Re: [R] 3 questions regarding matrix copy/shuffle/compares

2009-04-25 Thread David Winsemius
On Apr 26, 2009, at 12:28 AM, Esmail wrote: Hello all, I have the following function call to create a matrix of POP_SIZE rows and fill it with bit strings of size LEN: pop=create_pop_2(POP_SIZE, LEN) Are you construction a vector or a matrix? What are the dimensions of your matrix?

Re: [R] constrained optimization

2009-04-25 Thread David Winsemius
http://search.r-project.org/cgi-bin/namazu.cgi?query=%22constrained+optimization%22&max=100&result=normal&sort=score&idxname=functions&idxname=Rhelp08 And that is only the help messages from the last two years.' On Apr 26, 2009, at 12:00 AM, wrote: Is there any R package addressing problems

Re: [R] Nomogram with stratified cph in Design package

2009-04-25 Thread David Winsemius
On Apr 25, 2009, at 6:57 PM, reneepark wrote: Hello, I am using Dr. Harrell's design package to make a nomogram. I was able to make a beautiful one without stratifying, however, I will need to stratify to meet PH assumptions. This is where I go wrong, but I'm not sure where. Non-Stra

[R] 3 questions regarding matrix copy/shuffle/compares

2009-04-25 Thread Esmail
Hello all, I have the following function call to create a matrix of POP_SIZE rows and fill it with bit strings of size LEN: pop=create_pop_2(POP_SIZE, LEN) I have 3 questions: (1) If I did keep_pop[1:POP_SIZE] == pop[1:POP_SIZE] to keep a copy of the original data structure before

[R] constrained optimization

2009-04-25 Thread mauede
Is there any R package addressing problems of constrained optimization ? I have the following "apparently" simple problem: Given a set V with fixed cardinality:nv Given a set S whose cardinality is a parameter:nHat Let the cardinality of the intersection S.and.V be:

[R] Nomogram with stratified cph in Design package

2009-04-25 Thread reneepark
Hello, I am using Dr. Harrell's design package to make a nomogram. I was able to make a beautiful one without stratifying, however, I will need to stratify to meet PH assumptions. This is where I go wrong, but I'm not sure where.

Re: [R] Multiple Imputation in mice/norm

2009-04-25 Thread Frank E Harrell Jr
David Winsemius wrote: On Apr 25, 2009, at 9:25 AM, Frank E Harrell Jr wrote: Emmanuel Charpentier wrote: Le vendredi 24 avril 2009 à 14:11 -0700, ToddPW a écrit : I'm trying to use either mice or norm to perform multiple imputation to fill in some missing values in my data. The data has so

[R] fclustindex, e1071 package

2009-04-25 Thread Caroline Wallis
Hi, I'm using e1071 package to do fuzzy cluster analysis. My dataset (ra) has 5237 observations and 2 variables - depth and velocity. I used fuzzy cmeans to create 6 fuzzy classes. >ra.flcust6<-cmeans(ra,6,iter.max=100,verbose=F,dist="euclidean",method="cmea ns",m=1.7,rate.par=NULL,weights=1)

Re: [R] plm Hausman-Taylor model

2009-04-25 Thread William Dunlap
The problem arises because your data.frame contains no factors and plm:::lev2var implicitly assumes that its input data.frame, x, contains both factor and non-factor columns. That is because, e.g., the output of sapply(zeroLongInput, func) has class NULL, not the class of the output of func()

Re: [R] plm Hausman-Taylor model

2009-04-25 Thread Achim Zeileis
On Sat, 25 Apr 2009, Ron Burns wrote: Dear all- I am have trouble in using the model="ht" option in function plm from the plm library. I am using Package: plm Version: 1.1-1; R version 2.8.1 (2008-12-22) running on a FC-8 linux machine. Here is what I am trying to do: ##--

Re: [R] saved workspace

2009-04-25 Thread Greg Snow
There are functions for that, see ?unlink and ?file.rename (and several others on that same page). They can be used to remove or rename the .Rdata file, but there are several other ways to remove/rename the file as well. Under windows you can click on the file menu, choose "Load Workspace", th

Re: [R] ANOVA/statistics question

2009-04-25 Thread Tal Galili
Hi Douglas. So you want to check for correlation or regression ? how many levels does "pre" have ? you could subset the variables you want to check correlation on, by the pre levels. for example: Let's say pre has two levels: 1 and 2. then you can do: cor(y[pre == 1], x[pre == 1]) cor(y[pre == 2]

Re: [R] saved workspace

2009-04-25 Thread bogdanno
OK, I found the file and moved and renamed it And now it doesn't load anymore. It's a weird method though-there should be a command for that purpose. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the pos

Re: [R] saved workspace

2009-04-25 Thread Jorge Ivan Velez
Hi bogdanno, Do right click on the R-icon (on your desktop) and then click on Properties. On the window that pops up, go to Target and modify what it shows. On my computer I have something like "C:\Program Files\R\R-2.9.0pat\bin\Rgui.exe" --no-save --max-mem-size=2047M which means that I do not w

[R] plm Hausman-Taylor model

2009-04-25 Thread Ron Burns
Dear all- I am have trouble in using the model="ht" option in function plm from the plm library. I am using Package: plm Version: 1.1-1; R version 2.8.1 (2008-12-22) running on a FC-8 linux machine. Here is what I am trying to do: ##--

Re: [R] saved workspace

2009-04-25 Thread bogdanno
I am using it from Windows XP. I have never used Linux or Unix. I do not have a terminal window, so --no-restore doesn't work.(I think) I open R just by clicking on the R icon and a console opens up. I have tried to move and rename the file but still R loads it-which makes me think it was copied so

Re: [R] ANOVA/statistics question

2009-04-25 Thread drmh
Hi, thanks for your prompt reply In my situation, the dependent variable is "post-test" and the independent variables are "pre" and "coh". Howw would I find the correlation between coh and post with the effect of "pre" regressed using your commands? Tal Galili wrote: > > Hi Douglas > I would

Re: [R] Multiple Imputation in mice/norm

2009-04-25 Thread David Winsemius
On Apr 25, 2009, at 9:25 AM, Frank E Harrell Jr wrote: Emmanuel Charpentier wrote: Le vendredi 24 avril 2009 à 14:11 -0700, ToddPW a écrit : I'm trying to use either mice or norm to perform multiple imputation to fill in some missing values in my data. The data has some missing values bec

Re: [R] Request for some help

2009-04-25 Thread Tom Backer Johnsen
Abdul: First, read the posting guide. You will find a link to that one at the bottom of all messages. Also, read some of the documentation for R. Sorry, there is no way to avoid that. A very good source is the R web page (Google for the letter R, the link will be at the top of the list).

Re: [R] ANOVA/statistics question

2009-04-25 Thread Tal Galili
Hi Douglas I would go for a different command then aov. something like: ?cor or ?cor.test To also get the p value of the correlation. Cheers, Tal On Sat, Apr 25, 2009 at 8:27 AM, drmh wrote: > > (Have searched for this already) > > Hi, > > How do you find the strength of correlation between tw

[R] heatmap.2 does not accept dendogram passed to Rowv param

2009-04-25 Thread Mark Borowsky
heatmap.2() from gplots does not seem to accept a dendrogram produced by the stats package function heatmap(): > testHeatmap=heatmap(test[,1:40],Colv=NA,col=bluewhitered(256),labRow=testL,keep.dendro=TRUE) # draws expected image # to prove this dendro is OK, redraw with same function: > heat

Re: [R] Multiple Imputation in mice/norm

2009-04-25 Thread Emmanuel Charpentier
Danke sehr, herr Professor ! This one escaped me (notably because it's a trifle far from my current interests...). Emmanuel Charpentier Le samedi 25 avril 2009 à 08:25 -0500, Frank E Harrell Jr a écrit : > Emmanuel Charpentier wrote: > > Le vendredi 24 avri

[R] ANOVA/statistics question

2009-04-25 Thread drmh
(Have searched for this already) Hi, How do you find the strength of correlation between two variables using an ANOVA table? "Pr(>F)" gives the statistical significance of the association, but not the strength of the correlation. See data (from R) below Readable: "Df"

Re: [R] Multiple Imputation in mice/norm

2009-04-25 Thread Frank E Harrell Jr
Emmanuel Charpentier wrote: Le vendredi 24 avril 2009 à 14:11 -0700, ToddPW a écrit : I'm trying to use either mice or norm to perform multiple imputation to fill in some missing values in my data. The data has some missing values because of a chemical detection limit (so they are left censored

Re: [R] Multiple Imputation in mice/norm

2009-04-25 Thread Emmanuel Charpentier
Le vendredi 24 avril 2009 à 14:11 -0700, ToddPW a écrit : > I'm trying to use either mice or norm to perform multiple imputation to fill > in some missing values in my data. The data has some missing values because > of a chemical detection limit (so they are left censored). I'd like to use > MI

Re: [R] Tinn-R and latex

2009-04-25 Thread jcfaria
The prior answer of Stefan is correct! You have now two options: 1. To uninstall Tinn-R and to install it newly, but don not check the extension related with latex 2. To change the association file inside of the Windows Operational System. HTH, JCFaria -- View this message in context: http://

Re: [R] ordinal logistic regression for longitudinal data set

2009-04-25 Thread David Winsemius
On Apr 24, 2009, at 5:22 PM, joy_stat wrote: Hi, Can one tell me which procedure will fit an ordinal logistic regression model for longitudinal data set. To be precise, I have both dichotomous and polytomous items. Also, I would like to specify different covariance structures (unst

Re: [R] Reading files

2009-04-25 Thread David Winsemius
On Apr 25, 2009, at 2:46 AM, Santosh wrote: Dear R-sians Quick question... 1) From a flat (data) file with 100+ columns, how do I read specific columns instead of reading the entire dataset? I am trying to avoid reading the entire file followed by "subsetting". If you are asking about h

Re: [R] Sem and nlm and ols instead of ml

2009-04-25 Thread John Fox
Dear Adam, ML is indeed hard-coded into the sem() function. Depending upon its complexity, modifying the code to use a different "fitting function" shouldn't be difficult, particularly if you are content not to supply derivatives for the optimization. Providing for different "fitting functions" is

Re: [R] Reading files

2009-04-25 Thread jim holtman
On Sat, Apr 25, 2009 at 2:46 AM, Santosh wrote: > Dear R-sians > Quick question... > > 1) From a flat (data) file with 100+ columns, how do I read specific columns > instead of reading the entire dataset? I am trying to avoid reading the > entire file followed by "subsetting". In read.table you c

Re: [R] Text Contrast in a Plot

2009-04-25 Thread Jim Lemon
Rodrigo Aluizio wrote: Hi List, I would appreciate any suggestion on how can I make a text I’ve inserted in a plot show some contrast? With this I mean that I have a white text on a plot and I would like to make a tiny border around it in black, so even being small sized and the entire graphic b

Re: [R] plot() - thicker points when pair exist more than 1 time?

2009-04-25 Thread Jim Lemon
Knut Krueger wrote: Hi to all, is it possible to show in anyway that point 1,1 is existing more than 1one time? f.e.: f<- data.frame("x"=c(1,3,5,6,1),"y"=c(1,2,3,4,1)) plot(f) Hi Knut, Taka a look at cluster.overplot and count.overplot in the plotrix package. Jim ___

Re: [R] power.t.test formula

2009-04-25 Thread Karl Ove Hufthammer
Greg Snow: > Look at the pwr package, it has functions for 2 samples of different > sizes. > > Hope this helps, Great! Thanks. -- Karl Ove Hufthammer __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read t

Re: [R] Extracting an object name?

2009-04-25 Thread Gabor Grothendieck
On Sat, Apr 25, 2009 at 6:56 AM, Duncan Murdoch wrote: > On 24/04/2009 9:30 PM, greggal...@gmail.com wrote: >> >> Dear Sir or Madam: >> >> This is an extension to a earlier post, about looping through several >> thousand files, and testing student's models against a different >> data-set, called r

Re: [R] Extracting an object name?

2009-04-25 Thread Duncan Murdoch
On 24/04/2009 9:30 PM, greggal...@gmail.com wrote: Dear Sir or Madam: This is an extension to a earlier post, about looping through several thousand files, and testing student's models against a different data-set, called rclnow, for "recall now". The problem is, that the instructor never speci

[R] Multiple Imputation in mice/norm

2009-04-25 Thread ToddPW
I'm trying to use either mice or norm to perform multiple imputation to fill in some missing values in my data. The data has some missing values because of a chemical detection limit (so they are left censored). I'd like to use MI because I have several variables that are highly correlated. In

[R] ordinal logistic regression for longitudinal data set

2009-04-25 Thread joy_stat
Hi, Can one tell me which procedure will fit an ordinal logistic regression model for longitudinal data set. To be precise, I have both dichotomous and polytomous items. Also, I would like to specify different covariance structures (unstructured, ar1 etc) for trial runs. Thanks -- V

[R] Request for some help

2009-04-25 Thread abdul hanan
Dera Graham I would highly be thankful if u help me how to do 1. Wilk's Lambda test 2. Box plots and 3. pooled within group standardization in discriminant analysis with 6 variables in R. Actually I am new to R but I have an assignment to analyse some questions only in R and there is drawback for

Re: [R] Loess over split data

2009-04-25 Thread Emmanuel Charpentier
Dear Luc, I stumbled on your unanswered question only this morning. Sorry for this lateness... Le jeudi 23 avril 2009 à 15:56 -0400, Luc Villandre a écrit : > Dear R users, > > I am having trouble devising an efficient way to run a loess() function > on all columns of a data.frame (with the x f

Re: [R] Can't install package "glmnet"

2009-04-25 Thread Tobias Verbeke
Uwe Ligges wrote: Liang Zhang wrote: I am just wondering how to solve this installation problem. As I said, ask your admin to install suitable compilers. And 'suitable compilers' in this case means to install the GNU compiler collection gcc 4.x.y. Contrary to gcc 3.x.y (which only has a F

Re: [R] Tinn-R and latex

2009-04-25 Thread Stefan Grosse
On Fri, 24 Apr 2009 22:35:05 -0700 (PDT) Roslina Zakaria wrote: RZ> I installed new version of R and Tinn-R and I just wonder why all RZ> my latex document change to Tinn-R symbol? Because Tinn-R also is able to edit tex documents and you probably missed the default document settings during the

[R] Reading files

2009-04-25 Thread Santosh
Dear R-sians Quick question... 1) From a flat (data) file with 100+ columns, how do I read specific columns instead of reading the entire dataset? I am trying to avoid reading the entire file followed by "subsetting". 2) is the a way to a call a column of dataframe through a variable.. e.g. e,g