Displaying 20 results from an estimated 500 matches similar to: "Hmisc: can not reproduce figure 4 of Statistical Tables and Plots using S and LATEX"
2008 Nov 24
1
Discrepancy in the PBC data set
The data set in R is wrong. I've found mistakes on 2 lines in a quick look.
I don't know if the data is incorrect in the Appendix of Fleming and
Harrington as well (someone seems to have borrowed my copy), which is where the
data set appears to have been taken from, given all the "-9" codes in it. (Note,
Tom Fleming originally got the data from me, so I'm fairly
2011 Apr 20
2
survexp with weights
Hello,
I probably have a syntax error in trying to generate an expected
survival curve from a weighted cox model, but I can't see it. I used
the help sample code to generate a weighted model, with the addition
of a "weights=albumin" argument (I only chose albumin because it had
no missing values, not because of any real relevance). Below are my
code with the resulting error
2008 Nov 21
1
Discrepancy in the regression coefficients for Cox regression - PBC data set
Hi,
When I run the following Cox proportional hazards model on the Mayo clinic's
PBC data set (given in the "survival" package), the regression coefficients
do not agree with the results presented in Table 4.6.3 (p. 195) of Fleming &
Harrington's book.
library(survival)
data(pbc)
ans.cox <- coxph(Surv(time, status) ~ log(bili) + log(alb) + age +
log(protime) +
2006 Sep 03
2
Running cox models
Hi,
I'm reading van Belle et al "Biostatistics" and trying to run a cox test using
a dataset from:
http://faculty.washington.edu/~heagerty/Books/Biostatistics/chapter16.html
(Primary Biliary Cirrhosis data link at top of the page),
I'm using the following code:
--------------- start of code
library(survival)
liver <-
2008 Mar 02
0
new to latex to pdf
Dear All,
I'm trying to teach myself latex along with the latex function in Hmisc
and have hit a roadblock that I can't seem to get around. I'd greatly
appreciate any pointers.
I'm running R 2.6.0 on Windows XP and have Miktex 2.7 installed.
I've reproduced the code below, taken from Frank Harrell's latexsummary
introduction. My question relates to getting a pdf
2003 Aug 04
1
coxph and frailty
Hi:
I have a few clarification questions about the elements returned by
the coxph function used in conjuction with a frailty term.
I create the following group variable:
group <- NULL
group[id<50] <- 1
group[id>=50 & id<100] <- 2
group[id>=100 & id<150] <- 3
group[id>=150 & id<200] <- 4
group[id>=200 & id<250] <- 5
group[id>=250
2004 Oct 15
1
categorical varibles in coxph
Hello,
I wonder when I do coxph in R:
coxph( Surv(start, stop, event) ~ x, data=test)
If x is a categorical varible (1,2,3,4,5), should I creat four dummy
varibles for it? if yes, how can I get the overall p value on x other
than for each dummy variable?
Thanks
Lisa Wang
Princess Margaret Hospital
Phone 416 946 4501
2010 Sep 13
0
using survexp and ratetable with coxph object that includes a factor term
Hello,
I'm attempting to use the ratetable argument to
survexp in the survival package. I use
the example from the ?survexp help page below,
and then slightly modify it to produce an error.
library(survival)
data(pbc)
#fit a model without any factors
pfit1 <- coxph(Surv(time, status > 0) ~ trt + log(bili) +
log(protime) + age + platelet, data=pbc)
#this works as expected
2004 Apr 09
2
Regression models w/ splines
Hi - I am fitting various Cox PH models with spline predictors. After
fitting the model, I would like to use termplot() to examine the
functional form of the fitted model (e.g., to obtain a plot of the
relative risk (or log r.r.) versus the predictors).
When there is only 1 predictor in the model, termplot returns a "?".
In this case, I have not been able to figure out how to create
2009 Jul 13
0
pbc data
Hi there,
Can anyone please help me because I am going to get crazy with the pbc data set. I just want to apply simple cox regression in the data set. I am a beginner in R but I don't think I am doing anything wrong.
I have the book of Fleming and Harrington 1990. I perform cox regression by typing:
out<- coxph(Surv(times/365,status)~log(bili)+log(proth)+edema+log(albumin)+age)
out
2012 Apr 29
1
Error in if (nuhat < 2) stop("The degrees of freedom must be greater than or equal to 2") : missing value where TRUE/FALSE needed
Hi,
i am trying to run an ANCOVA and a bootstrapped ANCOVA analysis on a specific data set. I am using the ancova and ancboot functions as in the following code:
setwd("C:/Users/User/Desktop/Rdatabilingualstudy2012")
bilingualismdata<-read.spss("bilingualdataforconferences2012.sav", use.value.labels = TRUE, to.data.frame = TRUE)
2008 Jan 29
2
Direct adjusted survival?
Hello,
I am trying to find an R function to compute 'direct adjusted survival'
with standard errors. A SAS-macro to do this is presented in Zhang X,
Loberiza FR, Klein JP, Zhang MJ. A SAS macro for estimation of direct
adjusted survival curves based on a stratified Cox regression model.
Comput Methods Programs Biomed 2007;88:95-101. It appears that this
method is not implemented in R.
2008 Oct 30
1
[LLVMdev] Using patterns inside patterns
I do not have access to a subtraction routine, as it is considered add
with negation on the second parameter, so I have this pattern:
// integer subtraction
// a - b ==> a + (-b)
def ISUB : Pat<(sub GPRI32:$src0, GPRI32:$src1),
(IADD GPRI32:$src0, (INEGATE GPRI32:$src1))>;
I am attemping to do 64 bit integer shifts and using the following
pattern:
def LSHL :
2010 Dec 02
1
thunderbird crashed-mail_max_userip
thunderbird just crashed, and I've never seen this before. Any idea what
happened?
this was in the dovecot log:
2010-12-02 13:06:40 imap-login: Info: Maximum number of connections from
user+IP exceeded (mail_max_userip_connections): user=<pbc>,
method=PLAIN, rip=127.0.0.1, lip=127.0.0.1, secured
2010-12-02 13:06:40 imap-login: Info: Maximum number of connections from
user+IP exceeded
2008 Feb 15
12
Transfer Crosstable to Word-Document
# Dear list,
# I am an R-beginner and
# spent the last days looking for a method to insert tables produced
# with R into a word document. I thought about SPPS: copy a table from
# an SPO-file and paste it into a word document
# (if needed do some formatting with that table).
# Annother idea was, to produce a TEX-file,
# insert it and make it a word-table.
# I found the following libraries, which
2005 Sep 19
2
Problem with tick marks in lines.survfit (package survival)
I have attempted to follow posting guidelines but I have failed to find out
what I am doing wrong here.
I am trying to use lines.survfit to plot a second curve onto a survival
curve produced by plot.survfit. In my case this is to be a progression free
survival curve superimposed upon an overall survival curve, but I will
illustrate my problem using the example given in the help for
2007 May 17
1
MICE for Cox model
R-helpers:
I have a dataset that has 168 subjects and 12 variables. Some of the
variables have missing data and I want to use the multiple imputation
capabilities of the "mice" package to address the missing data. Given
that mice only supports linear models and generalized linear models (via
the lm.mids and glm.mids functions) and that I need to fit Cox models, I
followed the previous
2011 Jan 06
1
Hmisc, summary.formula and catTest
Dear all,
I?m specifying the fisher.exact test for use with summary.formula as follows:
u<-function(a,b){
j<-fisher.test(a)
p<-list(P=j$p.value,stat=NA,df=NA,testname=j$method,statname="")
return(p)
}
However I?m also required to specify stat & df. However this doesnt apply to the fisher test. I?ve tried specifying them as NA and "" without
2008 Oct 30
0
[LLVMdev] Using patterns inside patterns
I am not sure what you are looking to do. Please provide a mark up
example.
Evan
On Oct 28, 2008, at 11:00 AM, Villmow, Micah wrote:
> Is there currently a way to use a pattern inside of another pattern?
>
> Micah Villmow
> Systems Engineer
> Advanced Technology & Performance
> Advanced Micro Devices Inc.
> 4555 Great America Pkwy,
> Santa Clara, CA. 95054
> P:
2008 Oct 28
4
[LLVMdev] Using patterns inside patterns
Is there currently a way to use a pattern inside of another pattern?
Micah Villmow
Systems Engineer
Advanced Technology & Performance
Advanced Micro Devices Inc.
4555 Great America Pkwy,
Santa Clara, CA. 95054
P: 408-572-6219
F: 408-572-6596
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