Displaying 15 results from an estimated 15 matches for "bili".
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2011 Apr 20
2
survexp with weights
...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 messages. Thanks in advance!
> pfit <- coxph(Surv(time,status>0) ~ trt + log(bili) + log(protime) + age +
+ + platelet, data=pbc
+ )
>
> pfit
Call:
coxph(formula = Surv(time, status > 0) ~ trt + log(bili) +
log(protime) +
age + +platelet, data = pbc)
coef exp(coef) se(coef) z p
trt -0.000624 0.999 0.17304 -0.003...
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
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 <- scan("liver2.txt",list(age=0,albumin=0,alkphos=0,ascites=0,bili=0,
cholest=0,edema=0,edmadj=0,hepmeg=0,obstime=0,platelet=0,protime=0,...
2008 Nov 21
1
Discrepancy in the regression coefficients for Cox regression - PBC data set
...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) + edema)
ans.cox
> ans.cox <- coxph(Surv(time, status) ~ log(bili) + log(alb) + age +
log(protime) + edema)
> ans.cox
Call:
coxph(formula = Surv(time, status) ~ log(bili) + log(alb) + age +
log(protime) + edema)
coef exp(coef) se...
2007 Nov 24
1
Hmisc: can not reproduce figure 4 of Statistical Tables and Plots using S and LATEX
...oduce figure 4 of *Statistical Tables and Plots using S and
LATEX* by Prof. Frank Harrell with the following code:
rm(list=ls())
library(Hmisc)
getHdata(pbc)
attach(pbc)
age.groups <- cut2(age, c(45,60))
g <- function(y) apply(y, 2, quantile, c(.25,.5,.75))
y <- with(pbc, cbind(Chol=chol,Bili=bili))
# You can give new column names that are not legal S names
# by enclosing them in quotes, e.g. 'Chol (mg/dl)'=chol
vars <- with(pbc, c(label(chol), label(bili)))
label(y) <- paste(vars, collapse=' and ') # Will make nice caption in table
s3 <- summary(y ~ age.groups...
2008 Nov 24
1
Discrepancy in the PBC data set
...lt;- read.table(pbcurl, header=F,
col.names=c('id', 'time', 'status', 'trt', 'age', 'sex',
'ascites', 'hepato', 'spiders', 'edema',
'bili', 'chol', 'albumin', 'copper',
'alk.phos', 'ast', 'trig', 'platelet',
'protime', 'stage'),
na.strings='.')
pbc$age <- pbc$age/...
2004 Apr 09
2
Regression models w/ splines
...tors).
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 the
desired plot. Otherwise,termplot is easy to use.
Example:
library(survival)
library(splines)
data(pbc)
fit1<-coxph(Surv(time,status)~ns(bili,4)+ns(age,4), data=pbc)
fit2<-coxph(Surv(time,status)~ns(bili,4), data=pbc)
par(mfrow=c(2,2))
termplot(fit1) # returns two plots (one for bili and one for age)
termplot(fit2) # returns a "?" prompt
Does anyone have any suggestions for obtaining a plot of the log
relative risk as a fu...
2010 Sep 13
0
using survexp and ratetable with coxph object that includes a factor term
...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
survexp(~ trt, ratetable = pfit1, data = pbc)
#now I fit a similar model, simply adding the 'sex' term
#note sex is now the only factor in the model
pfit2 <- coxph(Surv(time, status > 0) ~ trt + log(bili...
2009 Jul 13
0
pbc data
...oing 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
Call:
coxph(formula = Surv(times/365, status) ~ log(bili) + log(proth) +
edema + log(albumin) + age)
coef exp(coef) se(coef) z p
log(bili) 0.8636 2.3716 0.08294 10.41 0.0e+00
log(proth) 2.3868 10.8791 0.76851 ...
2003 Aug 04
1
coxph and frailty
...0] <- 4
group[id>=200 & id<250] <- 5
group[id>=250 & id<300] <- 6
group[id>=300] <- 7
I estimate the following model, using the Pbc data (with time-varying
covariates) from Therneau and Grambsch's book:
fitf <- coxph(Surv(start,stop,event==2) ~ age + log(bili) + log(protime) +
log(albumin) + edema + frailty(group),
na.action=na.exclude, data=Pbcseq)
Then I obtain:
> fitf[10]
$frail
[1] 0.06273372 0.16192093 0.10050877 0.37716999 -0.20853156 -0.71887977
[7] -0.10922275
And:
> fitf[11]
$fvar...
2010 Jun 21
5
when to use e1/t1 card?
This is a really rookie question: when should i use TE110P ISDN PRI Card?
--
Necati DEM?R
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2008 Jan 29
2
Direct adjusted survival?
Hello,
I am trying to find an R function to compute 'direct adjusted survival'
with standard errors. A SAS-macro to do this is presented in Zhang X,
Loberiza FR, Klein JP, Zhang MJ. A SAS macro for estimation of direct
adjusted survival curves based on a stratified Cox regression model.
Comput Methods Programs Biomed 2007;88:95-101. It appears that this
method is not implemented in R.
2008 Mar 02
0
new to latex to pdf
...=times, method='constant', f=0)$y
}
describe.survival <- function(y) {
km <- kmsurv(y, c(2,5))
c('2 Year'=km[1], '5 Year'=km[2], 'Mean, y'=sum(y[,1])/sum(y[,2]))
}
S <- with(pbc, Surv(fu.days/365.25, status))
s1 <- summary(S ~ age + albumin + ascites + bili + drug + edema + chol,
fun=describe.survival, data=pbc)
for(w in 1:2) {
if(w==1) setpdf(f1a,sublines=1,h=5.25) else
setpdf(f1b,sublines=1,h=5)
plot(s1, which=if(w==1)1:2 else 3,
cex.labels=.7, cex.group.labels=.7*1.15, subtitles=T, main='',
pch=if(w==2) 16 else c('2','5'),...
2014 Sep 14
0
Snimanja energetskih fenomena na bosanskim piramidama
...ma i u podzemnim prahistorijskim
tunelima. Betz je autor vi?e knjiga, a njegova posljednja pod nazivom
?Krafte aus dem Nichts ? Geheimnisvolle Orte und ratselhafte Energien?
tretira drevne megalitne lokacije, menhire, dolmene i sveti?ta. Prave?i
komparativnu analizu zaklju?io je da su drevni narodi bili tehnolo?ki i
nau?no mnogo napredniji nego ?to im to dozvoljava konvencionalna nauka.
Nakon mjerenja u Visokom Betz je odr?ao predavanje za stru?ni tim
Fondacije i volontere Pete smjene zaklju?uju?i da postoji prisustvo
elektromagnetnog zra?enja na vrhu Bosanske piramide Sunca frekvencije
28.125 kHz...
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