Re: [R] likelihood ratio test

karuna m yahoo.com> writes: > Can anybody tell me which R package has Lo-Mendell Rubin LR test and > Bootstrap > LR test to compare the model fit between k class and k+1 class model > for Latent class analysis? I don't know, but library("sos") findFn("Lo-Mendell") findFn("{latent class ana

Re: [R] L-BFGS-B and parscale in optim()

Sebastian P. Luque gmail.com> writes: > > Hi, > > When using method L-BFGS-B along with a parscale argument, should the > lower and upper bounds provided be on the scaled or unscaled values? > Thanks. I think you can figure this out by experimentation on your own, but I believe that all of t

Re: [R] plotting texas school district using shape files

least on my system, read.shape() is *not* part of the maptools package. help.search("read.shape") finds maptools::readShapeSpatial. library("sos"); findFn("read.shape") discovers that there is a read.shape() function in the spsurvey package. Ben Bolker > > I was

Re: [R] Thiessen method

federico.eccel gmail.com> writes: > I try to search in the web and in the R forum for any package for computing > The thiessen method but I didn't find anything. I would like to ask if it > exists any package in R that provides the possiblity to compute the Thiessen > method for interpolating ra

Re: [R] plotting texas school district using shape files

he package first, too, right?) After you have done that I suspect you will still have a problem with finding the file -- I think you want something like library("maptools") txtshp <- read.shape("S:\\Districts_10_11.shp") Ben Bolker ___

Re: [R] Fortran DLL in Spotfire

found. I have used "setwd" to point to the location in the > spotfire statistical services server library. Is this the correct way to > call the DLL in spotfire??? > This is the R help list; you'd better contact spotfire (commercial) support with your

Re: [R] Interpreting the results of the zero inflated negative binomial regression

Vishnu B gmail.com> writes: > I am new to R and has been depending mostly on the online tutotials to learn > R. I have to deal with zero inflated negative binomial distribution. I am > however unable to understand the following example from this link > http://www.ats.ucla.edu/stat/r/dae/zinbreg.h

Re: [R] Formatting names.arg

Adrienne Keller umontana.edu> writes: > I am making a barplot using barplot2 from gplots and would like to > format the names of my categorical variables (tree species) on the x- > axis so that the genus name is above the species name (to save room). > My code so far is: [snip] Try "Dia

Re: [R] FW: getting time series into r

Heiman, Thomas J. mitre.org> writes: > tmp <- read.table("baltimore.csv", sep = " ") ##This is timeseries 2 > z <- zoo(tmp[, 2:20], as.Date(as.character(tmp[, 1]), format = "%y %m %d")) > > tmp1 <- read.table("baltimorefludata.csv", sep = " ") ##This is timeseries 1 > z2 <- zoo(tmp[,2], as.Date(

Re: [R] What are the common Standard Statistical methods used for the analysis of a dataset

"how long is a piece of string"? Furthermore, even if it were better phrased it would not be a question about R, but about statistics (sometimes tolerated here, but not appropriate). Finally, it sounds like a homework question (also inappropriate). Please read the posting g

Re: [R] how could I use function in-visible to user in my code?

Shuguang Sun gmail.com> writes: > How could I use function in-visible to user in my code? For example > 'survfitKM' or 'survfit.formula' in package survival. These functions > are in-visible to user. ?":::" e.g. survival:::survfit.formula __ R-help

Re: [R] outout clarification of fitdist {fitdistrplus} output

ty (p) . To me it is not > clear what these mu and size parameter declares. > See the help page for ?dnbinom, which gives the details of the different parameterizations ... Ben Bolker __ R-help@r-project.org mailing list https://stat.e

Re: [R] predict.gls choking on levels of factor

reproducible example (see below) > (2) Is it possible to get the "varIdent" into lm or ols from Design? No. > (3) is Yee's "smartpred" package, last updated for R 1.7, reliable > for current R? Can we have a reproducible example please? Ben Bolke

Re: [R] dbetagen function in mc2d package

he package maintainers [maintainer("mc2d")]. Seems fairly easy to fix for yourself, though -- just scale by the size of the domain (max-min). Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE

Re: [R] Parameter Estimates needed from lmer output

David Cross tcu.edu> writes: > > If I remember correctly, coef(m1) would do it ... > but it has been a while since I last used lmer, and I am > working only from memory. > fixef() for fixed effects only ranef() for random effects only coef() gives a matrix of the predicted coefficients in

Re: [R] R-code in R-file documentation

Brian Oney gmail.com> writes: > > Hello List, > I would like to insert code from .r files into a LaTeX appendix > (possibly using Sweave). > I was considering: > [snip] Wouldn't it be easier to use the LaTeX listings package?

Re: [R] Query Gene ontology

uld > you tell me if there is a way to do that? You will probably have better luck posting this question on the bioconductor mailing list (read the posting guide, and search the list archives, first ...) Ben Bolker __ R-help@r-project.org mailing li

Re: [R] extract value from mer object ?

Maas James Dr (MED uea.ac.uk> writes: > > > What is the easiest way to extract a value from a 'mer' > object from glmer? The first I need is the > trtpair Std.Dev. which in this case is 0.17542? > > I've managed to get the fixed effects numbers from > summary(fednmaout)@coeffs You sho

Re: [R] using glmer to fit a mixed-effects model with gamma-distributed response variable

transforming your data (dealing with zeros appropriately) and fitted a regular, linear mixed model ... Further discussions on this topic would probably be better on the r-sig-mixed-models list. Ben Bolker __ R-help@r-project.org mailing list https://st

Re: [R] to check if a group of values is randomly distributed

Your question above is different from the typical mid-domain hypothesis question, which is about the arrangement of ranges rather than their distribution of sizes. Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/

Re: [R] Format ddmmYYYY in date

smoff boku.ac.at> writes: > My problem is that I have a table containing dates in the first column of 10 > years. These dates have the format ddmm at least in the csv-file. After > importing the file using read.table() R deletes the first character if it is > a zero. [snip] > How do I solv

Re: [R] Categorical bubble plot

et quantitative information on the basis of size and colour. A dot chart of some form would probably convey the information more accurately. Ben Bolker > Thanks!!! > > On 21 April 2011 09:49, Jurgens de Bruin <mailto:debrui...@gmail.com>> wrote: > > Thanks for all the

Re: [R] Tests for the need of cluster analysis

don't think you should be testing _based on your data_ whether robust or robust cluster variance estimators are more appropriate; there's a fairly dangerous data snooping issue here. Rather, you should try to decide _a priori_ based on your data what's most appropriate. Ben Bolker

Re: [R] Convert filogenetic tree to binary matrix

as an ancestors() functions that could help you put together a solution, but there may well be a quicker, easier way. Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting gui

Re: [R] Accounting for overdispersion in a mixed-effect model with a proportion response variable and categorical explanatory variables.

> Although both models make the same effects to be significant, I would > like to know which one I should report and use as input to a > subsequent multiple comparisons analysis with multiicomp. I think so. It may however comfort you to see that the coefficients and their standard e

Re: [R] Simple question about symbols()

David Winsemius comcast.net> writes: > > > On Apr 19, 2011, at 10:51 PM, murilofm wrote: > > > Thanks for the answer; I see that col=c("blue","red")[inv$c+1] > > creates a > > vector of "red" and "blue" associated with the binnary c. > > But still I got everything red. > > If you want teste

Re: [R] Simple question about symbols()

murilofm gmail.com> writes: > > I'm new to R and i'm having some trouble with a bubble chart. > Basically I have 3 series (a,b,c), but the third one is a binnary variable > (assumes only 0 or 1 to the entire data). > How can I use these binnary information to make 2 different colours in a > bubb

Re: [R] reporting lme results

Pennell, Tanya exeter.ac.uk> writes: > I have used lme4 and I have found a significant result > when using anova to compare model 1 and model 2 (where I > took out an interaction). > > The result looks like this: > model.3: DIFFERENCE ~ (1 | MALE.ID) > model.2: DIFFERENCE ~ MALE.SPECIES + (1 |

Re: [R] altering identity column

Bodnar Laszlo EB_HU erstebank.hu> writes: > [snip snip ] > So I have a transformed dataframe now including 10,000 obeservations > (from 60,001 - to 70,000) and if you send > "head(transformed_dataframe)" into R it looks like this: [snip] > > Now is there a quick way to alter this indexin

Re: [R] Rsquared for anova

Dorien Herremans ua.ac.be> writes: > > Thanks Dieter, > > Even if I use lm(), I get the following output: > > > summary(fit) >              Df  Sum Sq Mean Sq F value    Pr(>F) > nh1            1   324.0  323.99  139.13 < 2.2e-16 *** > nh2            1   723.1  723.12  310.53 < 2.2e-16 *** > n

Re: [R] Help me create a hyper-structure

On 11-04-18 04:45 AM, Alaios wrote: > It seems you were right. > Now I can easily access my struct and substruct like this > > # all.str[[1]]] Gives access to the first struct of per.sr.struct which > containts 101 times the xorder,yorder,estimation.sr > # all.str[[1]][[2]] Gives access to the se

Re: [R] Help me create a hyper-structure

Alaios yahoo.com> writes: > > Dear all > I would like to have in R a big struct containing a smaller struct. > > 1) I would like to have a small struct with the following three fields > xorder (an integer ranging from 0 to 20) > yorder (an integer ranging from 0 to 20) > estimated (a 256*256

Re: [R] GLM and normality of predictors

! I think the original model using the binomial distribution for the response seems entirely appropriate. I agree with the comment about tiny data sets: the usual rule of thumb is that (# parameters) should be <(effective N)/10 -- so in practice estimating anything more than a single binary

Re: [R] Whole genome searching of 100bp "D" sequence

eople on this list. (Do mention that you posted here first.) Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: [R] Function for deleting variables with >=50% missing obs from a data frame

Rita Carreira hotmail.com> writes: > I have several data frames where some of the variables have many > missing observations. For example, Q1 in > one of my data frames has over 66% of its observations missing. > I have tried imputation with mice but it does > not work for all the data frames an

Re: [R] Conveting SAS Proc mixed to R code

is more appropriate than (1|Stream:Group:Treatment)? In general, what goes on the LEFT of the bar is an intercept or fixed effect (i.e. something that varies between groups); what goes on the RIGHT of the bar is a grouping variable. Thus if a fixed effect terms ends up on the right of the bar, someth

Re: [R] Categorical bubble plot

's easier to assess quantitative values plotted along a common scale than via size or colour ... ggplot(dd,aes(x=drugclass,y=fitvalue,colour=plant))+ geom_point()+geom_line(aes(group=plant)) > The size of the bubbles will be related to the fitvalues. > > > > On 14 April 201

Re: [R] mixed model random interaction term log likelihood ratio test

seatales uh.edu> writes: > > Hello, > I am using the following model > > model1=lmer(PairFrequency~MatingPair+(1|DrugPair)+(1|DrugPair:MatingPair), > data=MateChoice, REML=F) > > 1. After reading around through the R help, I have learned that the above > code is the right way to analyze a mi

Re: [R] Plotting an Underbrace in R

Michael McAssey gmail.com> writes: > > I need to include some mathematical expressions in a plot I am creating in > R, one of which requires an underbrace, which in LaTeX would be written like > > \underbrace{T \cdots T}_{n times} > > There does not appear to be a provision for this in plotmat

Re: [R] Categorical bubble plot

Jurgens de Bruin gmail.com> writes: > > Hi, > > I do not have much R experience just the basics, so please excuse > any obvious questions. > > I would like to create bubble plot that have Categorical data on the x and y > axis and then the diameter if the bubble the value related to x and y. >

Re: [R] Line plots in base graphics

Hadley Wickham rice.edu> writes: > On Wed, Apr 13, 2011 at 2:58 PM, Ben Bolker gmail.com> wrote: > > Hadley Wickham rice.edu> writes: > > > >> > >> Am I missing something obvious on how to draw multi-line plots in > >> base graphics? [snip]

Re: [R] latex, eps graphics and transparent colors

Thomas Lumley uw.edu> writes: > > On Thu, Apr 14, 2011 at 5:30 AM, > Michael Friendly yorku.ca> wrote: > > I have a diagram to be included in latex, where all my figures are .eps > > graphics (so pdflatex is not an option) > > You could use the pdf() device and then use pdf2ps to convert to

Re: [R] Line plots in base graphics

Hadley Wickham rice.edu> writes: > > Am I missing something obvious on how to draw multi-line plots in > base graphics? > > In ggplot2, I can do: > data(Oxboys, package = "nlme") library(ggplot2) qplot(age, height, data = Oxboys, geom = "line", group = Subject) > But in base graphics, the

Re: [R] latex, eps graphics and transparent colors

Michael Friendly yorku.ca> writes: > > I have a diagram to be included in latex, where all my figures are .eps > graphics (so pdflatex is not an > option) and I want to achieve something > like the following: three concentric filled circles varying in lightness > or saturation. It is easiest

Re: [R] How to get the names of all the packages that depend on a give package?

Dennis Murphy gmail.com> writes: > > Hi: > > Here's one way, assuming Matrix (or whichever package you want to > investigate) is installed on your system: > > u <- installed.packages() > u['Matrix', 'Depends'] > [1] "R (>= 2.10.0), stats, methods, utils, lattice" > > HTH, > Dennis > Or, i

Re: [R] glmnet

Janina Hemmersbach scai.fraunhofer.de> writes: > > Hello, > I´m trying to in install the package 'glmnet' > but I get always the error massage "package ‘Matrix’ is > not available". I search on you site, but I coundn´t > find the package there either. Is their still a > package called "Matrix"?

Re: [R] R plots pdf() does not allow spotcolors?

Prof Brian Ripley stats.ox.ac.uk> writes: > > On Wed, 13 Apr 2011, Ben Bolker wrote: > > > Matthieu Stigler gmail.com> writes: > > > >> > >> Hi > >> > >> We are about to publish a book, which contains figures made with R >

Re: [R] R plots pdf() does not allow spotcolors?

d/perl ?) ... if you don't use R, what is your alternative for creating the figures? Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: [R] How to set the dimension of a matrix correctly?

ode so it was readable. Often the process of trying to simplify the problem leads you to discover your own problem. good luck, Ben Bolker > > -- library(geoR) #functions for geostatistical data analysis coords<- as.matrix(read.table('/Users/R/Code/stncoor

Re: [R] 2-parameter MLE problems

Tyler Schartel msstate.edu> writes: > > Hi all, > > Sorry for the re-post, I sent my previous e-mail before it was complete. I > am trying to model seroprevalence using the differential equation: > dP/dt = beta*seronegative*.001*(seropositive)-0.35*(0.999)*(seropositive)- > r*seropositive.

Re: [R] plot3d crashes R

gmail.com> writes: > > Hi Duncan, > > I've just read the help for the plot3d function you've written > and tried out the example code given at the > bottom of the page. I then modified the function by adding > an aspect ratio of 0.1 and ran it again, which > crashed my R. I am using 2.12.2 o

Re: [R] question about optim

chirine wolley hotmail.com> writes: > Dear R-users, I would like to use optim( ) to minimize a function > which depends on 4 parameters: 2 vectors, a scalar, and a matrix. > And I have a hard to define the parameters at the beginning of the > function, and then to call optim. Indeed, all the exa

Re: [R] Is there some command or alternative using dist.dna in ape package for models not included like GTR?

Ignacio Quintero gmail.com> writes: > I am making some DNA distances and I would like to use dist.dna as matrix in > R, but this command does not include models like GTR... > Is there some command or alternative using dist.dna in ape package for > models not included like GTR? Try forwarding t

Re: [R] iterative methods in R

rvohen 126.com> writes: > does some know iterative methods in R ? thank you! Please read the posting guide and ask a more specific question; then someone may be able to help. Ben Bolker __ R-help@r-project.org mailing list https://stat.e

Re: [R] simple maths question

Georg Ehret gmail.com> writes: > > Hi Mrs & Ms "R", > A simple maths question that I am trying to resolve with R: I need to > calculate the SE from a pvalue and it's beta... How to do this...? > Thank you very much and best regards! > Georg Ehret, Geneva, Switzerland. Without more infor

Re: [R] Windrose Percent Interval Frequencies Are Non Linear! Help!

quot;wind rose") finds them in packages plotrix, openair, oce, climatol, IDPmisc, ggplot2 ... and that's not counting rose.diag in the CircStats package. I would take a quick look and see if any of those packages work for you. Ben Bolker _

Re: [R] How can I include a new book on the

Marcio Pupin Mello ieee.org> writes: > I've just published a new book for R beginners in Portuguese: > "Conhecendo o R: uma visão estatística" (something like "Knowing R: an > statistical approach"). I'd like to include it on the list "Books" at > R-project.org. How can I do it? > More informa

Re: [R] extract variance for random effects from "mer" object

Maas James Dr (MED uea.ac.uk> writes: > I get an output from a glmer package, but would like > to extract the variance of the Random effects, in this > case called trtpair and the value is 0. [snip] > > fednmaout > Generalized linear mixed model fit by the Laplace approximation > Formula: cbind

Re: [R] corSpatial and nlme

Robert Baer atsu.edu> writes: > > I noticed that ?corClasses in package nlme does not list corSpatial > among the standard classes. This might > either be intentional because corSpatial is not "standard" , > or it might be simply an oversight that needs correcting. > corSpatial is a virtu

Re: [R] Package diveMove readTDR problem

mwege zoology.up.ac.za> writes: > I am trying to read my TDR data into R using the readTDR function for the > diveMove package. > > > seal <- readTDR("file location and name here", dateCol=1, depthCol=3, > > speed=FALSE, subsamp=1, concurrentCols=4:5) > > But I keep getting the following error:

Re: [R] IFELSE function XXXX

William Dunlap tibco.com> writes: > Avoid assignments in arguments to function calls, especially > multiple assignments to the same object, except when you know > what you are doing and want to write obscure code. > > Change the above line to > data3$input1 <- ifelse(data3$res1==1, data3$input

Re: [R] Clarks 2Dt function in R

biologie.uni-marburg.de> writes: > > Dear Ben, > > you answerd to Nancy Shackelford about Clarks 2Dt function. > Since the thread ended just after your reply, > I would like to ask, if you have an idea how to use this function in R > Dear Ronald, I got started on your problem, but I didn

Re: [R] Poisson Regression

Jim Silverton gmail.com> writes: > > Is there R code that can do a Poisson Regression and plot the density of the > fitted values? > ?glm glm(...,family=poisson) ?predict.glm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listi

Re: [R] lme:correlationstructure AR1 and random factor

model you want (correlation within trap-field combinations, random effects across fields), but you might have some options/ get some ideas from posting to r-sig-mixed-models. Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mai

Re: [R] Intercept and slope of GLS model

John Haart me.com> writes: > With this truncated output from a GLS model the > intercept is 0.004634487 but where is the slope? > > Coefficients: >Value Std.Error > t-valuep-value > (Intercept) 0.004634487 0.000677339

Re: [R] Help with multidimensional array

Giuseppe gmail.com> writes: > > Dennis, > > Yes, Reduce works, but unfortunately it does not speed up the > evaluation time (actually, it makes it a little bit slower). > > Thank you anyway. I have an alternate solution that I would have expected to be faster but is actually much slower for

Re: [R] rtree() distances between tips as n by n matrix?

list rather than the general R help list; most of the people here have no idea that you're talking about the random tree generating function from the ape package ... Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listi

Re: [R] FW: Platform Compatibility

Shahriar, Khandaker (CONT capitalone.com> writes: > > > Good Afternoon, > I am trying to verify if R v2.10.1 can be run with HPUX 11.x or AIX? > > Thx! > Khan > 804-284-7201 > You might get a quick answer, but probably your best bet is simply to try compiling:

Re: [R] question about calculating derivatives for vectors

Mingwei Min cam.ac.uk> writes: > I am trying to calculating derivatives for vectors using R. I have a numerical vector, which is in time series manner and contains "NA"s. I want to know the changing rate throughout the whole time range. I am wondering if there is function in R can do this. In

Re: [R] matrix inverstion

Daniel Nordlund frontier.com> writes: > > On Behalf Of Rosario Garcia Gil > > I have this matrix which I am trying to invert. I get a message about > > reciprocal condition number, what that does mean? [snip] > > Well, it means exactly what the message says. Within the precision of your com

Re: [R] Degrees of freedom for lm in logLik and AIC

Rubén Roa azti.es> writes: > > > However, shouldn't _free parameters_ only be counted for degrees of > freedom and for calculation of AIC? > The sigma parameter is profiled out in a least-squares > linear regression, so it's not free, it's not a > dimension of the likelihood. > Just wondering

Re: [R] deleting the first two characters in each row of a factorized column

Bodnar Laszlo EB_HU erstebank.hu> writes: > I have a database and it has a column which looks like this one here: > > small_factor <- factor(c("d_variable1","d_variable2","d_variable3")) > small_factor > small_factor <- factor(gsub("^d_","",as.character(small_factor))) _

Re: [R] a question on R optimization functions

Paul Gilbert bank-banque-canada.ca> writes: > > It seems more likely that the return value from your function > is NA or NaN or Inf. This might then result in an > NA parameter value being calculated for the next step. > This is possible, for example, because the line > search extends outside

Re: [R] Removing object - searching/googlin' ..and more hasn't helped :(

agustgisla hi.is> writes: > > I know this is probably really easy thing but... > I've loaded data into R from the net. I've got 97 subjects (in a database). > I'm supposed to remove subjects "lower than 140 cm".. Of course it's easy to > find the subject (i.e. number 83 and 84) - but how can I d

Re: [R] a question on R optimization functions

e much more likely for it to be an infinite loop/hang somewhere inside your objective function. See ?setTimeLimit (which will fail if the problem is inside C code that you have written ...) Ben Bolker __ R-help@r-project.org mailing list https://sta

Re: [R] Looking for a repeated measure two groups comparison and a two factor ANOVA in Circular distribution

and glmer. You might be able to > write your own family function there and analyze your data in the > generalized mixed models context. Unfortunately this isn't so easy. GLM families are hard-coded in the underlying C code, so doing this would require a

Re: [R] Rmark and scientific notation issue

odaniel utas.edu.au> writes: > Just wondering if anyone might know a way to stop R reading my survival > history that has zeros at the beginning in as scientific notation. Gmane doesn't want me to quote much, but maybe read.table("myfile.dat",colClasses=c("character",rep("numeric",2)) ?

Re: [R] Feature request: rating/review system for R packages

sers and collecting more information; (c) consult with the fine folks running CRANtastic to see if they wanted to somehow integrate it into their infrastructure. The big advantage of this approach is that you don't need to convince anyone from R-core to do anything, you just need to convince users

Re: [R] problem running a function

garciap usal.es> writes: > > Dear people, > > I'm trying to do some analysis of a data using the models by Royle & Donazio > in their fantastic book, particular the following function: > http://www.mbr-pwrc.usgs.gov/pubanalysis/roylebook/panel4pt1.fn > [snip] I'm guessing you're fairly new

Re: [R] [R-sig-ME] PREDICTIONS from a PIECEWISE LINEAR (mixed) MODEL: THEY AIN'T LINEAR BETWEEN BREAK POINTS!!

t; > I sincerely express many thanks in advance .. > > Federico Bonofiglio > You have not given us a *reproducible* example ... I would guess that you need I(rt>15) rather than rt>15 in your formulae. good luck Ben Bolker __ R-help

Re: [R] Autocorrelation in linear models

Arni Magnusson hafro.is> writes: > > I have been reading about autocorrelation in linear models over the last > couple of days, and I have to say the more I read, the more confused I > get. Beyond confusion lies enlightenment, so I'm tempted to ask R-Help for > guidance. > > Most authors are

Re: [R] Strange R squared, possible error

On 11-03-16 07:55 PM, Peter Ehlers wrote: > On 2011-03-16 15:02, Ben Bolker wrote: >> ria.buffalo.edu> writes: >> >>> >>> lm(y~x+0) yields the regression on x without the constant, i.e., y=bx+e, >>> not y = a +e >>> >>> derek

Re: [R] Strange R squared, possible error

d submit it to Kurt Hornik for inclusion in the R FAQ? Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal

Re: [R] Re; Fitting a Beta distribution

Jim Silverton gmail.com> writes: > > I want to fit some p-values to a beta distribution. But the problem is some > of the values have 0s and 1's. I am getting an error if I use the MASS > function to do this. Is there anyway to get around this? The probability *density* of an exact 0 or 1 can

Re: [R] Error in X11

clinic.ub.es> writes: > I've installed R-2.12.2 on a server with Suse 10 linux OS. > When I try to create images I got this error: > > > png(filename="hola.png") > > Error in X11(paste("png::", filename, sep = ""), width, height, pointsize, : > FAQ 7.19:

Re: [R] how to set the starting value in lme

Daniel Kaschek physik.uni-freiburg.de> writes: > > Hi Jia, > > in order to test if the failing parameter estimation really has to do > with wrong initial values, you could first simulate data with your mixed > effects model. Just assume parameters, produce a data set with these > parameters, ad

Re: [R] (R) transitions in a Markov Chain

o you know how to do it with R? > This sounds like homework, and it is the policy of this list not to give answers to homework. To get you started, though, see ?matrix ?"%*%" and possibly ?eigen good luck Ben Bolker ___

Re: [R] betareg help

data=results, start=list(mu=qlogis(mean(results$cond)),logphi=0)) summary(m1) p1 <- profile(m1) plot(p1,show.points=TRUE) confint(p1) confint(m1,method="quad") ## not much difference coef(m1) coef(gyl) On 11-03-13 12:59 PM, Vlatka Matkovic Puljic wrote: > Sorry, here is my

Re: [R] Gnuplot fit function in R

Stefan me.com> writes: [snip] > I'm just wondering if there is a equivalent to the fit function of > gnuplot in R? > If not, s there any good resource on fitting gaussians into a curve? Try ?nls ?predict.nls __ R-help@r-project.org mailing li

Re: [R] betareg help

f you can't possibly post the data to the list, or put them on a web site somewhere, or randomize them a bit so you're not giving anything away, or find a simulated example that shows the same problem, you could as a last resort send them to me. Ben Bolker _

Re: [R] betareg help

in your data, but you seem to have taken care of that. Are you willing to post the whole data set (use dput() to get it in a useful form)? Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: [R] ERROR: gamm function (mgcv package). attempt to set an attribute on NULL

ia library(nlme) lme(A~B,random=~1|ID,na.action=na.omit,data=rs) good luck (it would still be a good idea to read the posting guide, for future reference!) Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help

[R] beamer overlays with Sweave?

annoying and error-prone. I could spend some more time hacking it, but I wondered if anyone else had already solved this ... (Brief googling of "beamer+Sweave+overlay" didn't find an obvious answer, but I might have missed something ...) thanks Ben Bolker ___

Re: [R] More appropriate optimization routine?

Dimitri Liakhovitski gmail.com> writes: > I have 2 variables - predictor "pred" and response variable "DV": > > pred<-c(439635.053, 222925.718, 668434.755, 194242.330, 5786.321, 115537.344, > 100835.368, 7133.206, 159058.286, 4079991.629, 3380078.060, 2661279.136, > 2698324.478, 1245213.965, 19

Re: [R] linear mixed model with nested factors

David Dudek student.umb.no> writes: > > Hi R-help. > > I am trying to run a linear mixed model with nested factors with either > lme or lmer and I am having no luck obtaining the same results as Minitab. > Here is Minitab's code: > > MTB > GLM 'count' = site year replicate(site year) site*year

Re: [R] AIC on GLMM pscl package

C value (which technically does not exist in this case). It is in principle possible to get a "quasi-AIC", but it is (a) delicate to define and (b) moderately challenging to extract the information from glmmPQL. Ben Bolker __ R-help@r-proj

Re: [R] message: please select CRAN mirror

Aggita eurotransplant.org> writes: > > > chooseCRANmirror() > Error in m[, 1L] : incorrect number of dimensions > > Can someone explain me why I can't choose the cran mirror, but get again and > again this error message. Have searched for this on several engines but > can't find explanation. >

Re: [R] Measuring correlations in repeated measures data

2 3 2 -0.099 3 0.021 -0.242 4 -0.298 0.184 0.262 (this is also shown at the end of summary(fit2)) This is the lower triangle of the (symmetric) correlation matrix; the diagonal is 1 by definition. Isn't that what you're looking for? (Sorry if I'm misunderstanding

Re: [R] Measuring correlations in repeated measures data

Brant Inman mac.com> writes: > > R-helpers: > > I would like to measure the correlation coefficient between the repeated measures of a single variable > that is measured over time and is unbalanced. As an example, consider the Orthodont dataset from package > nlme, where the model is: > > fit

Re: [R] Urgent Help: How I can open (Business Objects 6.0) data file? Any ideas?

Salaam Batur gmail.com> writes: > This maybe unrelated R-question, but I am sure some of you might have a same > problem like I do. I'd like to run some tests on files which need to be > opened by a software tool called Business Objects. Right now, I am having > problem with open the data files w

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