[R] Question on interpreting glmer() results

Hello, I originally posted this on the stats stack exchange site, but given its focus on R software, it was removed -- so I figured I'd post here. I'm having trouble interpreting a change in effect direction and significance when I add an interaction term to my glmer() model. *Part 1* I ran an

Re: [R] hourly prediction time series

Try the auto.arima function in the forecast package.. Regards, DR SEAN PORTER Scientist South African Association for Marine Biological Research Direct Tel: +27 (31) 328 8169 Fax: +27 (31) 328 8188 E-mail: spor...@ori.org.za Web: www.saambr.org.za 1 King Shaka Avenue, Point, Durban 4001

Re: [R] monte carlo simulations in permanova in vegan package

.. Apologies if I am missing something and if what you have said still applies (that is not appropriate to exceed the possible number of permutations), I am not a statistician..so any help/clarity would be welcome.. Regards, sean   -Original Message- From: R-help [m

Re: [R] monte carlo simulations in permanova in vegan package

.. Apologies if I am missing something and if what you have said still applies (that is not appropriate to exceed the possible number of permutations), I am not a statistician..so any help/clarity would be welcome.. Regards, sean   -Original Message- From: R-help [m

Re: [R] monte carlo simulations in permanova in vegan package

ion and aim? I was therefore hoping there was a way of coding for the Monte-Carlo permutation procedure into adonis? Thanks for your help! From: stephen sefick [mailto:ssef...@gmail.com] Sent: 27 October 2015 03:11 PM To: Sean Porter Cc: r-help@r-project.org Subject: Re: [R] monte carlo s

[R] monte carlo simulations in permanova in vegan package

done in the commercial package PERMANOVA+ for PRIMER. How can I adapt my code so that adonis will do so ? Many thanks, Sean > permanova <- adonis(species ~ time, data = time, permutations=99, method="bray") > permanova Call: adonis(formula = species ~ time, data = time

Re: [R] need help with excel data

pe: =LEFT(A1,2) This will extract the first 2 characters from the left. To extract "45" you would type: =Right(A1,2) To get 2 characters starting at position 4 you would type: =MID(A1, 4,2) Which will give you 23. Hope this helps. Regards, DR. SEAN PORTER Scientist South African As

[R] Calculating the focal mean of a raster using an annulus

. Please help if you can. Thank you, Sean Parks ## ## library(raster) the.raster <- raster(matrix(round(rep(seq(1,5, 0.0001), 250)),

[R] gradientForest input data structure

7.1 0 0 0 ... $ ct: num 2.7 0 0 0 0 0 0 0 0 0 ... $ cu: num 0 0 30.9 0 41.2 ... [list output truncated] I thought it may be that some values are numbers and some are integers but I tested this using only numbers and found that this is not the problem. How do I get my response/species

Re: [R] randomForest warning: The response has five or fewer unique values. Are you sure you want to do regression?

each of only 3 species when I have 100 species in the matrix, surely this is not correct, what am I doing wrong? Also, what did you mean when you said by using the code I am not using randomForest directly ? Many thanks, Sean > # For Andy > # get biological data into R > biological <

[R] randomForest warning: The response has five or fewer unique values. Are you sure you want to do regression?

ey get 500 trees from only 90 species even though they input 110 species in the response data. Why am I getting the warning/how do I solve it, and why is randomForest producing trees for only 3 species when I am looking at 100 species (response variables)? Many thanks Sean [[a

[R] pixel based percentile among rasters

offer suggestions on how to accomplish this task? Thanks for your help, Sean This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may

Re: [R] lattice yscale.components: use multiple convenience functions

m[2]] } It seems to do what I want: xyplot((1:200)/20 ~ (1:200)/20, type = c("p", "g"), scales = list(x = list(log = 10), y = list(log = 10)), yscale.components = yscale.components.logpowerTicks) Is there a way to automatically load this function when I start R so it is a

[R] lattice yscale.components: use multiple convenience functions

), scales = list(x = list(log = 2), y = list(log = 10)), xscale.components = xscale.components.fractions, yscale.components = function(...){ yscale.components.log10ticks yscale.components.logpower} ) Thanks! Sean Sean Taylor Post-doctoral Fellow Fred H

[R] Question regarding error "x and y lengths differ"

Hello, I'm a first semester statistics studentand I am using R for roughly the third time ever. I am following a tutorial and yet I still get the error "x and y lengths differ." I am very new to

[R] A==A false?

> > as.numeric(ImpVol[1,5,57]) == 0.0001 [1] FALSE > > as.numeric(ImpVol[1,5,57]) [1] 1e-04 > > 0.0001 [1] 1e-04 > Any tips? Thanks Sean R 2.15.3 windows 7 __ R-help@r-project.org mailing list https://stat.ethz.ch/ma

[R] Nested ANCOVA question

hy does the Number of Groups at the bottom say 11? and say treatment %in% tank...that makes me think that I didn't nest it properly. Well...I think that is it...I'm confused. please help!! --Sean [[alternative HTML version deleted]]

[R] R on a cluster head node and memory limits

only R) on the head node (the only node with an outside internet connection)? The goal is to allow a small R instance to run on the head node to allow package installation, but nothing more complicated than that. Thanks, Sean __ R-help@r-project.org ma

Re: [R] Vector size limit for table() in R-2.15.1

meone to do that. Much appreciated! Sean On Aug 9, 2012, at 10:05 PM, Prof Brian Ripley wrote: > As the posting guide asked you to before posting, try R-patched. That has > the NEWS items > >• duplicated(), unique() and similar now support vectors of > lengths abov

[R] Vector size limit for table() in R-2.15.1

dea how to troubleshoot. I have a work around that reads in chunks at a time, but I'm very interested in why there appears to be a limit at 2^29 when according to the unique.c file it should be twice that. Thanks for the help. -Sean [[alternative HTML version deleted]]

[R] trouble with png image creation in R v2.14.0 on Red Hat 6

Hello, Is anyone having trouble with png image generation with 2.14.0 on Red Hat 6? We recently updated our pipeline to Red Hat 6 (from 5) and R 2.14.0 (up from 2.9.0) and R shell scripts that worked fine before are now breaking in an unusual way. The source of the problem seems to be centered a

[R] Dependency-aware scripting tools for R

develop robust bioinformatic pipelines driven by scripts written in R. Thanks, Sean __ 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

Re: [R] Moore-Penrose Generalized determinant?

My colleague asked me to thank those of you who responded. Kind regards, Sean -- View this message in context: http://r.789695.n4.nabble.com/Moore-Penrose-Generalized-determinant-tp4471629p4475415.html Sent from the R help mailing list archive at Nabble.com

[R] Moore-Penrose Generalized determinant?

Is there a function in R to calculate the generalized determinant of a singular matrix? - similar to the ginv() used to compute the generalized inverse. I can't seem to find any R related posts at all. Thanks in advance, Sean O'Riordain Trinity College Dublin -- View this message

[R] lmer - error message

has one binary observation. But I don't know what to do to be able to fit this model. Any help would be greatly appreciated! -Sean [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/li

Re: [R] Trouble converting hourly data into daily data

Weather, FUN = which.min) n.obs <- cumsum(rle(as.double(Weather$Date))$lengths) n.obs <- c(0, n.obs[1:(length(n.obs) - 1)]) noon.ind <- agg$diff.time + n.obs subset <- Weather[noon.ind,] Cheers, Sean On Mon, Dec 19, 2011 at 6:03 AM, Jean V Adams wrote: > > Sean Baumgarten wr

[R] how to draw random numbers from many categorical distributions quickly?

better approach for speed? Thanks in advance. -Sean [[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-gui

[R] Trouble converting hourly data into daily data

quot;aggregated" data frame only has two columns: Date and Diff_from_noon. I can't figure out how to get the columns with the actual weather variables to carry over from the original data frame. Any suggestions you have would be much appreciated. Thanks, Se

[R] getting R2 (goodness of fit) result after using biglm()

help? Thanks, sean __ 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] Web based R-help not a list

On 11/9/11 7:22 PM, "David Winsemius" wrote: > > On Nov 9, 2011, at 5:38 PM, Cem Girit wrote: > >> Hello, >> >>Is there a web version of this R-Help user group >> (such as >> the ones under Google Groups) such that > > There is Nabble. It's not going to make you any friends

[R] [ reached getOption("max.print") -- omitted 8178 rows ]]

;max.print") -- omitted 8178 rows ]] Is there a setting somewhere that I can change to get to see all of my data? Thanks Sean [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLE

[R] Guidance with PCA and Regression using complex categorical variables

Hello. I need some guidance. I would like to run PCA and regression, and my predictor variables are mainly complex categorical variables (hundred's of levels for some of them). What packages and functions are useful for this? THanks. sean __ R

[R] sapply( ) a loop function

g into the loop if you want to try it. fish<-rep(1,241) d2p<-seq((50/241),50,(50/241)) my.data.frame<-data.frame(fish,d2p) thanks!! Sean [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/lis

[R] applying a loop to multiple dataframes

"data.csv" dataframes that I don't want But I can't figure out how to write a "for" loop that will apply the (top) code above to each data frame. Also, once I'm able to apply the loop to each data frame, I would like to organize the data in a manageable form so I

[R] Select Random Rows from a dataframe

Hi all, I have a dataframe of behavioral observations from 360 fish, each with 241 observation points(rows), which looks like this: > head(d) fishtreatment tank trial video tid pid ang.chgabs.ac t lenvel d2p x y 1 1

[R] Non-linear Regression best-fit line

func, data, mCall = as.list(match.call(func, : no 'getInitial' method found for "function" objects Can anyone help clarify how I can find the parameters for a best-fit curve for this data? Thanks!! Sean [[alternative HTML version deleted]] _

[R] In need of help with correlations

I am in need of someone's help in correlating gene expression. I'm somewhat new to R, and can't seem to find anyone local to help me with what I think is a simple problem. I need to obtain pearson and spearman correlation coefficients, and corresponding p-values for all of the genes in my dataset

[R] spatial stats - geoR - variogram - standard deviation

is the "standard deviation of the values in each bin". However, when I run this command, the standard deviation values are much larger than I would expect. I suspect my interpretation of the outputs from this command is wrong. I would appreciate your input. Please help. Than

[R] how to efficiently extract elements of a list?

3))) names(test.l)<-LETTERS[1:3] The following does not work. is there some command (I was thinking of do.call) that can do the job? test.l[[c('A','B')]] test.l[[c(1,3)]] do.call('[',c(test.l,c(1,3))) do.call('[[',c(test.l,c(1,3))) do.call('[',c

[R] using character vector as input argument to setkey (data.table pakcage)

7;,'b') as an input argument as below setkey.wanted(test.dt,c('a','b')) Your help will be highly appreciated. -Sean [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch

[R] How to get percent contribution of each factor of 1st component from Principal Component Regression (PCR)

one response. How can I get the contribution of each variable of 1st component? Are coef () or loadings() the right functions? But I don't know how to get the contribution from the values from these two functions. Thanks for your help. Sean -- View this message in context: http://r.7896

[R] how to cut a multidimensional array along a chosen dimension and store each piece into a list

o make it happen but I am searching for a better solution. Thanks in advance. -Sean [[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:/

[R] question about deparse(substitute(...))

? test.fun <- function(...){deparse(substitute(...))} test.fun(x) #this works test.fun(x,y,z) # I like c('x','y','z') be the output, but cannot get it. Thanks in advance. -Sean [[alternative HTML version deleted]] __

[R] Difficulty creating Julian day in data frame

55.2084 1916-01-06 5843 As you can see, the "temp.date" column behaves as expected, but the "julian.day" column is populated with the Julian day value from 1/1/1916. Please help me out if you have some ideas. Thanks, Sean * Sean Parks Eco

Re: [R] Cramer-von Mises test

Thanks Peter...I hadn't some across the sos package before, but I'm sure I'll be putting it to good use from now on! Sean. On Mon, Jul 19, 2010 at 2:55 PM, Peter Ehlers wrote: > On 2010-07-18 22:04, Sean Carmody wrote: >> >> I have found the Kolmogorov-Smirnov

[R] Cramer-von Mises test

rtest package). Any suggestions? Regards, Sean. -- Sean Carmody Twitter: http://twitter.com/seancarmody Stable: http://mulestable.net/sean The Stubborn Mule Blog: http://www.stubbornmule.net Forum: http://mulestable.net/ __ R-help@r-project.org mailing

Re: [R] Borders on a polygon

On Mon, Jun 7, 2010 at 6:55 PM, beloitstudent wrote: > [...] I am trying to do some shading in R and am using the polygon() setting. > I want the border on the top and bottom of the polygon, but not on the left > and right. [...] One way would be to add the borders after as lines. For example: pl

Re: [R] writing a matrix in a file

... Matrix: [,1] [,2] [,3] [,4] [,5] [,6] [1,]55 -1 -1 -1 -1 [2,]882765 [3,]668275 x <- matrix(1:12, nrow = 4) sink("test.txt") cat("Matrix:\n") x sink() Also look at ?write.table Sean __

Re: [R] [BioC] after updating biomaRt cannot connect any more

tch ? > > Read this page. http://bioconductor.org/docs/install/ If you have problems after following the instructions, please follow the instructions in the posting guide and ask your question again. Also, note that the newest version of R is 2.11 and not 2.10.1 Patched. Sean [

Re: [R] persp(); help with 'tck' option

of axis length */ ... So, it looks like the tick length is hard coded as 3% of the axis length. I suppose you could edit that and re-compile R from source, but maybe there's an easier way? Perhaps I'm mistaken? Sean __ R-help@r-projec

Re: [R] lines on plot

quot;)) > segments(0,2,2.3,2) > segments(0,3,2.3,3) > segments(0,4,2.3,4) > segments(0,5,2.3,5) > segments(0,6,2.3,6) > segments(0,7,2.3,7) abline(h = 2:7) grid() is another option also, axis(2, at = 2:7) is all you need Sean __ R-help@

[R] Fwd: [R-sig-DB] Package RPostgreSQL : Problem with dbWriteTable

-- Forwarded message -- From: PALMIER Patrick - CETE NP/INFRA/TRF < patrick.palm...@developpement-durable.gouv.fr> Date: Tue, May 18, 2010 at 8:05 AM Subject: Re: [R-sig-DB] Package RPostgreSQL : Problem with dbWriteTable To: "Davis, Sean (NIH/NCI) [E]" Hel

Re: [R] [R-sig-DB] Package RPostgreSQL : Problem with dbWriteTable

inserting rows > But If I send the "COPY FROM" as an sql query in R, the rows are then > well added > I think it is a problem with the temp file create by dbWriteTable > > As anyone solved this problem? > > Hi, Patrick. A reproducible example an

Re: [R] Vector recycling and zoo

Thanks David, You comment made me realise that whereas when x is a data frame, x$a is a numeric vector, when x is of class zoo, x$a is also of class zoo, so the following does what I was expecting: x$a/as.numeric(x$a[1]) Sean. On Sun, May 16, 2010 at 9:25 PM, David Winsemius wrote: > >

[R] Vector recycling and zoo

4 6 3 6 9 4 8 12 5 10 15 > x$a/x$a[1] [1] 1 2 3 4 5 > x <- zoo(x) > x$a/x$a[1] 1 1 > I feel understanding this difference would lead me to a greater understanding of the zoo module! Sean. -- Sean Carmody Twitter: http://twitter.com/seancarmody Stable: http://mulestable.net/sean

Re: [R] Histogram Bin

hist(dat, plot = FALSE) get.break.num <- function(x, breaks) { min((1:length(breaks))[x < breaks]) - 1 } # Then to use it: > get.break.num(6, hist.dat$breaks) [1] 1 > get.break.num(42, hist.dat$breaks) [1] 3 Sean __ R-help@r-project.org

[R] frequencies of time series data

I have an excel file in following shape: date Category 01/21/2010turf 01/21/2010jack 01/21/2010jack 01/22/2010 turf 01/22/2010 jack 01/22/2010 psi 01/22/2010 psi 01/22/2010 psi 01/23/2010 turf 01/23/2010 turf 01/23/2010 jack 01/23/2010 psi I need to outp

Re: [R] intersect

wrote: > how can I test every element in a vector whether appears in another vector? > such as > a<-c("aa", "bb", "ff", "cc") > b <-c("oo","jj","bb","cc") a %in% b [1] FALSE TRUE FALSE TRUE __ R-help@r-project.org mailing list https://stat.ethz.ch/ma

Re: [R] removing duplicate rows

On Tue, May 11, 2010 at 9:07 PM, Jim Bouldin wrote: > > I'm trying to identify and remove rows in a data frame that are duplicated > only on particular columns within it (i.e. not on all columns). This is probably the cleanest way: dat <- data.frame(x = c(1, 2, 3), y = c(1, 1, 3)) subset(dat, !d

[R] read.socket and timeout

a socket connection? Thanks, Sean __ 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

[R] number of clusters for k-means

I am currently working on a clustering project and would like to obtain statistics for the number of clusters to include. In SAS you get a pseudo-F statistic and a cubic clustering criterion. Has anyone developed a function to get these values? Sean

[R] Multiple comparisons with a mixed effects model

ee if there are significant differences between them? Is it even possible to do this? I have tried doing it the same way I've done with linear models in the past, but instead of a t-value I get a z-value? Below is the code for what I have done. Thank you very much for any help! Sean &g

Re: [R] [BioC] Suppress output from getGEO

nd to this? Hi, Craig. These dots are from the output from download.file(). GEOquery was modified to use "quiet=TRUE" on December 8, 2009. If you would like to take advantage of this change, you can use the development version of GEOquery. Sean _

Re: [R] Merge and join data

Thank you, that worked great! Sean Peter Alspach wrote: Tena koe Sean I suspect the apply() and merge() functions are working, but they may not be doing what you expect :-) You could try rbind() and aggregate(): data.frame1$HAD <- as.numeric(NA) data.both <- rbind(data.

[R] Merge and join data

Hi, I'm looking to combine two data frames. Several of the columns are in common while the others need to be summed up. The apply functions and the merge functions don't seem to be working. I've included a basic example of what I'm trying to do below. Thanks!

[R] table() and setting useNA to be there by default?

NA='ifany') I could say something like.. > tab1 <- function(t, ...) { table(t, ..., useNA='ifany') } > tab1(t1) t 123 1234 but this names it as 't' instead of 't1' which is ugly? Any other suggestions please? Thanks in a

Re: [R] how to replace a single backward slash with a double backward slash?

Correct me, if I misunderstand and there is no such a limitation. Thanks again. -Sean On Sun, Dec 13, 2009 at 5:26 PM, David Winsemius wrote: > > On Dec 13, 2009, at 5:11 PM, Sean Zhang wrote: > > Dear R-helpers: >> >> Hours ago, I asked how to replace a single

[R] how to replace a single backward slash with a double backward slash?

t; into "c:\\test" I tried the following but does not work. gsub("\\\","","c:\test") Can someone help? Thanks a lot in advance. -Sean [[alternative HTML version deleted]] __ R-help@r-project.org ma

[R] how to replace a single forward slash with a double backward slash in a string?

Dear R-helpers. Can someone kindly tell me how to replace a single forward slash with double backward slash in a string? i.e., from "a/b" to "a\\b" Many thanks in advance. -Sean [[alternative HTML version deleted]] __

[R] sample weight for box plot?

Hi, I would like to make a box and whisker plot but use a sample weight for each observation. I've searched around a bit and have not found a method of doing this. Anyone have any advice? Thanks much, Sean Parks -- View this message in context: http://www.nabble.com/sample-weight-fo

Re: [R] help sub setting data frame

Works perfectly! Thanks to all who responded. Sean On Thu, Oct 22, 2009 at 6:24 PM, Ista Zahn wrote: > Is this what you want? > > df = data.frame('id'=c(1:100),'res'=c(1001:1100)) > dfb=df[1:10,] > dfc = df[df$id %in% dfb$id,] > > Still not sure, but

Re: [R] help sub setting data frame

=df[1:2] > dfc = df[dfb$id,] I get something along the lines of what I'd expect where my new dataframe is a subset of the original based on the matching ids I specified in dfb$id. Is that wrong in my first example? Cheers, Sean On Thu, Oct 22, 2009 at 4:55 PM, Ista Zahn wrote: > Hi Sean

[R] help sub setting data frame

df$PN) Warning message: In PN == df$PN : longer object length is not a multiple of shorter object length I wasn't aware that both the larger data frame had to be a multiple of the object you were sub-setting . In any case I would appreciate any insight into what I may be doing wrong. Cheers, Sean

Re: [R] How to right-align labels in dotchart

only I can nudge the labels a little further to the right... Regards, Sean. On Sat, Oct 17, 2009 at 5:05 AM, John Kane wrote: > Oops replying to the wrong post but anyway > does this do what you want? > > aa <- c(3,6,3,5,8) > lbs <- c('cat','goat', 'e

Re: [R] How to right-align labels in dotchart

Pressed send too soon (apologies). Meant to say I have only just discovered the joys of the dotchart (since I am reading William Cleveland's "The Elements of Graphing Data"). However, I cannot work out how to change the alignment of the text labels from left to right. Regards, Sea

[R] How to right-align labels in dotchart

I have only just discovered the joys of the dotchart (since I am reading William Cleveland's -- Sean Carmody The Stubborn Mule http://www.stubbornmule.net http://twitter.com/seancarmody [[alternative HTML version deleted]] __ R-h

Re: [R] how to convert character string with only month and year into date

David, Gabor, and Henriuqe, Thanks a lot for help! Another (inelegant) way is to use ts() and then supply the start and end time. this inelegant way works (I guess at least for equally spaced data.) . -Sean On Tue, Sep 22, 2009 at 3:19 PM, David Winsemius wrote: > > On Sep 22, 2009, a

[R] how to convert character string with only month and year into date

failed. #R code below. strptime(c("03_1993"),"%m_%Y") strptime(c("03-1993"),"%m-%Y") Can you someone kindly show me to do it? Many thanks in advance! -Sean [[alternative HTML version deleted]] __

[R] why need a new database to store results generated from another database in filehash?

7;id')) dbList(db1) #however, a new database(db2) can store "a_and_b" dbCreate("myDB2") db2<-dbInit("myDB2") dbInsert(db2,"a_and_b",merge(db1$a,db1$b,by='id')) dbList(db2) db2$a_and_b #R code above Is it possible to

[R] how to pass more than one argument to the function called by lapply?

side.fun.hardcode.cutoff <- function(indf, cutoff) { unlist(lapply(split(indf, indf[,'id']), function(.x, cutoff) {.x[,'y'] < 3} )) } outside.fun.hardcode.cutoff(indf,) #R code above So, can someone kindly show me how to pass more than one ar

Re: [R] Saving plots to file

Thank you Cedric. That was a nice straight forward example that works great. Cheers, Sean On 8/10/09 11:45 AM, "Cedrick Johnson" wrote: > Try this: > > png(file="Desktop/hist1.png") > plot(glm1$residuals,gain,main = "Hist of residuals and gain"

[R] Saving plots to file

p/hist1.png") Thanks in advance, Sean Session Info: R version 2.9.1 (2009-06-26) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and

Re: [R] Draw plot.table axis on right hand side

;", "", "", "", "")[data$x] > > neither. > > So I would recommend to use package vcd instead, which has very detailed > detail handling. > > Dieter Thanks Dieter. I see vcd had a detailed vignette. That should help me get to grips wi

[R] Draw plot.table axis on right hand side

"Mouse", "Frog")[data$x] data$b <- c("Banana", "Apple", "Pear", "Orange", "Melon")[data$y] plot(table(data$a, data$b), col=rainbow(5), las=1, main="") Regards, Sean. -- Sean Carmody The Stubborn Mule http://www.s

[R] how to use do.call together with cbind and get inside a function

n my task, I have to run do.call("cbind",lapply(ColNameVec,get)) inside a function, can someone kindly help? Many thanks in advance! -Sean [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mai

Re: [R] A Harder Score Test Question

) vcov(fit0)*sum(coxph.detail(fit0)$score)^2 ### Score Test From coxph fit1 <- coxph( Surv(time,cens)~grp ) fit1$score Thanks again, Sean -Original Message- From: Charles C. Berry [mailto:cbe...@tajo.ucsd.edu] Sent: Saturday, July 25, 2009 3:07 PM To: Sean Cc: r-help@r-project.

[R] A Harder Score Test Question

xph I can always program it myself. Thanks in advance. Sean Sean Brummel M.S. Doctoral Candidate Dept. Statistics University of California, Irvine Irvine, CA 92797-1250 Ph: 949-307-1811 Fax: 949-824-9863 [[alternative HTML version de

Re: [R] Weibull Prediction?

e since my example it is greater than one. Sean On 7/16/09, David Winsemius wrote: > > > On Jul 16, 2009, at 8:19 PM, Sean Brummel wrote: > > Thanks for the help but... > > I did the required transformations at the end of the code. The thing that > I dont understand is: Wh

Re: [R] Weibull Prediction?

Thanks for the help but... I did the required transformations at the end of the code. The thing that I dont understand is: Why is the predicted value (from the predict function) not either the mean or median. Sorry I was not clear in my explanation. Thanks, Sean On 7/16/09, David Winsemius

[R] Weibull Prediction?

response"))[1] ### Here is the mean and median of the data mean(y) median(y) ### Fitted Mean and Median from survreg fitScale<-exp(model$coef) fitShape<-1/model$scale fitScale*gamma(1 + 1/fitShape) fitScale*(log(2))^(1/fitShape) Is this done on purpose? If so does anyone know wh

Re: [R] Plot Fonts in Windows vs Mac OSX

abled? Also, I have tried the trick of using larger graphics reduced in the browser, but I have found that the results look a little blurry. I am yet to produce a png plot on Windows that looks anything like as good as the ones produced on the Mac. Regards, Sean. On Sat, Jul 4, 2009 at 1:35 AM, Wins

[R] Plot Fonts in Windows vs Mac OSX

r the perspicacity of my choice of search terms), so any help would be greatly appreciated! Regards, Sean. -- Sean Carmody The Stubborn Mule http://www.stubbornmule.net http://twitter.com/seancarmody __ R-help@r-project.org mailing list https://stat.et

Re: [R] Reading 4-byte float into R from binary file

On Wed, Jun 24, 2009 at 2:55 PM, Duncan Murdoch wrote: > On 6/24/2009 2:41 PM, Sean Davis wrote: > >> A simple question, I hope I have a binary file format that I want to >> slurp into R using readBin. There are a couple of fields in the file that >> are 4-byte

[R] Reading 4-byte float into R from binary file

in C, but the format is pretty simple, so I wanted to do it using just R. I did see as.single, but it appears that is for passing things to C and not much more. Any suggestions appreciated. Thanks, Sean [[alternative HTML version deleted]] _

[R] Problem with storing a sequence of lmer() model fit into a list

x27;)]]<-fit_1 fit.list[[paste('fit_',indepvec[12],sep='')]]<-fit_2 so why cannot I store lmer() model fit in a list? Would someone kindly explain to me what the R error message(last line of this email) really means? You

[R] how to apply the dummy coding rule in a dataframe with complete factor levels to another dataframe with incomplete factor levels?

ata=dfA)) #matB_wanted is below (matB_wanted<-rbind(c(1,0,0,0,0),c(1,1,0,1,0),c(1,1,0,1,0)) ) colnames(matB_wanted)<-colnames(matA) matB_wanted Can someone kindly show me how to get matB_wanted? Many thanks in advance! -Sean [[alternative HTML version deleted]] __

[R] Sean / Re: question related to fitting overdispersion count data using lmer quasipoisson

Hey Buddy, Hope you have been doing well since last contact. If you have the answer to the following question, please let me know. If you have chance to travel up north. let me know. best, -Sean -- Forwarded message -- From: Sean Zhang Date: Sat, Apr 11, 2009 at 12:12 PM

[R] question related to fitting overdispersion count data using lmer quasipoisson

output of fit.lmer.over.quasi below). Can someone kindly explain to me what went wrong? Many thanks in advance. -Sean #data simulation (modified from code at http://markmail.org/message/j3zmgrklihe73p4p) set.seed(100) m <- 5 n <- 100 N <- n*m #X <- cbind(1,runif(N)) X <- cbin

[R] How to handle tabular form data in lmer without expanding the data into binary outcome form?

at https://stat.ethz.ch/pipermail/r-help/2008-May/161072.html Seems to me, that link is implementing data expansion approach (they have only 1600 obs after data expansion). If someone knows a neat solution other than data expansion, please help. Many thanks in advance! -Sean [[alternati

Re: [R] What is the best package for large data cleaning (not statistical analysis)?

Dear Jim: Thanks for your reply. Looks to me, you were using batching. I used batching to digest large data in Matlab before. Still wonder the answers to the two specifics questions without resorting to batching. Thanks. -Sean On Sat, Mar 14, 2009 at 10:13 PM, jim holtman wrote: > Exac

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