Re: [R] metafor package: study level variation

! -Jarrett Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ 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

Re: [R] metafor package: study level variation

trials. Statistical Methods in Medical Research, 17(3), 279-301. Thanks! -Jarrett [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r-project.org mailing list

Re: [R] need help to convert in to panel data format

version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ 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

[R] [R-pkgs] New package metap on CRAN

and a graphical display. There exist a number of packages on CRAN which use one or other of these techniques in the context of genetic studies but metap is designed for general purpose use. Comments welcome. Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html

Re: [R] metafor combining escalc effect-sizes

it as a .csv, open it and re-run it as I have done? That gets rid of the attributes. Thanks very much, and to Wolfgang thanks for a great programme! I am using it in my MSc teaching here for healthcare students. Edward [[alternative HTML version deleted]] Michael Dewey i

Re: [R] Meta-analysis of prevalence at the country level with mgcv/gamm4

found. Anyone who has done a review will sympathise with you, not that that is any consolation. Julien [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r

Re: [R] Meta-analysis of prevalence at the country level with mgcv/gamm4

At 13:17 10/04/2014, Julien Riou wrote: Message: 11 Date: Wed, 09 Apr 2014 18:39:30 +0100 From: Michael Dewey i...@aghmed.fsnet.co.uk To: Julien Riou julien.rio...@gmail.com, r-help@r-project.org Subject: Re: [R] Meta-analysis of prevalence at the country level with mgcv/gamm4

Re: [R] interpreting weight in meta-analysis of proportion

Department of Translational Medical Sciences Naples University Federico II Italy Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] R 3.0.3, Windows 7: Problem installing XML package

/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. Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r

Re: [R] metafor - rstudent(res) - omitted rows

. MSc.* Content-Type: application/pdf; name=Rplot.pdf Content-Disposition: attachment; filename=Rplot.pdf X-Attachment-Id: f_hub2q8dv0 Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r-project.org mailing list

Re: [R] Metafor: How to integrate effectsizes?

deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ 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

Re: [R] Metafor: How to integrate effectsizes?

, please keep it on the list so others may benefit and contribute. best regards, Verena On Fri, Apr 25, 2014 at 1:21 PM, Michael Dewey mailto:i...@aghmed.fsnet.co.uki...@aghmed.fsnet.co.uk wrote: At 13:15 24/04/2014, Verena Weinbir wrote: Hello! I am using the metafor package for my master's

Re: [R] Metafor: How to integrate effectsizes?

. Box 616 (VIJV1) 6200 MD Maastricht, The Netherlands +31 (43) 388-4170 | http://www.wvbauer.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Michael Dewey Sent: Friday, April 25, 2014 16:23 To: Verena Weinbir Cc: r-help@r

Re: [R] Metafor: How to integrate effectsizes?

, 2014 15:09 To: Michael Dewey Cc: Viechtbauer Wolfgang (STAT); r-help@r-project.org Subject: Re: [R] Metafor: How to integrate effectsizes? Thank you very much for your illustration, Wolfgang! It helped me a lot. And also thank you for the package-hint, Michael! Now, I have re-checked

Re: [R] Help conduction Egger's test

homogenous studies to synthesise. Many thanks Sultan Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http

Re: [R] Metafor: How to integrate effectsizes?

, May 6, 2014 at 7:14 PM, Michael Dewey mailto:i...@aghmed.fsnet.co.uki...@aghmed.fsnet.co.uk wrote: At 14:23 06/05/2014, Viechtbauer Wolfgang (STAT) wrote: Without the sample size of a study (i.e., either the group sizes or the total sample size), you cannot convert the p-value to a t-value

Re: [R] Metafor: Strange Trim and Fill Outcome?

interpret this? That its not a publication bias that influences my data set, but a lack of precision (studies missing that are precise -small SD- and have big SMD)? Sorry but that bit is not very clear to me. Many thanks in advance! Verena [[alternative HTML version deleted]] Michael Dewey

Re: [R] is there anything wrong with doing a multinomial logistic like it is a binary logistic regression?

? [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R

Re: [R] How can I make my functions run faster

Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ 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

Re: [R] predict.glm with constant non-zero response intercept

of 'newdata' and the original 'offset' vectors produce full-on errors. is there any way in formula(...) other than including offset(...) to force a CONSTANT non-zero intercept? thanks for any insight! -m Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html

Re: [R] Sensitivy / Specificity and nulls

understand them better) but not required. -- - Don Donald Catanzaro PhD dgcatanz...@gmail.com 16144 Sigmond Lane Lowell, AR 72745 479-751-3616 [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html

Re: [R] Packaging

do 2 - what did you think was going to happen 3 - what actually happened Thanks in advance. Regards. Eva [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r

Re: [R] meta-analysis of annualized event rate

of Translational Medical Sciences Naples University Federico II Italy Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] Arcsine transformation

help mailing list archive at Nabble.com. [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do

Re: [R] over dispersion plot

of Environmental Studies University of Wisconsin - Madison [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help

[R] Fortune?, was Re: Recovering object names when using the ... argument in a fn XXXX

Nonclinical Biostatistics (650) 467-7374 Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R

Re: [R] manipulating longitudinal data in r

(1,2,2,1,1,2),b=c(2,2,2,1,2,2)) Any help will be appreciated. Dear Kemi It is often easier to do some sorts of manipulations on the wide format of the data. I appreciate that you can always do it both ways. Oluwakemi [[alternative HTML version deleted]] Michael Dewey i

Re: [R] manipulating longitudinal data in r

--- Sent from my phone. Please excuse my brevity. Michael Dewey i...@aghmed.fsnet.co.uk wrote: At 08:56 17/11/2012, Kemi Racheal wrote: Dear list member, I have the following data example ke - data.frame(patid=c(1,1,1,2,3,3),a=c(1,2,2,1,1,2)) I want to add another variable b

Re: [R] Comparing linear regression coefficients to a slope of 1

Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ 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

Re: [R] Forest plot

with so many studies included so I assume you are doing something else. Thank you very much! Mindy [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r-project.org mailing

Re: [R] Beta-coefficients for ZINB model

on relative importance in regression. Not sure how directly this translates into the non-linear case though. J Stat Soft October 2006 vol 17 number 1 Thanks, Jeremy [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html

Re: [R] suggestions about import SAS results to R.

-project.org/web/packages/SASxport/index.html But I heard that there might be some issues with the newest SAS version but give it a try... -- This message, and any attachments, is for the intended...{{dropped:13}} Michael Dewey i

Re: [R] Q-Q plot for chi-quadrat w/o knowing the contingency table

you correctly ?qqplot should help you here. If yes, please let me know. If no, please let me know as well. Thanks Wim [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help

[R] Announcement of new CRAN task view on meta-analysis

Subject line says it all really. I would be pleased to receive feedback on what I have left out which I should have put in, and what I have put in which I should have left out. Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html

Re: [R] using metafor for meta-analysis of before-after studies

Professor of Radiology Department of Radiology, West China Hospital, Sichuan University Chengdu, 610041, China [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r-project.org mailing

Re: [R] using metafor for meta-analysis of before-after studies

Tel: 613-722-6521 ext. 6554 Associate Professor of Radiology Department of Radiology, West China Hospital, Sichuan University Chengdu, 610041, China [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html Michael Dewey i

Re: [R] Return a vector in Fibonacci sequence function

.n4.nabble.com/Return-a-vector-in-Fibonacci-sequence-function-tp4666756p4666796.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html

Re: [R] calculate correlation effect size using contrast analysis for an omnibus Chi-square test statistic

Cambridge, MA 02140 617 864-4307 www.freshpond.org [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r

Re: [R] metafor

. Jin Choi MSc (Epidemiology) Student McGill University, Montreal CANADA Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] Can't find the error in a Binomial GLM I am doing, please help

?relevel might help you here Again, thanks -- View this message in context: http://r.789695.n4.nabble.com/Can-t-find-the-error-in-a-Binomial-GLM-I-am-doing-please-help-tp4615340p4616786.html Sent from the R help mailing list archive at Nabble.com. Michael Dewey i...@aghmed.fsnet.co.uk http

Re: [R] Wrong Q3 + Mean.

2.15.0 (2012-03-30). Retep -- View this message in context: http://r.789695.n4.nabble.com/Wrong-Q3-Mean-tp4630223.html Sent from the R help mailing list archive at Nabble.com. Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html

Re: [R] How do I print predicted effect sizes in forest plot?

deliveres the same values as already computed in the rma object. I checked the manual for package metafor but was not able to find out how to print the predicted values per study. kind regards, Alma [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http

Re: [R] about R

checking. Best Regards, Sevda [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] changing font size in Forest plot code.

(fontsize=15)) grid.text(* Test of heterogeneity of subgroups using General Estimating Equation model., x = .38, y = .07, gp=gpar(fontsize=10)) [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html

Re: [R] metafor package

version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ 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

Re: [R] Compilation fails for package 'BayesTree' on R 3.0.1 for Windows

what to do. Thank you in advance for any help, Javier [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo

Re: [R] metafor package: changing decimal in forest plot to midline decimal

PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r-project.org mailing

Re: [R] Zeta-squared transformation use R?

Ã¯Â¼ÂÃ¯Â¼ÂÃ¯Â¼ÂÃ¯Â¼ÂÃ¯Â¼ÂÃ¯Â¼ÂÃ¯Â¼ÂÃ¯Â¼ÂÃ¯Â¼ÂÃ¯Â¼ÂÃ¯Â¼Â [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r-project.org mailing list https://stat.ethz.ch

Re: [R] Correlating multiple effect sizes within a study to study-level predictors: metafor package

misunderstanding how to use metafor to do so? Thanks very much for your help! Best, Megan [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r-project.org mailing list

Re: [R] Correlating multiple effect sizes within a study to study-level predictors: metafor package

Maastricht University, P.O. Box 616 (VIJV1) 6200 MD Maastricht, The Netherlands +31 (43) 388-4170 | http://www.wvbauer.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Michael Dewey Sent: Monday, July 14, 2014 14:42

Re: [R] Correlating multiple effect sizes within a study to study-level predictors: metafor package

understands the science of what you are doing and the statistics of mixed effects models. I am a bit concerned that without that knowledge we on the list may end up giving you misleading advice, Thanks, Megan On Wed, Jul 16, 2014 at 1:53 AM, Michael Dewey i...@aghmed.fsnet.co.uk wrote: At 23

Re: [R] programme bivariate binomial negative

a list of posibilities Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ 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

Re: [R] Metafor -can't calculate heterogeneity with non-positive sampling variances

. Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ 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

Re: [R] How can I merge data with differing length?

On 30/10/2014 16:03, Kuma Raj wrote: How can I merge data frame df and tem shown below by filling the head of tem with missing values? does c(rep(NA, nrow(df) - length(tem)), tem) help? a- rnorm(1825, 20) b- rnorm(1825, 30) date-seq(as.Date(2000/1/1), by = day, length.out = 1825)

[R] Fwd: Re: Function that create day of the year column.

Dear Federic You need to do something like function(p, weights = NULL, data = NULL, subset = NULL, na.action = na.fail) { # but you will have Day, Month, Year, data # instead of the first three if(is.null(data)) data - sys.frame(sys.parent()) mf - match.call() mf$data - NULL

Re: [R] VGAM package : Frechet distribution - 2 parameter estimation

On 06/11/2014 06:04, Katherine Gobin wrote: Dear R forum, I am trying to execute following code (Page no 259 - VGAM.pdf) # . library(VGAM) set.seed(123) fdata -

Re: [R] MAd and trim-and-fill plot in R meta-analysis

On 10/11/2014 14:20, huang jialin wrote: Hi, I am planning to use BHHR method to conduct a meta-analysis, including calculation of a summary effect size and subgroup analysis. Meanwhile, I need to draw a trim-and-fill plot of all the effect sizes. However, MAd package cannot achieve the goal,

Re: [R] metafor - code for analysing geometric means

On 13/11/2014 11:00, Purssell, Ed wrote: ?Dear All I have some data expressed in geometric means and 95% confidence intervals. Can I code them in metafor as: rma(m1i=geometric mean 1, m2i=geometric mean 2, sd1i=geometric mean 1 CI /3.92, sd2i=geometric mean 2 CI/3.92...etc,

Re: [R] merge 2 data.frames in dependence of 2 values

On 13/11/2014 14:02, Matthias Weber wrote: Hello togehter, i have a little problem. Maybe anyone can help me. I think you might find ?merge enlightening Indeed given that the word merge occurs in your subject line and your text it is surprising you have not already found it. I have 2

Re: [R] Comparing summary hazard ratios in meta-analysis

On 21/11/2014 08:51, Mario Petretta wrote: Dear all, I use R 3.1.1 for Windows. I performed two different meta-analysis assessing the prognostic value of two different tests in patients with coronary artery disease. The study included in the two analysis are different. That makes life

Re: [R] Error Missing values where true/false needed

You do not tell us what you are trying to do but I think there is something wrong in the logic of your thinking as on the one hand you are selecting just precisely those elements of data$Rain which are NA and then testing whether any of them equals 60. On 25/11/2014 12:19, Frederic

Re: [R] Error Missing values where true/false needed

...@aims.ac.za https://sites.google.com/a/aims.ac.za/fredo/ On Tue, Nov 25, 2014 at 3:51 PM, Michael Dewey i...@aghmed.fsnet.co.uk mailto:i...@aghmed.fsnet.co.uk wrote: You do not tell us what you are trying to do but I think there is something wrong in the logic of your thinking as on the one hand

Re: [R] please please unsubscribe!!!!!!!!!!!!!!!!

Dear John Perhaps you have set your mail client to hide them? Your email certainly has them when I go Options | View | Headers | All in Thunderbird. Michael On 30/11/2014 12:05, John Sorkin wrote: The headers listed below as being part of the ״raw email messages are not seen, at least not

Re: [R] Add group name in barchart

Comments in line On 02/12/2014 23:27, Silong Liao wrote: Dear ALL, I have a dataset contains 2 variables: mate (mating groups) and ratio (ratio of number of mothers and fathers). And mate is an identifer which consists three components: year, flock (flk), and tag. I am using command

Re: [R] 2 ablines dans 1 même plot vide

If I understand correctly plot(1:10, 1:10, type = n) should get you started. This is an Anglophone list by the way. On 04/12/2014 22:23, Adrien Bonvin wrote: Bonjour J’aimerais savoir comment créer un “plot vide”, dans lequel je pourrais ajouter deux valeurs d’abline, tracées à partir de

Re: [R] Help sought with 1. converting factor to numeric; 2. creating new dataframe

Comments in line On 16/12/2014 11:25, Aditya Singh via R-help wrote: Dear R-experts, I am relatively new to R. Please help me in converting a dataframe into a numeric and then creating a new dataframe. R-code attached: my_xtrain=read.table(./train/X_train.txt)

Re: [R] dotplot legend

On 17/12/2014 12:24, r...@openmailbox.org wrote: Subscribers, For this example: library(lattice) testmatrix-matrix(c(1,2,3,4,3,6,12,24),nrow=4,ncol=2) testylabels-c('w1','x1','y1','z1') dotplot(testmatrix, scales=list(y=list(labels=testylabels), xlab=NULL)) legend('bottomright', 'legend',

Re: [R] pairing columns based on a value

Not sure how much help it will be but there is a package on CRAN called icd9. Although clearly the codes are different in ICD 10 it may give you some hints. I suppose you could even email the maintainer to see whether there is an icd10 in the pipeline. On 17/12/2014 20:14, Robert Strother

Re: [R] combinations between two vectors

On 18/12/2014 14:56, Alaios via R-help wrote: Hi all,I am looking for a function that would give me all the combinations between two vectors.Lets take as example the test-seq(1,3,by=5000) Browse[2] test [1] 1 5001 10001 15001 20001 25001 I want all the combinations between two times

Re: [R] Cox model -missing data.

Comment inline On 19/12/2014 11:17, aoife doherty wrote: Many thanks, I appreciate the response. When I convert the missing values to NA and run the cox model as described in previous post, the cox model seems to remove all of the rows with a missing value (as the number of rows n in the cox

Re: [R] Getting HR from Cox model in R

Inline comments On 23/12/2014 09:42, Ruzan Udumyan wrote: Dear All, I am not familiar with R language well. Could you please help me interpret these commands?: TE = exp(sum(coef(cox)[c('aTRUE', 'bTRUE')])) - does it mean exp(coef(a variable) + coef(b variable)) ? You have not given us

Re: [R] Getting HR from Cox model in R

TE = exp(sum(coef(cox)[c('TrialTRUE', 'MedTRUE')])) DE = exp(unname(coef(cox)['TrialTRUE'])) IE = exp(sum(coef(cox)['MedTRUE'])) PM = log(IE) / log(TE) return(c(exp(coef(cox)), TE=TE, DE=DE, IE=IE, PM=PM)) } On Tue, Dec 23, 2014 at 6:21 PM, Michael Dewey i...@aghmed.fsnet.co.uk mailto:i

[R] Fwd: Re: multiple imputed files

Forgot to send to list Dear Analies Would the package mitools help you? It is available from CRAN. On 26/01/2015 10:23, hnlki wrote: Dear, My dataset consists out of 5 imputed files (that I did not imputed myself). Is was wondering what is the best way to analyse them in R. I am aware that

Re: [R] installing Packages

On 26/01/2015 16:51, Kenya Carpenter wrote: Dear R- Help When installing ggplot2 it seems to install correctly but then I can't load it. My R session is copied below. Can you help? See below install.packages(ggplot2) Installing package into ‘C:/Users/Kenya/Documents/R/win-library/3.1’

Re: [R] Interpreting a Logit regression result

Dear Mohamed Your dataset did not make it through, the list strips most attachments. In my area of application I would be suspicious that such an odds ratio was the result of a data error or my misunderstanding of the underlying science. You are probably in the best position to judge both of

Re: [R] subsamples and regressions for 100 times

Comment inline On 17/02/2015 12:40, Angela Smith wrote: Hi R user, I'm new to R so my problem is probably pretty simple but I'm stuck: my data is consist of 2 variables: co2, temp and one treatment (l_group). The sample size is different among the treatments. so that, I wanted to make

Re: [R] extracting significance test for individual lm() parameters after using by

Dear Jerad I may have completely misunderstood your question but you do know that you can write your own function and use it in sapply where you have summary? You could incorporate calls to summary or to coef or somet other extractor or you could use the $ tool. On 25/01/2015 02:01, Moxley,

Re: [R] nonmonotonic glm?

Comments in line On 12/01/2015 13:13, Vito M. R. Muggeo wrote: dear Stanislav, Your data show two slopes with a kink at around 0. Thus, yet another approach would be to use segmented regression to fit a piecewise linear relationship with unknown breakpoint (being estimated as part of model

Re: [R] horizontal bar plots for CI visualization

On 12/02/2015 13:56, michael.eisenr...@agroscope.admin.ch wrote: There are a number of options for doing this. You might consider using forest plots as provided by one of a number of the meta-analysis packages. See the CRAN MetaAnalysis task view for more details. -- Michael

Re: [R] R match - could be improved ?

Dear Jeremy The NAs do not seem random to me as the gaps between successive NAs are either 3, 8 or 11. Have you considered the possibility that the finite precision of real numbers in computers may be the issue here? On 15/03/2015 11:04, Jeremy Clark wrote: ​Dear All, The following gives

Re: [R] Ayuda con un árbol de regresión

Miguel, si prefieres escribir en espanol https://stat.ethz.ch/mailman/listinfo/r-help-es (This is the address of the Spanish language mailing list) On 23/03/2015 20:13, Miguel angel Lopez Martinez wrote: ARBOL-tree(PRECIO~CILINDRAJE_DEL_MOTOR+MODELO,data=CARROST) ARBOL plot(ARBOL)

Re: [R] Fitting a line on trellis plot

On 25/03/2015 12:30, Frederic Ntirenganya wrote: Hi all, I am doing analysis which involves fitting a line on trellis plot. But the commands below (or at least the output from them) are not plotting commands. The factor is month. As you know a year has 12 months and I expect to get 12

Re: [R] about model.matrix

This is really a question about statistics rather than R but see below On 01/04/2015 06:28, Fix Ace wrote: I tried to run the sample code from R: dd - data.frame(a = gl(3,4), b = gl(4,1,12)) a b 1 1 1 2 1 2 3 1 3 4 1 4 5 2 1 6 2 2 7 2 3 8 2 4 9 3 1 10 3 2 11 3 3 12 3 4

Re: [R] Substring replacement in string

Dear Alrik This may seem a silly suggestion but why not just define new functions PMIN and PMAX to call pmin and pmax. Obviously that does not solve your problem if it is more general than your example. On 28/02/2015 13:16, Alrik Thiem wrote: Dear Gabor, Many thanks. Works like a charm,

Re: [R] Substring replacement in string

With this string, I can then do: tt[pmin(pmax(pmin(1-tt$A,tt$B), pmin(1-tt$A,tt$C,1-tt$D))==tt$Y,pmax(tt$E,1-tt$E))==TRUE, ] A B C D Y E 1 0 0 0 0 0 0 2 0 0 0 0 0 1 . . . . . . . 61 1 1 1 1 0 0 62 1 1 1 1 0 1 -Ursprüngliche Nachricht- Von: Michael Dewey [mailto:i

Re: [R] xtable caption knitr

Dear Aurora I suspect the underscore character in your variable name is the problem. On 24/02/2015 11:16, AURORA GONZALEZ VIDAL wrote: Dear all, I have a problem with the caption option on the xtable function. Using Rmarkdown, knitr generates correctly a pdf when I write something like this:

Re: [R] library(multcomp) does not work for loading Tukey

Dear Xavier See below for comments On 26/02/2015 11:20, CHIRIBOGA Xavier wrote: Dear colleagues, For Tukey, I tried to load the function with library(multcomp) but again a message says: Error in library(multcomp) : any package called ‘multcomp’ has been found I suspect you

Re: [R] metafor - Cochrane on change score in pre-post design

Comment below On 13/04/2015 20:46, Antonello Preti wrote: Hi, this is another quesite related to the use of 'metafor' for calculation of standardized mean change in pre-post design studies. Essentially, my aim is to compare different method to arrive at the same conclusion: Does the treatment

Re: [R] Error in solve.default(-val)

Andrés Si prefieres escribir en español https://stat.ethz.ch/mailman/listinfo/r-help-es seria mejor (That is a link to the Spanish language version of R-help) On 23/04/2015 05:24, Andrés M wrote: Buenas noches, comedidamente me dirijo a ustedes para hacerles una consulta respecto a un error

Re: [R] generate a list as follows: 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, . . . . ., n, n, n, n

On 19/04/2015 15:34, John Sorkin wrote: Windows 7 64-bit R 3.1.3 RStudio 0.98.1103 I am trying to generate a list of length 4n which consists of the integers 1 to n repeated in groups of four, i.e. 1,1,1,1, 2,2,2,2, 3,3,3,3, . . . . , n,n,n,n (The spaces in the list are added only for

Re: [R] Metafor - rma.mv function - variance components

Dear Carlijn You might shed some light on what is going on by using profile.rma.mv Michael On 21/04/2015 09:42, Carlijn Wibbelink wrote: Thank you for your reaction, it worked. However, I'm wondering if this is the right way to test whether there is significant variation on one of the two

Re: [R] problem setting default timezone

In-line below On 23/04/2015 14:01, Bos, Roger wrote: Dear All, I would like to learn the proper way to set the default time zone so I get the correct date for my files. The code below is non-reproducible (sorry) because it is based on a file on my system, but I hope someone will be able to

Re: [R] create function to plot high density data using lattice

I suspect Luigi that if you wrap the call to xyplot in print( ) matters might be improved. On 23/04/2015 13:50, Luigi Marongiu wrote: Dear all, with the most useful help of Duncan I updated a script to plot high density data in the form of 384 squares containing tiny plots. The function

Re: [R] Help Interpreting Linear Mixed Model

Dear Joshua It would also help if you told us what your scientific question was. At the moment we know what R commands you used and have seen the head of your dataset but not why you are doing it. I would summarise what you have given us as 1 - most ID only occur once 2 - goal keepers do

Re: [R] Help with making Loop

Dear Fazal I think part of your problem can be addressed with merge go ?merge at the R prompt On 01/05/2015 21:05, Hadi Fazal wrote: Hi everyone, I am a real beginner to R and have probably a very naive issue. I've a small data frame with three columns: Unique Sample ID, Gene 1 and Gene 2 (the

Re: [R] Request for functions to calculate correlated factors influencing an outcome.

Dear Lalitha, see inline below On 03/05/2015 10:19, Lalitha Viswanathan wrote: Hi I have a dataset of the type attached. Here's my code thus far. dataset -data.frame(read.delim(data, sep=\t, header=TRUE)); newData-subset(dataset, select = c(Price, Reliability, Mileage, Weight, Disp, HP)); In

Re: [R] Wrong results from anova

See in-line On 14/04/2015 18:23, li li wrote: Hi all, I have following data. When I perform an anova, the residual sum of square returns to be zero. But this is wrong, since we can hand calculate the RSS to be around 0.0308. Did anyone come across the same problem before? Any suggestions?

Re: [R] : automated levene test and other tests for variable datasets

You ask quite a lot of questions, I have given some hints about your first example inline On 14/04/2015 09:07, Joachim Audenaert wrote: Hello all, I am writing a script for statistical comparison of means. I'm doing many field trials with plants, where we have to compare the efficacy of

Re: [R] BIG difficulties in Using boot.ci (bot package)

See in line On 13/04/2015 14:38, varin sacha wrote: Hi Jean, Many thanks, I got it but there is still a problem. When trying to bootstrap the confidence intervals, I get these messages. boot.ci(results,type=bca,index=1) [1] All values of t are equal to 5.75620151906917 \n Cannot calculate

Re: [R] friedman.test error: not an unreplicated complete block design

Dear Lindsay If the problem is that you have an excess of zeroes you might look at the vignette for the package pscl which is called something like Regression models for count data. On 13/04/2015 17:17, lindsay hanford wrote: Hello R Community, I am using the friedman.test() function to

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