Re: [R] How to calculate confidence interval of C statistic by rcorr.cens

Dear Prof. Harrell, I'm sorry to say this, but I'm afraid I cannot understand what you write very well. Do you mean that the method to calculate confidence intervals for Dxy or C statistics in logistic model penalized for overfitting has not been established yet and what I did is wrong? Could

[R] Help with isolating and comparing data from two files.

Hello, I was hoping that someone would be able to help me or at least point me in the right direction regarding a problem I am having. I am a new R user, and I've been trying to read tutorials but they haven't been much help to me so far. The problem is relatively simple as I've already created w

[R] SNA query

Hi R Users I am working with the very useful SNA package (v.2.2) in R and have a query I hope you may be able to help out with: I have been using gplot commands to plot an SNA graph. Here's the code and output: library(sna); library(network); library(RODBC) setwd("c:\\temp") x = read.csv(fi

Re: [R] Finding solution set of system of linear equations.

Thanks Robert. That all seems to work. I also found the MASS::Null() function that gives the null space for the matrix(transpose) given as argument. I am still trying to appreciate the math behind the Moore-Penrose inverse matrix. If you have any suggestions for understanding how to use R to solve

Re: [R] Convert dataframe with two factors from wide to long format

Just learned another trick today. Thanks a lot to both of you for the kind help! Gang On Sun, May 22, 2011 at 6:04 PM, Dennis Murphy wrote: > Hi: > > library(reshape2) > d1 <- melt(d, id = 'Subj') > d1 <- cbind(d1, colsplit(d1$variable, '_', c('Time', 'Cond'))) > d1 <- transform(d1, >

Re: [R] grep pattern

If you want to only match names of length 6, you will have to use this pattern: > x <- c("ZFHSJK", "ZFHJKZ","ZIOPWE","ZLKJSD","ZKFLPZ", "ZAAZ", "ZAZ", + "ZZAZ", "ZRITEZ") > # match exactly values of length 6 > len6 <- "^Z[[:alpha:]]{4}Z$" > grep(len6, x) [1] 2 5 9 > On Sun, May 22, 2

Re: [R] Convert dataframe with two factors from wide to long format

Hi: library(reshape2) d1 <- melt(d, id = 'Subj') d1 <- cbind(d1, colsplit(d1$variable, '_', c('Time', 'Cond'))) d1 <- transform(d1, Time = substr(Time, 2, 2), Cond = substr(Cond, 5, 5))[c(1, 4, 5, 3)] str(d1) d1 You can decide whether to leave Time and Cond as char

Re: [R] grep pattern

Thanks! On May 21, 7:09 am, David Winsemius wrote: > On May 20, 2011, at 11:57 AM, Kang Min wrote: > > > Hi all, > > > I'm trying to subset a pattern in a vector. Each argument has 6 > > letters, and I need those that start with Z and end with Z. > > > e.g. > > x <- c("ZFHSJK", "ZFHJKZ","ZIOPWE",

Re: [R] Convert dataframe with two factors from wide to long format

On May 22, 2011, at 5:25 PM, Gang Chen wrote: I know how to convert a simple dataframe from wide to long format with one varying factor. However, for a dataset with two factors like the following, Subj T1_Cond1 T1_Cond2 T2_Cond1 T2_Cond2 1 0.125869 4.108232 1.099392 5.556614 2 1.

[R] Convert dataframe with two factors from wide to long format

I know how to convert a simple dataframe from wide to long format with one varying factor. However, for a dataset with two factors like the following, Subj T1_Cond1 T1_Cond2 T2_Cond1 T2_Cond2 1 0.125869 4.108232 1.099392 5.556614 2 1.427940 2.170026 0.120748 1.176353 How to eleg

Re: [R] A better way to do this

Hi: Here are a few options for making this type of plot: # ggplot2 library(ggplot2) ggplot(dd, aes(x = Age.at.Sample.Collection, y = MCP1, group = Subject.ID, colour = Subject.ID, shape = Group)) + geom_point(size = 2.5) + geom_line(size = 0.6) + labs(x = 'Age') ggplot(dd,

[R] tm package, makeChunks

Hi all, i have a question about a makeChunks function from tm package. I have a text with constructed with a SQL qurey consisting of several rows in a table. The texts should be around 1000 lines but is now one long line of text. My question is : Does this matter in makeChunks()

[R] Manipulating rownames for nMDS

I am trying to plot an nMDS plot using ggplot2. My rownames are coded so that they can be broken down by Site, Species, Treatment, or Replicate based on unique separators. There are no column headers. I am having trouble coding ggplot2 to plot by Site -or- Species -or- Treatment and NOT by all u

Re: [R] How to intantiate a list of data.frames?

I will post the whole function, but I believe the problem is in the 3th part. The issue is that oilDF has different number of rows than oilDF2. Thank you, Rui myScan <- function(dirPath, num) { #dirPath is the name of the directory where we want to apply the function. It should be called from

Re: [R] unwanted coercion using apply

On May 22, 2011, at 3:40 PM, David Winsemius wrote: On May 22, 2011, at 2:11 AM, Jeroen Ooms wrote: I need to convert a dataframe to a record-structure, to be able to encode it later in JSON. Suppose this is the data: mydata <- data.frame(foo=1:3, bar=c("M","M","F")); I would like to con

Re: [R] unwanted coercion using apply

On May 22, 2011, at 2:11 AM, Jeroen Ooms wrote: I need to convert a dataframe to a record-structure, to be able to encode it later in JSON. Suppose this is the data: mydata <- data.frame(foo=1:3, bar=c("M","M","F")); I would like to convert this to a unnamed list (json array) of key- value

Re: [R] unwanted coercion using apply

On May 22, 2011, at 3:22 PM, Jeroen Ooms wrote: apply() operates on arrays and a data frame will be coerced to a matrix (which requires all elements to be of the same type). This is documented in ?apply. Thanks, I was not aware of that. I implicitly assumed there would be a specific ap

Re: [R] unwanted coercion using apply

> > apply() operates on arrays and a data frame will be coerced to a matrix > (which requires all elements to be of the same type). This is documented in > ?apply. > Thanks, I was not aware of that. I implicitly assumed there would be a specific apply.data.frame. > This may not be elegant, but

Re: [R] How to calculate confidence interval of C statistic by rcorr.cens

Hi Kohkichi, What we really need to figure out is how to make validate give you confidence intervals for Dxy or C while it is penalizing for overfitting. Some people have ad hoc solutions for that but nothing is nailed down yet. Frank khosoda wrote: > > Thank you for your comment, Prof Harrell.

Re: [R] using predict.lm function

On May 22, 2011, at 12:35 PM, Dave Evens wrote: Dear all, I'm fitting a linear model with numerous lag terms of the response variable [i.e. y(t-1), y(t-2),y(t-3)...,] and other explanatory variables [x(1), x(2), x(3),]- which go into my design matrix X. I'm fitting the linear model:

Re: [R] Adding dash-lines in R tables

On May 22, 2011, at 2:41 PM, David Winsemius wrote: On May 22, 2011, at 2:22 PM, David Hajage wrote: moreover: > library(ascii) Seems strange that the ascii.interger function doesn't set the digits argument to 0: ascii.integer > ascii(as.integer(c(3,4,5))) |= | 3

Re: [R] Adding dash-lines in R tables

On May 22, 2011, at 2:22 PM, David Hajage wrote: moreover: > library(ascii) Seems strange that the ascii.interger function doesn't set the digits argument to 0: > ascii(as.integer(c(3,4,5))) |= | 3.00 | 4.00 | 5.00 |= > ascii(as.integer(c(3,4,5)),

Re: [R] A better way to do this

here is the data set, yes i am doing spagghetti plots for each Subject for MCP1 with respect to the Age.at.Sample.Collection, with a final of all the controls and all the cases Subject.ID sample Group Age.at.Sample.CollectionMCP1 19 00173-0 3455 control11.767282 2

Re: [R] How to intantiate a list of data.frames?

Hi Josh, Sorry, your examples have equal number of rows in both df and df2. In my situation they haven't. Strangely, your solution have worked only when I am copy post the code into the command line. If I use the code inside of a function I get an error at: return(ds) ERROR: arguments imply d

[R] using predict.lm function

Dear all, I'm fitting a linear model with numerous lag terms of the response variable [i.e. y(t-1), y(t-2),y(t-3)...,] and other explanatory variables [x(1), x(2), x(3),]- which go into my design matrix X. I'm fitting the linear model: lm(Y ~ X, ...). I would like to use the predict.lm f

Re: [R] How to intantiate a list of data.frames?

Hi Rui, data frames must have the same number of rows, but two different data frames stored within a list do not need to have the same number of rows. Can you please post the code that is giving the error? Josh On Sun, May 22, 2011 at 9:41 AM, Rui Maximo wrote: > Hi Josh, > > Sorry, your examp

Re: [R] Adding dash-lines in R tables

moreover: > library(ascii) > M <- matrix(letters[1:10], 2) > M [,1] [,2] [,3] [,4] [,5] [1,] "a" "c" "e" "g" "i" [2,] "b" "d" "f" "h" "j" > ascii(M) | | a | c | e | g | i | b | d | f | h | j | > print(ascii(M), "rest") +---+---+---+---+---+ | a |

Re: [R] How to calculate confidence interval of C statistic by rcorr.cens

Thank you for your comment, Prof Harrell. I changed the function; CstatisticCI <- function(x) # x is object of rcorr.cens. { se <- x["S.D."]/2 Low95 <- x["C Index"] - 1.96*se Upper95 <- x["C Index"] + 1.96*se cbind(x["C Index"], Low95, Upper95) } > CstatisticCI(MyModel.lr

Re: [R] maximum likelihood convergence reproducing Anderson Blundell 1982 Econometrica R vs Stata

> From: marchy...@hotmail.com > To: rvarad...@jhmi.edu; pda...@gmail.com; alex.ols...@gmail.com > Date: Sat, 21 May 2011 20:40:44 -0400 > CC: r-help@r-project.org > Subject: Re: [R] maximum likelihood convergence reproducing Anderson Blundell > 1982 Eco

Re: [R] multilevel

I see.. Row1 of Table 2 gives averages for category 3 in the group with a zero in cols 6-8 AND col 2. I wanted to averages for category 3 in the group with a zero in cols 6-8 and a 1 in col 2. I still think its suspicious that cols V1 and V2 in Table 1 are the same. -- View this message in conte

Re: [R] Adding dash-lines in R tables

Axel, you may also be interested in the ascii function (in the ascii package). The ascii version of David's example is library(ascii) #may need install.packages("ascii") first ascii(M) ascii(table(sample(1:10, 100, replace=TRUE))) Best, Ista On Sun, May 22, 2011 at 9:52 AM, David Winsemius wrote

Re: [R] Shrink file size of pdf graphics

Thank you very much for the tip! Using imagemagick i got an image of reasonable quality without making the file size that large. Regards Roman Von: "Philipp Pagel-5 [via R]" Gesendet: 20.05.2011 09:50:42 An: Layman123 Betre

Re: [R] dealing with sweave.sty and pgfSweave

Hi Ravi, There are a couple of ways to do it. See chapter 4 of the MikTeX documentation. Best, Ista PS. List: Is there any reason why Sweave.sty should not be distributed with the major LaTeX distributions (TeXlive, MacTeX, MikTeX)? Every time I add Sweave.sty to my texmf directory I wonder about

Re: [R] How to calculate confidence interval of C statistic by rcorr.cens

S.D. is the standard deviation (standard error) of Dxy. It already includes the effective sample size in its computation so the sqrt(n) terms is not needed. The help file for rcorr.cens has an example where the confidence interval for C is computed. Note that you are making the strong assumption

Re: [R] Adding dash-lines in R tables

On May 22, 2011, at 7:47 AM, Axel Urbiz wrote: is it possible to add dash lines to tables or matrices when they are printed? An example of what I'm looking for is this: library(Design) y <- sample(c(0,1),100, replace = TRUE) x <- rnorm(100) summary(y ~ x) There is a method for summary on for

Re: [R] Plots: I've deleted axes, now to delete space

Hi Adele, it was not my intention to critizise you for posting your question. You are totally free to post whatever question you like and the reciepient is then free to answer it or not. I wanted, however, to demonstrate to you that it would have been easier in my opinion to research some of

Re: [R] multilevel

Thanks for your reply David. I didn't realize I could change the title of my post! Haha. I rather like the example because Table 1 actually appears in Cameron and Trivedi (potential error and all!). aperm is not the issue. I am not sure why you get different output, it should be the case. Other

[R] Adding dash-lines in R tables

is it possible to add dash lines to tables or matrices when they are printed? An example of what I'm looking for is this: library(Design) y <- sample(c(0,1),100, replace = TRUE) x <- rnorm(100) summary(y ~ x) Thanks, Axel. [[alternative HTML version deleted]] ___

Re: [R] Group close numbers in a vector

Hi Jim, I think i sorted it out how to read and write each vector separately. Thanks a lot. It was exactly what i wanted to do. best, salih On Sat, May 21, 2011 at 11:41 PM, jim holtman wrote: > Is this what you are after: > > > x = c(1 ,2 ,4 ,7 ,9 ,10 ,15) > > # partition if the difference is >

Re: [R] unwanted coercion using apply

On 2011-05-21 23:11, Jeroen Ooms wrote: I need to convert a dataframe to a record-structure, to be able to encode it later in JSON. Suppose this is the data: mydata<- data.frame(foo=1:3, bar=c("M","M","F")); I would like to convert this to a unnamed list (json array) of key-value pairs. For exa

[R] How to calculate confidence interval of C statistic by rcorr.cens

Hi, I'm trying to calculate 95% confidence interval of C statistic of logistic regression model using rcorr.cens in rms package. I wrote a brief function for this purpose as the followings; CstatisticCI <- function(x) # x is object of rcorr.cens. { se <- x["S.D."]/sqrt(x["n"]) Low95 <

[R] unwanted coercion using apply

I need to convert a dataframe to a record-structure, to be able to encode it later in JSON. Suppose this is the data: mydata <- data.frame(foo=1:3, bar=c("M","M","F")); I would like to convert this to a unnamed list (json array) of key-value pairs. For example like this: apply(data.frame(foo=1:3

Re: [R] source and localhost

"localhost" is the computer you are working at, and the ip assigned to the loob-back interface. This is normally used for testing networking interfaces. That being so, simply using the path to the file on your machine, e.g. "/home//data/somedata.csv" should work much better. JWD