[R] datatable using dt not able to print background colors

2022-12-16 Thread Matthew Pirritano
Hey, all! I've got a report that uses datatable from DT to create an rmarkdown html that looks great as an html but when I try to print it, to a printer, or to a pdf the colors I've assigned to cells are not displaying. I'm using chrome and I've clicked on the Background graphics button there,

Re: [R] Differential Gene Expression in R

2021-08-22 Thread Matthew McCormack
tle and you will see that edgeR is available. You will still have to learn a little about edgeR analysis, so reading the vignette will be very helpful.    Also, for the comparisons you want to do, statistical help is recommended. Matthew On 8/22/21 2:13 PM, Anas Jamshed wrote: Exte

Re: [R] Joining data frames

2021-06-29 Thread Matthew McCormack
nging df.) df_final<- full_join(df, df1, by = c(“Sample”, "Plot")) Matthew On 6/29/21 7:15 PM, Jim Lemon wrote: External Email - Use Caution Hi Esthi, Have you tried something like: df2<-merge(df,df1,by.x="Sample",by.y="Plot",all.y=TRUE) Thi

Re: [R] analyzing results from Tuesday's US elections

2020-11-16 Thread Matthew McCormack
Bye the way, I thought I had checked my e-mail before sending it, but my last e-mail had an unfortunate typo with an 'I' that originally belonged to the beginning of a deleted sentence. Matthew On 11/17/20 1:54 AM, Matthew McCormack wrote: External Email - Use Caution No

Re: [R] analyzing results from Tuesday's US elections

2020-11-16 Thread Matthew McCormack
e explored. A oncee-in-a-while dive into a practical application of statistics that has current interest can be fun and enlightening for those interested. Matthew On 11/16/20 9:01 PM, Abby Spurdle wrote: External Email - Use Caution I've come to the conclusion this whole

Re: [R] analyzing results from Tuesday's US elections

2020-11-15 Thread Matthew McCormack
both agree with Benfords Law. However, he uses the last digit and not the first. A word of caution before you click on that link: he uses Excel ! Matthew On 11/13/20 9:59 PM, Rolf Turner wrote: External Email - Use Caution On Thu, 12 Nov 2020 01:23:06 +0100 Martin Møller Skarbiniks P

Re: [R] analyzing results from Tuesday's US elections

2020-11-09 Thread Matthew McCormack
Benford Analysis for Data Validation and Forensic Analytics Provides tools that make it easier to validate data using Benford's Law. https://www.rdocumentation.org/packages/benford.analysis/versions/0.1.5 Matthew On 11/9/20 9:23 AM, Alexandra Thorn wrote: > External Ema

Re: [R] analyzing results from Tuesday's US elections

2020-11-08 Thread Matthew McCormack
om/statistical-anomalies-in-biden-votes-analyses-indicate_3570518.html?utm_source=newsnoe&utm_medium=email&utm_campaign=breaking-2020-11-08-5 Matthew On 11/8/20 11:25 PM, Bert Gunter wrote: > External Email - Use Caution > > NYT had interactive maps that reported votes by c

Re: [R] RNA Seq Analysis in R

2020-08-01 Thread Matthew McCormack
Excel and then inspect the logFC and p-values for the top 1250 genes. Matthew On 8/1/20 1:13 PM, Jeff Newmiller wrote: > External Email - Use Caution > > https://www.bioconductor.org/help/ > > On August 1, 2020 4:01:08 AM PDT, Anas Jamshed > wrote: >> I choo

Re: [R] Fwd: Re: transpose and split dataframe

2019-05-06 Thread Matthew
ate it with the column name ATG.  David's result complements Jim's, and both end up being very helpful to me.   Thanks again to both of you for your time and help. Matthew On 5/2/2019 8:40 PM, Jim Lemon wrote: > External Email - Use Caution > > Hi again, >

Re: [R] Fwd: Re: transpose and split dataframe

2019-05-01 Thread Matthew
at a time from each entry in the character matrix, but have not got anything near working yet. Matthew On 4/30/2019 6:29 PM, David L Carlson wrote > If you read the data frame with read.csv() or one of the other read() > functions, use the asis=TRUE argument to prevent conversion to facto

[R] Fwd: Re: transpose and split dataframe

2019-04-30 Thread Matthew
ith the greatest number of hits. The full joins I can do with dplyr, but getting up to that point seems rather difficult. This would get me what my ultimate goal would be; each Regulator is a column name (152 columns) and a given row has either NA or the same hit.    This seems ve

[R] transpose and split dataframe

2019-04-30 Thread Matthew
header of column 2 and AT2G85403 is row 1 of column 2, etc.   I have tried playing around with strsplit(TF2list[2:2]) and strsplit(as.character(TF2list[2:2]), but I am getting nowhere. Matthew __ R-help@r-project.org mailing list -- To UNSUBSCRIBE

Re: [R] Define pch and color based on two different columns

2019-04-09 Thread Matthew Snyder
You are not late to the party. And you solved it! Thank you very much. You just made my PhD a little closer to reality! Matt *Matthew R. Snyder* *~* PhD Candidate University Fellow University of Toledo Computational biologist, ecologist, and bioinformatician Sponsored Guest

Re: [R] Define pch and color based on two different columns

2019-04-09 Thread Matthew Snyder
I tried this too: xyplot(mpg ~ wt | cyl, data=mtcars, # groups = carb, subscripts = TRUE, col = as.factor(mtcars$gear), pch = as.factor(mtcars$carb) ) Same problem... *Matthew R. Snyder* *~* PhD Candidate University Fellow University of Toledo

Re: [R] Define pch and color based on two different columns

2019-04-09 Thread Matthew Snyder
unique in the whole plot. But when you add cyl as a factor. Those two points are only unique within their respective panels, and not across the whole plot. Matt *Matthew R. Snyder* *~* PhD Candidate University Fellow University of Toledo Computational biologist, ecologist, and

Re: [R] Define pch and color based on two different columns

2019-04-09 Thread Matthew Snyder
for single plots in ggplot. Maybe I should contact the authors of lattice and see if this is something they can help me with or if they would like to add this as a feature in the future... Matt *Matthew R. Snyder* *~* PhD Candidate University Fellow University of Toledo Computational

[R] Define pch and color based on two different columns

2019-04-09 Thread Matthew Snyder
ilter rule match" Thanks, Matt *Matthew R. Snyder* *~* PhD Candidate University Fellow University of Toledo Computational biologist, ecologist, and bioinformatician Sponsored Guest Researcher at NOAA PMEL, Seattle, WA. matthew.snyd...@rockets.utoledo.edu msnyder...@gmail.co

Re: [R] creating a dataframe with full_join and looping over a list of lists.

2019-03-25 Thread Matthew
, Jim, for the work you put into this. Matthew On 3/21/2019 11:01 PM, Jim Lemon wrote: External Email - Use Caution Hi Matthew, Remember, keep it on the list so that people know the status of the request. I couldn't get this to work with the "_source_info_" variable.

[R] creating a dataframe with full_join and looping over a list of lists.

2019-03-21 Thread Matthew
the same row. # I could rename the colname to 'AGI' so that I can join by 'AGI', # but then I would lose the name of the list. # In the final dataframe, I want to know the name of the original list # the column was made from. Matthew

[R] creating a dataframe with full_join and looping over a list of lists

2019-03-21 Thread Matthew
me, I want to know the name of the original list     # the column was made from. Matthew [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/

[R] Defining Variables from a Matrix for 10-Fold Cross Validation

2018-10-09 Thread matthew campbell
me across that specific message before, and am not exactly sure how to interpret its meaning. What exactly is this error message trying to tell me? Any suggestions or insights are appreciated! Thank you all, Matthew Campbell > library (ElemStatLearn) > library(kknn) > data(zip.train)

Re: [R] security using R at work

2018-08-09 Thread john matthew via R-help
Hi Katherina. Good point you make. What makes your IT department happy with the use of R studio server? What are the safe packages? Can I trust your answer? :) John. On 9 Aug 2018 10:38, "Fritsch, Katharina (NNL) via R-help" < r-help@r-project.org> wrote: > Hiya, > I work in a very security co

Re: [R] sub/grep question: extract year

2018-08-09 Thread john matthew via R-help
So there is probably a command that resets the capture variables as I call them. No doubt someone will write what it is. On 9 Aug 2018 10:36, "john matthew" wrote: > Hi Marc. > For question 1. > I know in Perl that regular expressions when captured can be saved if not > o

Re: [R] sub/grep question: extract year

2018-08-09 Thread john matthew via R-help
Hi Marc. For question 1. I know in Perl that regular expressions when captured can be saved if not overwritten. \\1 is the capture variable in your R examples. So the 2nd regular expression does not match but \\1 still has 1980 captured from the previous expression, hence the result. Maybe if you

Re: [R] security using R at work

2018-08-09 Thread john matthew via R-help
Hello Laurence. Taking a pragmatic approach. If the data is so valuable and secret but also needs some analysis in R, here is suggested steps to minimise security risks. 1. Plan the analysis up front, what exactly what you want and the outcomes. 2. Take a laptop with Internet, install R and all p

Re: [R] Breaking the samplesize package from CRAN

2018-07-27 Thread john matthew via R-help
ner. > > ?maintainer > > Cheers, > Bert > > Bert Gunter > > "The trouble with having an open mind is that people keep coming along and > sticking things into it." > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) > > On

[R] Breaking the samplesize package from CRAN

2018-07-26 Thread john matthew via R-help
Hello all, I am using the samplesize package (n.ttest function) to calculate number of samples per group power analysis (t-tests with unequal variance). I can break this n.ttest function from the samplesize package, depending on the standard deviations I input. This works very good. n.ttest(sd1

Re: [R] fwrite() not found in data.table package

2017-10-02 Thread Matthew Keller
ble example (check it with package reprex) and try again here, or > ask one of the maintainers of that package. > -- > Sent from my phone. Please excuse my brevity. > > On October 2, 2017 8:56:46 AM PDT, Matthew Keller > wrote: > >Hi all, > > > >I used to use fwri

[R] fwrite() not found in data.table package

2017-10-02 Thread Matthew Keller
a a namespace (and not attached): [1] tools_3.2.0 chron_2.3-47 tcltk_3.2.0 -- Matthew C Keller Asst. Professor of Psychology University of Colorado at Boulder www.matthewckeller.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing l

[R] Why does residuals.coxph use naive.var?

2017-03-02 Thread Matthew Burgess
Hi all, I noticed that the scaled Schoenfeld residuals produced by residuals.coxph(fit, type="scaledsch") were different from those returned by cox.zph for a model where robust standard errors have been estimated. Looking at the source code for both functions suggests this is because residuals.cox

Re: [R] use value in variable to be name of another variable

2016-07-11 Thread Matthew
Hi Rolf, Thanks for the warning. I think because my initial efforts used the assign function, that Jim provided his solution using it. Any suggestions for how it could be done without assign() ? Matthew On 7/11/2016 6:31 PM, Rolf Turner wrote: On 12/07/16 10:13, Matthew wrote: Hi

Re: [R] use value in variable to be name of another variable

2016-07-11 Thread Matthew
Hi Jim, Wow ! And it does exactly what I was looking for. Thank you very much. That assign function is pretty nice. I should become more familiar with it. Matthew On 7/11/2016 5:59 PM, Jim Lemon wrote: Hi Matthew, This question is a bit mysterious as we don't know what the object

[R] use value in variable to be name of another variable

2016-07-11 Thread Matthew
ame of 265 observations of 2666 variables, if this data structure makes things easier. My initial attempts are not working. Starting with a test data structure that is a little simpler I have tried: for (i in 1:4) { ATG <- tTargTFS[1, i] assign(cat(ATG)

Re: [R] identify duplicate entries in data frame and calculate mean

2016-05-24 Thread Matthew
Thank you very much, Dan. These work great. Two more great answers to my question. Matthew On 5/24/2016 4:15 PM, Nordlund, Dan (DSHS/RDA) wrote: You have several options. 1. You could use the aggregate function. If your data frame is called DF, you could do something like with(DF

Re: [R] identify duplicate entries in data frame and calculate mean

2016-05-24 Thread Matthew
Thanks, Tom. I was making a mistake looking at your example and that's what my problem was. Cool answer, works great. Thank you very much. Matthew On 5/24/2016 4:23 PM, Tom Wright wrote: > Don't see that as being a big problem. If your data grows then dplyr > supports connect

Re: [R] identify duplicate entries in data frame and calculate mean

2016-05-24 Thread Matthew
<-data.frame(Length=c(321,350,340,180,198), > ID=c(rep('A234',3),'B123','B225') ) > $ x %>% group_by(ID) %>% summarise(m=mean(Length)) > > > > On Tue, May 24, 2016 at 3:46 PM, Matthew > <mailto:mccorm...@molbio.mgh

[R] identify duplicate entries in data frame and calculate mean

2016-05-24 Thread Matthew
report the mean to get this: Length Identifier 337 A234 180 B123 198 B225 Matthew __ 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 ht

Re: [R] fast way to create composite matrix based on mixed indices?

2015-09-18 Thread Matthew Keller
d <- cbind(rep(index[,2], ind_len), ind) > # > # new indices > new.ind <- cbind(rep(index[,1], ind_len), ind) > # > # create the new matrix > result <- matrix(NA_integer_, max(index[,1]), max(index[,4])) > # > # fill the new matrix > result[new.ind] <- old.mat

[R] fast way to create composite matrix based on mixed indices?

2015-09-17 Thread Matthew Keller
or loop would be prohibitively slow. I may resort to unix tools and use a shell script, but wanted to first see if this is doable in R in a fast way. Thanks in advance! Matt -- Matthew C Keller Asst. Professor of Psychology University of Colorado at Boulde

Re: [R] reshape: melt and cast

2015-09-01 Thread Matthew Pickard
don't understand > exactly what you want, but does sum work? If there is more than one record > for a given set of factors the sum is the sum of the counts. If only one > record, then the sum is the same as the original number. > > On Tue, Sep 1, 2015 at 10:00 AM, Matthew Pick

[R] setting up R -- VM Fusion, WIndows7

2015-07-30 Thread Matthew Johnson
Hi, As i need R to speak to Bloomberg (and big only runs on windows), i'm running windows 7 via VM Fusion on my mac. I think i am having permission problems, as i cannot use install.packages, and cannot change .libPaths via either a .Rprofile, or Profile.site. I've posted more detail in this sup

Re: [R] tcltk2 entry box

2015-07-10 Thread Matthew
do with them. Matthew On 7/9/2015 5:31 PM, Greg Snow wrote: If you want you script to wait until you have a value entered then you can use the tkwait.variable or tkwait.window commands to make the script wait before continuing (or you can bind the code to a button so that you enter the value

Re: [R] tcltk2 entry box

2015-07-08 Thread Matthew McCormack
Wow ! Very nice. Thank you very much, John. This is very helpful and just what I need. Yes, I can see that I should have paid attention to tcltk before going to tcltk2. Matthew On 7/8/2015 8:37 PM, John Fox wrote: Dear Matthew, For file selection, see ?tcltk::tk_choose.files or ?tcltk

[R] tcltk2 entry box

2015-07-08 Thread Matthew
would like a way for the user to input that information as the script ran. Matthew McCormack __ 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] simple question - mean of a row of a data.frame

2015-02-11 Thread Matthew Keller
m = 0) : argument is not numeric or logical: returning NA I get that rock[2,] is itself a data.frame of mode list, but why the inconsistency between functions? How can you figure this out from, e.g., ?mean ?sum Thanks in advance, Matt -- Matthew C Keller Asst. Professor of Psychology University of Colora

Re: [R] need help with excel data

2015-01-21 Thread Matthew
plit columns. You may have to do some 'cleaning' of individual cells, such as removing leading and/or trainling spaces. A lot of this can be one with the ASAP Utilities 'Text' pull down menu. Matthew On 1/21/2015 3:31 PM, Dr Polanski wrote: Hi all! Sorry to bother you, I am tr

[R] change default installation of R

2014-10-30 Thread Matthew
get if I just type at the command line: /usr/local/R-3.1.1/bin/R. Matthew [[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/

Re: [R] find the data frames in list of objects and make a list of them

2014-09-04 Thread Matthew
go. Matthew On 8/13/2014 7:40 PM, William Dunlap wrote: > Previously you asked >> A second question: is this the best way to make a list >> of data frames without having to manually type c(dataframe1, dataframe2, >> ...) ? > If you use 'c' there you

Re: [R] find the data frames in list of objects and make a list of them

2014-08-13 Thread Matthew
something like: dplyr::rbind_all(list of data frames), but when I try dplyr::rbind_all(lsDataFrame(ls())), I get the error: object at index 1 not a data.frame. So, I am going to have to learn some more about lists in R before proceding. Thank you for your help and code. Matthew Matthew On 8

Re: [R] find the data frames in list of objects and make a list of them

2014-08-13 Thread Matthew
t various times of the day, so I want to automate the process so it does not need anyone to manually sit at the computer and type the list of data frames. Matthew On 8/13/2014 3:06 PM, jim holtman wrote: > Here is a function that I use that might give you the res

[R] find the data frames in list of objects and make a list of them

2014-08-13 Thread Matthew
. Which objects are data frames ? How to then make a list of these data frames. A second question: is this the best way to make a list of data frames without having to manually type c(dataframe1, dataframe2, ...) ? Matthew __ R-help@r-project.org

Re: [R] working on a data frame

2014-07-28 Thread Matthew
ackground noise' in the measurement process, but it is somewhat arbitrary. Matthew On 7/28/2014 2:43 AM, PIKAL Petr wrote: Hi I like to use logical values directly in computations if possible. yourData[,10] <- yourData[,9]/(yourData[,8]+(yourData[,8]==0)) Logical values are automagi

Re: [R] working on a data frame

2014-07-25 Thread Matthew
rom Perl to Python or Java etc., but it seems like R programming works differently. Matthew On 7/25/2014 12:06 AM, Peter Alspach wrote: Tena koe Matthew " Column 10 contains the result of the value in column 9 divided by the value in column 8. If the value in column 8==0, then the division

Re: [R] working on a data frame

2014-07-24 Thread Matthew McCormack
On 7/24/2014 8:52 PM, Sarah Goslee wrote: > Hi, > > Your description isn't clear: > > On Thursday, July 24, 2014, Matthew <mailto:mccorm...@molbio.mgh.harvard.edu>> wrote: > > I am coming from the perspective of Excel and VBA scripts, but I >

[R] working on a data frame

2014-07-24 Thread Matthew
me started ? Matthew __ 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] odd behavior of seq()

2014-07-03 Thread Matthew Keller
[1] 0 > > z[2]==0.15 > [1] TRUE > > Peter > > On Thu, Jul 3, 2014 at 11:28 AM, Matthew Keller > wrote: > > Hi all, > > > > A bit stumped here. > > > > z <- seq(.05,.85,by=.1) > > z==.05 #good > > [1] TRUE FALSE FALSE FALSE

[R] odd behavior of seq()

2014-07-03 Thread Matthew Keller
darwin9.8.0" $status [1] "" $major [1] "2" $minor [1] "13.1" $year [1] "2011" $month [1] "07" $day [1] "08" $`svn rev` [1] "56322" $language [1] "R" $version.string [1] "R version 2.13.1 (2011-07-08)&q

[R] lm models over all possible pairwise combinations of the columns of two matrices

2014-04-22 Thread Matthew Robinson
Dear all, I am working through a problem at the moment and have got stuck. I have searched around on the help list for assistance but could not find anything - but apologies if I have missed something. A dummy example of my problem is below. I will continue to work on it, but any help would be

Re: [R] [e1071] Features that are factors when exporting a model with write.svm

2014-02-21 Thread Matthew Wood
the scale file. On Fri, Feb 21, 2014 at 1:50 PM, Matthew Wood wrote: > I have a trained SVM that I want to export with write.svm and > eventually use in libSVM. Some of my features are factors. Standard > libSVM only works with features that are doubles, so I need to figure > ou

[R] [e1071] Features that are factors when exporting a model with write.svm

2014-02-21 Thread Matthew Wood
I have a trained SVM that I want to export with write.svm and eventually use in libSVM. Some of my features are factors. Standard libSVM only works with features that are doubles, so I need to figure out how my features should be represented and used. How does e1071 treat factors in an SVM? For fe

Re: [R] Biomod model access

2014-02-13 Thread Matthew Bayly
Hi great that was easy I feel like a bit of a fool for not figuring this out. TO LOAD ALL SAVED MODELS AT ONCE: library(biomod2) # change directory to where you stored you’re original models (my documents is default if you did not specify). Go into the file models *# TO LOAD ALL SAVED MODELS

Re: [R] Biomod model access

2014-02-12 Thread Matthew Bayly
I have been struggling with this same problem. I always have to re-run. PLEASE HELP!! I have however figured out the whole data-format issue & am now able to save grid files for use in other GIS programs after they are re-exported. On Thursday, August 15, 2013 1:32:31 AM UTC-7, Jenny Williams w

Re: [R] SDM using BIOMOD2 error message

2014-02-12 Thread Matthew Bayly
> > I think it is a problem with your directory setting & changing your > directory. When you make your enviro stack you set your directory to: setwd("V:/BIOCLIM") Then when you import your species coordinates and presence/absence status you change your directory to: setwd("C:/Users/Linds

Re: [R] Handling large SAS file in R

2014-02-05 Thread Matthew Shotwell
Completing the reverse engineering effort is the principle barrier to fully incorporating the sas7bdat file format. Of course, SAS may change the format specification at any time, and without our knowledge. The sas7bdat package is a repository for the results of our (myself, Clint Cummins, and seve

[R] geo_bar x= and y= warnings and error help

2014-01-22 Thread Matthew Henn
Any insight on issues leading to the following error modes would be appreciated. #Version_1 CALL alphaDivOTU <- ggplot(data=alphaDivOTU_pt1to5, aes(y = Num.OTUs,x = Patient,fill = Timepoint)) + geom_bar(position = position_dodge) + theme(text = element_text(family = 'Helvetica-Narrow',

Re: [R] Help with removing extra legend elements in ggplot

2013-11-19 Thread Matthew Van Scoyoc
Awesome! Thanks for the fix Dennis, and thanks for clearing up aes() too. It makes sense now. Cheers, MVS = Matthew Van Scoyoc Graduate Research Assistant, Ecology Wildland Resources Department <http://www.cnr.usu.edu/wild/> & Ecology Center <http://www.usu.edu/ecology/> Qu

Re: [R] Help with removing extra legend elements in ggplot

2013-11-19 Thread Matthew Van Scoyoc
No dice. I still get the "10" legend element. Thanks for the quick reply. Cheers, MVS ===== Matthew Van Scoyoc Graduate Research Assistant, Ecology Wildland Resources Department <http://www.cnr.usu.edu/wild/> & Ecology Center <http://www.usu.edu/ecology/> Quinney Co

[R] Help with removing extra legend elements in ggplot

2013-11-19 Thread Matthew Van Scoyoc
ank(), >legend.key = element_rect(color = "white") >) I have been messing around with > theme(..., legend.key.size = unit(1, "cm")) but I keep getting the error "could not find function unit". I'm not sure why, isn't unit supposed t

[R] Save intermediate result in a same file

2013-10-01 Thread Matthew
Hello everybody, i have to save a 100 iteration computation in a file every 5 iterations until the end. I first give a vector A of 100 elements for the 100 iterations and i want to update A every 5 iterations. I use "save" but it doesn't work. Someone has an idea, i need a help Cheers. -

Re: [R] Confusing behaviour in data.table: unexpectedly changing variable

2013-09-25 Thread Matthew Dowle
you have tried the maintainer first but didn't hear from them; i.e., r-help isn't for support about packages. I don't follow r-help, so please continue to cc me if you reply. Matthew On 25/09/13 00:47, Jonathan Dushoff wrote: I got bitten badly when a variable I created for the

Re: [R] Regularized Discriminant Analysis scores, anyone?

2013-06-02 Thread Matthew Fagan
:39 AM, Uwe Ligges wrote: On 02.06.2013 05:01, Matthew Fagan wrote: Hi all, I am attempting to do Regularized Discriminant Analysis (RDA) on a large dataset, and I want to extract the RDA discriminant score matrix. But the predict function in the "klaR" package, unlike the pre

[R] Regularized Discriminant Analysis scores, anyone?

2013-06-01 Thread Matthew Fagan
Hi all, I am attempting to do Regularized Discriminant Analysis (RDA) on a large dataset, and I want to extract the RDA discriminant score matrix. But the predict function in the "klaR" package, unlike the predict function for LDA in the "MASS" package, doesn't seem to give me an option to

Re: [R] Contour lines in a persp plot

2013-05-17 Thread Matthew
Thanks a lot, that is all i want. If someone is interessed, see the code below panel.3d.contour <- function(x, y, z, rot.mat, distance, nlevels = 20, zlim.scaled, ...) # les3 points de suspension pour dire les autres paramètres sont ceux données par défaut { add.line <- trel

[R] expanding a presence only dataset into presence/absence

2013-04-29 Thread Matthew Venesky
and haven't found a resolution (and note that a similar question was asked sometime in 2011 without an answer). Does anyone have any thoughts? Thank you in advance. -- Matthew D. Venesky, Ph.D. Postdoctoral Research Associate, Department of Integrative Biology, The University of South

Re: [R] Factor to numeric conversion - as.numeric(levels(f))[f] - Language definition seems to say to not use this.

2013-04-01 Thread Matthew Lundberg
is is OK, since this can change if the implementation > does. Which is the whole point, of course. > > -- Bert > > > > On Mon, Apr 1, 2013 at 12:16 PM, Matthew Lundberg > wrote: > > > > When used as an index, the factor is implicitly converted to integer. In >

Re: [R] Factor to numeric conversion - as.numeric(as.character(f))[f] - Language definition seems to say to not use this.

2013-04-01 Thread Matthew Lundberg
, Apr 1, 2013 at 1:49 PM, Peter Ehlers wrote: > On 2013-04-01 10:48, Matthew Lundberg wrote: > >> These two seem to be at odds. Is this the case? >> >> From help(factor) - section Warning: >>> >> >> To transform a factor f to approximately its origin

[R] Factor to numeric conversion - as.numeric(as.character(f))[f] - Language definition seems to say to not use this.

2013-04-01 Thread Matthew Lundberg
These two seem to be at odds. Is this the case? >From help(factor) - section Warning: To transform a factor f to approximately its original numeric values, as.numeric(levels(f))[f] is recommended and slightly more efficient than as.numeric(as.character(f)). >From the language definition - secti

Re: [R] Problem with R CMD check and the inconsolata font business

2013-03-05 Thread Matthew Dowle
t into the Windows Font directory was not necessary. I'm including the solution in case anyone else has this problem. Many thanks Brian Diggs! I just had the same problem and that fixed it. Matthew __ R-help@r-project.org mailing list https://stat.

Re: [R] low pass filter analysis in R

2013-02-07 Thread Shotwell, Matthew Stephen
Janesh, This might help get you started: http://biostatmatt.com/archives/78 (apologies for linking to my own blog) Regards, Matt -- Message: 51 Date: Wed, 6 Feb 2013 18:50:43 -0600 From: Janesh Devkota To: r-help@r-project.org Subject: [R] low pass filter analysi

[R] Rscript on Mac : specify R64 over R (32-bit version)

2013-01-16 Thread Matthew Pettis
Hi, I have both R and R64 installed on Mac OSX 10.8 Mountain Lion (64-bit). When I run the command sessionInfo() from within Rscript, I get: R version 2.15.2 (2012-10-26) Platform: i386-apple-darwin9.8.0/i386 (32-bit) Is there a way to make Rscript point at the R64 rather than R (32-bit)? Th

[R] SQLDF column errors

2013-01-15 Thread Matthew Liebers
I am trying to exclude integer values from a small data frame 1, d1 that have matching hits in data frame 2, d2 (Very big) which involves matching those hits first. I am trying to use sqldf on the df's in the following fashion: df1: V1 12675 14753 16222 18765 df2: head(df2) V1 V2 13

[R] sqldf merging with subset in specific range

2012-12-26 Thread Matthew Liebers
Hi all: I have two data sets. Set A includes a long list of hits in a single column, say: m$V1 10 15 36 37 38 44 45 57 61 62 69 ...and so on Set B includes just a few key ranges set up by way of a minimum in column X and a maximum in column Y. Say, n$X n$Y 30 38 # range from 30 to 38 52 6

[R] confirming a formula for use with lmer

2012-12-19 Thread Matthew Panichello
Hello, I recently began using R and the lme4 package to carry out linear mixed effects analyses. I am interested in the effects of variables 'prime','time', and 'mood' on 'reaction_time' while taking into account the random effect 'subjects.' I've read through documentation on lme4 and came

[R] Updating Tom Short's R Reference Card, contacting him?

2012-11-21 Thread Matthew Baggott
I am uncertain about how to acknowledge the fact that $ can do partial matching in the space of about 30 characters. One option is this: x[["name"]] column named "name" x$name same as above (almost always) Is that better or worse than ignoring this issue, or is there an even bett

[R] Updating Tom Short's R Reference Card, contacting him?

2012-11-20 Thread Matthew Baggott
I made an update/reboot of Tom Short's classic and public domain "R Reference Card". His is from late 2004 and I've found myself giving it to new R users with additional notes about packages. If anyone knows how to reach Tom, that would be great. I am titling this reboot "Short R Reference", in

[R] Clustering groups according to multiple variables

2012-10-31 Thread Matthew Ouellette
Dear R help, I am trying to cluster my data according to "group" in a data frame such as the following: df=data.frame(group=rep(c("a","b","c","d"),10),(replicate(100,rnorm(40 I'm not sure how to tell hclust() that I want to cluster according to the group variable. For example: dfclust=hc

[R] Clustering groups according to multiple variables

2012-10-31 Thread Matthew Ouellette
Dear R help, I am trying to cluster my data according to "group" in a data frame such as the following: df=data.frame(group=rep(c("a","b","c","d"),10),(replicate(100,rnorm(40 I'm not sure how to tell hclust() that I want to cluster according to the group variable. For example: dfclust=hc

[R] optimize and mcparallel problem

2012-10-03 Thread Matthew Wolak
my first question is whether or not there is a better way to return all of the values over which "optimize" evaluates my function. The second question is if I do use my solution to the first question, how can I get the "vals" object returned from the child process? Thanks anyon

[R] Hosted R

2012-08-24 Thread Matthew K. Hettinger
son I ask is that I'm looking at the possibility of establishing an R grid if one doesn't already exist, and if one does, then I'm looking for interfaces, protocols, and guidelines for adding an R node. -- Matthew K. Hettinger, Enterprise Architect and Systemist Ma

[R] how to sort huge (> 2^31 row) dataframes quickly

2012-07-30 Thread Matthew Keller
s, but again, maybe I'm wrong. My computer programmer writes in C++, so if you have ideas in C++, that works too. Any help would be much appreciated... Thanks! Matt -- Matthew C Keller Asst. Professor of Psychology University of Colorado at Boulder www.matthewckeller.com _

Re: [R] Extracting standard errors for adjusted fixed effect sizes in lmer

2012-07-22 Thread Matthew Ouellette
Dear R help, Does no one have an idea of where I might find information that could help me with this problem? I apologize for re-posting - I have half a suspicion that my original message did not make it through. I hope you all had a good weekend and look forward to your reply, MO On Fri, Jul

[R] Extracting standard errors for adjusted fixed effect sizes in lmer

2012-07-20 Thread Matthew Ouellette
Dear R help list, I have done a lot of searching but have not been able to find an answer to my problem. I apologize in advance if this has been asked before. I am applying a mixed model to my data using lmer. I will use sample data to illustrate my question: >library(lme4) >library(arm) >data

Re: [R] how to convert list of matrix (raster:extract o/p) to data table with additional colums (polygon Id, class)

2012-06-29 Thread Matthew Dowle
AKJ, Please see this recent answer : http://r.789695.n4.nabble.com/data-table-vs-plyr-reg-output-tp4634518p4634865.html Matthew -- View this message in context: http://r.789695.n4.nabble.com/how-to-convert-list-of-matrix-raster-extract-o-p-to-data-table-with-additional-colums-polygon-Id

Re: [R] data.table vs plyr reg output

2012-06-29 Thread Matthew Dowle
x27;d suggest the data.table tag on Stack Overflow (which I subscribe to) : http://stackoverflow.com/questions/tagged/data.table Btw, I recently presented at LondonR. Here's a link to the slides : http://datatable.r-forge.r-project.org/LondonR_2012.pdf Matthew -- View this messag

Re: [R] templated use of aggregate

2012-06-13 Thread Matthew Johnson
thank you for your patience. i assure you i will get better with the appropriate etiquette - and hopefully eventually contribute. On 13 June 2012 16:18, David Winsemius wrote: > > On Jun 13, 2012, at 10:09 AM, Matthew Johnson wrote: > >> my sessioninfo was as follows: >

Re: [R] templated use of aggregate

2012-06-13 Thread Matthew Johnson
ethods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique mnz[, 1] mnz[, -1] 197.90 408 297.89 208 So is this a bug in XTS? thanks for your patience mj On 13 June 2012 15:53, David Winsemius wrote: > > On Jun 13, 2012, at 9:38 AM, Matthe

Re: [R] templated use of aggregate

2012-06-13 Thread Matthew Johnson
mand could be made to be: px_ym1 count vol_ym1 1 97.90 11 408 2 97.89 10 208 where we have the price traded, the number of trades (a count of px_ym1 / mn[,1], and the sum of vol_ym1 (mn[,2]). thanks and best regards matt johnson On 13 June 2012 15:06, David Winsemius wrote: >

[R] templated use of aggregate

2012-06-12 Thread Matthew Johnson
Dear R-help, I have an xts data set that i have subset by date. now it contains a date-time-stamp, and two columns (price and volume traded): my objective is to create tables of volume traded at a price - and i've been successfully using aggregate to do so in interactive use. say the data looks

Re: [R] what does .indexDate() do - R::xts

2012-06-12 Thread Matthew Johnson
thanks. i think i understand: the difference is that the first command converts my 'searched-for' date to a number and matches it, but the second does not? On 13 June 2012 12:58, Joshua Ulrich wrote: > On Tue, Jun 12, 2012 at 9:48 PM, Matthew Johnson > wrote: > > Dear R

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