Displaying 9 results from an estimated 9 matches for "platelet".
2011 Apr 20
2
survexp with weights
...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 -0.00360 1.0000
log(bili) 0.985497 2.67...
2007 May 31
0
Using MIcombine for coxph fits
...o help with. I will work through a
reproducible example to demonstrate the issue.
First, make a dataset from the pbc dataset in the survival package
---------------
# Make a dataset
library(survival)
d <- pbc[,c('time','status','age','sex','hepmeg','platelet',
'trt', 'trig')]
d[d==-9] <- NA
d[,c(4,5,7)] <- lapply(d[,c(4,5,7)], FUN=as.factor)
str(d)
summary(d)
---------------
Second, since there is missing data for several (but not all) of the
variables, investigate the patterns.
---------------
library(Hmisc)
na.pattern(d...
2006 Sep 03
2
Running cox models
...hapter16.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,
sex=0,sgot=0,spiders=0,stage=0,status=0,treatmnt=0,
triglyc=0,urinecu=0))
fit<-coxph(Surv(obstime,status)~bili+edmadj+albumin+protime+age,data=liver)
summary(fit)
----------------- End of code
but the answer is rather different from that in the book (p.688 - for
any...
2007 May 17
1
MICE for Cox model
...hat I encounter occurs when I try to use the "pool"
function to pool the fitted models into one general model. Here is some
code that reproduces the error using the pbc dataset.
------------
d <- pbc[,c('time','status','age','sex','hepmeg','platelet', 'trt',
'trig')]
d[d==-9] <- NA
d[,c(4,5,7)] <- lapply(d[,c(4,5,7)], FUN=as.factor)
str(d)
imp <- mice(d, m=10, maxit=10, diagnostics=T, seed=500,
defaultImputationMethod=c('norm', 'logreg', 'polyreg'))
fit <- cox.mids(Surv(time,status)...
2010 Sep 08
1
XML getNodeSet syntax for PUBMED XML export
...ny suggestions?
Thanks in advance.
Prototype text from PUBMED
<MeshHeadingList>
<MeshHeading>
<DescriptorName MajorTopicYN="Y">Antibodies, Monoclonal</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Blood Platelets</DescriptorName>
<QualifierName MajorTopicYN="N">immunology</QualifierName>
<QualifierName MajorTopicYN="Y">physiology</QualifierName>
<QualifierName MajorTopicYN="N">ultrastructure</QualifierName>
</MeshHeading>
</Me...
2010 Sep 13
0
using survexp and ratetable with coxph object that includes a factor term
...t 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) +
log(protime) + age + platelet...
2008 Nov 24
1
Discrepancy in the PBC data set
...,
'ascites', 'hepato', 'spiders', 'edema',
'bili', 'chol', 'albumin', 'copper',
'alk.phos', 'ast', 'trig', 'platelet',
'protime', 'stage'),
na.strings='.')
pbc$age <- pbc$age/365.25
newfit <- coxph(Surv(time, status==2) ~ age + edema + log(bili) +
log(protime) + log(albumin), data=pbc)
newfit
coef exp(coef) se(c...
2015 Jun 19
2
Sobre data.table
Mª Luz,
si el comando de Carlos te devuelve 0 es que no hay NA's.
Da igual que tus columnas sean caracteres o número.
Lo que intuyo es que tienes celdas con la frase "NA" que interpretas como NA.
Mandanos el summary de tu data.table y lo vemos...
----- Mensaje original -----
De: "MªLuz Morales" <mlzmrls en gmail.com>
Para: "Carlos J. Gil Bellosta"
2009 Dec 17
2
some help regarding combining columns from different files
Dear all,
Here is my code which am using to combine 5th column from different data
sets.
Here is the function to do my job
genesymbol.append.file <-NULL
gene.column <- NULL
readGeneSymbol <- function(files,genesymbol.column=5){
for(i in fnames){
temp <- read.table(fnames,header=T,sep="\t",stringsAsFactors=F,quote="\"")