Re: [R] : Ramanujan and the accuracy of floating point computations - using Rmpfr in R

2015-07-03 Thread Hadley Wickham
It doesn’t appear to me that mpfr was ever designed to handle expressions as the first argument. >>> >>> This could be a start. Obviously one would wnat to include code to do other >>> substitutions probably using the all.vars function to pull out the other >>> “constants” and ’numeric

Re: [R] : Ramanujan and the accuracy of floating point computations - using Rmpfr in R

2015-07-03 Thread David Winsemius
> On Jul 3, 2015, at 11:05 PM, Duncan Murdoch wrote: > > On 04/07/2015 3:45 AM, David Winsemius wrote: >> >>> On Jul 3, 2015, at 5:08 PM, David Winsemius wrote: >>> >>> >>> >>> It doesn’t appear to me that mpfr was ever designed to handle expressions >>> as the first argument. >> >> This

Re: [R] : Ramanujan and the accuracy of floating point computations - using Rmpfr in R

2015-07-03 Thread Duncan Murdoch
On 04/07/2015 3:45 AM, David Winsemius wrote: > >> On Jul 3, 2015, at 5:08 PM, David Winsemius wrote: >> >> >> >> It doesn’t appear to me that mpfr was ever designed to handle expressions as >> the first argument. > > This could be a start. Obviously one would wnat to include code to do other

Re: [R] what constitutes a 'complete sentence'?

2015-07-03 Thread Duncan Murdoch
On 04/07/2015 12:26 AM, Rolf Turner wrote: > On 04/07/15 06:27, Yihui Xie wrote: >> Sigh, how natural it is to say "This package ...", but you probably >> don't know a package can be easily rejected by CRAN simply because of >> this phrase "This package" (it has been clearly stated in the R-exts >>

Re: [R] question

2015-07-03 Thread Mark Sharp
Lida, I expect that there is a better way to solve your problem than the process you propose. However, something like this may do what you want. ### ## met <- read.csv("your_met_file”) ## Since I do not have your file a made a small 5*1 character vector. met <- c("glycine_imp", "Nac

Re: [R] How to feed graphic device (png, jpeg etc) with different files names

2015-07-03 Thread Jeff Newmiller
Use dev.off and re-open the device. --- Jeff NewmillerThe . . Go Live... DCN:Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#

[R] How to feed graphic device (png, jpeg etc) with different files names

2015-07-03 Thread Jun Shen
Dear list, I define a function to export a bunch of plots. A sample code is something like the follow export.plots<-function(export.type='pdf',...){ match.fun(export.type) (...) print(plot.func1(...)) print(plot.func2(...)) print(plot.func3(...)) ... print(plot.funcn(...)) dev.off() } If I d

Re: [R] : Ramanujan and the accuracy of floating point computations - using Rmpfr in R

2015-07-03 Thread David Winsemius
> On Jul 3, 2015, at 5:08 PM, David Winsemius wrote: > > > > It doesn’t appear to me that mpfr was ever designed to handle expressions as > the first argument. This could be a start. Obviously one would wnat to include code to do other substitutions probably using the all.vars function to p

Re: [R] Lattice: set col = "black" for box.rectangle and box.umbrella

2015-07-03 Thread Duncan Mackay
Rich Just a thought Have you set pch colour values somewhere else? see also https://stat.ethz.ch/pipermail/r-help/2010-March/230329.html Duncan -Original Message- From: rshep...@localhost.appl-ecosys.com [mailto:rshep...@localhost.appl-ecosys.com] On Behalf Of Rich Shepard Sent: Saturday

Re: [R] : Ramanujan and the accuracy of floating point computations - using Rmpfr in R

2015-07-03 Thread David Winsemius
It doesn’t appear to me that mpfr was ever designed to handle expressions as the first argument. — David > On Jul 3, 2015, at 12:01 PM, Ravi Varadhan wrote: > > Thank you all. I did think about declaring `pi' as a special constant, but > for some reason didn't actually try it. > Would i

Re: [R] : Ramanujan and the accuracy of floating point computations - using Rmpfr in R

2015-07-03 Thread Ravi Varadhan
Thank you all. I did think about declaring `pi' as a special constant, but for some reason didn't actually try it. Would it be easy to have the mpfr() written such that its argument is automatically of extended precision? In other words, if I just called: mpfr(exp(sqrt(163)*pi, 120), then al

Re: [R] [FORGED] Re: matrix -> delete last row -> list

2015-07-03 Thread Rolf Turner
On 04/07/15 03:43, Sarah Goslee wrote: Hi, On Fri, Jul 3, 2015 at 10:33 AM, Zander, Joscha wrote: Good day R-community, i just wondered if it is a bug or a feature... When i have a matrix "mat" with one column and i delete the last row with mat <- mat[-nrow(mat),] the result is a list. I

Re: [R] what constitutes a 'complete sentence'?

2015-07-03 Thread Rolf Turner
On 04/07/15 06:27, Yihui Xie wrote: Sigh, how natural it is to say "This package ...", but you probably don't know a package can be easily rejected by CRAN simply because of this phrase "This package" (it has been clearly stated in the R-exts manual). Urrr! I *did* "know" that, but had for

Re: [R] what constitutes a 'complete sentence'?

2015-07-03 Thread Yihui Xie
Sigh, how natural it is to say "This package ...", but you probably don't know a package can be easily rejected by CRAN simply because of this phrase "This package" (it has been clearly stated in the R-exts manual). I don't think the grammar is the problem here. When in doubt, I always check what

Re: [R] : Ramanujan and the accuracy of floating point computations - using Rmpfr in R

2015-07-03 Thread David Winsemius
> On Jul 3, 2015, at 8:08 AM, John Nash wrote: > > > > > Third try -- I unsubscribed and re-subscribed. Sorry to Ravi for extra > traffic. > > In case anyone gets a duplicate, R-help bounced my msg "from non-member" (I > changed server, but not email yesterday, > so possibly something chang

Re: [R] no slot of name "fixef" for this object of class "lmerMod"

2015-07-03 Thread Thierry Onkelinx
Yes, use fixef(mod) instead of mod@fixef. It is recommended to use the accessor functions instead of reading the slots with the @. ​ ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality As

Re: [R] matrix -> delete last row -> list

2015-07-03 Thread Sarah Goslee
Hi, On Fri, Jul 3, 2015 at 10:33 AM, Zander, Joscha wrote: > Good day R-community, > > i just wondered if it is a bug or a feature... > > When i have a matrix "mat" with one column and i delete the last row with > > mat <- mat[-nrow(mat),] the result is a list. I have no idea how you're getting

Re: [R] matrix -> delete last row -> list

2015-07-03 Thread Marc Schwartz
> On Jul 3, 2015, at 9:33 AM, Zander, Joscha wrote: > > Good day R-community, > > i just wondered if it is a bug or a feature... > > When i have a matrix "mat" with one column and i delete the last row with > > mat <- mat[-nrow(mat),] the result is a list. > > So my next call mat[10,] will t

Re: [R] what constitutes a 'complete sentence'?

2015-07-03 Thread Berend Hasselman
> On 03-07-2015, at 14:18, Federico Calboli > wrote: > > As I said, I found a formulation that pleased the check and that’s it for me. > I am befuddled by the check in the first place though. > And what would that formulation be (replacing the original one) ? Berend > BW > > F > > >> O

Re: [R] what constitutes a 'complete sentence'?

2015-07-03 Thread Federico Calboli
As I said, I found a formulation that pleased the check and that’s it for me. I am befuddled by the check in the first place though. BW F > On 3 Jul 2015, at 15:14, PIKAL Petr wrote: > > Hi > > without going deep into this matter, what if you remove "/" from your > sentence. > > Cheers >

Re: [R] no slot of name "fixef" for this object of class "lmerMod"

2015-07-03 Thread Iker Vaquero Alba
   Dear Thierry,    Thank you very much. Do you mean I should add a line to the function with the code "fixef(my.model)", retaining everything else, even the "beta0    <- as.numeric(mod@fixef)" line? Or should I replace something?   Also, when you say "fixef(my.model), do you mean "fixef(mod)"

Re: [R] : Ramanujan and the accuracy of floating point computations - using Rmpfr in R

2015-07-03 Thread John Nash
Third try -- I unsubscribed and re-subscribed. Sorry to Ravi for extra traffic. In case anyone gets a duplicate, R-help bounced my msg "from non-member" (I changed server, but not email yesterday, so possibly something changed enough). Trying again. JN I got the Wolfram answer as follows: l

Re: [R] what constitutes a 'complete sentence'?

2015-07-03 Thread Federico Calboli
That exists already: last slide here — it looks like it is a know issue. BW F > On 3 Jul 2015, at 14:13, Hadley Wickham wrote: > > In that case, you need to create a minimal reproducible example and make it > publicly available. > > Hadley > > On Friday, July 3, 2015, Federico Calboli

[R] matrix -> delete last row -> list

2015-07-03 Thread Zander, Joscha
Good day R-community, i just wondered if it is a bug or a feature... When i have a matrix "mat" with one column and i delete the last row with mat <- mat[-nrow(mat),] the result is a list. So my next call mat[10,] will throw an "wrong dimension" error. The proper call must be: mat <- as.matrix

[R] timePlot legend

2015-07-03 Thread ulasim77
Dear all I am plotting a time series using time Plot function. All goes well until i try to modify the legend by taking it from the standard location at the bottom, to the right side in a vertical way. How can i do this? This is my code: filename <- sprintf('%s/TS_CO_all.png',folderPLOTS) y_la

Re: [R] : Ramanujan and the accuracy of floating point computations - using Rmpfr in R

2015-07-03 Thread RK
Also when I try the following with Rmpfr, it works jut fine. > exp(sqrt(mpfr(163, 120)) * Const("pi", 120)) 1 'mpfr' number of precision 120 bits [1] 262537412640768743.25007601 and > exp(sqrt(mpfr(163, 400)) * Const("pi", 400)) 1 'mpfr' number of precision 400 bits [1] 2625

Re: [R] what constitutes a 'complete sentence'?

2015-07-03 Thread Federico Calboli
> On 3 Jul 2015, at 12:14, Hadley Wickham wrote: > > It might be a line break problem - I think you want: > > Description: Functions designed to test for single gene/phenotype > association and >for pleiotropy on genetic and genomic data. Tried this and unfortunately it does not help. BW

[R] Variance estimates for survreg vs. lm

2015-07-03 Thread Richard Perry
I would like help understanding why a survival regression with no censored data-points does not give the same variance estimates as a linear model (see code below). I think it must be something to do with the fact that the variance is an actual parameter in the survival version via the log(scale),

Re: [R] igraph plot slowness

2015-07-03 Thread jim holtman
Here is what it does locally on my PC: > library("igraph") > topo_data <- read.table(text = "ibcore01ibswitch01 + ibcore01ibswitch02 + ibcore01ibswitch03 + ibcore02ibswitch01 + ibcore02ibswitch02 + ibcore02ibswitch03 + ibswitch01 node001

Re: [R] what constitutes a 'complete sentence'?

2015-07-03 Thread Rolf Turner
On 03/07/15 20:09, Federico Calboli wrote: Hi All, I am upgrading a package for CRAN, and I get this note: checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. This is puzzling because: cat DESCRIPTION ... Description: Fun

Re: [R] Lattice: set col = "black" for box.rectangle and box.umbrella

2015-07-03 Thread Rich Shepard
On Fri, 3 Jul 2015, Duncan Mackay wrote: I usually avoid global settings as they may change between graphs therefore I use the par.settings in each plot My settings are ... Duncan, Thank you very much. Sound advice and excellent example. I suspect that part of my issues with tryin

Re: [R] what constitutes a 'complete sentence'?

2015-07-03 Thread PIKAL Petr
Hi without going deep into this matter, what if you remove "/" from your sentence. Cheers Petr > -Original Message- > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Hadley > Wickham > Sent: Friday, July 03, 2015 1:14 PM > To: Federico Calboli > Cc: R-help > Subject: Re:

Re: [R] what constitutes a 'complete sentence'?

2015-07-03 Thread Hadley Wickham
In that case, you need to create a minimal reproducible example and make it publicly available. Hadley On Friday, July 3, 2015, Federico Calboli wrote: > > > On 3 Jul 2015, at 12:14, Hadley Wickham > wrote: > > > > It might be a line break problem - I think you want: > > > > Description: Funct

Re: [R] no slot of name "fixef" for this object of class "lmerMod"

2015-07-03 Thread Thierry Onkelinx
Dear Iker, The internals of the mer model have changed. Use fixef(your.model). Best regards, ​ ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070 Anderl

Re: [R] question

2015-07-03 Thread Jim Lemon
Hi Ati, Let's start from the top and see where we finish up. I'll use a somewhat smaller matrix: met<-matrix(runif(5),ncol=1) rownames(met)<-c("glycine_imp","Nacetylglycine_imp","sarcosine_imp", "dimethylglycine_imp","betaine_imp") met [,1] glycine_imp 0.61532855

[R] Getting predictions for skewed t-distribution

2015-07-03 Thread Patrick Connolly
I have a small dataframe xxF, a summary of which looks like this: > summary(xxF) T Dev Min. :10.44 Min. :0.008929 1st Qu.:10.44 1st Qu.:0.012048 Median :18.61 Median :0.031250 Mean :17.87 Mean :0.028286 3rd Qu.:22.24 3rd Qu.:0.041667

Re: [R] what constitutes a 'complete sentence'?

2015-07-03 Thread Hadley Wickham
It might be a line break problem - I think you want: Description: Functions designed to test for single gene/phenotype association and for pleiotropy on genetic and genomic data. Hadley On Fri, Jul 3, 2015 at 10:09 AM, Federico Calboli wrote: > Hi All, > > I am upgrading a package for CRAN,

Re: [R] question

2015-07-03 Thread PIKAL Petr
Hi I cannot test it in absence of data. Anyway I would not use saving single objects but use list instead. Something like lll <- vector(mode="list", nrow(met)) for (i in 1:nrow(met)) { form <- as.formula(paste(met[i], "~ egfr_v1_ckdepi+pc1+pc2+pc3+V1AGE01+GENDER")) lll[i] <- Scores(Z=metalofGT

[R] what constitutes a 'complete sentence'?

2015-07-03 Thread Federico Calboli
Hi All, I am upgrading a package for CRAN, and I get this note: checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. This is puzzling because: cat DESCRIPTION ... Description: Functions designed to test for single gene/pheno

Re: [R] : Ramanujan and the accuracy of floating point computations - using Rmpfr in R

2015-07-03 Thread Ravi Varadhan
Hi Rich, The Wolfram answer is correct. http://mathworld.wolfram.com/RamanujanConstant.html There is no code for Wolfram alpha. You just go to their web engine and plug in the expression and it will give you the answer. http://www.wolframalpha.com/ I am not sure that the precedence matters

Re: [R] Removing rows in a data frame

2015-07-03 Thread Sergio Fonda
In my experience package "dplyr" has all functions to deal with this kind of problems in a simple and compact way Sergio Il 03/lug/2015 07:26, "Charles Thuo" ha scritto: > I have a data frame whose rows are 678013 . I would like to remove rows > from 30696 to 678013 and then attach a new column

Re: [R] Removing rows in a data frame

2015-07-03 Thread Rainer Schuermann
Try y <- x[ -( 30596:678013 ), ] Please note that I have replaced 30595 with 30596 which is I think what you mean. You can add a new column with y$new <- new_column # this is your vector of length 30595 Good luck, Rainer On Friday 03 July 2015 07:23:28 Charles Thuo wrote: > I have a data

[R] igraph plot slowness

2015-07-03 Thread Loris Bennett
Hi, With the following data ibcore01ibswitch01 ibcore01ibswitch02 ibcore01ibswitch03 ibcore02ibswitch01 ibcore02ibswitch02 ibcore02ibswitch03 ibswitch01 node001 ibswitch01 node002 ibswitch01 node003 ibswitch02 node004 ibswitch02