Re: [R] incidence_fit model for simulation

dear all, In addition to the thorough and intuitive incidence package, I would like to indicate a technical report on the same topic. R code and worked examples are reported. https://www.researchgate.net/publication/340664370_Modelling_COVID-19_outbreak_segmented_regression_to_assess_lockdow

Re: [R] Efficient way to update a survival model

dear Frank, update() does not update actually.. It just builds a new call which is evaluated. To speed up the procedure you could try to supply starting values via argument 'init'. The first values come from the previous fit, and the last one referring to new coefficients is set to zero (or

Re: [R] Model studies in one analysis using treatment as a five level moderator in a meta-regression

hi Jay, Consult a local statistician. Statistics is not you think is (namely simple computations, R and probably plotting..). regards, vito Jay Zola ha scritto: Hello, I am medical student, writing a meta-analysis on complication and reoperation rates after the five most common treat

Re: [R] Piecewise continuous Poisson regression

dear John, The package segmented can help you. ?plot.segmented includes a Poisson example best, vito "Sorkin, John" ha scritto: Is there an R package that will perform a piecewise continuous Poisson regression? I want to model two linear segments that intersect at a common knot. Thank

Re: [R] Fitting quantile (or cdf?) function to data with specified percentiles

A possible (simple) solution is to use a binomial GLM which guarantees fitted values (percentiles) in (0,1): plot(percentile, score) o<-glm(percentile~sc, family=binomial) points(fitted(o), sc, col=2) You can "predict" percentiles given score via predict.glm() best, vito Franco Danilo Roca L

Re: [R] structural equation modeling in sem, error, The model has negative degrees of freedom = -3, and The model is almost surely misspecified...

he abundance of some microbial groups (Nitrosotalea, Nitrosos_Cl1, Nitrosos_Cl3, Nitrosos_Cl4 e Nitrosos_Cl7), and on enzyme activity (PNA). Thanks in advance, Best regards Michele mod.pnr1 <- specifyModel() PD_AOA -> PNA, B1, NA Nitrosotalea -> PNA, B2, NA Nitrosos_Cl1 -> PNA,

[R] Biclustering issues with biclust()

ix) <- colnames(xs) standardMatrix } Without stdm not even BCCC can find anything. Am I missing something? Best, Michele __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http:

[R] rgenoud and snow

Hello everyone. I am trying to use rgenoud in a parallel environment. While making some tests, I noticed that rgenoud seems not to be using the cluster created by makeCluster, doing all the computation in the main node. Following is the example: ncores <- 5 cl <- makeCluster(rep('localhost', nco

Re: [R] Sweave, Texshop, and sync with included Rnw file

the two files. % Sweavetest.Rnw \documentclass{article} \begin{document} \SweaveOpts{concordance=TRUE} \title{an Sweave inclusion test} \author{Michele} \maketitle This is an example for the inclusion of RNW files and forward-inverse search. following is a chunk of sweave

Re: [R] Sweave, Texshop, and sync with included Rnw file

exworks but I had no luck On Jan 10, 2013, at 11:23 AM, Duncan Murdoch wrote: > On 13-01-09 9:09 PM, Duncan Murdoch wrote: >> On 13-01-09 3:25 PM, michele caseposta wrote: >>> Hello everyone. >>> I am in the process of writing a book in Latex with Texshop, on M

Re: [R] Sweave, Texshop, and sync with included Rnw file

> 2215 Snedecor Hall, Ames, IA > > > On Wed, Jan 9, 2013 at 2:25 PM, michele caseposta wrote: >> Hello everyone. >> I am in the process of writing a book in Latex with Texshop, on Mac. >> This book contains a lot of R code, hence the need to use Sweave. >> I was

[R] Sweave, Texshop, and sync with included Rnw file

Hello everyone. I am in the process of writing a book in Latex with Texshop, on Mac. This book contains a lot of R code, hence the need to use Sweave. I was able to compile Rnw files, and to sync back and forth from the pdf to the source Rnw. My problem now is that the book is divided in Chapters,

Re: [R] Multiple groups barplot

Hi Jim, thanks again for your support. Yes, I meant the subject codes; I will add a new variable and set the color to white all over. Thanks, Michele On Nov 15, 2012, at 1:13 AM, Jim Lemon wrote: > On 11/15/2012 07:21 AM, michele caseposta wrote: >> Back again. >> Is there a q

Re: [R] Multiple groups barplot

Back again. Is there a quick way to add the sample names in the plot? I was not able to find anything other than creating a new category with the name in it (and the same color all over). Thanks, Michele On Nov 14, 2012, at 2:45 PM, michele caseposta wrote: > Hi Jim, > sizetree was what

Re: [R] Multiple groups barplot

Hi Jim, sizetree was what I was looking for. I am going to play with the options a bit. Thanks a lot, Michele On Nov 14, 2012, at 2:55 AM, Jim Lemon wrote: > On 11/14/2012 11:04 AM, michele caseposta wrote: >> Hi everyone, >> I have a certain number of samples and I want to visua

[R] Multiple groups barplot

Hi everyone, I have a certain number of samples and I want to visualize the groups those samples belong to. For example, suppose to have three variables, age, sex, and smoker/nonsmoker, and three samples, S1, S2, S3. S1 is 35, male, nonsmoker S2 is 24, female, nonsmoker S3 is 24, female, smoker

Re: [R] Fit continuous distribution to truncated empirical values

Bert, I think there is a misunderstanding here. Some data is censored, but I want to fit the data with a distribution in the interval [0,24] only. Also, please note that I have other datasets having values larger than 1000. Cheers, Michele On 14 Nov 2011, at 18:28, Bert Gunter wrote: A

Re: [R] Fit continuous distribution to truncated empirical values

have a "good" fit over the interval of interest rather than a "reasonable" fit over the whole data. 3 - I went though those tutorials, but couldn't find an answer. That's probably due to the fact that those tutorials are "general", as you pointed out, while

Re: [R] Fit continuous distribution to truncated empirical values

Hello David, thanks for your answer. I have done as you told me, however the fit is very poor, much worse than that obtained from using the whole dataset (without upper bound). Any idea? Thanks, Michele On Nov 4, 2011, at 8:56 PM, David Winsemius wrote: > > On Nov 3, 2011, at 7

[R] Dunif and Punif

Hi, I am trying to use dunif and runif however, I have two problems: if I do dunif(1:10, min=1, max=10) I get 10 values, which summed give me 1. I understand that the probability is computed as f(x) = 1 / (max-min) but in this case it looks wrong: I have 10 values, each one equiprobable, and

[R] Fit continuous distribution to truncated empirical values

NaNs produced Am I doing something wrong? Thanks, Michele p.s. I have seen similar posts, e.g., http://tolstoy.newcastle.edu.au/R/help/05/02/11558.html, but I am not sure whether I can apply the same approach here. __ R-help@r-project.or

[R] (no subject)

dear R-utents, does anybody of you knows if there are some specific function, already stored in some libraries, which allow me to calculate straightforward McFadden-R^2,,pseudo-R^2, p-hat (the ML estimator for p) and the goodness of fit R^2p? thanks in advance! michi [[al

[R] memisc output to latex

Hi, I am trying to output a table in a Latex format with write.mtable. This is my code: h.summary <- mtable("linear" = hlm, "quadratic" = hqd, summary.stats=c("R-squared","adj. R-squared", "p")) h.summary <- relabel(h.summary, "J" = "J", "I(J^2)" = "J^2") write.mtable(h.summary, forLatex=TRUE, fil

[R] Sweave and multiple figures from an R source file

This is a simple Sweave test \includegraphics{coupling_images_report-gethypergraphs_rhea} \\ End of the simple sweave test \end{section} \end{document} When I compile the .tex file, however, the figures are overlapped one on top of the other. I tried to search for a solution, but found none...

[R] StepAIC with coxph

ybody know this error?? Thanks. Michele [[alternative HTML version deleted]] __ 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 pr

[R] X matrix deemed to be singular;

Hello, i'm tring to use a cox's model for a survival analysis. I have a dataset, this is a part: VOD SESSO fonte_sct donor RT_CGY STATOBMT TEMPO morto 1 0 F midrelated 1200 CP651 2 0 M mid

[R] X matrix deemed to be singular;

: X matrix deemed to be singular; variable 10 14 15 18 20 21 22 24 25 26 why??? anyone know the solution of this?? Thanks Michele [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/li

[R] read a xls file

Hello, i have a xls file. I will read it in r, what library-command i use for this?? any ideas?? Thanks Michele [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do

[R] anova with ordered groups

ank you Michele Pinelli ---- Michele Pinelli, MD, PhD Complex Disease Genetics Unit Department of Cellular and Molecular Biology and Pathology "L. Califano" University "Federico II", Naples Italy [EMAIL PR

[R] error on predict

ve this error: Warning message: 'newdata' had 1 rows but variable(s) found have 23 rows why?? thanks. Michele [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLE

[R] force glm estimates to be nonnegative

ver, I don't want to allow for that. In such a case, glm should solve > capacity ~ Student and I will set the slope to zero. Is there an option to constrain a parameter set to nonnegative values? Many thanks in advance! Michele Itten, BS. Carn

[R] Proportional Hazard mixture cure model

ch can do PHMCM? Regards, Michele Petteni --- Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place London W2 1PG [[alternative HTML version deleted]] _