) run(c(20, 22, 24, 26, 1,

Re: [R] help with nprmpi

2011-07-06 Thread p_connolly
Quoting Ouattara : Dear I have been trying to a program which requires "nprmpi". However, I have tried to install the downloaded zip file but get the error: "cannot open compressed file 'npRmpi_0.40-7.tar.gz/DESCRIPTION'" Since you didn't tell us any basic information, we have to guess what y

[R] Seasonal correlations

2011-07-06 Thread Ira Sharenow
I am an R newbie, and I am facing what is for me a challenging problem. I am trying to write functions to solve the following problems. It seems as though R offers so many options I am not sure how to approach the problem. I have a data frame with dates in the first column and returns in th

Re: [R] identifying a 'run' in a vector

2011-07-06 Thread B77S
well.. the following works, but if you have another idea I am still interested. 1:(which(diff(x)!=1)[1]) B77S wrote: > > Hi, > > How can I discern which elements in x (see below) are in 'order', but more > specifically.. only the 1st 'ordered run'? > I would like for it to return eleme

Re: [R] identifying a 'run' in a vector

2011-07-06 Thread Joshua Wiley
Hi, If an "ordered run" means the difference is between the ith and ith + 1 position is 1, then: out <- rle(diff(x)) ?diff gives you the differences (i + 1) - (i), and then run length encoding encodes how long a run of the same number is. In this case, there first run is length 7. rle() output

[R] identifying a 'run' in a vector

2011-07-06 Thread B77S
Hi, How can I discern which elements in x (see below) are in 'order', but more specifically.. only the 1st 'ordered run'? I would like for it to return elements 1:8... there may be ordered values after 1:8, but those are not of interest. x <- c(1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 45) Thanks fo

Re: [R] How to Execute A Query Stored In Access 2007

2011-07-06 Thread Steven Kennedy
What package are you using to connect to the Access database? On Thu, Jul 7, 2011 at 7:02 AM, Alex Zhang wrote: > Hey guys, > > Could you please teach me how to run or execute a query stored in an Access > 2007 database? > > I can connect and run queries from my Access database without any prob

Re: [R] The BiodiversityR can't work

2011-07-06 Thread David Cross
I have not used BiodiversityGUI.R, but it looks like it needs Rcmdr ... are you using Rcmdr? In case you are not, here is the url: http://socserv.mcmaster.ca/jfox/Misc/Rcmdr/ Cheers David Cross d.cr...@tcu.edu www.davidcross.us On Jul 6, 2011, at 5:37 PM, Aishuijiao wrote: > Sourced: Biod

[R] The BiodiversityR can't work

2011-07-06 Thread Aishuijiao
Sourced: BiodiversityGUI.R Error : .onAttach failed in attachNamespace() for 'Rcmdr', details: call: get(Menus[m, 5]) error: object 'chisquareDistributionPlot' not found Error in BiodiversityRGUI() : needs Rcmdr Hi Guys, I am from China, I wanna use Biodiversity R, but it can't work. Can so

Re: [R] Wrong environment when evaluating and expression?

2011-07-06 Thread William Dunlap
No, it is not in any package. Feel free to use it as you wish - it has no licensing restrictions. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com > -Original Message- > From: Joshua Wiley [mailto:jwiley.ps...@gmail.com] > Sent: Wednesday, July 06, 2011 1:23 PM > To: William Dun

[R] problem loading rgdal with Rapache, problem solved due to libexpat with apache.

2011-07-06 Thread Mike Marchywka
Has anyone had problems with Rapache that don't show up on command line execution of R? I just ran into this loading rgdal in Rapache page and having a problem with loading shared object. The final complaint was that Stop_XMLParser was undefined- this was surprising since grep -l showed it in ex

Re: [R] Split a row vector into columns

2011-07-06 Thread Peter Maclean
That is what I wanted  Peter Maclean Department of Economics UDSM - Original Message From: Sarah Goslee To: Peter Maclean Cc: r-help@r-project.org Sent: Wed, July 6, 2011 1:15:31 PM Subject: Re: [R] Split a row vector into columns You mean like: > myvec <- c(1,2,3,1,2,3,1,2,3) > myv

Re: [R] finding the intersection of two vectors

2011-07-06 Thread David Winsemius
On Jul 6, 2011, at 4:43 PM, Data Analytics Corp. wrote: Hi, Suppose I have two vectors, not necessarily the same length (in fact, they usually are different lengths): y.1 that has increasing values between 0 and 1; y.2 that has decreasing values between 1.0 and 0. You can picture these

[R] How to Execute A Query Stored In Access 2007

2011-07-06 Thread Alex Zhang
Hey guys, Could you please teach me how to run or execute a query stored in an Access 2007 database? I can connect and run queries from my Access database without any problem. But I have an append query stored there. Say called "Append2Tbl". How do I execute it without copying and pasting the

[R] finding the intersection of two vectors

2011-07-06 Thread Data Analytics Corp.
Hi, Suppose I have two vectors, not necessarily the same length (in fact, they usually are different lengths): y.1 that has increasing values between 0 and 1; y.2 that has decreasing values between 1.0 and 0. You can picture these as being supply (= y.1) and demand (= y.2) curves from econom

Re: [R] Dealing with missing values in a linear mixed model

2011-07-06 Thread Christine
Hi, within lme(), I think it is only possible to do na.action = na.omit. The default action (= na.fail) causes lme() to print an error message and terminate if there are any incomplete observations Best, Christine - -- Christine Adrion, Dipl.-Stat.,MPH Ludwig-Maximilians-Universität München

Re: [R] Subset creates row_names column when exported to MYSQL

2011-07-06 Thread Steven Kennedy
What function are you using to export your data.frame to MySQL? On Wed, Jul 6, 2011 at 10:41 PM, Thiago Clark wrote: > Dear R-helpers, > > I have a huge dataset and I create a filter selecting only the cases I want > using: >>data <- subset(data, data$var=='x' | data$var=='y' | data$var=='z' |

Re: [R] trouble parsing a date using strptime()

2011-07-06 Thread jim holtman
paste on a 'day' since it is trying to convert to something that is ambigous: > strptime("2011010","%Y%W%w") [1] "2011-01-02" > strptime("2011520","%Y%W%w") [1] "2011-12-25" > strptime("2011120","%Y%W%w") [1] "2011-03-20" > strptime("2011200","%Y%W%w") [1] "2011-05-15" On Wed, Jul 6, 2011 at 3:

Re: [R] Showing which bars in a bar chart are significantly different

2011-07-06 Thread John Kane
# Incremental approach bb <- c(23, 45, 67) bsp <- barplot(bb,beside=TRUE) # get midpoints of the bars and plot # draw lines segments( .7, 50, 1.9, 50) segments(.7, 50, .7, 48) segments(1.9, 50, 1.9, 48) # Or all in one go segments(c(.7, .7, 1.9), c(50,50,50), c(1.9,.7,1.9), c(50, 48, 48)) ---

Re: [R] Showing which bars in a bar chart are significantly different

2011-07-06 Thread Joshua Wiley
On Wed, Jul 6, 2011 at 1:37 PM, omernevo wrote: > Hello, > > a probably rather stupid question to which I can't find an answer: > > I have a bar chart, and I want to present which bars are significantly > different by placing a line with an asterisk above then (similarly to fig. 3 I would highly

Re: [R] Showing which bars in a bar chart are significantly different

2011-07-06 Thread Sarah Goslee
I'd do it by hand with either segments() or arrows() and text(), but without a reproducible example I can't give you specific instructions. Sarah On Wed, Jul 6, 2011 at 4:37 PM, omernevo wrote: > Hello, > > a probably rather stupid question to which I can't find an answer: > > I have a bar chart

[R] Piecewise distribution function estimation with Generalized Pareto for tail

2011-07-06 Thread Edwin Sun
Hello all, I am trying to estimate the cumulative distribution function for a single stock return time series. A piecewise estimation is composed of three parts: parametric generalized Pareto (GP) for the lower tail (10% of the observation), non-parametric kernel-smoothed interior (80% of the obse

[R] help with nprmpi

2011-07-06 Thread Ouattara
Dear I have been trying to a program which requires "nprmpi". However, I have tried to install the downloaded zip file but get the error: "cannot open compressed file 'npRmpi_0.40-7.tar.gz/DESCRIPTION'" I tried the command: install.packages("nprmpi") but get the message "package 'nprmpi' is no

r-help@r-project.org

2011-07-06 Thread Sam Steingold
> * Sam Steingold [2011-07-05 15:30:02 -0400]: > > I want to modify etr.rt (or create a new frame etr.rt.md) which would > have all the columns of etr.rt plus 5 additional columns > > market.cap > X52.week.low > X52.week.high > X3.month.average.daily.volume > X50.day.moving.average.price > > whic

Re: [R] question about getting things out of an lapply

2011-07-06 Thread Joshua Wiley
Dear Annemarie, Can you replicate the problem using a madeup dataset or one of the ones built into R? It strikes me as odd to pass tree1$edge directly to lapply, when it is also hardcoded into the function, but I do not have a sense exactly for what you are doing and without data it is hard to pl

[R] significant results with KW but not in post-hoc test

2011-07-06 Thread Silvia Lomascolo
Dear all, I did a Kruskall-Wallis test for a comparison of a variable of interest between 10 sites and I get a significant result (p=0.0019). however, when I perform a post-hoc test using kruskalmc from the pgirmess package, I get no difference between any of the paired comparisons. I cannot find

[R] Showing which bars in a bar chart are significantly different

2011-07-06 Thread omernevo
Hello, a probably rather stupid question to which I can't find an answer: I have a bar chart, and I want to present which bars are significantly different by placing a line with an asterisk above then (similarly to fig. 3 in: http://jnm.snmjournals.org/content/46/4/574.figures-only). Does anyone

[R] question about getting things out of an lapply

2011-07-06 Thread Annemarie Verkerk
Dear R-help subscribers, I have a quite stupid question about using lapply. I have the following function: create.gradient <- function(i){ colorgrad01<-color.scale(seq(0,1,by=0.01), extremes=c("red","blue")) tree1$edge[i,1] -> x tree1$edge[i,2] -> y print(x) print(y) all2[x] -> z all2[y] -> z2

[R] trouble parsing a date using strptime()

2011-07-06 Thread David Pitkin
Hi, I am having a trouble parsing dates using strptime() that I get in the format of year and week number. The data looks like this "201127" which means year 2011 and week 27. I would like to graph this using ggplot but then I get a gap between 201054 and 201101 so I thought I would just easily co

Re: [R] Split a row vector into columns

2011-07-06 Thread John Kane
t(matrix(rep(1:3, 3), nrow=3)) --- On Wed, 7/6/11, Peter Maclean wrote: > From: Peter Maclean > Subject: Re: [R] Split a row vector into columns > To: r-help@r-project.org > Received: Wednesday, July 6, 2011, 2:06 PM > I want to create columns from this > row vector. From: >     x1 x2 x3 x1 x2

Re: [R] Unusual graph- modified wind rose perhaps?

2011-07-06 Thread John Kane
Thanks Michael. It looked like a decent display but it's nice to know what is going on. I has figured out something to do with milk but that was my total knowledge.. --- On Wed, 7/6/11, Michael Dewey wrote: > From: Michael Dewey > Subject: Re: [R] Unusual graph- modified wind rose perhap

Re: [R] Wrong environment when evaluating and expression?

2011-07-06 Thread Joshua Wiley
Thanks Bill! That is very useful. Is the str.language function in any package (findFn("str.language") came up empty)? It certainly helped me, not only to understand this particular problem, but in trying to wrap my head around language objects (which I only very poorly grasp) in general. Josh

Re: [R] accessing names of lists in a list

2011-07-06 Thread Greg Snow
In general, if the data frames are all related then it is best to keep them together in a list like you have. But if you want to change the names of the component data frames then you can use a loop, or sometimes better use the lapply function. Here is a basic example: tmp <- list( df1=data.f

Re: [R] reading data from password protected url

2011-07-06 Thread Steven R Corsi
Hi Duncan Your method works well for my situation when I make only one call to the database/URL with the login info. Our database is configured like the first situation (cookies) that you described below. Now, I will need to make multiple successive calls to get data for different sites in the

Re: [R] Reshape from long to wide format with date variable

2011-07-06 Thread Dennis Murphy
Hi: Here's one way with the reshape package. I converted ref to numeric and date to character string first. Sometimes these little things matter... library(plyr) library(reshape) # Modified original data; note the option in the data.frame() statement id=c("034","034","016","016","016","340","340

Re: [R] Unusual graph- modified wind rose perhaps?

2011-07-06 Thread Michael Dewey
At 12:21 04/07/2011, John Kane wrote: In a OpenOffice.org forum someone was asking if the spreadsheet could graph this http://www.elmundo.es/elmundosalud/documentos/2011/06/leche.html I didn't think it could. :) I don't think I've ever seen exactly this layout. Does anyone know if there is

Re: [R] Writing dataframes side by side in a file

2011-07-06 Thread Steve Lianoglou
Hi, On Wed, Jul 6, 2011 at 1:18 PM, Cliff Clive wrote: > Is there a quick and easy way to write data frames side-by-side in a csv file > with one column separating them? > > I could just fill them with empty rows so they all have the same height, > then cbind them with empty columns in between, b

[R] accessing names of lists in a list

2011-07-06 Thread tomtomme
After importing multiple files to data.frames in R, I want to rename all their columns and do other operations with them. The data.frame names are not continuous like 1, 3, 4, 6. I could not find a way of creating a list of the data.frames and loop this and ended up putting them into a list first:

[R] Dealing with missing values in a linear mixed model

2011-07-06 Thread Debs Majumdar
Hello,    I am trying to run a linear mixed model using model.a <- lme(Psstotals ~ Visit, data=caf, random= ~ Visit|Id) My dataset looks lie the following:     Id   Visit  Agecorrected Psstotals 1 106 0   19    8 2 106 1   19    9     3

Re: [R] elegant way of removing NA's and selecting specific values from a data.frame

2011-07-06 Thread William Dunlap
The question was whether you could do this 'in a single line' and the word 'elegant' was in the subject line. Those two things don't always go together. You can put semicolons between the statements so they all can go on one line, but that isn't very elegant. You could collapse the three assignm

Re: [R] Split a row vector into columns

2011-07-06 Thread Sarah Goslee
You mean like: > myvec <- c(1,2,3,1,2,3,1,2,3) > myvec [1] 1 2 3 1 2 3 1 2 3 > matrix(myvec, ncol=3, byrow=TRUE) [,1] [,2] [,3] [1,]123 [2,]123 [3,]123 > Or do you actually have more complex requirements? Sarah On Wed, Jul 6, 2011 at 2:06 PM, Peter Macle

[R] Writing dataframes side by side in a file

2011-07-06 Thread Cliff Clive
Is there a quick and easy way to write data frames side-by-side in a csv file with one column separating them? I could just fill them with empty rows so they all have the same height, then cbind them with empty columns in between, but I'm looking for a more elegant solution, if one exists. Than

Re: [R] very large pair() plot

2011-07-06 Thread ahrager
Uwe, This worked. Thank you so much, Audrey -- View this message in context: http://r.789695.n4.nabble.com/very-large-pair-plot-tp3634075p3649361.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list htt

Re: [R] Split a row vector into columns

2011-07-06 Thread Peter Maclean
I want to create columns from this row vector. From:     x1 x2 x3 x1 x2 x3 x1 x2 x3 1  2 3  1  2  3  1   2  3 to: x1 x2 x3 1  2   3 1  2   3 1  2   3 Peter Maclean Department of Economics UDSM __ R-help@r-project.org mailing list https://stat.ethz

Re: [R] BY GROUP in evir R package

2011-07-06 Thread Peter Maclean
Dr. Pfaff: After using str; can you give an example on data extration (e.g. for $par.ests and @residuals) - Original Message From: "Pfaff, Bernhard Dr." To: Peter Maclean ; Dr. Bernhard Pfaff Cc: "r-help@r-project.org" Sent: Wed, July 6, 2011 8:17:12 AM Subject: AW: [R] BY GROUP i

Re: [R] wgcna

2011-07-06 Thread Peter Langfelder
On Wed, Jul 6, 2011 at 8:27 AM, Raquel Martinez Garcia wrote: > Hi, > > I'm running a tutorial ("Meta-analyses of data from two (or more) microarray > data sets"), which use wgcna package. I have an error in the function > modulePreservation (it is below). > I'm using R2.13 > Can you help me? Do

Re: [R] Reshape from long to wide format with date variable

2011-07-06 Thread Joshua Wiley
Hi Pete, Try the reshape function (see ?reshape for documentation). It can be a bit confusing, but its worth learning if you deal with multiple observations per unit much. Code inline does what you want (though you might need a bit of tweaking to get pretty names, etc. HTH, Josh On Wed, Jul 6

[R] wgcna

2011-07-06 Thread Raquel Martinez Garcia
Hi, I'm running a tutorial ("Meta-analyses of data from two (or more) microarray data sets"), which use wgcna package. I have an error in the function modulePreservation (it is below). I'm using R2.13 Can you help me? Do you know, what is happens? Thanks Raquel multiExpr = list(A = list(data

Re: [R] hdf5 library install issue

2011-07-06 Thread Nicola Soranzo
On Fri Feb 18 17:48:11 CET 2011 Jérôme wrote: > I'm trying to install the hdf5 library into R. The HDF5 package is > installed in a special directory, distributed accross my cluster: > /share/apps/HDF5 > > So i put the args option to the configure command as i read in previous > post in the list:

[R] working with values from ranef()

2011-07-06 Thread Jamie Smith
I am fitting a series of models using lmer(). I'd like to be able to manipulate the coefficients generated by ranef() to facilitate comparisons between models, and I can't figure out how to do it. (This is probably old news for most of you, but the problem is that although the ranef() output is in

Re: [R] superimposing network graphs

2011-07-06 Thread Mike Marchywka
> Date: Wed, 6 Jul 2011 13:10:14 +0200 > To: r-help@r-project.org > CC: but...@uci.edu > Subject: [R] superimposing network graphs > > Dear all, > > I have a undirected network (g), representing all the sexual relationships > that ever existed in a model community. > I also have a directed edg

[R] Create simulated data's using mvrnorm

2011-07-06 Thread Aparna Sampath
Hi All This might be something very trivial but I seem to miss something in the syntax or logic which makes me keep wandering around the problem without arriving at a solution. What I want to do is to simulate a sample data for performing cluster analysis. I tried to use x1= mvrnorm(10,rep(0.8,

[R] Reshape from long to wide format with date variable

2011-07-06 Thread Pete Pete
Hi, I need to reshape my dataframe from a long format to a wide format. Unfortunately, I have a continuous date variable which gives me headaches. Consider the following example: > id=c("034","034","016","016","016","340","340") > date=as.Date(c("1997-09-28", "1997-10-06", "1997-11-04", "2000-09-

[R] relative euclidean distance

2011-07-06 Thread Sarah Leclaire
Hi, I would like to calculate the RELATIVE euclidean distance. Is there a function in R which does it ? (I calculated the abundance of 94 chemical compounds in secretion of several individuals, and I would like to have the chemical distance between 2 individuals as expressed by the relative

Re: [R] clustering based on most significant pvalues does not separate the groups!

2011-07-06 Thread pguilha
Yes absolutely, your explanation makes sense. Thanks very much. rgds Paul -- View this message in context: http://r.789695.n4.nabble.com/clustering-based-on-most-significant-pvalues-does-not-separate-the-groups-tp3644249p3649233.html Sent from the R help mailing list archive at Nabble.com. _

[R] mlogit: nested model with constant option in degenerate partition

2011-07-06 Thread Felix Eggers - Uni Hamburg
Dear R users, I am trying to estimate a nested logit model that has a constant option in a degenerate partition. The data set is a conjoint survey where respondents were asked to answer multiple choice sets. The choice sets consist of three alternatives (described by four varying attributes) and a

Re: [R] time zone issue - beginners question

2011-07-06 Thread Jeff Newmiller
A) ?str A common mistake by beginners is to fail to import to the appropriate data type. Learn to confirm your data types. B) ?dput Provide reproducible examples. dput is one useful tool for creating such. C) Sys.setenv(TZ="CEST") If you can't use ?chron or ?Date, then setting the default timezone

Re: [R] time zone issue - beginners question

2011-07-06 Thread Gabor Grothendieck
On Wed, Jul 6, 2011 at 10:37 AM, B Laura wrote: > Hello all! > > As beginner I'm struggling for a while with time zones issue and can't find > a suitable solution. > I would be grateful for any help. > > Dataset imported from excel has a variable transplant.date which has been > recorded with CET

Re: [R] elegant way of removing NA's and selecting specific values from a data.frame

2011-07-06 Thread Bert Gunter
?"&" This is basic. Please read "An Intro to R" before posting any more such questions if you have not already done so. -- Bert On Wed, Jul 6, 2011 at 8:35 AM, Jim Maas wrote: > I have a data.frame "e" and would like to extract the 23rd column, remove > any NA's and then remove any values >= 30

[R] elegant way of removing NA's and selecting specific values from a data.frame

2011-07-06 Thread Jim Maas
I have a data.frame "e" and would like to extract the 23rd column, remove any NA's and then remove any values >= 30. I can do it in steps such as this but have failed to figure out how to do it in a single line any suggestions? first <- e[,23] second <- first[!is.na(first)] third <- seco

[R] matching, treatment effect-ATT and Zelig package

2011-07-06 Thread Ana Kolar
Hi there, I'm wondering what Zelig in the following situation (code below) actually does. Is this considered as a so called regression adjustment after the propensity score matching? library(MatchIt) library(Zelig) data(lalonde) re78 represents the outcome variable 1. With Zelig m.out <- m

Re: [R] including figures in html documentation/help

2011-07-06 Thread Duncan Murdoch
On 06/07/2011 10:37 AM, Jannis wrote: Dear Duncan, OK, my fault. I did not realize that you only refer to r-devel. I found however a way for standard R by putting this into the Rd file: \details{ \if{html}{\out{}}\ifelse{latex}{}{} } And saving the figure in inst/doc. I think that will wor

[R] Install.package error

2011-07-06 Thread justin bem
When try to use install.package I have this error message : Error in m[, 1L] : incorrect dimensions number What the matter with my installation ? I run R2.13 on Window 7 32bits.   Justin BEM BP 1917 Yaoundé Tél (237) 76043774 [[alternative HTML version deleted]] ___

[R] forecast: bias in sampling from seasonal ARIMA model?

2011-07-06 Thread Nicolas Chapados
[Reposting, since there was problems with encodings the first time around.] Dear all, I stumbled upon what appears to be a troublesome issue when sampling from an ARIMA model (from Rob Hyndman's excellent 'forecast' package) that contains a seasonal AR component. Here's how to reproduce the issu

[R] time zone issue - beginners question

2011-07-06 Thread B Laura
Hello all! As beginner I'm struggling for a while with time zones issue and can't find a suitable solution. I would be grateful for any help. Dataset imported from excel has a variable transplant.date which has been recorded with CET time zone. > subDataset$transplant.date [1] "2000-01-01 CET"

Re: [R] including figures in html documentation/help

2011-07-06 Thread Jannis
Dear Duncan, OK, my fault. I did not realize that you only refer to r-devel. I found however a way for standard R by putting this into the Rd file: \details{ \if{html}{\out{}}\ifelse{latex}{}{} } And saving the figure in inst/doc. Now I just need to find a way to get Inlinedocs to pass this

Re: [R] including figures in html documentation/help

2011-07-06 Thread Duncan Murdoch
On 06/07/2011 10:03 AM, Jannis wrote: Thanks for your advice Duncan. In which file should I put the \figure{} command? I tried the *.Rd file, but the html files created are without the figure. Are you sure I only need to include the filename and no path? Yes, in the .Rd file. Can't really d

Re: [R] including figures in html documentation/help

2011-07-06 Thread Jannis
Thanks for your advice Duncan. In which file should I put the \figure{} command? I tried the *.Rd file, but the html files created are without the figure. Are you sure I only need to include the filename and no path? Jannis --- Duncan Murdoch schrieb am Mi, 6.7.2011: > Von: Duncan Murdoch

[R] superimposing network graphs

2011-07-06 Thread Wim Delva
Dear all, I have a undirected network (g), representing all the sexual relationships that ever existed in a model community. I also have a directed edgelist (e) which is a subset of the edgelist of g. e represents the transmission pathway of HIV. Now I would like to superimpose the picture of th

[R] aggregation question

2011-07-06 Thread Dr Eberhard Lisse
Hi, I am reading payment data like so 2010-01-01,100.00 2010-01-04,100.00 ... 2011-01-01,200.00 2011-01-07,100.00 and plot it aggregated per month like so library(zoo) df <- read.csv("daily.csv", colClasses=c(d="Date",s="numeric")) z <- zoo(df$s, df$d) z.mo <- aggregate(z, as.yearmon, sum) barp

[R] Subset creates row_names column when exported to MYSQL

2011-07-06 Thread Thiago Clark
Dear R-helpers, I have a huge dataset and I create a filter selecting only the cases I want using: >data <- subset(data, data$var=='x' | data$var=='y' | data$var=='z' | ... ) The problem is, when i check my new data it doen't show a row_names column but when the data is exported to MYSQL (using R

Re: [R] BY GROUP in evir R package

2011-07-06 Thread Pfaff, Bernhard Dr.
Hello Peter, str(rg2) us quite revealing for this; by() returns a list and hence lapply() can be employed, e.g.: lapply(rg2, rlevel.gev, k.blocks = 5) By the same token, you can extract the relevant bits and pieces and put them together in a data.frame. Best, Bernhard > -Ursprüngliche N

Re: [R] including figures in html documentation/help

2011-07-06 Thread Duncan Murdoch
On 11-07-06 8:47 AM, Jannis wrote: Dear list members, is it somehow possible to include figures to the html help pages of individueal functions (containing for example a plot produced by that function?) I thought about adding these figures into a 'graphs' subfolder of the package folder and t

Re: [R] Speed Advice for R --- avoid data frames

2011-07-06 Thread Frank Harrell
On occasion, as pointed out in an earlier posting, it is efficient to convert to a matrix and when finished convert back to a data frame. The Hmisc package's asNumericMatrix and matrix2dataFrame functions assist by converting character variables to factors if needed, and by holding on to original

[R] including figures in html documentation/help

2011-07-06 Thread Jannis
Dear list members, is it somehow possible to include figures to the html help pages of individueal functions (containing for example a plot produced by that function?) I thought about adding these figures into a 'graphs' subfolder of the package folder and then to somehow insert some sort of ht

Re: [R] permil symbol linux

2011-07-06 Thread Gavin Simpson
On Wed, 2011-07-06 at 12:24 +0200, mathew brown wrote: > To all in R land, > > Here is what I would like to do. > x = c(1:10) > y = c(1:10) > plot(x,y) > mtext(side=2, line=1.5, expression(""*delta*""^18*"O [permill]"), cex=1, > adj=0.5) > > That's it. Except I would like to replace "permill" wi

Re: [R] gradient generation

2011-07-06 Thread Jim Lemon
On 07/06/2011 04:19 PM, Annemarie Verkerk wrote: Dear R-help subscribers; I have a question regarding making gradients in R. I've searched on the web, but was only able to find functions that make a gradient between color X and Y, which is not what I want. I want to 'pick out' individual, small

Re: [R] matching items in a data frame

2011-07-06 Thread Jim Holtman
table(dat$word) Sent from my iPad On Jul 6, 2011, at 1:41, Lee Averell wrote: > I have a data frame with 2 columns, the first is an index of participants and > the second is a list of words presented to the participant (see below). > >> head(dat) > sword > 1a pianist > 1a sweat > 1a

Re: [R] permil symbol linux

2011-07-06 Thread mathew brown
To all in R land, Here is what I would like to do. x = c(1:10) y = c(1:10) plot(x,y) mtext(side=2, line=1.5, expression(""*delta*""^18*"O [permill]"), cex=1, adj=0.5) That's it. Except I would like to replace "permill" with the symbol. Thanks for the help On Wed, 6 Jul 2011 11:07:55 +0100 (BST

Re: [R] Group Data indexed by n Variables

2011-07-06 Thread Paolo Rossi
Actually to get exactly what I want I need to add no.dimnames(AvgDemand ) where no.dimnames <- function(a) { ## Remove all dimension names from an array for compact printing. d <- list() l <- 0 for(i in dim(a)) { d[[l <- l + 1]] <- rep("", i) } di

Re: [R] clustering based on most significant pvalues does not separate the groups!

2011-07-06 Thread S Ellison
t-tests and the like test for a difference in mean value, not for non-overlapping populations or data sets. The fact that the mean of one data set differs significantly from the mean of the other does not mean that the ranges of the individual points in each data set are disjoint. set.seed(10

[R] How to use "Update" for an object of clss GOGARCH

2011-07-06 Thread massa1234
Hi, I am using gogarch from the package "gogarch". i have 13 series. the univariate model for the one of the series has a statistically insignificant constant term (garch(1,1)). so I want to re fit the model assuming the constant term top be zerocan i use "update" method to do soif not ple

[R] matching items in a data frame

2011-07-06 Thread Lee Averell
I have a data frame with 2 columns, the first is an index of participants and the second is a list of words presented to the participant (see below). > head(dat) sword 1a pianist 1a sweat 1a carnage 1a nymph 1ahank 1a waist > tail(dat) sword 4a package 4a

[R] gradient generation

2011-07-06 Thread Annemarie Verkerk
Dear R-help subscribers; I have a question regarding making gradients in R. I've searched on the web, but was only able to find functions that make a gradient between color X and Y, which is not what I want. I want to 'pick out' individual, smaller pieces of a gradient based on a range of nu

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