Re: [R] mgcv: bam(), error in models with random intercepts and random slopes

2016-09-22 Thread Simon Wood
Hi Fotis, Thanks for the report, and sending me the data and code (off list). The problem is triggered by 'ctrial' being a (one column) matrix. An immediate fix is data_a$ctrial <- as.numeric(data_a$ctrial) - mgcv 1.8-16 will catch the problem automatically internally. best, Simon On 20/09

Re: [R] if/else help

2016-09-22 Thread Crombie, Burnette N
Thanks very much for your detailed reply to my post. Very helpful/useful tool(s) you’ve provide me. Best wishes, B. From: William Dunlap [mailto:wdun...@tibco.com] Sent: Wednesday, September 21, 2016 10:48 AM To: Crombie, Burnette N Cc: r-help@r-project.org Subject: Re: [R] if/else help If yo

Re: [R] if/else help

2016-09-22 Thread Crombie, Burnette N
Thank you for your time, Don. Exactly what I was looking for - a one-liner. Feedback from others on this post has been good to expand my knowledge, though. I'm too old for homework but have just started using R if/else, loops, and functions and trying to get the hang of them. Best wishes - B

[R] `head` doesn't show all columns for an empty data.frame

2016-09-22 Thread Colin Phillips
I'm sure I'm doing something wrong, but I'm seeing strange behaviour using the `head` and `tail` functions on an empty data.frame. To reproduce: # create an empty data frame. I actually read an empty table from Excel using `readWorkbook` from package `openxlsx` test <- structure(list(Code = NUL

Re: [R] "invalid argument to unary operator" while selecting rows by name

2016-09-22 Thread Pauline Laïlle
Hi, thanks for the answer. In this case, the row named "601" is not the 601st row of the table, but the 117th. data[601,] actually refers to a non existing row. I was wondering why data[-"601,] generates an error message whereas data["601",] does not? 2016-09-20 19:08 GMT+02:00 Bert Gunter : > Hi

Re: [R] "invalid argument to unary operator" while selecting rows by name

2016-09-22 Thread Pauline Laïlle
Works like a charm, thanks! Still don't know what that error message means though. Any idea? 2016-09-20 20:13 GMT+02:00 : > Sorry, I've made a stupid mistake. > It's obviously the other way around. > > ix <- which(rownames(data) %in% c("601", "604")) > clean <- data[-ix, ] > > > Rui Barradas > >

Re: [R] "invalid argument to unary operator" while selecting rows by name

2016-09-22 Thread Pauline Laïlle
Tanks for all your answers and for taking the time to help me better understand my mistake. I will take your advice and do some reading! Best, P. Le mercredi 21 septembre 2016, William Dunlap a écrit : > The OP cannot be entirely blamed for thinking that x[,-"ColName"] > would omit x's "ColName"

[R] Add annotation text outside of an xyplot (lattice package)

2016-09-22 Thread Jun Shen
Dear list, Just wonder if there is a way to add annotation text outside an xyplot, (e.g. the bottom of the plot). the panel.text seems only add text within the plot. Thanks. Jun [[alternative HTML version deleted]] __ R-help@r-project.org mail

Re: [R] `head` doesn't show all columns for an empty data.frame

2016-09-22 Thread Duncan Murdoch
On 22/09/2016 4:45 AM, Colin Phillips wrote: I'm sure I'm doing something wrong, but I'm seeing strange behaviour using the `head` and `tail` functions on an empty data.frame. To reproduce: # create an empty data frame. I actually read an empty table from Excel using `readWorkbook` from packa

Re: [R] Add annotation text outside of an xyplot (lattice package)

2016-09-22 Thread Carlos Ortega
Hi, Yes, you can use "latticeExtra" package and use a text layer on top of your current chart. Thanks, Carlos Ortega 2016-09-22 16:04 GMT+02:00 Jun Shen : > Dear list, > > Just wonder if there is a way to add annotation text outside an xyplot, > (e.g. the bottom of the plot). the panel.text see

Re: [R] "invalid argument to unary operator" while selecting rows by name

2016-09-22 Thread ruipbarradas
Hello, data["601",] doesn't generate an error because you can also refer to a row by its name, as an alternative to refering to it by row number. It's the same with vectors, just consider the following case. (x <- c("601"=1, b=2)) x[1] x["601"] # the same But when you want to remove it yo

[R] Variable String formation

2016-09-22 Thread Roy Mendelssohn - NOAA Federal
Hi All: I am trying to write code to create a string to be executed as a command. The string will be of the form: "param <- param[,rev(seq_len(dataYLen)),,drop = FALSE]" Now just creating that string is simple enough. Where the problem arises is the array param could be 2, 3, or 4 dimensions

[R] Memory not release when an environment is created

2016-09-22 Thread Olivier Merle
Dear, When I use big data for a temporary use it seems that the memory is not released when a function/environement is created nearby. Here the reproducible exemple: test<-function(){ x=matrix(0,5,1) y=function(nb) nb^2 return(y) } xx=test() # 3 Go of Ram is used gc() # Memory is not rele

Re: [R] Memory not release when an environment is created

2016-09-22 Thread Ismail SEZEN
> On 22 Sep 2016, at 18:41, Olivier Merle wrote: > > Dear, > > When I use big data for a temporary use it seems that the memory is not > released when a function/environement is created nearby. > Here the reproducible exemple: > > test<-function(){ > x=matrix(0,5,1) > y=function(nb) nb

Re: [R] Memory not release when an environment is created

2016-09-22 Thread David Winsemius
> On Sep 22, 2016, at 8:41 AM, Olivier Merle wrote: > > Dear, > > When I use big data for a temporary use it seems that the memory is not > released when a function/environement is created nearby. > Here the reproducible exemple: > > test<-function(){ > x=matrix(0,5,1) > y=function(nb)

Re: [R] Memory not release when an environment is created

2016-09-22 Thread David Winsemius
> On Sep 22, 2016, at 9:45 AM, Ismail SEZEN wrote: > > >> On 22 Sep 2016, at 18:41, Olivier Merle wrote: >> >> Dear, >> >> When I use big data for a temporary use it seems that the memory is not >> released when a function/environement is created nearby. >> Here the reproducible exemple: >>

Re: [R] Variable String formation

2016-09-22 Thread David Winsemius
> On Sep 22, 2016, at 8:01 AM, Roy Mendelssohn - NOAA Federal > wrote: > > Hi All: > > I am trying to write code to create a string to be executed as a command. > The string will be of the form: > > "param <- param[,rev(seq_len(dataYLen)),,drop = FALSE]" > > Now just creating that string i

Re: [R] Memory not release when an environment is created

2016-09-22 Thread William Dunlap via R-help
I like to have my function-returning functions use new.env(parent=XXX) to make an environment for the returned function and put into it only the objects needed by the function. The 'XXX' should be a an environment which will hang around anyway. It could be globalenv(), but if your function is in

Re: [R] Memory not release when an environment is created

2016-09-22 Thread luke-tierney
My preference is to use a top level function in the package or global env that takes as arguments just the variables I want in the parent frame. That avoids the explicit environment manipulations. Here that would be makeFunc0 <- function(xmin, xmax) function(y) (y - xmin) / (xmax - xmin)

Re: [R] Memory not release when an environment is created

2016-09-22 Thread luke-tierney
On Thu, 22 Sep 2016, luke-tier...@uiowa.edu wrote: My preference is to use a top level function in the package or global env that takes as arguments just the variables I want in the parent frame. That avoids the explicit environment manipulations. Here that would be makeFunc0 <- function(xmin,

Re: [R] mgcv: bam(), error in models with random intercepts and random slopes

2016-09-22 Thread Fotis Fotiadis
Dear Professor Wood, Thank you for taking the time to fix the problem. Best, Fotis On Thu, Sep 22, 2016 at 4:25 PM, Simon Wood wrote: > Hi Fotis, > > Thanks for the report, and sending me the data and code (off list). The > problem is triggered by 'ctrial' being a (one column) matrix. An imm

Re: [R] Help with PCA data file prep and R code

2016-09-22 Thread David L Carlson
Looking at your data there are several issues. 1. Tank is an integer, but it sounds like you intend to use it as a categorical measure. If so that it should be a factor, but factors cannot be used in pca. Is Tank 10 10 times more of something than Tank 1? 2. Date is a factor. That means you are

Re: [R] [R-pkg-devel] doc url to vignette

2016-09-22 Thread S Ellison
> In other words, try to mislead CRAN. Well, no. The thought was that if CRAN has agreed an exception, as Uwe had indicated, you might want a simpler way of maintaining it than discussing it on every update. I can see that that would sidestep an enforced regular review, though. Keep up the g

Re: [R] Memory not release when an environment is created

2016-09-22 Thread peter dalgaard
> On 22 Sep 2016, at 21:24 , luke-tier...@uiowa.edu wrote: > > On Thu, 22 Sep 2016, luke-tier...@uiowa.edu wrote: > >> My preference is to use a top level function in the package or global >> env that takes as arguments just the variables I want in the parent >> frame. That avoids the explicit e

[R] Replacing value with "1"

2016-09-22 Thread Saba Sehrish via R-help
Hi I have a matrix that contains 1565 rows and 132 columns. All the observations are either "0" or "1". Now I want to keep all the observations same but just one change, i.e. whenever there is "1", the very next value in the same row should become "1". Please see below as a sample: >df 0

Re: [R] Replacing value with "1"

2016-09-22 Thread Richard M. Heiberger
tmpf <- function(x) { n <- length(x) indices <- which(match(x,1) == 1) x[indices+1] <- 1 x[1:n] ## needed for the case when the last item in a row has value 1 } tmp <- matrix(c(0,0,1,0,0, NA,0,1,1,0, 0,1,0,0,NA, 1,0,1,0,1), ## last item in r

Re: [R] Replacing value with "1"

2016-09-22 Thread Jim Lemon
Hi Saba, Try this: df<-matrix(c(0,NA,0,0,0,1,1,1,0,0,1,0,0,0,NA),nrow=3) dimdf<-dim(df) df1<-df==1 df[cbind(rep(FALSE,dimdf[1]),df1[,-dimdf[2]])]<-1 Jim On Fri, Sep 23, 2016 at 12:27 PM, Saba Sehrish via R-help wrote: > Hi > > I have a matrix that contains 1565 rows and 132 columns. All the o

Re: [R] Replacing value with "1"

2016-09-22 Thread Henrik Bengtsson
which(df == 1, arr.ind=TRUE) is useful here: > df <- matrix(c(0,NA,0,0,0,1,1,1,0,0,1,0,0,0,NA), nrow=3) > df [,1] [,2] [,3] [,4] [,5] [1,]00100 [2,] NA0110 [3,]0100 NA > ## Identify (row,col) indices for 1:s > idxs <- which(df == 1, arr