[R] Problem of data format using function of tmerger()

We want to perform a survival analysis using time-dependent covariates in the Cox regression. In this analysis, ESRD1_END and ESRD1_TIME are the outcome and follow-up time,respectively. AKI_END is a binary time-dependent variable, while AKI_TIME is the time point for AKI_END measurement. The Cox mo

[R] Fitting problem for Cox model with Strata as interaction term

Dear All, I got a warning message "X matrix deemed to be singular" in Cox model with a time dependent coefficient. In my analysis, the variable "SEX" is a categorical variable which violate the PH assumption in Cox. I first used the survSplit() function to break the data set into different time i

[R] Help with SpaceCAP

Hi there, I am trying to load csv files into the spacecap program in R, but I keep getting either or both of the following error messages: Error - mismatch in animal capture details and trap deployment details files : location id 29 not deployed on SO 22 Error in if (locso[loc, so + 3] == 0)

[R] How to pass a variable to a function which use variable name as a parameter

There are functions which use variable names as parameters in some R packages. However, if the variable name is stored in another variable, how can I pass this variable to the function. Taking the "rms" package as an example: library(rms) n <- 1000 age <- rnorm(n, 50, 10) sex <- factor(sample(c('f

Re: [R] how update to latest version of R on mac

Thanks for your response Tom, now I have successfully upgraded and my affy package problem seems to be is solved with this latest version of R and latest version of Bioconductor. Thanks! /Jane --- Jane Synnergren, PhD

Re: [R] how update to latest version of R on mac

installation. /Jane --- Jane Synnergren, PhD Systems Biology Research Center School of Bioscience University of Skövde Sweden Contact: email: jane.synnerg...@his.se mobile: +46 (0)708 806495 webpage: his.se/synj Postal

[R] how update to latest version of R on mac

le and reliable? I also need a guide of how to update to latest version of bioconductor on mac. Descriptions for windows is available everywhere. /Jane --- ---- Jane Synnergren, PhD Systems Biology Research Center Sch

[R] Cox regression model for matched data with replacement

My problem was how to build a Cox model for the matched data (1:n) with replacement. Usually, we can use stratified Cox regression model when the data were matched without replacement. However, if the data were matched with replacement, due to the re-use of subjects, we should give a weight for eac

Re: [R] Problem Creating Partial Dependence Plot

Hi Jean, I did use a formula and a data frame in creating the rpart model, and the variable names are quite simple. And rpart is definitely supported. Best, Jane On Tue, May 27, 2014 at 5:44 AM, Adams, Jean wrote: > Jane, > > Page 9 of the reference manual, > http://cran.r-pro

[R] Problem Creating Partial Dependence Plot

plotmo is supposed to be able to handle NA's in rpart models. What I might do about this? Thanks, Jane -- ----- Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org “Those who say it cannot be done should not interfere with thos

[R] Restricted Cubic Spline using rms package

I am trying to use restricted cubic spline to examine the association between an independent variable and outcome. When I plot the relationship between HR and the independent variable, I found the HR is not equal to 1 for the specified reference value. For example: dat <- read.table("mydata.csv")

[R] MuMIn Random Effects Variance

according to AIC.  Is there a preferred approach to getting these? I would be grateful for any insights. Stephen Jane __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R

[R] step halving factor reduced below minimum

Hello,   I am attempting to use nlme to model the response of 19 groups.  I am able to get a reasonable fit of all of the groups to the observed data using an exponential decay model (a*exp-x*b).  The problem is that when I plot the fitted values to residuals, it demonstrates a pattern of increa

[R] glht multiple comparisons for glm with 2 factors

Hi All, I have used glm to model my data, I have two factors and a covariate as described in the example code below (mod.1). I have been able to "force" glht to perform multiple comparisons by creating a combined variable for the factors, accepting that there will be a loss of statistical power

[R] How to calculate confidence interval using bootstrap

Dear List, If I build a model based on training set, and calculate the predictive AUC on test set using that model, how should I calculate the 95%CI for this predictive AUC using bootstrap method? The SE should be calculated on training set or test set, or combine them together? I feel confused ab

[R] please remove me from this list

[[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained

Re: [R] Logical inconsistency

Data Center Intermountain Healthcare [EMAIL PROTECTED] 801.408.8111 > -Original Message- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > project.org] On Behalf Of emma jane > Sent: Tuesday, December 09, 2008 7:02 AM > To: Bernardo Rangel Tura; Wacek Kusnierc

Re: [R] Logical inconsistency

uzzled that it only apparently applies to certain elements, as follows: 8.8 - 7.8 > 1 > TRUE 8.3 - 7.3 > 1 > TRUE   However,   10.2 - 9.2 > 1 >FALSE   11.3 - 10.3>1 > FALSE Emma Jane From: Bernardo Rangel Tura <[EMAIL PROTECTED]>

[R] Logical inconsistency

Dear colleagues Please could someone kindly explain the following inconsistencies I've discovered when performing logical calculations in R: 8.8 - 7.8 > 1 > TRUE 8.3 - 7.3 > 1 > TRUE Thank you, Emma Jane [[alternative HTM

[R] mean computation for external data

__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

[R] Mean Computation for Data from External File

__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.