[R] Unexpected behaviour with MBA algorithm

Hello helpers, I get some curious results, when I apply the MBA algorithm to my test set of scattered points. I'm using R v2.11.1 on Win XP with the package MBA v0.0-7 installed. Here is my code: rm(list=ls(all=TRUE)) library(MBA) library(fields) #regular 3x3 grid with all values zero, except

[R] Loading .RData from Internet

Dear All, Can you please suggest me a correct way to load the following R data frame from the internet and save it to the hard drive? The following is what I tried: raceprofiling - read.table(http://rss.acs.unt.edu/Rdoc/library/twang/data/raceprofiling.RData;) save(raceprofiling, file =

[R] lattice: strip panel function question

Dear list, If have some repeated measurement data which looks something like: time - rep(1:5 , each=2*4) groups - rep(c(Case, Control), each=4) subjects - factor(rep(1:(2*4), 5)) responses - time + rnorm(5*2*4) + as.integer(factor(groups)) data - data.frame(responses, time, groups, subjects)

Re: [R] knowing the code-number of factors in a vector

Hi! As Ben Bolker told you already, the levels are alphabetically ordered by default. When you print rfactor, the last line shows you the different levels, in the saved order. rfactor [1] c c c d b a b d d a a e e b b e c e e a a b b b a b a e a a b d b b c a b b [39] d c a e c d e d a a a

Re: [R] Loading .RData from Internet

Try with load() instead of read.table() read.table() is for csv, txt... files. load() is for R files Ivan Le 12/6/2010 09:35, zhiji19 a écrit : Dear All, Can you please suggest me a correct way to load the following R data frame from the internet and save it to the hard drive? The following

Re: [R] Loading .RData from Internet

I tried the load() already. It does not work. The erro is shown as following: Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection In addition: Warning message: In readChar(con, 5L, useBytes = TRUE) : cannot open compressed file

[R] Odp: Help with diff(sqrt()) function in terms of time series

Hi r-help-boun...@r-project.org napsal dne 05.12.2010 00:19:17: year1 is the time series data set below 11.64 11.50 11.49 11.16 11.15 11.37 11.37 11.57 11.83 11.87 11.85 11.92 11.77 11.71 11.57 11.24 11.27 11.33 11.17 . With a total of 1304 rows of data.

Re: [R] Loading .RData from Internet

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 12/06/2010 10:29 AM, zhiji19 wrote: I tried the load() already. It does not work. The erro is shown as following: load() works - I downloaded the data and then used load() - it works. I don't know if load() accepts an URL as a source, because

Re: [R] Loading .RData from Internet

On Mon, Dec 6, 2010 at 8:29 PM, zhiji19 zhij...@gmail.com wrote: I tried the load() already. It does not work. The erro is shown as following: Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection In addition: Warning message: In readChar(con, 5L, useBytes = TRUE) :  

[R] Help with capture.output

Hi Im trying to capture the output of HTML but dont really get what I want As an example: y-data.frame(a=c(1,2,3),b=c(1,2,3),c=c(1,2,3)) toReturn-capture.output(HTML(y,file=)); This gives me the output of toReturn as an vector: toReturn [1]

Re: [R] Loading .RData from Internet

You can create a connection to the URL and load() the connection. Like this: con - url('http://rss.acs.unt.edu/Rdoc/library/twang/data/raceprofiling.RData') load(file=con) close(con) str(raceprofiling) But the easiest way is to save the file and then load it. Ivan Le 12/6/2010 10:44, Rainer

Re: [R] Help with capture.output

Why to you always find the answer as soon as you have posted the Q here :P paste(toReturn, collapse=) But if anyone have a better solution plz share. //Joel -- View this message in context: http://r.789695.n4.nabble.com/Help-with-capture-output-tp3074192p3074199.html Sent from the R help

[R] [plyr] Question regarding ddply: use of .(as.name(varname)) and varname in ddply function

Dear R-Helpers: I am using trying to use *ddply* to extract min and max of a particular column in a data.frame. I am using two different forms of the function: ## var_name_to_split is a string -- something like var1 which is the name of a column in data.frame ddply( df,

[R] Help with GAM (mgcv)

Please help! Im trying to run a GAM: model3=gam(data2$Symptoms~as.factor(data2$txerad)+s(data2$maritalStatus),family=binomial,data=data2) But keep getting this error: Error in dl[[i]] : subscript out of bounds Can someone please tell me what this error is? Thanks -- View this message in

[R] Urgent Help with R calculation correlation coefficient

Hi, I am trying to calculate correlation coefficient for gene expression data. Tab delimited file looks like this Id v1 v2v3 df 56 9045 gh 87 9878 ty 897867 I used this code [code] gse20437 - read.csv(C:/Users//Desktop/data/GSE20437_matrix.txt,header = TRUE, sep =

Re: [R] plot more plots from one matrix

Hi r-help-boun...@r-project.org napsal dne 03.12.2010 16:56:37: I solved the 1° problem with this command: matrix2plot2[,sensor_data]-as.numeric(as.character((matrix2plot2[,sensor_data]))) In fact before the previous command I if write: str(matrix2plot2[,sensor_data]) I get:

Re: [R] lattice: strip panel function question

Dear Maarten xyplot has the argument groups which allows you to create nested groupings. data$subjectID - paste(data$groups, data$subjects) # create a character label xyplot(responses~time|subjectID, groups = groups, data = data, aspect=xy) # or change to a factor to define the plot order

Re: [R] How to catch both warnings and errors?

Hmm... still not quite what I was hoping for... but thanks anyway. I would like to have the output in the following form: f(1) $result [1] 0 $warning [1] NULL # or $error [1] NULL # or f(-1) $result [1] NaN $warning [1] Warning in log(-1) : NaNs produced # or something similar $error

[R] R 2.12.1 scheduled for December 16

This is to announce that we plan to release R version 2.12.1 on Thursday, December 16, 2010. Those directly involved should review the generic schedule at http://developer.r-project.org/release-checklist.html The source tarballs will be made available daily (barring build troubles) via

Re: [R] Urgent Help with R calculation correlation coefficient

On Mon, Dec 6, 2010 at 11:02 AM, chintan85 chintanpatha...@yahoo.com wrote: Hi, I am trying to calculate correlation coefficient for gene expression data. Tab delimited file looks like this Id v1   v2    v3 df 56   90    45 gh 87   98    78 ty 89    78    67 I used this code [code]

[R] Odp: Urgent Help with R calculation correlation coefficient

Hi r-help-boun...@r-project.org napsal dne 06.12.2010 11:02:03: Hi, I am trying to calculate correlation coefficient for gene expression data. Tab delimited file looks like this Id v1 v2v3 df 56 9045 gh 87 9878 ty 897867 I used this code [code]

Re: [R] Odp: Urgent Help with R calculation correlation coefficient

On Dec 6, 2010, at 11:28 , Petr PIKAL wrote: Hi r-help-boun...@r-project.org napsal dne 06.12.2010 11:02:03: Hi, I am trying to calculate correlation coefficient for gene expression data. Tab delimited file looks like this Id v1 v2v3 df 56 9045 gh 87 9878

Re: [R] Urgent Help with R calculation correlation coefficient

On 2010-12-06 02:02, chintan85 wrote: Hi, I am trying to calculate correlation coefficient for gene expression data. Tab delimited file looks like this Id v1 v2v3 df 56 9045 gh 87 9878 ty 897867 I used this code [code] gse20437-

Re: [R] Help with GAM (mgcv)

On Monday 06 December 2010 09:33, Stressed1985 wrote: Please help! Im trying to run a GAM: model3=gam(data2$Symptoms~as.factor(data2$txerad)+s(data2$maritalStatus),fa mily=binomial,data=data2) But keep getting this error: Error in dl[[i]] : subscript out of bounds Can someone please tell

Re: [R] Urgent Help with R calculation correlation coefficient

Try excluding the first column. cor(gse20437[, 2:4]) chintan85 wrote: Tab delimited file looks like this Id v1 v2v3 df 56 9045 gh 87 9878 ty 897867 I used this code [code] gse20437 - read.csv(C:/Users//Desktop/data/GSE20437_matrix.txt,header =

Re: [R] [plyr] Question regarding ddply: use of .(as.name(varname)) and varname in ddply function

On 2010-12-06 01:58, Sunny Srivastava wrote: Dear R-Helpers: I am using trying to use *ddply* to extract min and max of a particular column in a data.frame. I am using two different forms of the function: ## var_name_to_split is a string -- something like var1 which is the name of a column in

Re: [R] [plyr] Question regarding ddply: use of .(as.name(varname)) and varname in ddply function

Here is another approach to try: require(data.table) var - g10 df - data.table(df) str(df) Classes ‘data.table’ and 'data.frame': 6 obs. of 5 variables: $ g10: int 1 1 1 10 10 10 $ l1 : num 0.41 0.607 0.64 -1.478 -1.482 ... $ d1 : num 0.918 0.959 0.773 0.474 0.591 ... $ l13: num

[R] make check from R2.12.0.exe installation

Hi, I typically install new versions of R on windows using the downloadable executable file rather than the full tar. I need to now document the success of the installation in addition to my preferred procedure of running an old dataset against the new build. I found quickly that this is

Re: [R] Urgent Help with R calculation correlation coefficient

On Mon, Dec 6, 2010 at 11:30 AM, Peter Ehlers ehl...@ucalgary.ca wrote: If you have a *tab*-delimited file, then why are your using read.csv?? Try this: 1. read your data with read.table() or read.delim() If you're very new to R, try Rcmdr. Data Import Text file. Liviu

Re: [R] Help with GAM (mgcv)

Thank you for your reply! It says: This is mgcv 1.5-5 . For overview type `help(mgcv-package)'. Its version: R 2.9.2 And summary(data2) gives: id age bmi siblingsgender Min. : 1.0 Min. :32.19 Min. :16.41 Min. :0.000

[R] Understanding the output from lme.anova

I have a question regarding understanding the output from a nested linnear mixed effect model. My model looks like the following lme(Poaceae~Site+Ditch_block+Tree_cut+as.factor(Dist_start)+(as.factor(Dist_start)*Tree_cut)+((as.factor(Dist_ditch))/Ditch_block),random=~1|Mainplot/Transect/Obsplot)

[R] Understanding the output from lme anova

I have a question regarding understanding the output from a nested linnear mixed effect model. My model looks like the following lme(Poaceae~Site+Ditch_block+Tree_cut+as.factor(Dist_start)+(as.factor(Dist_start)*Tree_cut)+((as.factor(Dist_ditch))/Ditch_block),random=~1|Mainplot/Transect/Obsplot)

Re: [R] Runif Help: same variable, 3 different parameters

On 05/12/2010 10:13 PM, pythonomics wrote: So I am working on an economic model and I need to change the parameters of the runif statement as time goes on. Ex. X-runif(1:50,0,5) X-runif(51:100,100,150) X-runif(100:T, 1,2) Not sure how to go about entering this in to R properly. It's not

[R] as.xts error

Dear all, I am using the as.xts function to transfer a data frame to the xts The following is the code and result: a-read.csv(price.csv) a$Date-as.POSIXct(a$Date) str(a) 'data.frame': 15637 obs. of 2 variables: $ Date : POSIXct, format: 2010-01-04 09:45:01 2010-01-04 09:45:02

Re: [R] Help with GAM (mgcv)

Probably the problem is with trying to smooth maritalStatus, which is a factor variable. Smooths are generally functions of metric variables (i.e. variables that take numerical values, where the ordering is meaningful). You can have random effect smooths and markov random field smooths in more

Re: [R] as.xts error

On Mon, Dec 6, 2010 at 6:52 AM, Ted Zeng (曾振兴) zengzhenx...@gmail.com wrote: Dear all, I am using the as.xts function to transfer a data frame to the xts The following is the code and result: a-read.csv(price.csv) a$Date-as.POSIXct(a$Date) str(a) 'data.frame':   15637 obs. of  2

Re: [R] Help with GAM (mgcv)

Ok, i just tried this: library(mgcv) model3=gam(data2$Symptoms~as.factor(data2$txerad)+as.factor(data2$maritalStatus),family=binomial,data=data2) And im still getting this error! Error in dl[[i]] : subscript out of bounds -- View this message in context:

Re: [R] Help with GAM (mgcv)

OK, try... model3=gam(Symptoms~as.factor(txerad)+as.factor(maritalStatus),family=binomial,data=data2) or model3=gam(data2$Symptoms~as.factor(data2$txerad)+as.factor(data2$maritalSt atus),family=binomial) ... both types of construction work with the current mgcv:gam (and with glm). Your

Re: [R] Help with GAM (mgcv)

Ye Thank you so much, finally i have something to look at. Just got to interpret the bloomin' thing now! -- View this message in context: http://r.789695.n4.nabble.com/Help-with-GAM-mgcv-tp3074165p3074414.html Sent from the R help mailing list archive at Nabble.com.

[R] Error with Rserv

Hi I get this error with Rserve: eval failedeval failed, request status: R parser: syntax erroreval failed, request status: R parser: input incompleteorg.rosuda.REngine.Rserve.RserveException: eval failed at org.rosuda.REngine.Rserve.RConnection.eval(RConnection.java:233) at

Re: [R] Tinn-R 2.3.7.0 released

I am also finding the link between TINN - R (2.3.7.0) and R (2.12.0 2010 - 10 - 15) to be problematic. source(.trPaths[5], echo=TRUE, max.deparse.length=150) Error in source(.trPaths[5], echo = TRUE, max.deparse.length = 150) : object '.trPaths' not found Steve Friedman Ph. D. Ecologist

[R] R CMD SHLIB Error

Hi! I'm a new programmer in R Last week i wrote many function in C and i used R CMD SHLIB to make dll. Since friday i have this error: cygwin warning: MS-DOS style path detected: C:\PROGRA~1\R\R-211~1.1/bin/SHLIB.sh Preferred POSIX equivalent is:

[R] Optimize multiple variable sets

Hi, I usually use optimize function for ML Estimation. Now I´ve got a data frame with many sets, but I can´t save estimates each time I run the code for each data set (I´m using a for loop with my loglikelihood function and works ok but when I apply another for loop to:

Re: [R] lattice: strip panel function question

Thanks Chris Campbell, I didn't though about that. Cheers, Maarten On Mon, 2010-12-06 at 10:08 +, Chris Campbell wrote: data$subjectID - paste(data$groups, data$subjects) # create a character label xyplot(responses~time|subjectID, groups = groups, data = data, aspect=xy) --

Re: [R] Optimize multiple variable sets

Correct me if I'm wrong, but isn't the minimal x value in your example the same regardless of what positive coefficient you apply to x? If that is the case, you would expect the same min(x) for each iteration. i.e. in the interval [0,1] the minimum x value of x^2 + x is the same as x^2 +

Re: [R] Optimize multiple variable sets

On Dec 6, 2010, at 15:15 , Jonathan P Daily wrote: Correct me if I'm wrong, but isn't the minimal x value in your example the same regardless of what positive coefficient you apply to x? If that is the case, you would expect the same min(x) for each iteration. i.e. in the interval [0,1]

[R] Change intervals in apply.weekly

I am using the function apply.weekly() from the xts package and I realized that for the program the week starts Tuesday. So for instance, with a series like this: Close 2006-07-03 3.00 2006-07-04 36738.00 2006-07-05 36207.00 2006-07-06 36534.00 2006-07-07 36434.00 2006-07-10

[R] From ts to xts

I have the following problem. After having created an xts importing data from a csv with: data - read.csv(mib.csv, header = TRUE, dec = ., sep=\t) dates - as.POSIXct(strptime(data[,1],format=%m/%d/%Y)) mib - xts(data[,c(2:6)],order.by=dates)) I work out weekly log returns: p -

Re: [R] Optimize multiple variable sets

I suppose I should have been more clear. I saw that her interval did not include the actual minimum, but I was asking if (and if, why) she was expecting the minimum x value to be different for each run. If the y value were returned the same on each run that would be puzzling. As for the

[R] Connect SQL Oracle server

Hi, I use Oracle sql developer to connect to a server. I would like to connect to the server directly from R by using odbcConnect(DB name) function. I am trying to make first the connection below Control Pannel-Datasource (ODBC). Which software should I select here? Which one is suitable for

[R] help getting data in correct format

Dear All, I am having trouble getting my data into R as i need it! I am used to using read.delim() to open .txt files to do work on. The function i am using requires a matrix like the one below. My data is from excel and then saved as a txt file. I have tried the usual read.delim() approach

[R] npRmpi memory error

Hi List, I'm using npRmpi to run some density equality tests and place the output into a matrix. I've put together some crude functions for the purpose, but I'm receiving the following error when npdeneqtest() reached the bootstrap; FATAL ERROR: Memory allocation failure (type DBL_VECTOR).

[R] less than full rank contrast methods

I'd like to make a less than full rank design using dummy variables for factors. Here is some example data: when - data.frame(time = c(afternoon, night, afternoon, morning, morning, morning, morning, afternoon, afternoon),

Re: [R] Can't read data coded in Cyrillic

I suspect that R is reading the data just fine, but is not displaying it as you want to see it. Read the R Windows FAQ 3.3. Dan Winetsky dwine...@gmail.com wrote: To whom it may concern, I have a database (an SPSS .sav file) with some vectors containing strings of words in Cyrillic. My

[R] How to formulate constraint like abs(x) = y in constrOptim (or other)

Hello list reader, I am trying to form some constraints for an optimization I am working on. I think I have understand the use of the constraints in matrix form. I use them like: constr_mat- -diag(2) constr_vec- rep(-0.05,2) constr_mat- rbind(constr_mat, diag(2)) constr_vec- c(constr_vec,

Re: [R] help getting data in correct format

When I try to read data from excel, I save it in csv-format and read the files via: fileData -read.csv(fkFileName, header = fkHasHeader, stringsAsFactors=FALSE, sep=fkSep) where fkSep is depending on your localization of excel (I think). For some columns that don’t get the correct data format

Re: [R] as.xts error

On Mon, Dec 6, 2010 at 5:57 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Mon, Dec 6, 2010 at 6:52 AM, Ted Zeng (曾振兴) zengzhenx...@gmail.com wrote: Dear all, I am using the as.xts function to transfer a data frame to the xts The following is the code and result:

[R] use pcls to solve least square fitting with constraints

Hi, I have a least square fitting problem with linear inequality constraints. pcls seems capable of solving it so I tried it, unfortunately, it is stuck with the following error: M - list() M$y = Dmat[,1] M$X = Cmat M$Ain = as.matrix(Amat) M$bin = rep(0, dim(Amat)[1])

[R] How can I refer to actual (n) and previous (n-1) elements in a vector?

Hello, How can I apply a function on a vector that refers to actual (n) and previous elements in the vector (e.g. n-1)? For example: I would like to calculate the sum of (n-1) + n for each element of a vector and get a vector as a result. Besides others I tried this:

Re: [R] How can I refer to actual (n) and previous (n-1) elements in a vector?

-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Marianne Stephan Sent: Monday, December 06, 2010 9:13 AM To: r-help@r-project.org Subject: [R] How can I refer to actual (n) and previous (n-1) elements in a vector? Hello,

Re: [R] How can I refer to actual (n) and previous (n-1) elements in a vector?

-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Nordlund, Dan (DSHS/RDA) Sent: Monday, December 06, 2010 9:21 AM To: r-help@r-project.org Subject: Re: [R] How can I refer to actual (n) and previous (n-1) elements in a vector?

Re: [R] How can I refer to actual (n) and previous (n-1) elements in a vector?

Hi Marianne, You have to be very careful with subsetting when doing something like that - that's where you went wrong with your original construct. This version works: v-c(3,6,8,1,1,3,9,5,6,3) a - numeric(length(v)-1) for (i in 2:length(v)) {a[i-1] - v[i-1] + v[i]} a [1] 9 14 9 2 4 12 14

Re: [R] book about support vector machines

My favorite book on SVM is Learning with Kernels by Scholkopf and Smola. You might also want to consider a relevance vector machine, which is a more recent development. RVM is Bayesian-based and usually produces a sparser representation than a SVM. Check out Mike Tipping's web site at

Re: [R] Optimize multiple variable sets

Let us look at the objective function: f(x) = x^2 + Si * x, where Si is the sum of the i-th column. This function has a stationary point at x = -Si/2, and the second derivative is 2, so it is a minimum. Now, the column sums of your data matrix are all positive. So, your minimum has to be

Re: [R] book about support vector machines

hi: i don't know that book but there's another pretty new book on svms by lutz hamel. It's pretty gentle but very nice, especially if you have ZERO background on svms. there's also another one titled an introduction to svms by cristianini and shawne-taylor that's also quite good but much more

[R] Cutting Matrix

I have got a matrix with 100 values. Is there a easy way to cut the upper 10% (every value which is above 90%) and the lower 10% of my matrix-values away and create a new matrix with all the rest. Thx for your help Marty -- View this message in context:

Re: [R] Quadratic programming with semi-definite matrix

Andreas Jensen bentrevisor at gmail.com writes: Hello. I'm trying to solve a quadratic programming problem of the form min ||Hx - y||^2 s.t. x = 0 and x = t using solve.QP in the quadprog package but I'm having problems with Dmat not being positive definite, which is kinda okay since I

Re: [R] Optimize multiple variable sets

peter dalgaard pdalgd at gmail.com writes: On Dec 6, 2010, at 15:15 , Jonathan P Daily wrote: Correct me if I'm wrong, but isn't the minimal x value in your example the same regardless of what positive coefficient you apply to x? If that is the case, you would expect the same min(x) for

Re: [R] How to formulate constraint like abs(x) = y i n constrOptim (or other)

Benjamin B. benj.bad.ac at googlemail.com writes: Hello list reader, I am trying to form some constraints for an optimization I am working on. I think I have understand the use of the constraints in matrix form. I use them like: [...] Now I would like to formulate a constraint like

Re: [R] Tukey Test, lme, error: less than two groups

Hi Steven, thank you again so much for your help and for the transformation of the data. In fact I knew that there are these empty lines in the data. I couldn't take them off with the program I have. I tried to solve this problems with using the levels. You are right, the statistical tests

Re: [R] Cutting Matrix

You can use quantile and cut: x - runif(1000) x.cut - cut(x, c(-Inf, quantile(x, prob=c(.1, .9)), Inf), labels=c('lo','mid','hi')) table(x.cut) x.cut lo mid hi 100 800 100 On Mon, Dec 6, 2010 at 12:53 PM, Marty_H churc...@alpenjodel.de wrote: I have got a matrix with 100 values. Is

Re: [R] less than full rank contrast methods

Have you tried setting singular.ok=TRUE in the call to lm? This will start with the full set of contrasts, but only fit those that it is able to. Otherwise you can set specific contrasts or subsets using the C (note case) or contrasts functions. -- Gregory (Greg) L. Snow Ph.D. Statistical

Re: [R] How to get 'R' to talk BACK to other languages / scripts??

Ista, Thanks for this method, it works! Unfortunately 'R' still spits everything out to std out, but the variable as you describe below grabs only the final output variable, similar to how functions or scripts work internally within 'R'. Thanks! Kjetil, Thanks also for your input, but

[R] package ca/rgl for ubuntu?

hi, for some unknown reason i cannot install the package ca in R running in a ubuntu mint system. i keep getting the following error message: configure: error: missing required header GL/gl.h ERROR: configuration failed for package ‘rgl’ * removing

Re: [R] package ca/rgl for ubuntu?

On 06/12/2010 1:45 PM, Manderscheid Katharina wrote: hi, for some unknown reason i cannot install the package ca in R running in a ubuntu mint system. i keep getting the following error message: You need the development package for OpenGL or MesaGL to install rgl. I don't know Ubuntu so I

[R] Sparse matrix performance question

I have a very sparse square matrix which is 20K rows columns and I am trying to row standardize the matrix for the rows that have non-missing value as follows: row_sums - rowSums(M,na.rm=TRUE) nonzero_idxs - which(row_sums0) nonzero_M - M[nonzero_idxs,]/row_sums[nonzero_idxs] M[nonzero_idxs,] -

Re: [R] package ca/rgl for ubuntu?

thanks a lot, duncan for that super-fast reply and help! i could install rgl via synaptic and afterwards ca in R directly. and it works! :-) have a nice evening, kat Von: Duncan Murdoch [murdoch.dun...@gmail.com] Gesendet: Montag, 6. Dezember 2010 19:55

Re: [R] Sparse matrix performance question

Btw, forgot to mention I am using the standard Matrix package and I am running version 2.10.1 of R. On Mon, Dec 6, 2010 at 11:04 AM, scott white distributedin...@gmail.comwrote: I have a very sparse square matrix which is 20K rows columns and I am trying to row standardize the matrix for the

Re: [R] book about support vector machines

Hi, On Fri, Dec 3, 2010 at 10:23 AM, manuel.martin manuel.mar...@orleans.inra.fr wrote: Dear all, I am currently looking for a book about support vector machines for regression and classification and am a bit lost since they are plenty of books dealing with this subject. I am not totally new

Re: [R] Perl cut equivalent in R

if(FALSE) { stuff your don't want executed          } Switching a block of code off/on with editing a single character may be done using 0/1 instead of FALSE/TRUE. Or even F/T -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering Cancer Center  |

[R] getting the exact p value

I was wondering if there is a way to get an exact p-value at times where R gives me just a range . for example t.test(x,y) p-value 2.2e-16 thanks, -- View this message in context: http://r.789695.n4.nabble.com/getting-the-exact-p-value-tp3075107p3075107.html Sent from the R help mailing

[R] read ESRI file geodatabase feature classes

Hello- Does anyone know if R can read in ESRI file geodatabase feature classes, directly from the file geodatabase? I currently have to export the data out of Arc, to a csv file, then read the csv file. I'd like to bypass this step and read directly from the file geodatabase. Thanks for your

[R] Loglinear models for missing data

Dear, I have the data in the following form: head(matrices_m) Location Variable Value Week 1 Africa Africa21 4 weeks 2 Asia Africa 0 4 weeks 3 Canada Africa17 4 weeks 4China Africa29 4 weeks 5 Europe AfricaNA 4 weeks 6Japan Africa68 4

Re: [R] Cutting Matrix

In this case I only get three values back. My intention was to get every value between 10% and 90% i.e. let's say i have a matrix 1 2 3 4 5 6 7 8 9 10 11 12 i only want the values above 10% and under 90%. Maybe i should try it with a loop. -- View this message in context:

Re: [R] getting the exact p value

Hi, It depends on the function used to calculate it---each has their own way of extracting particular values. Here's an example for t.test: x - rnorm(10, 100, .1); y - x - 100 t.test(x, y)$p.value You could find this yourself by looking at the documentation for t.test() ?t.test The heading

[R] waldtest and nested models - poolability (parameter stability)

Dear All, I'm trying to use waldtest to test poolability (parameter stability) between two logistic regressions. Because I need to use robust standard errors (using sandwich), I cannot use anova. anova has no problems running the test, but waldtest does, indipendently of specifying vcov or

Re: [R] use pcls to solve least square fitting with constraints

Baoqiang Cao bqcaomail at gmail.com writes: I have a least square fitting problem with linear inequality constraints. pcls seems capable of solving it so I tried it, unfortunately, it is stuck with the following error: M - list() M$y = Dmat[,1] M$X = Cmat M$Ain = as.matrix(Amat)

Re: [R] mgcv package plot superimposing smoothers

Hi Jef, I would extract the information about the smoothers and plot them using standard plotting routines. After Mtest - gam(outcome ~ s(age, by=as.numeric(gender==0)) + s(age,by=as.numeric(gender==1))+factor(Gender)) run something similar to: smoothers - predict(s,type='terms') and you

Re: [R] read ESRI file geodatabase feature classes

No there is no open software to read ESRI file geodatabases (the .gdb ones). If it's not .gdb but .mdb (personal geodatabase, built on Microsoft Access database) then you can read it with generic tools (such as RODBC package) or with an appropriate build of GDAL as part of the rgdal package.

Re: [R] waldtest and nested models - poolability (parameter stability)

On Mon, 6 Dec 2010, Roberto Patuelli wrote: Dear All, I'm trying to use waldtest to test poolability (parameter stability) between two logistic regressions. Because I need to use robust standard errors (using sandwich), I cannot use anova. anova has no problems running the test, but

Re: [R] waldtest and nested models - poolability (parameter stability)

Dear Achim, Thanks a lot for the superquick reply! Somehow with your suggestion I can get around the problem, but of course I run into other problems, such as this: waldtest(inv.log.leva.base, inv.log.leva, test = Chisq, vcov = sandwich) Error in bread. %*% meat. : non-conformable arguments

Re: [R] waldtest and nested models - poolability (parameter stability)

On Mon, 6 Dec 2010, Roberto Patuelli wrote: Dear Achim, Thanks a lot for the superquick reply! Somehow with your suggestion I can get around the problem, but of course I run into other problems, such as this: waldtest(inv.log.leva.base, inv.log.leva, test = Chisq, vcov = sandwich) Error

[R] R cmd batch with parameters

hello! I'm trying to make a very simple calculation using R that would called from bash with two parameters, the names of the input and output files. the first one is just an 4 by 100 numerical table- the function finds the index of the maximal elements in each columns and writes it into the

[R] Help with plit plot design in logit model

Hi, I'm trying to fit a logit model to a set of data that was collected under a split plot scheme. The structure of the data is Whole plot factors: Watering Frequency (2 levels: Hi/Lo) and Fertilizer type (3 factors A/B/C) Subplot factor: slope type (2 factors up/down) Response: Proportion of

Re: [R] Troubles in plotting to a postscript file (not to png)

Hi I think the problem is that the viewer you are using for the PS file cannot find the ComputerModern fonts that are referenced in the PS file. If you use something like ghostscript to process the file you can see this happening ... [pmur...@stat18 Temp]$ gs plot_example.ps ESP

[R] Appearance of Forest Plot

Hi All, I have conducted a meta analysis using the metabin function. I want to plot 5 subgroups on the same forest plot. I have managed to do this using the byvar argument but when i plot the forest plot in R graphics I am unable to view the very top and very bottom of the image. It is as though

Re: [R] Appearance of Forest Plot

Hi, Can you give a reproducible example of what you did? My intuition is that you could do it using par(), but I am not sure what package metabin() is from (certainly none of the ones that load by default), and I have even less idea how you created a forest plot (there are many ways in R). If

Re: [R] Cutting Matrix

With the result of the 'cut' you can get a direct index for the values: x - runif(20) x [1] 0.26550866 0.37212390 0.57285336 0.90820779 0.20168193 0.89838968 0.94467527 0.66079779 0.62911404 [10] 0.06178627 0.20597457 0.17655675 0.68702285 0.38410372 0.76984142 0.49769924 0.71761851 0.99190609

Re: [R] [plyr] Question regarding ddply: use of .(as.name(varname)) and varname in ddply function

On Mon, Dec 6, 2010 at 3:58 AM, Sunny Srivastava research.b...@gmail.com wrote: Dear R-Helpers: I am using trying to use *ddply* to extract min and max of a particular column in a data.frame. I am using two different forms of the function: ## var_name_to_split is a string -- something like

[R] Please help with write.foreign(SPSS)

Dear all, I get stuck when i try to export the data into SPSS format/file using write.foreign() Do you know how to do it exactly? What i have done is 1) First i type the following code in R: df-data.frame(id,year,res1) names(df)-c(idcode,year,resarrvl)

  1   2   >