[R] How to include static PDFs vignettes in an R package

Hi all, prior to R version 3.0 I used to include a static PDF file as package vignette following the instructions in http://www.icesi.edu.co/CRAN/web/packages/R.rsp/vignettes/NonSweaveVignettes.pdf (I know this is a little bit old), except that the relevant files where in vignette/ directory o

Re: [R] density in hist does not come as 1

Hello, What you are doing wrong? Correctly read the help page. >From the help page: "if FALSE, probability densities, component density, are plotted (so that the histogram has a *total area of one*)" > sum(check$density * diff(check$breaks)) [1] 1 HTH, Pascal On Tue, May 20, 2014 at 3:06 PM, v

[R] density in hist does not come as 1

Dear List, I am trying to make a histogram with following data: dput(a) c(1, 0, 1.5, 1, 0, 0, 0, 1, 1.5, 0, 0, 1, 0, 0, 0, 1, 1, 2, 1, 0, 0, 0, 1, 1, 1, 0, 1, 0.5, 1, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1.5, 0, 0, 0, 0, 1, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 1, 1, 1,

Re: [R] How could I graph a special coordinate

Check out the R Graph Gallery for ideas. http://rgraphgallery.blogspot.com/ Cheers, Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom." H. Gilbert Welch On Mon, May 19, 2014 at 5:

Re: [R] R save with encoding...

Hi See ?plotmath. Something like this: plot(1, 1, main = expression(paste("INTERVALS ", lambda))) Yours sincerely / Med venlig hilsen Frede Aakmann Tøgersen Specialist, M.Sc., Ph.D. Plant Performance & Modeling Technology & Service Solutions T +45 9730 5135 M +45 2547 6050 fr...@vestas.com

[R] How could I graph a special coordinate

hi, I'v got some data attached as apx.csv. It shows the relationship about a kind of enzyme and the temperature. "yhf" and "xbt" are 2 kind of cowpea. "apx" is the kind of enzyme and "low" means the lowest temperature intraday. "date" means 1 to 121 days. What I want to show with it is how is "a

Re: [R] Boxplots

Another method uses the core boxplot() function but replaces the usual call to split() with a variant that puts all the data at the end of the list of splits: > splitPlusAll <- function(x, ...) c(split(x, ...), list(All=x)) > boxplot(with(mtcars, splitPlusAll(wt, list(gear,am), drop=TRUE))) > boxp

Re: [R] Subsets of a function

It would have been nice if you at least supplied a subset of the data, but here is a try at it: myList <- split(size, list(size$Year, size$Season)) result <- lapply(myList, function(.sub){ smooth.spline(.sub$Size, spar = 0.25) }) Jim Holtman Data Munger Guru What is the problem that you a

Re: [R] Subsets of a function

Have you read "An Introduction to R" and sections on indexing (?"[") where this is discussed. Have you read about apply type functions there like ?tapply. If not, don't you think you should. If so, read again. Cheers, Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 "Data is

[R] Subsets of a function

Hi all, this is a reoccurring theme in my programming and I need some help with it. When I use a built in function and need to use it on a subset of my data frame, I always end up using the subset function first, but this seems very clunky. For example, if I have years 2003:2013 with season "a" a

Re: [R] solve scalar linear equation

Hello, Try ?uniroot instead. Your equation is equivalent to 5x - 55 = 0, so the instruction would be uniroot(function(x) 5*x - 55, c(0, 20)) Hope this helps, Rui Barradas Em 19-05-2014 14:46, message escreveu: Readers, The function 'solve' states that it is applicable to a vector or matrix

Re: [R] Boxplots

Great, Thanks everyone :-) On Monday, May 19, 2014, Richard M. Heiberger wrote: > tmp <- data.frame(y=c(rnorm(20), rnorm(20), c=rnorm(20)), > g=rep(letters[1:3], each=20)) > > library(lattice) > library(latticeExtra) > A <- bwplot(y ~ g, data=tmp) > B <- bwplot(y ~ rep("Y",60), data=tmp, horizo

[R] R save with encoding...

Hello everybody!! I'm trying to plot a graphic with the title: INTERVALS λ. But the special character λ can't be encoded using ISO8859-1. Which another encoding I need to choose? Att. Alexsandro Cândido de Oliveira Silva ___

Re: [R] converting a matrix to array

Hi, If you meant to convert the matrix to a 3D array, check this link: http://stackoverflow.com/questions/9572656/how-to-convert-matrix-into-array A.K. On Monday, May 19, 2014 2:18 AM, Effat Habibi wrote: Dear Sir/ Madam, I have a problem with converting a matrix (247 rows, 16 columns) t

[R] solve scalar linear equation

Readers, The function 'solve' states that it is applicable to a vector or matrix object. Please what is the syntax to solve a very simple equation like: 5x + 1 = 56 The books read so far give explanations for simultaneous linear equations or differential equations, but there have not been a

Re: [R] substring if value starts with a character

Hi, Try:  dat <- read.table(text="A 1  R5000 2  R4800 3  R4700 4  3500 5  3800",sep="",header=TRUE,stringsAsFactors=FALSE)  dat$A <- as.numeric(gsub("[[:alpha:]]+","",dat$A)) A.K. On Monday, May 19, 2014 9:02 AM, Mat wrote: Hello togehter, i have a litte problem to convert a data.frame. My

Re: [R] Is there an easier way than this to list all functions in the global environment?

Thanks. That's the answer I was looking for. It not only lists the function names by also the arguments required.  I wonder why I was unable to find that command in all the searching I did (?).     - - Byron To: "r-help@r-project.org" Cc: Peter Alspach ;

Re: [R] Is there an easier way than this to list all functions in the global environment?

Thanks. Good suggestion. I completely forgot about the *apply() functions -- a symptom of my R-neophyte status. ;-)  From: Peter Alspach ct.org> Sent: Sunday, May 18, 2014 4:24 PM Subject: RE: [R] Is there an easier way than this to list all functions in

Re: [R] Boxplots

tmp <- data.frame(y=c(rnorm(20), rnorm(20), c=rnorm(20)), g=rep(letters[1:3], each=20)) library(lattice) library(latticeExtra) A <- bwplot(y ~ g, data=tmp) B <- bwplot(y ~ rep("Y",60), data=tmp, horizontal=FALSE) resizePanels(c(Individual=A, "All Together"=B, layout=c(2,1)), w=c(3,1)) ## for ev

Re: [R] Boxplots

> I have boxplots by factors for a dataset and trying to include a boxplot to > represent the entire dataset. Have a look at last the example in ?boxplot which plots a second set of values beside a first set. In your case, specifying xlim larger than needed by one and then using boxplot(x, at=

Re: [R] extract duplications from list

Hi, You may try: myList <- list(structure(list(X = c("FBgn008", "FBgn014", "FBgn028", "FBgn109", "FBgn114", "FBgn120"), NAME = c("FBgn008", "FBgn014", "FBgn028", "FBgn109", "FBgn114", "FBgn120" ), MEM.SHIP = c(0.9304502, 1, 1, 1, 0.4839886, 1)),

Re: [R] How to Optimize two functions together in R

Use defaul values initially, to see if you got reasonable results. See here for the details of nsga2 http://dx.doi.org/10.1109/4235.996017 On 19 May 2014 16:42, Mingxuan Han wrote: > I try to use NSGAII function in the mco but I am kind of confusing about the > numbers of input and output dimensi

Re: [R] How to define and calculate volume of 3D polygon?

On 19/05/2014, 10:42 AM, Alexander Shenkin wrote: Hi Folks, I have a set of x,y,z points in 3D space that defines the outline of a tree crown (5 - 15 perimeter points + 1 top & bottom point). I would like to calculate the volume of the corresponding 3D polygon based on those points. I have been

Re: [R] level for confint (nls)

I believe this has to do with numeric issues in nonlinear fitting and interpolation, and is neither concerned with R programming nor trivial to answer. I therefore suggest you post on the stats.stackexchange.com for a fuller discussion of the issues. Cheers, Bert Bert Gunter Genentech Nonclinical

[R] XML pkg. Namespace message

I am getting messages like: Namespace prefix ccd on el-418bd009-f19a-4107-bc7b-2abb83748bbb is not defined Namespace prefix mlhim244 on interval-type is not defined when retrieving nodesets like this: pct <- getNodeSet(root, '//ccd:el-6acf3ae9-222c-4f71-8120-76375db84177', nsDEF) nsDEF is defin

Re: [R] How to Optimize two functions together in R

I try to use NSGAII function in the mco but I am kind of confusing about the numbers of input and output dimension in the argument. Could you explain a little about this? Thank you. -- View this message in context: http://r.789695.n4.nabble.com/How-to-Optimize-two-functions-together-in-R-tp469

[R] How to define and calculate volume of 3D polygon?

Hi Folks, I have a set of x,y,z points in 3D space that defines the outline of a tree crown (5 - 15 perimeter points + 1 top & bottom point). I would like to calculate the volume of the corresponding 3D polygon based on those points. I have been able to use geometry::convhulln, but I think t

[R] level for confint (nls)

Dear list, I have this nls model and trying to calculate the confidence interval for some parameter. I found if I use the default value level=0.95, confint can calculate a value; when I change the level=0.9, then it return :Error in prof$getProfile() : number of iterations exceeded maximum of 50.

Re: [R] Boxplots

Read the posting guide, which tells you to provide a minimal reproducible example [1] (there it's more than one way to accomplish what you have done already) and post using plain text (so your R code comes through without being corrupted). [1] http://stackoverflow.com/questions/5963269/how-to-

Re: [R] dev-lang/R-3.1.0: biocLite("vsn") removes all files in /

On 05/19/2014 01:09 AM, Henric Winell wrote: On 2014-05-18 20:43, peter dalgaard wrote: On 18 May 2014, at 07:38 , Jeff Newmiller wrote: Then you had best not do it again if you don't like that result. 1) This is not the right mailing list for issues having to do with bioconductor. Please g

[R] Boxplots

Hi, I have boxplots by factors for a dataset and trying to include a boxplot to represent the entire dataset. Any idea how this would be done? Thanks -- Shane [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https:/

[R] K-mean Clustering in URL's

Hi , I have some URL's like :- 2 facebook http://www.facebook.com http://twitter.com/facebook http://en.wikipedia.org/wiki/Facebook http://play.google.com/store/apps/developer

Re: [R] substring if value starts with a character

Hi Mat, Try that: gsub("[A-Za-z]", "", df$A) This is a regular expression that looks for all characters (A to Z and a to z) and replaces it with nothing ("") You will need to convert the column to numeric after this operation. HTH, Ivan -- Ivan Calandra University of Franche-Comté Laboratoir

Re: [R] extract duplications from list

Here is one way of doing it: ## > files <- list(file1 = "XNAME MEM.SHIP + 1 FBgn008 FBgn008 0.9304502 + 2 FBgn014 FBgn014 1.000 + 3 FBgn028 FBgn028 1.000 + 4 FBgn109 FBgn109 1.000 + 5 FBgn114 FBgn114

Re: [R] substring if value starts with a character

Hello, Try the following. dat <- read.table(text = " A 1 R5000 2 R4800 3 R4700 4 3500 5 3800 ", header = TRUE) dat dat2 <- dat dat2[] <- lapply(dat, function(x) sub("^[[:alpha:]]*(.*$)", "\\1", x)) dat2 Hope this helps, Rui Barradas Em 19-05-2014 14:00, Mat escreveu: Hello togehter,

Re: [R] Testing parallel regression assumption

Hello, Take a look at http://stats.stackexchange.com/questions/58772/brant-test-in-r Hope this helps, Rui Barradas Em 19-05-2014 01:40, caoweina escreveu: Dear Rose : I saw your questions about the R function that performs brant test. Have you worked out ? Please give some advice. I n

[R] substring if value starts with a character

Hello togehter, i have a litte problem to convert a data.frame. My data.frame looks like this one A 1 R5000 2 R4800 3 R4700 4 3500 5 3800 I need now a command, which outputs all the numbers, without the character in front. The solution look like this one: A 1 5000 2 4800 3

Re: [R] Second axis on bottom of graph

On Mon, 19 May 2014 05:23:20 AM Hurr wrote: > Thanks again Jim. > Sorry, again I'm enclosing incomplete not-runnable code. > Modified like this it works with the new staxlab function which > I inserted before the second staxlab call. > How long before I don't need to insert it? > I didn't see a way

[R] Spatial Quantile Regression: Extracting residuals

Dear R users, Could anyone tell me if there is a way to obtain the residuals from a model fitted by qregspiv(y ~ x,wmat=wmat,inst=NULL,tau=.5,rhomat = seq(-1,1,.01),printsariv=T,silent=F, nboot=300,data=) in McSpatial, using the Chernozhukov and Hansen (2006) method. Many thanks in advance

[R] extract duplications from list

Hi, I have a list of 40 data.frames. I would like to identify duplicated entries in the whole list, not only in one specific data.frame, but in all 40. Here is my list: > myList [[1]] XNAME MEM.SHIP 1 FBgn008 FBgn008 0.9304502 2 FBgn014 FBgn014 1.000 3 F

Re: [R] Second axis on bottom of graph

Thanks again Jim. Sorry, again I'm enclosing incomplete not-runnable code. Modified like this it works with the new staxlab function which I inserted before the second staxlab call. How long before I don't need to insert it? I didn't see a way to select the specific axis, so I used top.line=5. Is

[R] Course: Introduction to GAM and GAMM with R

We would like to announce the following stats course: Course: Introduction to Generalized Additive Models and Generalized Additive Mixed Effects Models with R Where: Deakin University, Melbourne, Australia When: 25 - 29 August, 2014 URL Flyer: http://www.highstat.com/Courses/Flyer2014_08Deakin

Re: [R] dev-lang/R-3.1.0: biocLite("vsn") removes all files in /

On 2014-05-18 20:43, peter dalgaard wrote: On 18 May 2014, at 07:38 , Jeff Newmiller wrote: Then you had best not do it again if you don't like that result. 1) This is not the right mailing list for issues having to do with bioconductor. Please go to the bioconductor mailing list for that.

[R] could I smooth the geom_line output on ggplot2?

hi, I have got some data and draw a line graph with ggplot2 geom_line. The output seems too sharp to me, is there any way to smooth it? I mean smooth the line, NOT ADDING a smooth line. Or there is other functions in ggplot2 can help me out with a smooth line? Thank you. -- Stand Alone Complex

Re: [R] help with xts

Thanks to all for your ideas and inspirations Il 18/05/2014 18.35, Joshua Ulrich ha scritto: Using subset assignment with an array usually doesn't work well with xts/zoo objects. Your case wouldn't even work with a matrix because you have NA in your array. In this case, you can achieve the sam

Re: [R] filename of current device

On 18/05/2014 18:08, Prof Brian Ripley wrote: > On 14/05/2014 23:04, Andreas Leha wrote: >> Hi all, >> >> how do I find out about the filename, the currently open (let's say pdf) >> device is writing to? >> >> If I find 'dev.cur()' returning 'pdf 3' when I expect 'nulldevice 1' I >> would like to

Re: [R] solution for r-help to the problem of yahoo addresses bouncing?

Hi David, thanks for your reply. On 16.05.2014 23:07, David Winsemius wrote: On May 16, 2014, at 2:25 AM, Jannis wrote: Hi R users, I suspect this is due to yahoo recently changing its handling of DMARC policies. Yes. It is due to ISP bounces coming back to the ETHZ server. You do not sa

Re: [R] converting a matrix to array

On Sun, 18 May 2014 08:18:18 PM Effat Habibi wrote: > Dear Sir/ Madam, > > I have a problem with converting a matrix (247 rows, 16 columns) to an array > in R. > > Would you please help me in this regard. > Hi Effat, "A two-dimensional array is the same thing as a matrix." >From the help page

Re: [R] Second axis on bottom of graph

On Sun, 18 May 2014 11:12:21 PM Hurr wrote: > Thanks Jim, I see you are the author of staxlab. > In the second staxlab I have tried line=3.5 like in axis, and > top.line=3.5, separately, with no apparent effect. > We should have to select the second axis somehow. > Hurr > > You are correct, as I