Re: [R] Fitdistr and mle

Tia Borrelli yahoo.it> writes: > Thanks for answering, in ret i've the returns of FTSE MIB (the > benchmark stock market index in Italy) and i'm estimating the > parametres of the distribution of the returns of the index using > different methods.  OK, but this still isn't a *reproducible* ex

Re: [R] Fitdistr and mle

al optimization that you're never going to get exactly the right answer, due to various forms of numerical "fuzz" -- you just have to know enough about the methods, and about your problem, to know whether the answers are correct within sensible error bounds. > > Il Mercoledì

Re: [R] need help with distribution graphics

y gao wrote: > I need to graph > categorical data like a or b in the the following figure. Could > anybody let me know what command line I should go with? These are called "beeswarm plots". Try googling "beeswarm plot R" for a variety of options ... Ben Bolk

Re: [R] R crashes with memory errors on a 256GB machine (and system shoes only 60GB usage)

k whether gc(), memory.profile(), etc. give sensible results in a clean R session (R --vanilla). 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/postin

Re: [R] zero-inflated negative binomial model with random effects

Santiago Guallar yahoo.com> writes: > > Hi, > I'd like to incorporate a random intercept in a > zero-inflated negative binomial model. Package pscl is > great but does not allow random effects, and package > MCMCglmm doesn't support the negative binomial. I'm > aware that package glmmADMB supp

Re: [R] likelihood ratio test for mean difference assuming unequal variance

you don't have a random effect. (3) I really hope this is a toy example and that your real data are larger, because estimating means and variance for three groups from 7 data points is *extremely* optimistic. (If you look at intervals(lme1) you'll see that the confidence intervals are very wide .

Re: [R] Model averaging using QAICc

overdispersion. You probably need to look at your data more carefully -- do the model fits seem reasonable? Are there big outliers, or zero-inflation, or ... ? If you are using glmmADMB for mixed model fitting, I would suggest follow-ups go to r-sig-mixed-mod...@r-project.org ... Ben Bolker __

Re: [R] degrees of freedom

e of points for you to think about that might help: * since you only have two treatments, I think you can analyze this as a _paired_ model, that is, reduce the data to (treatment-control, i.e. overload - non_overload) for each animal. Then you'll have 6 data points, 3 in each group,

Re: [R] Regression on presence/absence matrix

Daniel Patón Domínguez gmail.com> writes: > > > The library of packages that installs with R includes the stats > > package, in the stats package is the glm function for fitting > > generalized linear models. Using glm with a binomial family will fit > > a logistic regression which can be used

Re: [R] RSA and lmer

package maintainer, and that you are likely to have to do a lot of re-engineering from scratch. Maybe as a shortcut you could figure out a way to get robust (Huber-White/sandwich) estimates of the standard errors? Ben Bolker __ R-help@r-projec

Re: [R] Regression on presence/absence matrix

penalized regression (glmnet package), random forests, MARSS, ... figuring out which is best in your case isn't trivial ... Ben Bolker On 14-01-25 01:52 PM, Daniel Patón Domínguez wrote: > Dear all: > > In the book "Logistic Regression: An Overview Lawrence M. Healy > Eastern

Re: [R] package opVar

Pascal Oettli ymail.com> writes: > > Hello, > > There is no package "opVar" in the available CRAN packages list. > > Regards, > Pascal > > On Sat, Mar 8, 2014 at 6:06 PM, Charles Thuo > gmail.com> wrote: [snip] > > Warning message: > > package '' is not available (for R version 3.0.2) >

Re: [R] R bug on survival library Windows 7

CASTELLI christel chu-nimes.fr> writes: > > Dear All, > > I have updated my OS - Windows 7, and I found a > situation where R stops working > with reported error "R for Windows GUI front-end has > stopped working". My script worked before (on windows XP). > > The error occured when I perfor

Re: [R] Negative binomial models and censored observations

; > Thanks, Tim It's not quite out of the box, but if you defined a censoring level it wouldn't be *too* hard to write a log-likelihood model for the truncated/censored case and using bbmle. It would be much less efficient and stable than pscl, but it should work ... Ben Bolker

Re: [R] lme4: How to specify nested factors, meaning of : and %in%

Shouli Li utu.fi> writes: > > I have the same problem. I am wondering have you solved the problem already? > > [[alternative HTML version deleted]] > > It's completely unclear from this message what the context is, so it's unanswerable -- sorry. (Perhaps there was a link to the ori

Re: [R] glmer vs glmmadmb

1 0.075400.068191.11 0.2689 > time.f2:intrv.f1 0.021480.023950.90 0.3698 > time.f3:intrv.f1 -0.048350.02394 -2.02 0.0435 * Otherwise I'm stumped. The numbers of observations etc. etc. seem consistent. It's hard to compare

Re: [R] Arcsine transformation

peake osu.edu> writes: > > I am tryin to perform an arcsine transformation on my data containig > percentages as the dep. variable. Does anyone have a code that I could use > to do that? I am relatively new to R. Thanks for your help! asin(x/100) ? or asin(x/100)*2/pi if you want the results

Re: [R] Arcsine transformation

oi/full/10.1890/10-0340.1. I think the title is a little silly, but it's worth reading. > Peter Alspach > > -Original Message- From: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] On Behalf Of Ben Bolker Sent: > Monday, 23 September 2013 1

Re: [R] Slight misinformation in OSX version of R

Erich Neuwirth univie.ac.at> writes: > > I just installed R on a Mac without any traces of earlier versions. > It exhibited a well know problem: > > WARNING: You're using a non-UTF8 locale, therefore only ASCII > characters will work. > Please read R for Mac OS X FAQ (see Help) section 9 and

Re: [R] Is it possible with two random effects in lme()?

n > so I need use lme. > Bettina This (crossed random effects) is possible but not that easy: you should (1) study the later chapters of Pinheiro and Bates 2000 and (2) re-post this question to r-sig-mixed-mod...@r-project.org. good luck, Ben Bolker ___

Re: [R] Error: C stack usage is too close to the limit when using list.files()

Jonathan Greenberg illinois.edu> writes: > > R-helpers: > > I'm running a file search on my entire drive (Mac OS X) using: > > files_found <- list.files(dir="/",pattern=somepattern,recursive=TRUE,full.names=TRUE) > where somepattern is a search pattern (which I have confirmed via a > unix "fin

Re: [R] na.action within glmmADMB package?

Marta Lomas hotmail.com> writes: > > Hello everybody, > > I would like to know if within the glmmADMB package into R interface > there is a way to deal with the NAs > different than applying "dataformodeling= na.omit(dataframe)". > This way as you may know removes all > the rows of the data

Re: [R] Problems with lme random slope+intercept model

g) ... I would guess that your model is overfitted/unidentifiable, but I would have to look a lot more carefully to know for sure. Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the po

Re: [R] Comparison of two weibull distributions

kmmoon100 student.unimelb.edu.au> writes: > > Hello, > > How can I do a test of two weibull distributions? > I have two weibull distribution sets from two wind datasets in order to > check whether they are same. > I thought 2 sample t-test would be applicable but I couldn't find any ways > to d

Re: [R] Error message glmer using R: “ 'what' must be a character string or a function”

both r-help and Stack Overflow tends to lead to duplicated effort/ frustration. Please choose one or the other (in my opinion it's OK to cross-post after a few days if you don't get any responses in one place, provided that you say that you've cross-posted and ideally provide a referenc

Re: [R] problem with interaction in lmer even after creating an "interaction variable"

a_lampei uni-tuebingen.de> writes: > > Dear all, > I have a problem with interactions in lmer. I have 2 factors (garden and > gebiet) which interact, plus one other variable (home), > dataframe arr. When > I put: > / > lmer (biomass ~ home + garden:gebiet + ( 1|Block), data = arr)/ > > it wri

Re: [R] Adding the complementary log-link to binomial() and make.link()

Ken Knoblauch inserm.fr> writes: > > Roland Deutsch tuwien.ac.at> writes: > > in my research I frequently work with binomial > response models, which > > are of course part of the generalized linear > models. While I do use > > common link functions such as the logit, probit > and cloglog,

Re: [R] Error running MuMIn dredge function using glmer models

Martin Turcotte gmail.com> writes: > Dear list, > I am trying to use MuMIn to compare all possible mixed models > using the dredge function on binomial data but I > am getting an error message that I cannot decode. This error > only occurs when I use glmer. When I use an lmer > analysis on a d

Re: [R] problem with interaction in lmer even after creating an "interaction variable"

compare > explained variability. Is there some option, or it is simply impossible? > Thank you, Anna The development version of lme4 has an (experimental) feature that automatically removes collinear columns of the model matrix; you could try that. Further discussion on r-sig-mix

Re: [R] Getting residual term out of lmer summary table

wsl.ch> writes: > > Hello > I'm working with mixed effects models using lmer() and have some > problems to get all variance components of the model's random > effects. I can get the variance of the random effect out of the > summary and use it for further calculations, but not the variance >

Re: [R] Repeated measures with categorical data

s probably considered 'ordinal', i.e. ordered categorical, which may be helpful terminology in searching for solutions.) Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the po

Re: [R] nlme function summary.lmList cannot be found with new versions

megan herting chla.usc.edu> writes: > > Hello, > > I installed the newest version of R (3.0.2) as well as the > newest version of > nlme (3.1-113) in order to use summary.lmList and other > nlme functions. Once > loading the new library, lmList and summary.lm can be found, > but a number of

Re: [R] Inverse of Probit

David Winsemius comcast.net> writes: > > > On Nov 19, 2013, at 10:59 AM, Calum wrote: > > > Hi there, > > I hope someone can help me. > > > > I have a dataset of Concentration against Mortality, and I am trying to > > compare the use of Logit and Probit models using this data. [snip snip sn

Re: [R] Binomial GLM in Stata and R

Floor Biemans hotmail.com> writes: [snip] > The stata code I have is: > > glm c IndA fia, family(binomial s) link(cloglog) offset(offset) > > The R code is: > > glmt <- glm(data=dataset, c ~ IndA + fia, offset = offset, family = binomial(link = cloglog)) > > Which yields different results fr

Re: [R] Thoughts for faster indexing

Neal Fultz gmail.com> writes: > > Noah, > > If N is # of rows, k is # of unique IDs > > Using which() is O(N), using which() in a loop is going to be O(Nk); > > sorting the entire data is O(N ln N) and then you can process it in > contiguous blocks, no which required. > > -Neal > You mi

Re: [R] Independent variable dependent on offset in GLMM

Jonas Josefsson slu.se> writes: > > Hi! (I was initially going to say that this question would probably be better on r-sig-mixed-mod...@r-project.org, but now that I've been through it I've changed my mind -- there aren't really any issues here that are specific to mixed models ... it's real

Re: [R] Direct (null) hypothesis testing using GLMMs - possible?

Tomer Czaczkes biologie.uni-regensburg.de> writes: > > Dear Forumites, > > Hi, I'm a long time eavesdropper, first time poster, but I simply couldn't > find any answer to this perhaps rather naive question: > > I am trying to see if my data is significantly different from a null > hypothesis u

Re: [R] Etimating time to run an analysis?

Erika Barthelmess stlawu.edu> writes: > Hi everyone, > > I'm new to this list and have searched R help prior for an answer > to this question, without luck. If I'm > posting in error, please forgive. > > I'm thinking about using package MuMIn to do multimodel inference > with logistic regres

Re: [R] date format

eliza botto hotmail.com> writes: > > Dear Users of R, > I have a data frame with three column, the first column contains years, the second one months and third one, > the days (cbind( mm dd)). I want to combine them so that i have one column with the date format as (dd.mm.). > Is there a

Re: [R] R lmer debugging: Error in [[<-.data.frame(*tmp*, i, value = integer(0)) : replacement has 0 rows, data has 117

r-message-even-after-grouping-variables- within-the-dat/20353535#20353535 (broken URL to make Gmane happy) These questions are probably more appropriate for r-sig-mixed-mod...@r-project.org ... Ben Bolker __ R-help@r-project.org mailing list https:

Re: [R] R lmer debugging: Error in [[<-.data.frame(*tmp*, i, value = integer(0)) : replacement has 0 rows, data has 117

Cynthia Tedore biol.lu.se> writes: > > males is a factor. If I don't specify that, then it > treats it as a numeric. > any other suggestions? transform(spiders,focal.chel=as.numeric(focal.chel), opponent.chel=as.numeric(opponent.chel),fmales=factor(males)) model1<-lmer(threatened~focal

Re: [R] mixed model ANCOVA

laurie bayet gmail.com> writes: > > Hi, > > I want to set up a mixed model ANCOVA but cannot find a way to do it. > > There is: > > * 1 subject factor (random, between subjects) called Subject > * 3 categorical within subjects factors called Emotion, Sex, Race > * 1 continuous covariate (**WI

Re: [R] help with the nested anova formulas

Robert Lynch gmail.com> writes: > I am modeling grade as a function of membership in > various cohorts. There > are four "cohorts". (NONE, ISE07,ISE08,ISE09) and two times of cohorts > coded as ISE = TRUE (ISE0#) or FALSE (NONE). There is clear co-linearity > but that is to be expected. > >

Re: [R] p value for mu: anova()

url.com/reproducible-000 What *exact* code are you running? "an anova analysis" is too vague. 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

Re: [R] 3-D interpretation

Shane Carey gmail.com> writes: > > it just keeps crashing on me, > > It seems to crash on this line > > rgl.surface(akima.li$x,akima.li$y,akima.li$z,color="green",alpha=c(0.5)) When I run the code you gave us along with the data you gave us, I get Error in rgl.surface(akima.li$X, akima.li$

Re: [R] 3-D interpretation

out that other people can plot your akima.li surface without any trouble ...) Ben Bolker > > > On Wed, Dec 11, 2013 at 3:24 PM, Ben Bolker wrote: > >> Shane Carey gmail.com> writes: >> >>> >>> it just keeps crashing on me, >>> >>&g

Re: [R] R crashes with large vectors

Jeremie Smaga 4ecap.com> writes: > > Good afternoon, > > I have been experiencing a lot of crashes working with large vectors in R. > > Specifically, I am using XTS of length of minimum 120k elements. > > My problem is that I cannot display the vector (otherwise R crashes), I > cannot plot it

Re: [R] how to update a bugs-model from inside R using R2WinBUGS

quot;debug=TRUE", then the > window remains open and updating is possible, but it is no longer > written into the R-object. Is it generally impossible? > > Thanks, > Frederic > > As far as I know (not having checked carefully), it's impossible -

Re: [R] R's Data Dredging Philosophy for Distribution Fitting

emorway engr.colostate.edu> writes: > > > Forum, > > I'm a grad student in Civil Eng, took some Stats classes that required > students learn R, and I have since taken to R and use it for as much as I > can. Back in my lab/office, many of my fellow grad students still use > proprietary softwa

Re: [R] qustion-binomial Ancova

the results of fitting the statistical model. In general, giving a more detailed example will get you better answers. Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://

Re: [R] log transformation

jarry hotmail.com> writes: > > > Hi, > > I am reading an article in which, first, some given "p-results" are > obtained, and, second, these are afterwards transformed and expressed as the > "NEGATIVE base-10 logarithm of the p-value". > > My question is if anyone could indicate how is such t

Re: [R] possible bug in ape::extract.clade()

> http://www.mail-archive.com/r-sig-phylo r-project.org/msg00537.html > If you don't see any action on this in the near future I would try re-posting to r-sig-ph...@r-project.org ... Ben Bolker __ R-help@r-project.org mailing list

Re: [R] logistic regression with repeated measures for spec ies-habitat associations

visit the r-sig-mixed-models mailing list with additional questions ... Missing data should not be a big problem. 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.

Re: [R] RGoogleDocs ability to write to spreadsheets broken as of yesterday

s as though one might be able to fix this by hacking the hard-coded URLs in the code, but as you suggest that might be above your head. good luck ... Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLE

Re: [R] RGoogleDocs ability to write to spreadsheets broken as of yesterday

On Wed, Jul 21, 2010 at 10:38 AM, Henrique Dallazuanna wrote: > > Maybe: > packageDescription('RGoogleDocs', fields = 'Author') > >> or rather packageDescription('RgoogleDocs', fields='Maintainer') (usually but not always the same person) thanks Ben ___

Re: [R] prediction from a logistic mixed effects model

kdionisio gmail.com> writes: > > > Hi, > Is there any similar command to "predict" which can be used with a logistic > random effects model? Poke around on http://glmm.wikidot.com , let me know how you do. Ben Bolker ___

[R] overriding axis limits in hexbin plot?

devices I will probably hack a version of the plot method that has explicit xlim and ylim arguments, but I wanted to (1) check that I wasn't missing anything obvious and (2) see if the package maintainer would be interested in a patch ... I think hexbin is reasonably widely used (or should be

Re: [R] glm - prediction of a factor with several levels

given ? It's not sufficiently clear (to me at least) what you're trying to do. Please provide a minimal reproducible example ... As far as I know, polr is the right way to do ordinal regression; it's not clear how you were trying to use glm to do it. Ben Bolker

Re: [R] Bug on r-bc?

Paul Smith gmail.com> writes: > > Dear All, > > The following code should return 1, but it returns 0: > > source("http://r-bc.googlecode.com/svn/trunk/R/bc.R";) > bc("9 % 2") > > Do you confirm this bug? > It's not a bug in r-bc, it's a misfeature (?) in bc. It has to do with the 'scale'

Re: [R] Bug on r-bc?

Gabor Grothendieck gmail.com> writes: > See FAQ 2 on the r-bc package home page: > http://r-bc.googlecode.com This is getting a little bit self-referential -- that FAQ refers to the previous message in this thread ... __ R-help@r-project.org mailin

Re: [R] confidence intervals around p-values

as an index of effect size (e.g. translating a t- or Z-score into a p-value), why not calculate the confidence interval on the effect size? This is off-topic for the group (not an R question), but if you gave a sense of the problem you were trying to solve you might get some a

Re: [R] lme vs. lmer, how do they differ?

nce of effects. lme is older, better documented (Pinheiro and Bates 2000), more stable, and handles 'R-side' structures (heteroscedasticity, within-group correlations). r-sig-mixed-models is a good place for questions about these packages. Ben Bolker ___

Re: [R] Maximum log likelihood estimates of the parameters of a nonlinear model.

Odette Gaston gmail.com> writes: > > Dear all, > > Is it possible to generate AIC or something equivalent for nonlinear > model estimated based on maximum log likelihood l in R? > I used nls based on least squares to estimate, and therefore I cannot > assess the quality of models with AIC. nlme

Re: [R] lmer output

unibas.ch> writes: > I have a question regarding an output of a binomial lmer-model. > The model is as follows: > lmer(y~diet * day * female + (day|female),family=binomial) A reproducible example would always be nice. > The corresponding output is: > Generalized linear mixed model fit by th

Re: [R] gee p values

John Sorkin grecc.umaryland.edu> writes: > > Peng, > If the answer were as simple as you suggest, I would expect that gee would automatically produce the p > values. Since gee does not produce the values, I fear that the computation may be more complex, or perhaps > computing p values from gee m

Re: [R] R-equivalent Stata command: poisson or quasipoisson?

Wil M Contreras Arbaje gmail.com> writes: > > Thanks Bill! > > Not asking for help with Stata at all, on the contrary: the article > mentioned using Stata to fit the model described earlier, and I wasn't > sure how to do the same in R (which is what I've used since college). > > Thanks aga

Re: [R] average matrices across a list

Gregory Ryslik comcast.net> writes: > Browse[2]> Reduce["+",results] > Error in Reduce["+", results] : > object of type 'closure' is not subsettable > You need to use parentheses, not square brackets. __ R-help@r-project.org mailing list https:/

Re: [R] average matrices across a list

My next suggestion (I don't have time to work out or test an example at the moment): library(abind) tmparr <- abind(m1,m2,m3,...,along=3) OR tmparr <- do.call(c(matlist,list(along=3))) apply(tmparr,c(1,2),mean,na.rm=TRUE) or something along those lines. __

Re: [R] Transforming character vector

LCOG1 lcog.org> writes: [snip] > > I need to do the same for a fueltype where each record has a character > representing the data instead of a numeral(as in year). No reproducible > code or data because i think this is pretty straight forward. I could do > this using a series of loops but i t

Re: [R] Stats Question

David Winsemius comcast.net> writes: > On Sep 13, 2010, at 8:27 PM, csiro.au> wrote: > > > I have site data with variables that vary across sites (like wind > > speed, moisture content) and within sites I have experimental units > > (logs) with associated variables (like decay class, suspen

Re: [R] average matrices across a list

Gregory Ryslik comcast.net> writes: > mymats <- vector('list', 5) > set.seed(246) > > # Generate a list of five 3 x 3 matrices > for(i in 1:5) mymats[[i]] <- matrix(sample(1:9), nrow = 3) > > mymats[[5]][1,1]<-NA > mymats[[4]][2,2]<-NA > mymats > > matrixadder<-function(u,v){ > na.u<-is

[R] predict(backSpline(x)): losing my marbles?

art of the range but goes crazy elsewhere. I would have expected it to be reasonably close to this well-behaved curve over the whole range. I have looked at the docs for interpSpline, backSpline, predict.bSpline, ... and nothing jumps out at me. Please be gentle, if possible, in explaining

Re: [R] Model averaging with (and without) interaction terms

Leslie Young gmail.com> writes: > > I’ve used logistic regression to create models to assess the effect of > 3 variables on the presence or absence of a species, including the > interaction terms between variables and model averaging using MuMI: > model.avg > > The top models (delta<4) include

Re: [R] HDP and 99% contour lines

Peter Spencer murdoch.edu.au> writes: > > Dear all, > > I have a very simple question about how I can include HPD confidence > lines in a Marginal posterior distribution scatterplot > I have the following code to draw the scatterplot(s) from an output > table; I think the code in HPDregionpl

Re: [R] IP address

Jorge Nieves moorecap.com> writes: > > > Hi, > > We have some tight controls in our systems and I am having difficulty > downloading/upgrading R packages. The IT department will configure our > system to let me download packages from two or three R depositories. > How do I find out what the I

Re: [R] More accurate ODE solver?

Tianchan Niu isis.georgetown.edu> writes: > > Dear All, > > I was using rk4 and lsoda to solve a ODE system. However, both of them gave > bad accurate solutions, especially compared with Matlab solver ODE45. For > example, ODE45 gave solutions that can go to a stable level (about 1.6) when > ti

Re: [R] Preparing data frame for Plotrix kiteChart

Graham Smith myotis.co.uk> writes: > > Although, I can fix this, I am trying to sort out something as > straighforward as possible for my students, and I have some questions > that hopefully someone can help me with. > > My data is: > > Species DistanceCount > A 5

Re: [R] Is there a project to compile R scripts into stand-alone executable file?

yehengxin hotmail.com> writes: > I know Matlab's M file can be converted to a stand-alone executable file. I > wonder if there is a project aimed at compiling R scripts into stand-alone > executable file. I think it will be very promising for R to be more widely > used in different fields.

Re: [R] ergm crashes

rtainly) a bug in the ergm package: contact the maintainer (maintainer("ergm")). 3. We, and they, are unlikely to be able to help without a reproducible example. cheers Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mail

Re: [R] Data Cube in R from CSV

dajohnst ucdavis.edu> writes: > Why not use an array? > > An array can be indexed in as many dimensions as you would like, and do not > require any extra packages. > > x = array(1:27, dim = c(3, 3, 3)) > x > x[1, , ] > x[ , 1, ] > x[ , , 1] > An array is certainly the right structure to

Re: [R] plotting convex hull for 3D

cassie jones gmail.com> writes: > I have a 3 dimensional data and I need to plot a convex hull to it. I have > done it for 2 dimensional case using chull command in R. But I think it does > not work for more than 2 dimension. > Can anyone help me with this? Is there anyway to plot the convex hull

Re: [R] boyplots nearly identical but still highly significant effect?

Jake Kami gmail.com> writes: > > dear list, > > i am running a within-design ANOVA with 4 factors (4,4,2 and 2 levels each). > the last one is a time factor comprising two different treatment timepoints. > i fit a mixed-effects model using lme and apply the anova function to the > outcome. acco

Re: [R] select affy probes of cancer-related genes

Unger Kristian imperial.ac.uk> writes: > I would like to select probes (affy expression set) of genes that are > "cancer-related". Conventionally the decision whether a gene is > cancer-related or not is made by looking up the literature. Since this > is not possible for all genes on the array

Re: [R] how to show the number of each axis interval (plot)

Duncan Murdoch gmail.com> writes: > > On 20/09/2010 9:44 AM, elaine kuo wrote: > > Dear List, > > > > I am using plot for homework. > > You should ask your instructor or teaching assistant for help on homework. > > Duncan Murdoch > > > The x-axis covered from 0 to 80, with 4 intervals. > >

Re: [R] Composing Music - R Package

C.H. gmail.com> writes: > http://r-forge.r-project.org/projects/tuner/ > > On Mon, Sep 20, 2010 at 8:35 AM, Deb Midya yahoo.com> wrote: [snip] > > 1.   Is there any R-package or if any to compose music? > > 2.   Is there any R-package or if any to analyse music? Also RSiteSearch("mu

Re: [R] Depletion of small p values upon iterative testing of identical normal distributions

A gmail.com> writes: > > Dear all, [snip] > Here are two key parts of my code to show what functions I'm working with: > > #Calculating the p values > while(i Group1<-rnorm(6,-0.0065,0.0837) > Group2<-rnorm(6,-0.0065,0.0837) > PV<-t.test(Group1,Group2)$p.value > pscoresvector<-c(PV,pscoresve

Re: [R] Survival curve mean adjusted for covariate: NEED TO DO IN NEXT 2 HOURS, PLEASE HELP

mark.fisher123 gmail.com> writes: [snip] > library(survival) > survdata<-read.csv("data.csv") > > ##Fit Weibull model to data > > WeiModel<-survreg(Surv(survdata$Time,survdata$Status)~survdata$gender) > summary(WeiModel) > > P<-pweibull(n, scale=exp(WeiModel$coef[1]), shape=1/WeiModel$sca

Re: [R] removed data is still there!

Ivan Calandra uni-hamburg.de> writes: > > Hi, > > I knew about that way already, with factor(). Isn't there another > possibility, directly at the subsetting step? That would be of great help > iris1 <- iris[iris$Species == 'setosa',] ## I mean here > > Ivan Not as far as I know. See

Re: [R] Uncertainty propagation

Maayt hotmail.com> writes: [snip] > My first intention was to use a kind of monte carlo routine and run the > model many times by changing the power law parameters. These power laws were > obtained by fitting data points under R. I thus have std error associated to > them: alpha (±da) * WaterHigh

Re: [R] Help required

Malik Shahzad live.com> writes: > > > Is it possible to read jpeg files into R? > > If yes please guide, Thanks.. I tried to search many time but failed to do. > install.packages("sos") library("sos") findFn("read jpeg") (I initially tried findFn("import jpeg") and didn't get any hits, then

Re: [R] Fitting GLMM models with glmer

Clodio Almeida gmail.com> writes: > > Hi everybody: > [snip] > > I obtained the same results for parameters estimates and > standarderrors, by using: > > glmer(cens ~ treat + heart + offset(log(SURVT) + (1 | INST), > data=liver, family=poisson) It's nice that this check works. I would li

Re: [R] 3D plot

jethi hotmail.com> writes: > hey, is there anybody who can help me? its very urgent because i have to > send my bachelor thesis on monday. pls help me I'm really sorry that you're stuck, but ... waiting until a few days before an important assignment is due and then depending on the gener

Re: [R] Uncertainty propagation

Maayt hotmail.com> writes: > I linearized my power relations en fitted them with a linear rlm() function. > When I re-sample my pairs from a bivariate normal distribution for my power > law what transformation do I need to apply a transformation to my covariance > (vcov) matrix to get back from m

Re: [R] Problem with unlist

Luis Felipe Parra quantil.com.co> writes: > > Hello, I am trying to unlist a list, which is attached, and I am having the > problem that when I unlist it the number of elements changes from 5065 to > 5084 > > > x <- lapply(SumaPluvi, FUN="[", 1); > > n <- sapply(x, FUN=length); > > print(tabl

Re: [R] 95% confidence intercal with glm

zozio32 gmail.com> writes: > > > Hi > > I had to use a glm instead of my basic lm on some data due to unconstant > variance. > > now, when I plot the model over the data, how can I easily get the 95% > confidence interval that sormally coming from: > > > yv <- predict(modelVar,list

Re: [R] Best package for time series analysis with wavelets???

specific to your field, and see what scholarly/ peer-reviewed articles you can turn up. That's what I would do. Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://w

Re: [R] A problem with plotting a long expression in ylab ?

y documented property of R's X11 graphics model, rather than a bug ... I have no idea where to start looking for more information about what defines this behavior -- if I were desperate to know I would probably try asking Paul Murrell ... I would be very interested to see this discussed

Re: [R] 95% confidence intercal with glm

gt; i use family="binomial" is this wrong if i use this method to > calculate 95% CI? > > Thanks > > Sam On 28 Sep 2010, at 14:50, Ben Bolker wrote: > > zozio32 gmail.com> writes: > >> >> >> Hi >> >> I had to use a glm instead

Re: [R] 3D Graphics

Duncan Murdoch gmail.com> writes: > > On 29/09/2010 6:00 AM, JoH wrote: > > Are there anyother ways in which I can create a surface plot? persp() (in base R) is less flexible than rgl::persp3d, doesn't do hidden line removal, etc., but does appear in the regular R graphics window and can be

Re: [R] how to rotate the x axis lable to an interested angle?

komais yahoo.com.cn> writes: > how to rotate the x axis lable to an interested angle as the picture show? __ R-help@r-project.org mailing list https://stat.ethz

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