Displaying 20 results from an estimated 4000 matches similar to: "Partial proportional odds logistic regression"
2007 Jan 06
2
Using VGAM's vglm function for ordinal logistic regression
R-Experts:
I am using the vglm function of the VGAM library to perform proportional
odds ordinal logistic regression. The issue that I would like help with
concerns the format in which the response variable must be provided for
this function to work correctly. Consider the following example:
------
library(VGAM)
library(MASS)
attach(pneumo)
pneumo # Inspect the format of the original dataset
2012 Oct 23
1
Testing proportional odds assumption in R
I want to test whether the proportional odds assumption for an ordered
regression is met.
The UCLA website points out that there is no mathematical way to test the
proportional odds assumption (http://www.ats.ucla.edu/stat//R/dae/ologit.htm),
and use graphical inspection ("We were unable to locate a facility in R to
perform any of the tests commonly used to test the parallel slopes
2008 Feb 01
3
Converting a character string into an object variable
R-helpers:
Assume that I want to create a series of sequentially named R objects. For
example, I might want to call these objects V1, V2, V3 ... V50. To do this,
I thought of some sort of looping function like:
input.value <- seq(1:50) * 3
for(i in 1:50){
paste("V", i, sep="") <- input.value[i]
}
Of course this loop will not work since the paste function
2007 Jul 16
2
Error while fitting Partial Proportional Odds model using vglm
Dear R developers:
I am trying to fit a PPO model using vglm from the library VGAM, and get an
error while executing the code. Here is the data, code, and error:
Data: first row is the column names. a = age, and 1,2,3, 4 and 5 are
condition grades.
a 1 2 3 4 5
1 1 0 0 0 0
2 84 2 7 10 2
3 16 0 6 6 2
4 13 0 3 4 0
5 0 0 0 1 0
Library(VGAM)
2007 Apr 20
3
Opinion on R plots: connecting X and Y
Attention R users, especially those that are experienced enough to be
opinionated, I need your input.
Consider the following simple plot:
x <- rnorm(100)
y <- rnorm(100)
plot(x, y, bty='n')
A colleague (and dreaded SAS user) commented that she thought that my
plots could be "cleaned up" by connecting the X and Y axes. I know that
I can do that with bty='l' but I
2006 Oct 31
3
Missing data analysis in R
I am looking for a book that discusses the theory of multiple imputation
(and other methods of dealing with missing data) and, just as
importantly, how to implement these methods in R or S-Plus. Ideally,
the book would have a structure similar to Faraway (Regression),
Pinheiro&Bates (Mixed Effects) and Wood (GAMs) and would be very modern
(i.e. published within the last couple of years).
2007 Mar 13
1
Freeman-Tukey arcsine transformation
R-Experts:
Does anyone know if there are R functions to perform the Freeman-Tukey
double arcsine transformation and then backtransform it?
Thanks,
Brant Inman
Mayo Clinic
2007 Jan 05
1
Calling "confint.glm" from within another function
On July 12, 2004 Spencer Graves wrote an email describing essentially
the same issue that I would like help on: calling the confint function
from within another homemade function. Because he provided many good
examples of the problem, I will not reproduce them here but will instead
refer readers to the original posting:
http://www.mail-archive.com/r-help at stat.math.ethz.ch/msg23826.html
It is
2006 Nov 03
6
Import problem with S-Plus 7.0 dataset
I am running R 2.3.1 on a Windows XP machine. I am trying to import
some data into R that is stored as an S-Plus 7.0 .sdd file.
When I run the following command, I get this error:
> library(foreign)
> d <- read.S(file='H:\\Research\\data.sdd')
Error in read.S(file = "H:\\Research\\data.sdd") :
not an S object
The dataset is fairly large, roughly 13000 rows
2006 Nov 03
6
Import problem with S-Plus 7.0 dataset
I am running R 2.3.1 on a Windows XP machine. I am trying to import
some data into R that is stored as an S-Plus 7.0 .sdd file.
When I run the following command, I get this error:
> library(foreign)
> d <- read.S(file='H:\\Research\\data.sdd')
Error in read.S(file = "H:\\Research\\data.sdd") :
not an S object
The dataset is fairly large, roughly 13000 rows
2007 Jan 12
7
Making TIFF images with rtiff
Many medical journals and publishers require that images, whether
photographs or line art, be submitted as high resolution .TIFF images.
One option for R users is to produce an image in one format and to
convert it to a .TIFF file using a second software program. My
experience has been that this option often results in images of poorer
quality, often with blurry contours, and a loss of
2010 Nov 17
1
Error: package 'pcvsuite' was built before R 2.10.0: please re-install it
R-helpers,
I have had difficulty installing the "pcvsuite" package on R version 2.12.0 (2010-10-15). The pcvsuite package is not available on CRAN, but is located for download at the following website at the University of Washington:
Windows version
http://labs.fhcrc.org/pepe/dabs/pcvsuite_1.0.zip
Mac version
2008 Jan 21
3
'matrix' returns integer instead of decimal
R-helpers:
I am experiencing some odd behavior with the 'matrix' function that I have
not experienced before and was wondering if there is something that I was
missing in my code.
---------------------------------
> sessionInfo()
R version 2.6.1 (2007-11-26)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
2007 Apr 25
1
prelim.norm() function not working
R-experts:
I am trying to reproduce some of Paul Allison's results in his little
green book on missing data (Sage 2002). The dataset for which I am
having problems, "usnews", can be found at:
http://www.ats.ucla.edu/stat/books/md/default.htm. I am working on a
Windows machine with R 2.5 installed, all packages up-to-date.
The problem has to do with the prelim.norm() function of the
2007 May 02
1
? R 2.5.0 alpha bug
This email is intended to highlight 2 problems that I encountered
running R 2.5.0 alpha on a Windows XP machine.
#1 - Open script error
If I click the "Open folder" icon on the toolbar, R opens my script
files perfectly. However, when I select "File > Open Script >
MyFileLocation", I get a fatal error that causes R to close immediately.
This error was reproduced on 3
2010 Nov 28
1
predict.drm not generating confidence intervals
R-helpers,
I recently submitted a help request for the predict.drm function found in the drc package. I am still having issues with the function and I am submitting reproducible code hoping that somebody can help me figure out what is going on.
--------
library(drc)
# Fit a 4 parameter logistic model to ryegrass dataset
fit <- drm(rootl ~ conc, data = ryegrass, fct = LL.4())
summary(fit)
#
2006 Nov 13
3
Profile confidence intervals and LR chi-square test
System: R 2.3.1 on Windows XP machine.
I am building a logistic regression model for a sample of 100 cases in
dataframe "d", in which there are 3 binary covariates: x1, x2 and x3.
----------------
> summary(d)
y x1 x2 x3
0:54 0:50 0:64 0:78
1:46 1:50 1:36 1:22
> fit <- glm(y ~ x1 + x2 + x3, data=d, family=binomial(link=logit))
>
2007 Apr 20
2
Using power.t.test over a range of conditions
R-Helpers:
I would like to perform sample size calculations for an experiment. As
part of this process, I would like to know how various assumptions
affect the sample size calculation. For instance, one thing that I
would like to know is how the calculated sample size changes as I vary
the difference that I would like to detect. I tried the following
first, but got the associated error
2006 Oct 27
1
Censored Brier Score and Royston/Sauerbrei's D
System: R 2.3.1 on a Windows XP computer.
I am validating several cancer prognostic models that have been
published with a large independent dataset. Some of the models report a
probability of survival at a specified timepoint, usually at 5 and 10
years. Others report only the linear predictor of the Cox model.
I have used Harrell's c index for censored data (rcorr.cens) as a
measure of
2007 Mar 05
3
Mixed effects multinomial regression and meta-analysis
R Experts:
I am conducting a meta-analysis where the effect measures to be pooled
are simple proportions. For example, consider this data from
Fleiss/Levin/Paik's Statistical methods for rates and proportions (2003,
p189) on smokers:
Study N Event P(Event)
1 86 83 0.965
2 93 90 0.968
3 136 129 0.949
4 82 70 0.854
Total