Re: [R] Math ops behaviour with multiple classes

2017-06-08 Thread Jeff Newmiller
Cole, that cow left the barn decades ago. You really should read Patrick Burns' discussion of the history of R [1]. [1] http://www.burns-stat.com/documents/presentations/inferno-ish-R/ -- Sent from my phone. Please excuse my brevity. On June 8, 2017 3:48:23 PM PDT, "Beck, Cole" wrote: >Thanks

Re: [R] Math ops behaviour with multiple classes

2017-06-08 Thread Hadley Wickham
On Thu, Jun 8, 2017 at 2:45 PM, Bert Gunter wrote: > I think you may be confusing (S3) class and ?mode. Your point is well made, but to be precise, I think you should talk about the "type of" an object, not it's mode. mode() is a wrapper around typeof(), designed (I believe) for S compatibility.

Re: [R] Math ops behaviour with multiple classes

2017-06-08 Thread Beck, Cole
Thanks Bert, I think we agree on the current behaviour, but I'm still not sure if it's desirable. The mode isn't used for method dispatch. In the following example, I have to write `log.foo` in order for the correct method to be called. > x <- seq.int(5) > class(x) <- c("integer", "foo") > hal

Re: [R] Math ops behaviour with multiple classes

2017-06-08 Thread Bert Gunter
I think you may be confusing (S3) class and ?mode. > x <- seq.int(1:3) > class(x) [1] "integer" > mode(x) [1] "numeric" > class(x+.5) ## coercion [1] "numeric" > mode(x+.5) [1] "numeric" But note: > y <- as.integer(1) > class(y) [1] "integer" > class(y) <- "foo" > mode(y) [1] "numeric" > class(y

Re: [R] help regarding r-project

2017-06-08 Thread John Kane via R-help
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example On Thursday, June 8, 2017 6:57 AM, Michael Dewey wrote: I do not think anyone is going to be able to help you unless you can provide a reproducible example with a clear account of what it dies and

Re: [R] Plot MArginal distribution in the correct place

2017-06-08 Thread Pedro páramo
Many thanks Jim. What I,m trying to show with the fhist plot is the empirical distribution of the values of the left plot simulation. You say: However, I don't think that this plot illustrates quite what you think it does. Can you give me a clue to try to illustrate better if it is not showing w

[R] Math ops behaviour with multiple classes

2017-06-08 Thread Cole Beck
I would expect that several math operations should always return values with a class of numeric. If the input is defined with multiple classes, however, the class attribute is preserved. I would think this may have some unintended side-effects. Here's an example: > sessionInfo()$R.version$v

Re: [R] DESeq2 pairwise compasion

2017-06-08 Thread Jeff Newmiller
I think you are asking on the wrong mailing list. Perhaps you should be asking this question on the Bioconductor mailing list? -- Sent from my phone. Please excuse my brevity. On June 8, 2017 7:35:55 AM PDT, Yogesh Gupta wrote: >There are two line 216 and 218 > >Three development stages 5 WEEK

Re: [R] rmarkdown and font size

2017-06-08 Thread Nordlund, Dan (DSHS/RDA)
You can change the style, modifying a variety of things. E.g, --- title: Test --- body{ /* Normal */ font-size: 12px; } td { /* Table */ font-size: 8px; } h1.title { font-size: 38px; color: DarkRed; } h1 { /* Header 1 */ font-size: 28px; color: DarkBlue; } h2 { /* Header 2

[R] DESeq2 pairwise compasion

2017-06-08 Thread Yogesh Gupta
There are two line 216 and 218 Three development stages 5 WEEK (5W), 7W, 9W. Three tissue: Ca, Co, Pa each with 2 biological replicate. With two biological replicate. I want to do differential gene expression analysis using DESeq2 so I tried these codes after reading about DESeq2: ,my aim is to

Re: [R] Paths in knitr

2017-06-08 Thread Duncan Murdoch
On 08/06/2017 7:15 AM, g.maub...@weinwolf.de wrote: Hi All, I have to compile a report for the management and decided to use RMarkdown and knitr. I compiled all needed plots (using separate R scripts) before compiling the report, thus all plots reside in my graphics directory. The RMarkdown repo

Re: [R] Paths in knitr

2017-06-08 Thread Yihui Xie
Why do you have to set the base.dir option? Regards, Yihui -- https://yihui.name On Thu, Jun 8, 2017 at 6:15 AM, wrote: > Hi All, > > I have to compile a report for the management and decided to use RMarkdown > and knitr. I compiled all needed plots (using separate R scripts) before > compilin

Re: [R] Rainbow in loop

2017-06-08 Thread WRAY NICHOLAS
Yep fabbo I can then call each vector as a separate element in a list and it gives the colours... Thanks aleph-null times Nick > > On 08 June 2017 at 14:13 Boris Steipe wrote: > > > Does: > > rainbow(3)[1] > rainbow(3)[2] > rainbow(3)[3] > > ... solve your issue? >

Re: [R] Rainbow in loop

2017-06-08 Thread Boris Steipe
Does: rainbow(3)[1] rainbow(3)[2] rainbow(3)[3] ... solve your issue? B. > On Jun 8, 2017, at 8:20 AM, WRAY NICHOLAS wrote: > > Hi R folk I have a distance time graph for a locomotive and at various times > different events occur on board the loco. I want to put a vertical line on

Re: [R] I don't want to receive mail from questioner

2017-06-08 Thread John C Frain
Unsubscribe by following the instructions at https://stat.ethz.ch/mailman/ listinfo/r-help. There is a message to this effect at the end of each message from r-help. If you are going to use R you should stay subscribed as you may find that some of the answers provide valuable information to users a

[R] Rainbow in loop

2017-06-08 Thread WRAY NICHOLAS
Hi R folk I have a distance time graph for a locomotive and at various times different events occur on board the loco. I want to put a vertical line on the speed time graph for each event, but I want to colour each different kind of event differently to see visually whether there's any pattern to

Re: [R] regular expression help

2017-06-08 Thread Ashim Kapoor
Dear Enrico, Many thanks and Best Regards, Ashim. On Thu, Jun 8, 2017 at 5:11 PM, Enrico Schumann wrote: > > Zitat von Ashim Kapoor : > > > Dear All, >> >> My query is: >> >> Do we always need to use perl = TRUE option when doing ignore.case=TRUE? >> >> A small example : >> >> my_text = >> "RE

[R] I don't want to receive mail from questioner

2017-06-08 Thread Sara Edi via R-help
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } How can I cancel R-help mail?I do not want to receive questions of questioner becouse I do not have enough information about R.  

Re: [R] regular expression help

2017-06-08 Thread Enrico Schumann
Zitat von Ashim Kapoor : Dear All, My query is: Do we always need to use perl = TRUE option when doing ignore.case=TRUE? A small example : my_text = "RECOVERY OFFICER-II\nDEBTS RECOVERY TRIBUNAL-III\n RC No. 162/2015\nSBI VS RAMESH GUPTA.\nDated: 01.03.2016 Item no.01

[R] Paths in knitr

2017-06-08 Thread G . Maubach
Hi All, I have to compile a report for the management and decided to use RMarkdown and knitr. I compiled all needed plots (using separate R scripts) before compiling the report, thus all plots reside in my graphics directory. The RMarkdown report needs to access these files. I have defined ```

Re: [R] help regarding r-project

2017-06-08 Thread Michael Dewey
I do not think anyone is going to be able to help you unless you can provide a reproducible example with a clear account of what it dies and what you expected it to do. On 08/06/2017 06:34, Sai Sathvick wrote: hello sir/ma'am, trying to build a small prototype of resum

Re: [R] Operating on RC in a list

2017-06-08 Thread Mohan.Radhakrishnan
I am replying to my question. AFAIK dplyr works only with data frames. So I flattened the RC's like this. A pure OO approach and a functional representation of it are at loggerheads. I think. filteredmeasurements <- keep(measure

[R] regular expression help

2017-06-08 Thread Ashim Kapoor
Dear All, My query is: Do we always need to use perl = TRUE option when doing ignore.case=TRUE? A small example : my_text = "RECOVERY OFFICER-II\nDEBTS RECOVERY TRIBUNAL-III\n RC No. 162/2015\nSBI VS RAMESH GUPTA.\nDated: 01.03.2016 Item no.01\n Present: Ms. Sonakshi, t

[R] help regarding r-project

2017-06-08 Thread Sai Sathvick
hello sir/ma'am, trying to build a small prototype of resume filter but not able to get expected intercept values, could you please help regarding this project ASAP. to predict, skills + experience =result -- *With Regards,* *C Sai Sathvick* ___

Re: [R] stepAIC() that can use new extractAIC() function implementing AICc

2017-06-08 Thread Marc Girondot via R-help
I have found the problem and a solution. The problem comes from the functions addterm.glm() and dropterm.glm() from MASS package. They use extractAIC() without transmitting the ... argument: aic <- aic + (extractAIC(object, k = k)[2L] - aic[1L]) I replace the call with: aic <- aic + (extract