[R] De-serialization vulnerability?

info. Thanks, Tim __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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

Re: [R] Missing shapes in legend with scale_shape_manual

s", "Missed exercise"), values = c(20, 4) ) Note that this method then gets very close without the scale_shape_manual, too. Hope that helps. Tim > Date: Mon, 30 Oct 2023 20:55:17 + > From: Kevin Zembower > To:

Re: [R] win110 + R 4.3.0 dowload only when method = "wininet"

://bugs.r-project.org/show_bug.cgi?id=18379 If you are in this situation, the fix is to add a new User Environment Variable: R_LIBCURL_SSL_REVOKE_BEST_EFFORT and set it to TRUE Tim >>>>>> Date: Thu, 11 May 2023 09:39:25 +0300 From: Ivan Krylov To: =?UTF-8?B?U2ViYXN0acOhbg==

Re: [R] Regex Split?

If you only want the character strings, this seems a little simpler: > strsplit("a bc,def, adef ,,gh", "[ ,]+", perl=T) [[1]] [1] "a""bc" "def" "adef" "gh" If you need delime

Re: [R] R version 4.2.1 install.packages does not work with IE proxy setting

is in R-4.2.1 Patched (I don't know if it has made it out to the full distribution) and works in my 'corporate' environment. Perhaps it also applies to your environment. Tim Date: Wed, 5 Oct 2022 10:34:02 + From: PIKAL Petr To: Ivan Krylov Cc: r-help mailing list Subject: Re: [R]  R

[R] Formula compared to call within model call

Manipulating formulas within different models I notice the following: m1 <- lm(formula = hp ~ cyl, data = mtcars) m2 <- update(m1, formula. = hp ~ cyl) all.equal(m1, m2) #> [1] TRUE identical(m1, m2) #> [1] FALSE waldo::compare(m1, m2) #> `old$call[[2]]` is a call #> `new$call[[2]]` is an S3

[R] Potential Bug: file.show does not support double-byte characters in the file path

hs do not. For example, the content for "C:\Test\test.txt" can be "Testing 123 测试". file.show("C:\\Test\\test.txt") would open this file and display its content correctly without specifying the encoding parameter. Thanks, Tim [[alternative HTML version deleted]

[R] [R-pkgs] weibulltools version 2.0.0 released on CRAN

sed vector-based approach has been largely preserved but is no longer recommended. Examples for the usage of the new interface, the documentation of all functions, as well as further changes can be found at https://tim-tu.github.io/weibulltools/ If you notice a bug or have suggesti

Re: [R] understanding as.list(substitute(...()))

Cheers Denes, That's useful to know. I'll stick with the match.call version instead. Interestingly I initially tried to post to R-devel (as I thought it may involve something internal) but was asked to post here instead. Best Tim On Tue, 6 Oct 2020 at 08:22, Dénes Tóth wrote: > >

Re: [R] understanding as.list(substitute(...()))

. dots <- function (...) { exprs <- substitute(list(...)) as.list(exprs[-1]) } In the original, dots <- function(...) as.list(substitute(...())), Does ...() get parsed in a special way? Tim On Tue, 6 Oct 2020 at 05:30, Bert Gunter wrote: > > You need to understand

[R] understanding as.list(substitute(...()))

Could someone explain what is happening with the ...() of the following function: dots <- function(...) as.list(substitute(...())) I understand what I'm getting as a result but not why. ?dots and ?substitute leave me none the wiser. regards

[R] Compositional Data Analysis

Hi All, I am currently working on a project examining the health effects of physical activity using a compositional data (CoDa) approach. I am using a linear regression to measure the effect of physical activity. What I want to do is predict an outcome, e.g. body mass index, based on the mean

Re: [R] project path in Rmd (Ivan Calandra)

You also should be able to reference locations from the 'root' of your project using the here() package. https://here.r-lib.org/ Best, Tim Howard > Date: Thu, 2 Apr 2020 10:21:47 +0100 > From: Rui Barradas > To: Ivan Calandra > Cc: "r-help@r-project.org" >

Re: [R] substr gives empty output

In y <- substr(x, i, 1) your third integer needs to be the location not the number of digits, so change it to y <- substr(x, i, i) and you should get what you want. Cheers, Tim > Date: Sun, 21 Jan 2018 10:50:31 -0500 > From: Ek Esawi <esaw...@gmail.com> &g

[R] Interesting behavior of lm() with small, problematic data sets

ct fit, but a p-value of 0.3112 doesn’t seem reasonable. As a side note, the various r^2 values seem odd too. Tim Glover Senior Scientist II (Geochemistry, Statistics), Americas - Environment & Infrastructure, Amec Foster Wheeler 271 Mill Road, Chelmsford, Massachusetts, USA 01824-4105 T +01

Re: [R] CRAN I-MR / Xbar-R / Xbar-S control chart package ?

Interesting, thanks for that. I came accross qcc but my quick scan of the docs is that it only did xbars but maybe I need to re-read the docs, I guess it does the individual plot versions (I-MR) too. Tim On 8 July 2017 at 20:53, Rui Barradas <ruipbarra...@sapo.pt> wrote: > Hello, &

[R] CRAN I-MR / Xbar-R / Xbar-S control chart package ?

Hi, I've had a quick look through the package list, and unless I've missed something, I can't seem to find anything that will do I-MR / Xbar-R / Xbar-S control charts ? Assuming there is something out there, can anyone point me in the right direction ? Thanks ! TIm

[R] [R-pkgs] CRAN updates: rpg and odeintr

rpg is a package for working with postgresql: https://github.com/thk686/rpg odeintr is a package for integrating differential equations: https://github.com/thk686/odeintr Cheers, THK http://www.keittlab.org/ [[alternative HTML version deleted]]

[R] Problem installing/loading packages from Africa

See error messages below. Thanks -- Tim - When attempting to install, the print-out I get in the Console in RStudio is any length of: > install.packages("swirl") % Total% Received % Xferd Average Speed TimeTime Time Current Dload

Re: [R] How to conduct a PERMANOVA using a dissimilarity matrix

;, "0.401", "0.358", "0.317", "0.39", "0", "0.371", "O", "0.479", "0.399", "0.374", "0.348", "0.354", "0.365", "0.371", "0"), .Dim = c(9L, 9L), .Dim

[R] Regular R freezes

leshooting or finding out who the culprit is? Thanks. -- Tim Richter-Heitmann (M.Sc.) PhD Candidate International Max-Planck Research School for Marine Microbiology University of Bremen Microbial Ecophysiology Group (AG Friedrich) FB02 - Biologie/Chemie Leobener Straße (NW2 A2130) D-28359 Bremen Tel.:

Re: [R] How to find out if two cells in a dataframe belong to the same pre-specified factor-level

sign NA so i can proceed with ggplot(final, aes(value.x,value.y, col=group)) + geom_point() So, in the example, the pairs A1-A1, A1-A2, A2-A1, A2-A2 should be identified as "both cats", hence should get the factor "cat". Thank you very much! Tim

[R] Download showing as exploit

Hi , I work for the NHS, and our IT service has been unable to download as its anti-virus software says it contains an exploit. Is this normal? Is there a way around this? Kind regards, Tim Kingston Sent from my HTC [[alternative HTML version deleted

Re: [R] Cross correlation between two time series over nested time periods?

correlation between two time series over nested time periods? Date: Thursday, May 14, 2015, 6:14 AM On 2015-05-14 , at 02:11, Tim via R-help r-help@r-project.org wrote: Hello Tim, Re: I have two time series Calculate and plot cross correlation between two time series over

[R] Cross correlation between two time series over nested time periods?

maximum lag), and plot A and B in a single plot? Thanks and regards, Tim __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting

Re: [R] Split a dataframe by rownames and/or colnames

! Thanks, On 20.02.2015 20:36, David Winsemius wrote: On Feb 20, 2015, at 9:33 AM, Tim Richter-Heitmann wrote: Dear List, Consider this example df - data.frame(matrix(rnorm(9*9), ncol=9)) names(df) - c(c_1, d_1, e_1, a_p, b_p, c_p, 1_o1, 2_o1, 3_o1) row.names(df) - names(df) indx - gsub

[R] Split a dataframe by rownames and/or colnames

rows x 3 columns). I could do as.data.frame(t(df_x), but maybe that is not elegant. What would be the solution for splitting the dataframe by rows? Thank you very much! -- Tim Richter-Heitmann __ R-help@r-project.org mailing list -- To UNSUBSCRIBE

[R] read.table with missing data and consecutive delimiters

NA6 What am I missing? Thanks, Tim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R

[R] Network graph google maps‏

appreciated! Tim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http

[R] rtmvnorm {tmvtnorm} seems broken

General linear constraints don't seem to work. I get an error message if I have more constraint equations than variables. E.g. executing the following code print(R.version) library('tmvtnorm') cat('tmvtnorm version ') print(packageVersion('tmvtnorm')) ## Let's constrain our sample to the dwarfed

[R] Creating submatrices from a dataframe, depending on factors in sample names

] }) unique_values - lapply(sub.matrices, function(x) x[upper.tri(x)]) names(unique_values) - unique(indx) This code needs to be expanded to form sub.matrices for any combination of unique indices in temp. Thank you so much! -- Tim Richter-Heitmann (M.Sc.) PhD

[R] big datasets for R

Another source of large datasets is the Public Data Sets on AWS http://aws.amazon.com/public-data-sets/ Tim Hoolihan @thoolihan http://linkedin.com/in/timhoolihan On Oct 28, 2014, at 7:00 AM, r-help-requ...@r-project.org wrote: -- Message: 2 Date: Mon, 27 Oct

[R] How can I overwrite a method in R?

How can I create an improved version of a method in R, and have it be used? Short version: I think plot.histogram has a bug, and I'd like to try a version with a fix. But when I call hist(), my fixed version doesn't get used. Long version: hist() calls plot() which calls plot.histogram() which

[R] [vegan] Error in as.vector(x, mode) : , cannot coerce type 'builtin' to vector of type 'any' when performing anova on CCA objects

, as the data sets are pretty large. -- Tim Richter-Heitmann (M.Sc.) PhD Candidate International Max-Planck Research School for Marine Microbiology University of Bremen Microbial Ecophysiology Group (AG Friedrich) FB02 - Biologie/Chemie Leobener Stra�e (NW2 A2130) D-28359 Bremen Tel.: 0049(0

Re: [R] How can I overwrite a method in R?

:10), graphics) hist(1:10) Haley On Thu, Oct 9, 2014 at 1:14 AM, Tim Hesterberg timhesterb...@gmail.com wrote: How can I create an improved version of a method in R, and have it be used? Short version: I think plot.histogram has a bug, and I'd like to try a version with a fix

[R] gplot heatmaps: clustering according to rowsidecolors + key.xtickfun

this sequential ordering to key.xtickfun? May i ask for an example code? Thank you very much! -- Tim Richter-Heitmann (M.Sc.) PhD Candidate International Max-Planck Research School for Marine Microbiology University of Bremen Microbial Ecophysiology Group (AG Friedrich) FB02 - Biologie/Chemie

[R] [vegan]Envfit, pvalues and ggplot2

created by envfit to rows meeting a criterion in $pval (via unlist and which, i suppose). However, i have difficulties to work out the correct code. Any help is much appreciated! -- Tim Richter-Heitmann (M.Sc.) PhD Candidate International Max-Planck Research School for Marine Microbiology

[R] problem with labeling plots, possibly in font defaults

Hello, I am using R 3.1.1 on a (four year old) MacBook, running OSX 10.9.4. I just tried making and labeling a plot as follows: x-rnorm(10) y-rnorm(10) plot(x,y) title(main=random points) which produces a scatter plot of the random points, but without the title and without any numbers

[R] Problems with read.table and data structure

file seems fine with me on surface (i dont know how the numbers are stored internally). I just see correct numbers, also the View command yields the correct content. Anyone knows help? Its pretty annoying. Thank you! -- Tim Richter-Heitmann [[alternative HTML version deleted

[R] x,y scatterplots, with averaging by a column

with lines. Also of interest would be annotating the whispers with their sample ID (because the whiskers basically represent the values for y1,2 (11,12; 21,22)). Any help is welcome! I am new to R, so please bear with me. Thank you! -- Tim Richter-Heitmann (M.Sc.) PhD Candidate International

[R] Large matrices and pairs/ggpairs

are not too stupid. -- Tim Richter-Heitmann (M.Sc.) PhD Candidate International Max-Planck Research School for Marine Microbiology University of Bremen Microbial Ecophysiology Group (AG Friedrich) FB02 - Biologie/Chemie Leobener Straße (NW2 A2130) D-28359 Bremen Tel.: 0049(0)421 218-63062 Fax: 0049(0

Re: [R] ggplot2: using coord_trans for logit - probability

scale gg - ggplot(pred, aes(x=Age, y=fit)) + geom_line(size = 2) + theme_bw() + geom_ribbon(aes(ymin = fit - 1.96 * se.fit, ymax = fit + 1.96 * se.fit,), alpha = 0.2, color = transparent) + labs(x = Age, y = Log odds (Better)) gg -Tim On Wed, Apr 16, 2014 at 7:03 PM, Michael

Re: [R] ggplot2: using coord_trans for logit - probability

Sorry I jumped the gun. That does not provide you with the same plot as gg2 that you are aiming for. -T On Wed, Apr 16, 2014 at 7:37 PM, Tim Marcella timmarce...@gmail.com wrote: I think all you have to do is add type=response to your call for the predictions. Does this work for you

[R] Plot mlogit object

Hi, I cannot figure out how or if I even can plot the results from a nested multinomial logit model. I am using the mlogit package. Does anyone have a lead on any tutorials? Both of the vignettes are lacking plotting instructions. Thanks, Tim -- Tim Marcella [[alternative HTML

[R] Time interactions for coxph object

CSHR.shore.fly - coxph(Surv(entry, exit, to == 1) ~ shore.cat, data glba.mod) My variable shore.cat is violating the proportional hazards assumption so I am trying to add in an interaction with time. Do I interact exit? entry? or the range of the two? Thanks, Tim -- Tim Marcella 508.498.2989

[R] Nested Logit Model

) or not, and then once a reaction has been made, which one is chosen and how these decisions relate to perpendicular distance to the ship's path. Thanks, Tim -- Tim Marcella 508.498.2989 timmarce...@gmail.com [[alternative HTML version deleted]] __ R-help@r

[R] multicore - handling a list of return values

Hi, I was trying to gather/combine the results returned from the mclapply function. This is how I do it if only one data object is returned: #= This works fine === library(multicore) frandom1 - function(iter,var1 = 3,var2 =2){     mat - matrix(rnorm(var1*var2),nrow=var1,ncol=var2)    

[R] Coding for segmented regression within a hurdle model

to worry about this and can just report the original std.errors and associated p values from the segemented object in the pub. Question # 2: If the count model uses the std.errors, how can I reformulate this equation to generate the original std.errors. Thanks, Tim [[alternative HTML version

[R] Negative binomial models and censored observations

this be accounted for in the hurdle() function? Thanks, Tim [[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

[R] Calculating RMSE in R from hurdle regression object

Hi, My data is characterized by many zeros (82%) and overdispersion. I have chosen to model with hurdle regression (pscl package) with a negative binomial distribution for the count data. In an effort to validate the model I would like to calculate the RMSE of the predicted vs. the observed

[R] ifelse...

Hi, Sorry for the newbie question! My code: x - 'a' ifelse(x == 'a',y - 1, y - 2) print(y) Shouldn't this assign a value of 1? When I execute this I get: x - 'a' ifelse(x == 'a',y - 1, y - 2) [1] 1 print(y) [1] 2 Am I doing something really daft??? thanks! sessionInfo() R version

[R] set new path for package installation, because In normalizePath(path.expand(path), winslash, mustWork) :

, a few users having this problem: Whenever i am starting R, i am welcomed with: Warning message: In normalizePath(path.expand(path), winslash, mustWork) : path[1]=//x/home$/tim/Documents/R/win-library/3.0: Access is denied And i am not allowed to install packages or manipulate objects in my

[R] Append text to panels of lattice::barchart()

I could use a little help writing a panel function to append text to each panel of a lattice::barchart(). Below is a modified version of the barley dataset to illustrate. data(barley) # add a new variable called samp.size barley$samp.size-round(runif(n=nrow(barley), min=0, max=50),0) # Below is

Re: [R] Append text to panels of lattice::barchart()

looking for. I'll look into trellis.focus to see if the light bulb comes on in my head. I'd still appreciate a more efficient way to do this given the number of plots and panels I need. Thanks, Tim On Tue, Nov 26, 2013 at 2:08 PM, Duncan Mackay dulca...@bigpond.com wrote: Hi Try barchart(yield

[R] spsurvey analysis

. Tim __ 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] spsurvey analysis

was worried it was detecting and treating polygons as classes, somehow (ecoregions in example below). I had already reached out to Kincaid and Olsen but had not received an answer yet so I moved on to R-help. I'll go back to them. Thanks again. Best, Tim Law, Jason jason

[R] Selecting maximums between different variables

), it looks like this and works perfectly: oil2 - data.frame ( names = c('YEAR', 'TX', 'CA', 'AL', 'ND'), oil_2011 = c(2011, 2, 4, 2, 21000), oil_2012 = c(2012, 3, 25000, 21000, 6) ) attach(oil2) oil2[c(oil_2012 == max(oil_2012)),] Any help is much appreciated. Thanks, Tim

Re: [R] update.packages fails on pdf write - CSAgent

= y, repos = NULL, lib = C:/pathToLocationWhereWritesAreAllowed) #now manually copy the folders to the R installation and overwrite the existing ones. Tim Date: Wed, 02 Oct 2013 11:17:29 -0400 From: Tim Howard tghow...@gw.dec.state.ny.us To: r-help@r-project.org Subject: [R] update.packages

[R] update.packages fails on pdf write - CSAgent

=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_3.0.2 Thanks for any help Tim __ R-help@r-project.org mailing list

[R] GGally installation problems

Hi, I was trying to install the GGally package, but was getting errors. Here is what I get: install.packages(GGally) Installing package(s) into ‘/Users/ts2w/Library/R/2.15/library’ (as ‘lib’ is unspecified) Warning in install.packages :   package ‘GGally’ is not available (for R

[R] #Keeping row names when using as.data.frame.matrix

#question I have the following data set: Date-c(9/7/2010,9/7/2010,9/7/2010,9/7/2010,9/7/2010,9/7/2010,9/8/2010) EstimatedQuantity-c(3535,2772,3279,3411,3484,3274,3305) ScowNo-c(4001,3002,4002,BR 8,4002,BR 8,4001) dataset- data.frame(EstimatedQuantity,Date,ScowNo) #I'm trying to convert the

Re: [R] read.csv quotes within fields

Yes! This does this trick. Thank You! Tim peter dalgaard pda...@gmail.com 1/26/2013 11:49 AM On Jan 26, 2013, at 16:32 , Tim Howard wrote: Duncan, Good point - I guess I am expecting too much. I'll work on a global replace before import or chopping with strsplit while importing. FYI

Re: [R] read.csv quotes within fields

=showCaseDownloadForm (see off-airport AEA 2005 for a csv with issues.) Thank you for the help. I really do appreciate the suggested solutions. Also, thanks to John Kane for the link to csvEdit. Tim Duncan Murdoch murdoch.dun...@gmail.com 01/25/13 6:37 PM On 13-01-25 4:37 PM, Tim Howard wrote: David, Thank

[R] read.csv quotes within fields

for a while! Thank you in advance, Tim __ 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

Re: [R] read.csv quotes within fields

[5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base Tim Howard 1/25/2013 1:42 PM All, I have some csv files I am trying to import. I am finding that quotes inside strings are escaped in a way R

Re: [R] read.csv quotes within fields

with the escape character within a single string. Tim David Winsemius dwinsem...@comcast.net 1/25/2013 2:27 PM On Jan 25, 2013, at 10:42 AM, Tim Howard wrote: All, I have some csv files I am trying to import. I am finding that quotes inside strings are escaped in a way R doesn't expect

Re: [R] read.csv quotes within fields

there would be a solution within read.csv() ... or perhaps scan()?, I just can't figure it out. best, Tim David Winsemius dwinsem...@comcast.net 1/25/2013 4:16 PM On Jan 25, 2013, at 11:35 AM, Tim Howard wrote: Great point, your fix (quote=) works for the example I gave. Unfortunately

Re: [R] Filling Lists or Arrays of variable dimensions

) width-c(slim,wide) l - vector(list,length(height)) names(l) - height for(i in 1:length(l)){ l[[i]] - vector(list,length(width)) names(l[[i]]) - width } Best Tim Date: Fri, 21 Dec 2012 11:34:06 +0100 From: Jessica Streicher j.streic...@micromata.de To: David Winsemius dwinsem

Re: [R] boot() with glm/gnm on a contingency table

of interest on the new table. } When f is called with 1:n, the table it creates should be the same as the original table. When called with a bootstrap sample of values from 1:n, it should create a table corresponding to the bootstrap sample. Tim Hesterberg http://www.timhesterberg.net (resampling

Re: [R] boot() with glm/gnm on a contingency table

Le mercredi 12 septembre 2012 à 07:08 -0700, Tim Hesterberg a écrit : One approach is to bootstrap the vector 1:n, where n is the number of individuals, with a function that does: f - function(vectorOfIndices, theTable) { (1) create a new table with the same dimensions, but with the counts

Re: [R] Histogram to KDE

bootstrap and jackknife methods won't work right. Tim Hesterberg http://www.timhesterberg.net New: Mathematical Statistics with Resampling and R, Chihara Hesterberg On Fri, Aug 31, 2012 at 12:15 PM, David L Carlson dcarl...@tamu.edu wrote: Using a data.frame x with columns bins and counts: x

[R] need help reshaping table using aggregate

I am trying to learn how to reshape my data set. I am new to R, so please bear with me. Basically, I have the following data set: site-c(A,A,B,B) bug-c(spider,grasshopper,ladybug,stinkbug) count-c(2,4,6,8) myf - data.frame(site, bug, count) myf site bug count 1A spider 2

Re: [R] ggplot2: legend for geom_rug() ..?

Hi, Here is the corrected code: library(ggplot2) ids - paste('id_',1:3,sep='') before - sample(9) after - sample(1:10,9) dat - as.matrix(cbind(before,after)) rownames(dat) - rep(ids,3) position - c(rep(10,3),rep(13,3),rep(19,3)) mdat - cbind(melt(dat),position) colnames(mdat) -

[R] [R-pkgs] dataframe package

* round(a data frame with numeric and factor columns) rounds the numeric columns and leaves the factor columns unchanged, rather than failing. Tim Hesterberg NEW! Mathematical Statistics with Resampling and R, Chihara Hesterberg http://www.amazon.com/Mathematical-Statistics-Resampling-Laura

[R] Possible artifacts in cross-correlation function (ccf)?

to, at least for specific situations, produce results with artifacts? It is very likely that the R-implementation, as opposed to the alternative algorithm described above and in the attachment, has a very good statistical explanation, but one that unfortunately is not dawning on me. Sincerely, Tim

[R] suggested method to transform list to a matrix

5 What is the suggested method to do this for 1 million rows, with 12 variables and ~ 4,000 unique users? Thank you, Tim Stutt t...@ischool.berkeley.edu [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https

Re: [R] [BioC] Read .idat Illumina files in R

Unfortunately, this won't help for expression arrays. Last time I checked, those IDATs appeared to be encrypted. crlmm, methylumi, and minfi can all read IDAT files... *if* they are version 3 or later (e.g. genotyping, methylation, etc). Otherwise you are probably stuck with GenomeStudio if it

Re: [R] detecting noise in data?

a reasonable level of homogeneity. Then from there, you can do a basic inference test for group means to detect whether there are significant differences detected between groups. Cheers, Tim -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org

[R] bootstrap means by strata

is the most efficient way to resample, with replacement, and generate means for each grouping variable? Thanks in advance, Tim sessionInfo() R version 2.12.2 (2011-02-25) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252

Re: [R] bootstrap means by strata

Answering my own question. ?sample (!) y - by(x, x$TrSeasYr, function(x) mean(sample(x[,1], size=999, replace = TRUE))) Tim Howard 10/13/2011 9:42 AM All - I have an uneven set of replicates and would like to sample from this set X number of times to generate a mean for each grouping

Re: [R] Permutation or Bootstrap to obtain p-value for one sample

, The permutation test answers the question - given that there is exactly 1 outlier in my combined data, what is the probability that random chance would give a difference as large as I observed. The bootstrap would answer some other question. Tim Hesterberg NEW! Mathematical Statistics with Resampling and R

[R] Can R be installed in a Hyper-V environment?

We are contemplating the installation of R on a Windows server with Hyper-V but we can't find any information on whether it can be done. This transmission is intended solely for the person or organization to whom it is addressed and it may contain

[R] ggplot2 freqpoly() layers..?

Hi, I was trying to overlay/combine two freqpoly plots. The sample code below illustrates the problem. Essentially, I want to do is: 1. Have the same colour for all the lines in 'Plot 1' (and 'Plot 2'). Currently, all the lines in Plot 1 have different colours and all the lines in Plot 2 have

[R] hide row and column-names in cat()

    53    11    7.7 What I want to have is this:  Nr   FraSand   FraSilt   FraClay   pH   (kg.kg-1) (kg.kg-1) (kg.kg-1) (-)  1    19    60    21    7.1  2    35    53    11    7.7 Thank you. TIM __ R-help@r-project.org

Re: [R] Extracting components from a 'boot' class output in R

' is not an exported object from 'namespace:boot'). Tim Hesterberg Do names(bootObj) to find out what the components are, and use $ or [[ to extract components. Do help(boot) for a description of components of the object (look in the Value section). That is general advice in R, applying to all kinds

Re: [R] Extracting components from a 'boot' class output in R

(), return lists with a class added, and you can operate on the object as a list using names(), $, etc. Tim Hesterberg Dear R user, I used the following to do a bootstrap. bootObj-boot(data=DAT, statistic=Lp.est, R=1000,x0=3) I have the following output from the above bootstrap. How can I extract

Re: [R] Pulling data from remote MySQL database

Agree - I started with RMySQL but eventually changed over to RODBC when I realised some of the additional functionality it contains and the fact that I needed to access different types of RDBMSs (e.g. acquire data from a Microsoft access database file). Cheers, Tim -Original Message

Re: [R] Sorting a data frame with values of different lengths

William, I think to convert to numeric, you might need to do something like: as.numeric(as.character()) ## and not just as.numeric() As it stands, it would appear that it is still being read as a character string. From: William Armstrong

Re: [R] Question on approximations of full logistic regression model

for the bootstrap biases, see e.g. Hesterberg, Tim C. (2004), Unbiasing the Bootstrap-Bootknife Sampling vs. Smoothing, Proceedings of the Section on Statistics and the Environment, American Statistical Association, 2924-2930. http://home.comcast.net/~timhesterberg/articles/JSM04-bootknife.pdf And other

Re: [R] memory and bootstrapping

estimated from the original data. And, you can compute the model matrix once and resample rows of that along with y, rather than computing a model matrix from scratch each time. Tim Hesterberg The only reason the boot package will take more memory for 2000 replications than 10 is that it needs

[R] Simple Missing cases Function

. Can anyone see a more efficient way to get the same results? Or is there existing function which does this? Thanks for your help Tim Function: miss - function (data) { miss.list - list(NA) for (i in 1:length(data)) { miss.list[[i]] - table(is.na(data[i

Re: [R] Simple Missing cases Function

Dear Petr Thanks so much. That is a LOT more efficient. Tim -Original Message- From: Petr PIKAL [mailto:petr.pi...@precheza.cz] Sent: Tuesday, April 19, 2011 3:37 PM To: tesutton Cc: r-help@r-project.org Subject: Odp: [R] Simple Missing cases Function Hi Hi try colSums(is.na(data.m

Re: [R] Simple Missing cases Function

Thanks Tyler This function has some useful features Tim From: Tyler Rinker [mailto:tyler_rin...@hotmail.com] Sent: Tuesday, April 19, 2011 3:52 PM To: tesutton; r-help@r-project.org Subject: RE: [R] Simple Missing cases Function I use the following code/function which gives me some

Re: [R] Bootstrap 95% confidence intervals for splines

is the range of the middle 95% of the recorded differences. Tim Hesterberg P.S. I think you're mixing up the response and explanatory variables. I'd think of eating hot dogs as the cause (explanatory variable), and waistline as the effect (response, or outcome). P.P.S. I don't like the terms independent

Re: [R] assign factor levels based on list

]] - factor(y[[x]] , levels= my.factor.defs[[x]])}) str(y) 'data.frame': 3 obs. of 3 variables: $ colOne : Factor w/ 6 levels 1,2,3,4,..: 1 2 3 $ colTwo : Factor w/ 5 levels apple,pear,..: 1 2 3 $ colThree: num 4 5 6 Thank you again! Best, Tim Howard William Dunlap wdun...@tibco.com 2

[R] assign factor levels based on list

= factor.defs[2][[1]]$lvl))) ##Error in function (x = character(), levels, labels = levels, exclude = NA, : ## object 'y$colTwo' not found Any help or perspective (or better way from the beginning!) would be greatly appreciated. Thanks in advance! Tim [[alternative HTML version

[R] Passing formula as an agrument

Hi, I had a function that looked like: diff - lm(x ~ y + z) How can I pass the argument to the 'lm' function on the fly? E.g., if I pass it in as a string (e.g. x ~ y + z), then the lm function treats it as a string and not a proper argument. many thanks [[alternative HTML

[R] legend not appearing in Word document

files. Thanks, Tim   library(plotrix)   Satelite.Palette - colorRampPalette(c(blue3,cyan,aquamarine,yellow,orange,red))   mycol-Satelite.Palette(ceiling(5000+1))#Max relative angle multiplied by 100 to give larger range.  Max is 3.1415, rounded up to 3.15 plus one.   col.labels

Re: [R] legend not appearing in Word document

Thanks, I will take it up with MS.  I just downloaded their latest converter and that hasn't fixed the issue.  Hopefully they will have additional advice. Aloha, Tim Tim Clark Marine Ecologist National Park of American Samoa Pago Pago, AS 96799 From

[R] apply over list of data.frames

6 10 3 12 7 11 #the result should be a b c 1 2.5 3.5 6 2 5 4.5 7 3 7.5 5.5 8 Can anyone direct me down the right path? Thanks in advance Tim Howard [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https

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