Re: [R] replicating C example from the Extensions Manual problem

2012-03-14 Thread Peter Langfelder
Seems you're missing the required header(s). Can't find the example in the extensions manual but you probably need #include or #include HTH, Peter On Wed, Mar 14, 2012 at 11:03 PM, Erin Hodgess wrote: > Dear R People: > > Here is something that I am sure is very simple.  I'm just trying t

Re: [R] replicating C example from the Extensions Manual problem

2012-03-14 Thread Jeff Newmiller
Do you really expect is to know how to figure out the error if you don't give us the code that the error is pointing at (or the code preceding the error, which may be at fault)? Please think before posting. --- Jeff Newmiller

Re: [R] replicating C example from the Extensions Manual problem

2012-03-14 Thread Joshua Wiley
Hi Erin, If you are just starting with including compiled code, I would highly recommend the Rcpp + inline packages. I attached a small example of how it works, but basically you get to inline C++ code in R files. Cheers, Josh P.S. I wrote this snippet awhile ago when I did not know much about

Re: [R] replicating C example from the Extensions Manual problem

2012-03-14 Thread Berwin A Turlach
G'day Erin, On Thu, 15 Mar 2012 01:03:59 -0500 Erin Hodgess wrote: > What is wrong, please? Missing #include #include In particular the latter is defining R_len_t. Guess that code snippet in the manual is only showing the code of the function, but not the complete file that needs to be com

[R] replicating C example from the Extensions Manual problem

2012-03-14 Thread Erin Hodgess
Dear R People: Here is something that I am sure is very simple. I'm just trying to re-create the C convolution example in the Extensions manual. Here is the subroutine: void convolve(double *a, int *na, double *b, int *nb, double *ab) { R_len_t i, j, nab = *na + *nb - 1; for(i = 0; i < nab; i++

[R] R CMD Rd2pdf [options] files

2012-03-14 Thread casperyc
Hi all, Sorry if I seem a bit pissed because I am! Basically, I have written some script and I wanted to make a "documentation" for it using .Rd format. I followed the example here in http://stat.ethz.ch/R-manual/R-de

[R] coloring wireframe plot with independent/separate matrix of color values.

2012-03-14 Thread Alex Miller
Dear R Users, I am trying to plot a matrix (a Digital Elevation Model) using wireframe [lattice] and color that matrix based on a separate/independent matrix of the same resolution (both have the same number of rows and columns) as the DEM. More specifically I would like to plot a DEM using wiref

[R] Re : ROC Analysis

2012-03-14 Thread Pascal Oettli
Hi Camille, I am surprised by your answer. If you do: pred <- prediction(ROCR.simple$predictions*1000, ROCR.simple$labels) x <- rev(unlist(pred@cutoffs)) You can see than x values are now between 0 and 1000. So, it should be probably the same for your data. Regards, Pascal -- View this me

Re: [R] subset problem

2012-03-14 Thread jim holtman
Supply an 'str' of your dataframe so we can see what its structure is. Do you have leading/trailing blanks in your ROUTE values. Print them out and see what their number of characters (nchar) are. Are they factors? You have not supplied enough information like a small subset. I bet when you c

Re: [R] qmvnorm function

2012-03-14 Thread Rui Barradas
Hello, > > Thanks Rui. > > Sorry I forgot to mention what is the "var" in the previous message. It > seems > that when the correlation is small, it does not work. > See below. > It works in my system: (your first example) var <- matrix(c(1,0.05,0.05,1), nrow=2, ncol=2, byrow=T) var [,1] [

[R] Logistic Regression Coding Help

2012-03-14 Thread Craig P O'Connell
Hello. I am beginning to analyze my work and have realized that a simple chi-square analysis will not suffice for my research, with one notable reason is that data are not discrete.  Since my data fit the assumptions of a logistic regression, I am moving forward with this analysis.  With t

Re: [R] sort list

2012-03-14 Thread sybil kennelly
O yea sure. So for example: grid <- read.table("table") ( i havent printed the output, as the table is 20,000 rows X 60 columns) point_of_interest <- c("row1", "row2") therefore all the other points in plot(table) are labelled green, but these two are labelled red. But at the minute, becaus

Re: [R] Maximization problem in the optim function

2012-03-14 Thread Niroshan
This is the part of the function in my likelihood function prob<-function(t1,t2,m1,m2,s_r,s_p,s_e,cor_m){ if ((t1==0) & (t2==0)) log_lik<-log(pmvnorm(lower=rep(-Inf, 2), upper=c(m1/sqrt(s_r+s_p+s_e+1),m2/sqrt(s_r+s_p+s_e+1)), mean=rep(0,2), corr=cor_m)) else if ((t1==0) & (t2==1)) log_lik<

Re: [R] Apply a loop containing a function on a list

2012-03-14 Thread jim holtman
Without a subset of data, it is hard to come up with a solution. Now here is a way of determining what names are in common and then maybe doing something: B.names <- names(B.list) A.names <- names(A.list) common <- intersect(B.names, A.names) for (i in common){ B.list[[i]] <- function(A.list[

[R] Help with operation on list of matrices

2012-03-14 Thread Axel Urbiz
I'll appreciate your help on this. I have values stored in a list as in "mylist" below. I need to sum the values over all elements of the list aggregated by the names of the matrices. mylist <- list(matrix(c(0.2, 0.4), 1, 2, dimnames = list(NULL, c("1", "2"))), matrix(c(0.1, 0.5

[R] subset problem

2012-03-14 Thread Farley, Robert
I'm having a simple problem with subset. I'm choosing what I think is a valid selection, but I either get everything or an empty dataframe. What am I doing wrong? > > describe(OBDataSumm) Description of OBDataSumm Numeric meanmedian varsd valid.n SAMP

Re: [R] NA - data.frame

2012-03-14 Thread R. Michael Weylandt
Try this. x <- matrix(1:3, nrow = 1) y <- matrix(1:6, nrow = 1) z <- matrix(1:10, nrow = 1) library(plyr) do.call("rbind.fill.matrix", list(x,y,z)) Note that x,y,z need to be made into matrices before this works. Michael On Wed, Mar 14, 2012 at 6:31 PM, Zenonn87 wrote: > Hello! > > How can I

Re: [R] qmvnorm function

2012-03-14 Thread li li
Thanks Rui. Sorry I forgot to mention what is the "var" in the previous message. It seems that when the correlation is small, it does not work. See below. > var <- matrix(c(1,0.05,0.05,1), nrow=2, ncol=2, byrow=T) > var [,1] [,2] [1,] 1.00 0.05 [2,] 0.05 1.00 > qmvnorm(0.05, tail="upper", s

Re: [R] sort list

2012-03-14 Thread R. Michael Weylandt
Errr...I'm still not sure how plot(table) gives you read and green points, but it sounds like the easiest thing to do would be to use the points() function to come back in and put new green points over the red ones. E.g. plot(runif(5000), runif(5000)) points(c(0.5, 0.25), c(0.5, 0.75), col = 2, pc

Re: [R] Maximization problem in the optim function

2012-03-14 Thread R. Michael Weylandt
What distribution's log-likelihood are you using? If sigma is supposed to be square-rooted, you may have to put a constraint or use of abs() might suffice -- though, admittedly I'm not sure what that will do to convergence behavior -- but it's hard to help without seeing the function at hand. Mich

[R] Improving help in R

2012-03-14 Thread Tomáš Křehlík
Hello R people I always wander what other people say about the R help. Finally after some years of using, I decided that it is probably time to try to do something about it, because the feeling of gritting teeth does not go away with years of usage. :) Moreover, I think it is one of the few thi

[R] Maximization problem in the optim function

2012-03-14 Thread Niroshan
Dear R Users I am maximizing a user defined log likelihood function. It includes variance parameter (sigma). I used R function optim with BFGS maximization method. However, it stops before the solution saying “sqrt(sigma): NaNs produced” Could anybody know a proper transformation for sigma which

[R] NA - data.frame

2012-03-14 Thread Zenonn87
Hello! How can I top up with NA instead of repeat numbers when I am making data.frame? I have made vectors (6. peace) form a table with different length (5,10,15,20,25,30 data). I want put these vectors into a data.frame but in the smaller columns the numbers repeat continuously to fill up the em

Re: [R] logical test not functioning correctly on zoo series...what the hell?

2012-03-14 Thread knavero
Thanks Gabor. colClasses did the trick. Also, I'll be sure to minimize the reproducible example the next time around using a text quote. Sorry about the noob mistake. -- View this message in context: http://r.789695.n4.nabble.com/logical-test-not-functioning-correctly-on-zoo-series-what-the-hell-

Re: [R] qmvnorm function

2012-03-14 Thread Rui Barradas
Hello, li li-13 wrote > > Dear all, >I need to use the "qmvnorm" function in mtvnorm package. > > Here is the error message I got >> qmvnorm(0.05, tail="upper", sigma=var)$quantile > Error in uniroot(pfct, interval = interval) : > f() values at end points not of opposite sign > > There is

Re: [R] Metropolis-Hastings in R

2012-03-14 Thread Michael Williams
Thanks, this isn't actually homework though. I'm researching MCMC methods but I've never really used R before so it's proved quite troublesome! my code is now: n=1 mu=0 sigma=1 lik<-function(theta) exp((-(theta-mu)^2)/2) alpha<-function(theta,phi) min(lik(phi)/lik(theta),1) theta1<-c(0,n) the

Re: [R] Using the mantel test in Ape Package

2012-03-14 Thread Sarah Goslee
Hi, On Wed, Mar 14, 2012 at 2:21 PM, Dorothea Hill wrote: > Hi, > > I am trying to use a mantel test on two distance matrices. The code I have > entered for each is: > > Gen_dists <- read.csv(file.choose(), >                                                stringsAsFactors = FALSE, >            

Re: [R] Help: problem converting character to numeric

2012-03-14 Thread Gabor Grothendieck
On Wed, Mar 14, 2012 at 6:07 PM, Aurélien PHILIPPOT wrote: > Dear R experts, > I have a dataframe imported from a csv file (with read.csv). > > Here is an example: > > mm<- c("19860228", "19860331","19860430","19860531") > id<-c("1","1","1","1") > re<- c("C","0.25", "0.98", "1.

Re: [R] Help: problem converting character to numeric

2012-03-14 Thread Aurélien PHILIPPOT
thanks for your suggestions, which work. In addition, I updated Rstudio to the latest version and my old code works again. Best, Aurelien 2012/3/14 Petr Savicky > On Wed, Mar 14, 2012 at 03:07:19PM -0700, Aurélien PHILIPPOT wrote: > > Dear R experts, > > I have a dataframe imported from a csv f

Re: [R] Help: problem converting character to numeric

2012-03-14 Thread Petr Savicky
On Wed, Mar 14, 2012 at 03:07:19PM -0700, Aurélien PHILIPPOT wrote: > Dear R experts, > I have a dataframe imported from a csv file (with read.csv). > > Here is an example: > > mm<- c("19860228", "19860331","19860430","19860531") > id<-c("1","1","1","1") > re<- c("C","0.25", "

Re: [R] Help: problem converting character to numeric

2012-03-14 Thread Jorge I Velez
Dear Aurelien, Thanks for the reproducible example. Here is one way: mm<- c("19860228", "19860331","19860430","19860531") id<-c("1","1","1","1") re<- c("C","0.25", "0.98", "1.34") mret <- data.frame(mm, id, re) subset(mret, !is.na(as.numeric(as.character(re HTH, Jorg

[R] Help: problem converting character to numeric

2012-03-14 Thread Aurélien PHILIPPOT
Dear R experts, I have a dataframe imported from a csv file (with read.csv). Here is an example: mm<- c("19860228", "19860331","19860430","19860531") id<-c("1","1","1","1") re<- c("C","0.25", "0.98", "1.34") mret<-data.frame(mm, id, re) mret<-as.numeric(as.character(mret

Re: [R] logical test not functioning correctly on zoo series...what the hell?

2012-03-14 Thread knavero
Heh, a one liner fix huh? This was going to be my alternative solution (got this coded as soon as the character strings theory arrived, and yes I'll use dput next time, sorry about that again and for all the miscommunication): require(zoo); require(chron) setwd("/home/knavero/Desktop") rawData =

Re: [R] Merging fully overlapping groups

2012-03-14 Thread mdvaan
Hi Jean and Peter, Thanks for the help. Both options are indeed faster than my initial procedure. Best, Mathijs -- View this message in context: http://r.789695.n4.nabble.com/Merging-fully-overlapping-groups-tp4470999p4473013.html Sent from the R help mailing list archive at Nabble.com. _

Re: [R] logical test not functioning correctly on zoo series...what the hell?

2012-03-14 Thread knavero
"If you showed the output of dput(yourData) or even str(yourData) others could see what types the columns are. Ordinary printed output can make numeric, character, and factor data look the same. Comparisons involving strings do not always return the same value as comparisons involving the equival

Re: [R] logical test not functioning correctly on zoo series...what the hell?

2012-03-14 Thread knavero
Additionally, the dput(rawData) output: dput(rawData) structure(list(Date...Time = structure(1:1040, .Label = c("2/11/12 12:45 ", "2/11/12 13:00 ", "2/11/12 13:15 ", "2/11/12 13:30 ", "2/11/12 13:45 ", "2/11/12 14:00 ", "2/11/12 14:15 ", "

[R] lme code help

2012-03-14 Thread harkiran
Hi guys, Got a few days left and I need to model a random effect of species on the body mass (logM) and temperature (K) slopes. This is what i've done so far that works: model1<-lme(logSSP~logM + K,random=~1|species,data=data1) model2<-lme(logSSP~logM + K,random=~K|species,data=data1) model3<-

[R] qmvnorm function

2012-03-14 Thread li li
Dear all, I need to use the "qmvnorm" function in mtvnorm package. Here is the error message I got > qmvnorm(0.05, tail="upper", sigma=var)$quantile Error in uniroot(pfct, interval = interval) : f() values at end points not of opposite sign There is no problem for 50th quantile. > qmvnorm(0.

Re: [R] logical test not functioning correctly on zoo series...what the hell?

2012-03-14 Thread knavero
"I'm getting a 404 on the dropbox linklooking at your pastebin link, my guess is that those numbers are in fact greater than zero, but are very small so they appear as zeros in the print method. If you want to send your data, it's easier to simply give us dput(rawData) and copy and paste the r

Re: [R] can not use plot.Predict {rms} reproduce figure 7.8 from Regression Modeling Strategies (http://biostat.mc.vanderbilt.edu/wiki/pub/Main/RmS/course2.pdf)

2012-03-14 Thread David Winsemius
On Mar 14, 2012, at 4:09 PM, John Smith wrote: With most current version of R and RMS, the 4 curves are drew in 4 separate panels. Can anyone show me how can I get the figure exactly like the figure 7.8 in *Regression Modeling Strategies* ( http://biostat.mc.vanderbilt.edu/wiki/pub/Main/RmS

Re: [R] Metropolis-Hastings in R

2012-03-14 Thread Patrick Breheny
This sounds like homework (in which case you should ask your instructor for help), but among the problems I see just glancing at it: * runif(-0.5,0.5) should be runif(1,-0.5,0.5) * there are a host of problems involved with the fact that you have set theta1 up as a two-column matrix, but repeat

Re: [R] How do I change the tick text on the x-axis of a plot and rotate them 90 degree?

2012-03-14 Thread David Winsemius
On Mar 14, 2012, at 5:30 PM, Michael wrote: How do I change the tick text on the x-axis of a plot and rotate them 90 degree? labs [1] "[-0.185,-0.0997]" "(-0.0997,-0.0549]" "(-0.0549,-0.0293]" [4] "(-0.0293,-0.00948]" "(-0.00948,0.00534]" "(0.00534,0.0178]" [7] "(0.0178,0.035]" "(0.035,

[R] How do I change the tick text on the x-axis of a plot and rotate them 90 degree?

2012-03-14 Thread Michael
How do I change the tick text on the x-axis of a plot and rotate them 90 degree? > labs [1] "[-0.185,-0.0997]" "(-0.0997,-0.0549]" "(-0.0549,-0.0293]" [4] "(-0.0293,-0.00948]" "(-0.00948,0.00534]" "(0.00534,0.0178]" [7] "(0.0178,0.035]" "(0.035,0.0566]" "(0.0566,0.0932]" [10] "(0.0932,0.183]"

Re: [R] Needing a better solution to a lookup problem.

2012-03-14 Thread Davis, Brian
Thanks for the idea. I think this example works fast mainly due to the limited number of matches. For each fdf1$chr there are only 2 potential matches in fdf2. In reality there are only 24 possible values for chr (1-22 and X, Y). When I replace the chr seq with more realistic values, I run o

Re: [R] logical test not functioning correctly on zoo series...what the hell?

2012-03-14 Thread Gabor Grothendieck
On Wed, Mar 14, 2012 at 12:43 PM, knavero wrote: > attached http://r.789695.n4.nabble.com/file/n4472408/dataout_2471_843.csv > dataout_2471_843.csv > Here is how the problem can be presented in a self contained, minimal, reproducible fashion (as per last two lines on every message to r-help): l

Re: [R] Merging fully overlapping groups

2012-03-14 Thread Petr Savicky
On Tue, Mar 13, 2012 at 08:56:33PM -0700, mdvaan wrote: > Hi, > > I have data on individuals (B) who participated in events (A). If ALL > participants in an event are a subset of the participants in another event I > would like to remove the smaller event and if the participants in one event > are

Re: [R] Glm and user defined variance functions

2012-03-14 Thread Ben Bolker
Craig Lyon rogers.com> writes: > > Hi, > > I am trying to run a generalized linear regression using a negative binomial > error distribution. However, I want to use an overdispersion parameter that > varies (dependent on the length of a stretch of road) so glm.nb will not do. > > >From what I'

Re: [R] where I can find more color names or color definition?

2012-03-14 Thread FJ M
Load package fBasics library(fBasics) colors() should give you what you want. Also helpful are colorTable() colorLocator() Which I found by searching for colors from the R console help menu. > Date: Wed, 14 Mar 2012 22:55:39 +0800 > From: totang...@gmail.com > To: r-help@r-project.org

Re: [R] check for data in a data.frame and return correspondent number

2012-03-14 Thread Jan van der Laan
Marianna, You can use merge for that (or match). Using merge: MyData <- data.frame( V1=c("red-j", "red-j", "red-j", "red-j", "red-j", "red-j"), V4=c(10.5032, 9.3749, 10.2167, 10.8200, 9.2831, 8.2838), redNew=c("appearance blood-n", "appearance ground-n", "appearance sea-n", "appeara

Re: [R] How can I save plot()/points() using SHP files into KML format?

2012-03-14 Thread MacQueen, Don
Since you found readOGR, you might want to look at writeOGR. -Don -- Don MacQueen Lawrence Livermore National Laboratory 7000 East Ave., L-627 Livermore, CA 94550 925-423-1062 On 2/22/12 3:43 PM, "gztourek" wrote: >Hi, > >I am new to R and am a very basic user. I'm importing SHP files,

Re: [R] Needing a better solution to a lookup problem.

2012-03-14 Thread ilai
You could try doing it without a loop (.C or other): (rgnsnp <- merge(region,snps)) (rgnsnp[with(rgnsnp,STOP>=POS & POS >= START),]) Here is my test for merge+search on 100k/200k: fdf1 <- data.frame(chr=1:10,p=runif(10),d=sample(10)) fdf2 <- data.frame(chr=rep(1:10,2),s=runif(2

Re: [R] logical test not functioning correctly on zoo series...what the hell?

2012-03-14 Thread R. Michael Weylandt
Just took a closer look at this, Bill Dunlap's guess was correct (mine wasn't): your data is stored as a character (or at least, mine is after the commands below) -- character sorting is highly platform dependent so that's probably why I got a different answer than you. rawData <- zoo(as.numeric(c

Re: [R] logical test not functioning correctly on zoo series...what the hell?

2012-03-14 Thread William Dunlap
Here is an example of the start of a self-contained way to reproduce your problem: > library(chron) > library(zoo) > rawData <- > read.zoo("http://r.789695.n4.nabble.com/file/n4472408/dataout_2471_843.csv";, > header = TRUE, + FUN = as.chron, format = "%m/%d/%Y %H:%M", index.column = 2

Re: [R] Export a plot/figure to excel or word?

2012-03-14 Thread Steve Taylor
Oops, this uses one of my own functions %like% "%like%" <- function(x,y) grepl(y,x,ignore=TRUE) Here's an improved version of word.tif ... word.tif <- function(filename="Word_Figure_%03d.tif", zoom=5, width=17, height=10, pointsize=10, ...) { if (!grepl("[.]ti[f]+$", filename,ignore.case=TRUE)

Re: [R] logical test not functioning correctly on zoo series...what the hell?

2012-03-14 Thread R. Michael Weylandt
That sure doesn't resemble the output of dput(). Still, I ran the following: rawData <- read.zoo("dataout_2471_843.csv", header = TRUE, FUN = as.chron, format = "%m/%d/%Y %H:%M", index.column = 2, sep = ",", aggregate = function(x) tail(x,1)) rawData$Meter.ID = NULL rawData[rawData$KW.ch..1..

Re: [R] Export a plot/figure to excel or word?

2012-03-14 Thread Aurelie Cosandey Godin
Thank you Michael, Yes it appeared odd to me too... I'll email them back to verify. Thanks! Aurelie On 2012-03-14, at 4:56 PM, R. Michael Weylandt wrote: > Hmmm, that seems an odd request: how could one make a plot in Excel > natively (excepting ASCII art)? > > Perhaps write and ask them if the

Re: [R] can not use plot.Predict {rms} reproduce figure 7.8 from Regression Modeling Strategies (http://biostat.mc.vanderbilt.edu/wiki/pub/Main/RmS/course2.pdf)

2012-03-14 Thread John Smith
With most current version of R and RMS, the 4 curves are drew in 4 separate panels. Can anyone show me how can I get the figure exactly like the figure 7.8 in *Regression Modeling Strategies* ( http://biostat.mc.vanderbilt.edu/wiki/pub/Main/RmS/course2.pdf) Thanks On Tue, May 17, 2011 at 4:04

Re: [R] Merging fully overlapping groups

2012-03-14 Thread Petr Savicky
On Tue, Mar 13, 2012 at 08:56:33PM -0700, mdvaan wrote: > Hi, > > I have data on individuals (B) who participated in events (A). If ALL > participants in an event are a subset of the participants in another event I > would like to remove the smaller event and if the participants in one event > are

Re: [R] Export a plot/figure to excel or word?

2012-03-14 Thread William Dunlap
Perhaps using the win.metafile() graphics device (instead of pdf()) would work. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On > Behalf > Of R. Michael Weylandt > Sent: Wednesday,

[R] Glm and user defined variance functions

2012-03-14 Thread Craig Lyon
Hi, I am trying to run a generalized linear regression using a negative binomial error distribution. However, I want to use an overdispersion parameter that varies (dependent on the length of a stretch of road) so glm.nb will not do. >From what I've read I should be able to do this using GLM by s

Re: [R] Export a plot/figure to excel or word?

2012-03-14 Thread Steve Taylor
I have found the TIF format (with lossless compression) most suitable for inclusion in Word documents. Here's my function for producing a tif plot... word.tif <- function(filename="Word_Figure.tif", zoom=5, res=96*zoom, width=17, height=10, pointsize=10, bg='white') { if (!filename %like% "

[R] Using the mantel test in Ape Package

2012-03-14 Thread Dorothea Hill
Hi, I am trying to use a mantel test on two distance matrices. The code I have entered for each is: Gen_dists <- read.csv(file.choose(), stringsAsFactors = FALSE, na.strings = c(" "),

[R] check for data in a data.frame and return correspondent number

2012-03-14 Thread mari681
Dear R-ers, still the newbie. With a question about coordinates of a vector appearing or not in a data.frame. I have a data.frame (MyData) with 3 columns which looks like this: V1V4 redNew red-j 10.5032 appearance blood-n

[R] Metropolis-Hastings in R

2012-03-14 Thread Michael Williams
Hi all, I'm trying to write a MH algorithm in R for a standard normal distribution, I've been trying for a good week or so now with multiple attempts and have finally given up trying to do it on my own as I'm beginning to run out of time for this, would somebody please tell me what is wrong with my

Re: [R] logical test not functioning correctly on zoo series...what the hell?

2012-03-14 Thread knavero
attached http://r.789695.n4.nabble.com/file/n4472408/dataout_2471_843.csv dataout_2471_843.csv -- View this message in context: http://r.789695.n4.nabble.com/logical-test-not-functioning-correctly-on-zoo-series-what-the-hell-tp4471654p4472408.html Sent from the R help mailing list archive at Nab

Re: [R] Export a plot/figure to excel or word?

2012-03-14 Thread R. Michael Weylandt
Hmmm, that seems an odd request: how could one make a plot in Excel natively (excepting ASCII art)? Perhaps write and ask them if they can take any image formats? R exports to most of them quite nicely: png, eps, jpeg, bitmap, svg, etc. Michael On Wed, Mar 14, 2012 at 3:49 PM, Aurelie Cosandey G

[R] Export a plot/figure to excel or word?

2012-03-14 Thread Aurelie Cosandey Godin
Hi all, I have created forest plots using the package "meta" that I submitted as pdf for publication. I just received an email from the editor asking me if I could send these files in an Excel or MS Word format such that they can treat them as tables with box plots. I am not sure if I can do t

Re: [R] Needing a better solution to a lookup problem.

2012-03-14 Thread Mikhail Titov
> -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On > Behalf Of Davis, Brian > Sent: Wednesday, March 14, 2012 2:28 PM > To: r-help@R-project.org > Subject: [R] Needing a better solution to a lookup problem. > > I have a solution (actually a f

Re: [R] Needing a better solution to a lookup problem.

2012-03-14 Thread David Winsemius
On Mar 14, 2012, at 3:27 PM, Davis, Brian wrote: I have a solution (actually a few) to this problem, but none are computationally efficient enough to be useful. I'm hoping someone can enlighten me to a better solution. I have data frame of chromosome/position pairs (along with other dat

[R] Needing a better solution to a lookup problem.

2012-03-14 Thread Davis, Brian
I have a solution (actually a few) to this problem, but none are computationally efficient enough to be useful. I'm hoping someone can enlighten me to a better solution. I have data frame of chromosome/position pairs (along with other data for the location). For each pair I need to determine

Re: [R] logical test not functioning correctly on zoo series...what the hell?

2012-03-14 Thread William Dunlap
If you showed the output of dput(yourData) or even str(yourData) others could see what types the columns are. Ordinary printed output can make numeric, character, and factor data look the same. Comparisons involving strings do not always return the same value as comparisons involving the equivale

Re: [R] gam - Y axis probability scale with confidence/error lines

2012-03-14 Thread Ben quant
Thank you. The binomial()$linkinv() is good to know. Ben On Wed, Mar 14, 2012 at 12:23 PM, Patrick Breheny wrote: > Actually, I responded a bit too quickly last time, without really reading > through your example carefully. You're fitting a logistic regression model > and plotting the results o

Re: [R] logical test not functioning correctly on zoo series...what the hell?

2012-03-14 Thread R. Michael Weylandt
Also, the term "error" means something specific so try not to misuse it (it will misdirect people as to the nature of your problem). An error looks like what you get if you do this: sqrt(list() + `if` / data) Michael On Wed, Mar 14, 2012 at 2:38 PM, R. Michael Weylandt wrote: > I'm getting a 40

Re: [R] logical test not functioning correctly on zoo series...what the hell?

2012-03-14 Thread R. Michael Weylandt
I'm getting a 404 on the dropbox linklooking at your pastebin link, my guess is that those numbers are in fact greater than zero, but are very small so they appear as zeros in the print method. If you want to send your data, it's easier to simply give us dput(rawData) and copy and paste the re

Re: [R] Rolling regressions with sample extended one period at a time

2012-03-14 Thread R. Michael Weylandt
My apologies: I was thinking of "rolling" more in the sense of "sliding" than "creeping". I'm not aware of anything suited for that, but it's not hard to "roll your own" with something like dats <- data.frame(x = 1:100, y = rnorm(100)) for(i in 80:100){ lm(y ~ x, data = dats[1:i, ]) } Michae

Re: [R] Merging fully overlapping groups

2012-03-14 Thread Jean V Adams
This code performs the same operation in about 1/10th the time on my machine. Give it a try. look <- function(i) { # look for subsets dif <- m[, i] - m apply(dif, 2, min) > -0.5 } nosubsets <- function(df) { # eliminate events that are subsets of other even

Re: [R] sort list

2012-03-14 Thread R. Michael Weylandt
What sort of plot are you using? I'm not really clear on what your data as a whole look like: if you use dput() you can create a representation and we can work from there. In addition to the resources Josh recommended, the following sites can direct you to all sorts of graphical goodies, all of wh

Re: [R] gam - Y axis probability scale with confidence/error lines

2012-03-14 Thread Patrick Breheny
Actually, I responded a bit too quickly last time, without really reading through your example carefully. You're fitting a logistic regression model and plotting the results on the probability scale. The better way to do what you propose is to obtain the confidence interval on the scale of th

Re: [R] gam - Y axis probability scale with confidence/error lines

2012-03-14 Thread Ben quant
That was embarrassingly easy. Thanks again Patrick! Just correcting a little typo to his reply. this is probably what he meant: pred = predict(fit,data.frame(x=xx),type="response",se.fit=TRUE) upper = pred$fit + 1.96 * pred$se.fit lower = pred$fit - 1.96 * pred$se.fit # For people who are interes

[R] statistical contrasts on 3-way interaction

2012-03-14 Thread array chip
Hi all,  I was trying to use glht() from multcomp package to construct a contrast on interaction term in a linear model to do some comparisons. I am little uncertain on how to construct contrasts on a 3-way interaction containing a continuous variable, and hope someone can confirm what I did i

Re: [R] How to use ggplot to do the binned quantile plots(one type of scatter plot)?

2012-03-14 Thread Michael
How to stack these subplots horizontally and vertically together in a nice way? Thank you! On Wed, Mar 14, 2012 at 11:04 AM, Clint Bowman wrote: > ?quantile on the individual bins, make your deciles, then plot the ten > series as usual with your x values at the midpoint of the bins. > > Clint B

Re: [R] How to test the statistical significance of the difference of two univariate Linear Regression betas?

2012-03-14 Thread Michael
Thank you! How large is large sample? What about 50 data points in D1 and another 50 data points in D2? Thanks a lot! On Wed, Mar 14, 2012 at 11:49 AM, peter dalgaard wrote: > > On Mar 14, 2012, at 16:21 , Michael wrote: > > > How to test the statistical significance of the difference of two

Re: [R] How to test the statistical significance of the difference of two univariate Linear Regression betas?

2012-03-14 Thread Bert Gunter
1. Is this homework? -- we don't do homework. 2. This is not an R question -- posting to stats.stackexchange.com or other statistics websites is usually more appropriate for such non-R statistical questions 3. General approach: Combine all data; model it with both a simpler (fewer parameter, sing

Re: [R] How to test the statistical significance of the difference of two univariate Linear Regression betas?

2012-03-14 Thread peter dalgaard
On Mar 14, 2012, at 16:21 , Michael wrote: > How to test the statistical significance of the difference of two > univariate Linear Regression betas? > > Hi all, > > There are two samples of data: D1 and D2. > > On data D1 we do a univariate Linear Regression and get the coefficient > beta1. >

[R] climate data, Netcdf

2012-03-14 Thread Amen
As you can see: time is from 1 to 1460, 1 means they the measure Tem for the globe at the first 6 hours , 2=after 12 hours .; and so on 1460 *6 = 8760 hours which equals 1 year first of all I want to convert all data from kelvin to degree second I want to convert from 6 hourly to daily a

[R] Reading and analyzing data with two headers

2012-03-14 Thread jorge Rogrigues
I have data that I would like to analyze in R with the following format: *,M1,,M2, *,S1,S2,S1,S2, p1,m1s1v1,m1s2v1,m2s1v1,m2s2v1 p2,m1s1v2,m1s2v2,m2s1v2,m2s2v2 ..,...,...,..., so I have a method M1 and M2 and each of these have attributes that I would like to analyze for the different problem

Re: [R] logical test not functioning correctly on zoo series...what the hell?

2012-03-14 Thread knavero
Here's the exact error I'm receiving: http://pastebin.com/mNsPauwk Tracked each output along the way. Starting to think there's a bug in the source code. -- View this message in context: http://r.789695.n4.nabble.com/logical-test-not-functioning-correctly-on-zoo-series-what-the-hell-tp4471654p

Re: [R] reshaping a dataset for a network

2012-03-14 Thread Marco Guerzoni
Il 3/14/2012 4:43 PM, William Dunlap ha scritto: I see you have a solution, but why do you want the results of split() in matrix form? E.g., does it make a nicer printout, is it needed to interface with other R functions, is it needed to interface with other I need matrix to export the data in t

Re: [R] logical test not functioning correctly on zoo series...what the hell?

2012-03-14 Thread knavero
"You're missing a comma between 0 and "]" in the last line if your goal is to retrieve the rows that satisfy that condition (and if the condition makes any sense). Haven't tested the rest of your code, though. ?Extract > The outputs that I'm getting, however, are > printing out 0's down th

Re: [R] gam - Y axis probability scale with confidence/error lines

2012-03-14 Thread Patrick Breheny
The predict() function has an option 'se.fit' that returns what you are asking for. If you set this equal to TRUE in your code: pred <- predict(fit,data.frame(x=xx),type="response",se.fit=TRUE) will return a list with two elements, 'fit' and 'se.fit'. The pointwise confidence intervals will

Re: [R] How to test the statistical significance of the difference of two univariate Linear Regression betas?

2012-03-14 Thread Mark Leeds
Hi: I'm jot sure if it's exactly what you want but check out Hotelling's paper from 1940. It should be in the archives because I answered this question before ( not from you ). If you can't find it, I'll find the title actually, here's the title: Hotelling, The Selection of Variates For Use i

Re: [R] Amount of memory occupied by data type

2012-03-14 Thread Folkes, Michael
Thanks David for the details and pointer to bitops functions. Buried a bit deep that was. I like to think the memory constraints of win xp keeps my code lean and efficient. RAM is like a suburban garage, the bigger it is, the more useless junk people stuff in there. Michael Folkes -Origina

Re: [R] logical test not functioning correctly on zoo series...what the hell?

2012-03-14 Thread David Winsemius
On Mar 14, 2012, at 11:47 AM, knavero wrote: "> Here's the raw data I'm working with (will be available temporarily): http://dl.dropbox.com/u/41922443/dataout_2471_843.csv Nothing appears. " ^ Clicking on the link should prompt you to download a csv file and save it somewhere in your H

Re: [R] help with expression

2012-03-14 Thread David Winsemius
On Mar 14, 2012, at 11:53 AM, ilai wrote: On Wed, Mar 14, 2012 at 8:56 AM, Thomas Hoffmann wrote: Hi all, I still fail to plot an axis title with the following expression: plot(0,xlab=expression('(SOC [' * kgm^{-2} * '])' * ^{-2})) the xlab should look like: (SOC [kgm^2])^0.25 with an o

Re: [R] MANOVA and Extra Sums-of-Squares Tests

2012-03-14 Thread chris33
Hi John, Thanks again. That looks like an easy and convenient approach. Regards, Chris -- View this message in context: http://r.789695.n4.nabble.com/MANOVA-and-Extra-Sums-of-Squares-Tests-tp4470077p4472265.html Sent from the R help mailing list archive at Nabble.com. ___

Re: [R] logical test not functioning correctly on zoo series...what the hell?

2012-03-14 Thread knavero
"> Here's the raw data I'm working with (will be available temporarily): > > http://dl.dropbox.com/u/41922443/dataout_2471_843.csv Nothing appears. " ^ Clicking on the link should prompt you to download a csv file and save it somewhere in your HDD. -- View this message in context: http://r.7896

Re: [R] extract values ​​for the dates and a new column

2012-03-14 Thread Jeff Newmiller
The error seems clear enough to me... you are trying to mix vectors of different lengths where one length is not a multiple of the other length. Your discussion is pretty confused though, referring to possible data frames x, x.sub, x.res and Dataset. You might benefit from reviewing ?str and ?dp

Re: [R] How to use ggplot to do the binned quantile plots(one type of scatter plot)?

2012-03-14 Thread Clint Bowman
?quantile on the individual bins, make your deciles, then plot the ten series as usual with your x values at the midpoint of the bins. Clint BowmanINTERNET: cl...@ecy.wa.gov Air Quality Modeler INTERNET: cl...@math.utah.edu Department of Ecology

Re: [R] logical test not functioning correctly on zoo series...what the hell?

2012-03-14 Thread knavero
"> The outputs that I'm getting, however, are > printing out 0's down the columns. I've tried various methods assuming > various theories, read the R manual via "?" for different possible > solutions, Googled stuff, tried the ifelse function which produces > the same > error, tried creating logic

Re: [R] Real-Time data transfer from Excel to R

2012-03-14 Thread Richard M. Heiberger
Yes. please look at RExcel. You can download it from rcom.univie.ac.at The wiki page there has many papers discussing similar projects (follow the Literature link in the left column). Followup should be on the rcom mailing list. Rich On Wed, Mar 14, 2012 at 7:12 AM, burcy wrote: > Hi All >

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