Displaying 20 results from an estimated 4000 matches similar to: "coxph models for insects"
2007 Oct 08
0
coxph() command design and data setup
Hello all:
I'm attempting to run a Cox proportional hazards function on survival data
from insects and I have a few questions.
My current command that I'm using to call the model is as follows (using
coxph() from the survival library):
coxph(Surv(day, censor) ~ treatment + room + chamber %in% treatment, data =
data.table)
Day indicates which day a particular observation occurred, and
2013 Jun 25
1
censor=FALSE and id options in survfit.coxph
Terry,
I recently noticed the censor argument of survfit. For some analyses it greatly reduces the size of the resulting object, which is a nice feature.
However, when combined with the id argument, only 1 prediction is made. Predictions can be made individually but I'd prefer to do them all at once if that change can be made.
Chris
#####################################
# CODE
# create
2011 Jun 16
0
coxph: cumulative mortality hazard over time with associated confidence intervals
Dear R-users,
I computed a simple coxph model and plotted survival over time with
associated confidence intervals for 2 covariate levels (males and
females).
M1 <- coxph(survobject~sex, data=surv)
M1
survsex <- survfit(survobject~sex,data=surv)
summary(survsex)
plot(survsex, conf.int=T, col=c("black","red"), lty = c(1,2),
lwd=c(1,2), xlab="Time",
2009 Sep 26
1
Multiple comparisons for coxph survival analysis model
Hello, all R-users!
I am working on fitting a survival analysis model using the coxph
function for Cox proportional hazards regression model. Data look like
usual:
==========================
group block death censor
Group1 1 4 1
Group1 1 12 1
...
Group2 30 4 1
Group2 30 4 1
...
Group3 57 16
2010 Feb 05
1
Using coxph with Gompertz-distributed survival data.
Dear list:
I am attempting to use what I thought would be a pretty straightforward practical application of Cox regression. I figure users of the survival package must have come across this problem before, so I would like to ask you how you dealt with it. I have set up an illustrative example and included it at the end of this post.
I took a sample of 100 data points from each of two populations
2008 Apr 29
0
Looking for Post-hoc tests (a la TukeyHSD) or interaction-level independent contrasts for survival analysis.
Hello all R-helpers,
I've performed an experiment to test for differential effects of
elevated temperatures on three different groups of corals. I'm
currently performing a cox proportional hazards regression with
censoring on the survivorship (days to mortality) of each individual
in the experiment with two factors: Temperature Treatment (2 levels:
ambient and elevated) and
2004 Apr 21
1
difference between coxph and cph
Hi. I am using Windows version of R 1.8.1. Being somewhat new to survival
analysis, I am trying to compare cph (Design) with coxph (survival) for use
with a survival data set.
I was wondering why cph and coxph provide me with different confidence
intervals
for the hazard ratios for one of the variables. I was wondering if I am
doing something wrong? Or if the two functions are calculating hazard
2007 Mar 14
0
Wald test and frailty models in coxph
Dear R members,
I am new in using frailty models in survival analyses and am getting
some contrasting results when I compare the Wald and likelihood ratio
tests provided by the r output.
I am testing the survivorship of different sunflower interspecific
crosses using cytoplasm (Cyt), Pollen and the interaction Cyt*Pollen
as fixed effects, and sub-block as a random effect. I stratified
2005 Sep 07
1
Survival analysis with COXPH
Dear all,
I would have some questions on the coxph function for survival analysis,
which I use with frailty terms.
My model is:
mdcox<-coxph(Surv(time,censor)~ gender + age + frailty(area, dist='gauss'),
data)
I have a very large proportion of censored observations.
- If I understand correctly, the function mdcox$frail will return the random
effect estimated for each group on the
2012 Feb 23
1
Schoenfeld residuals for a null model coxph
Hi,
I have a coxph model like
coxph(Surv(start, stop, censor) ~ x + y, mydata)
I would like to calculate the Schoenfeld residuals for the null, i.e the same model where the beta hat vector (in practical terms, the coeff vector spat out by summary()) is constrained to be all 0s --all lese stays the same.
I could calculate it by hand, but I was wondering if there is a way of doing it with
2009 Mar 25
2
Competing risks Kalbfleisch & Prentice method
Dear R users
I would like to calculate the Cumulative incidence for an event
adjusting for competing risks and adjusting for covariates. One way to
do this in R is to use the cmprsk package, function crr. This uses the
Fine & Gray regression model. However, a simpler and more classical
approach would be to implement the Kalbfleisch & Prentice method (1980,
p 169), where one fits cause
2003 Jun 16
0
new package: eha
A few days ago I uploaded to CRAN a new package called 'eha', which
stands for 'Event History Analysis'. Its main focus is on proportional
hazards modeling in survival analysis, and in that respect eha can
be regarded as a complement and an extension to the 'survival'
package. In fact eha requires survival. Eha contains three functions
for proportional hazards
2003 Jun 16
0
new package: eha
A few days ago I uploaded to CRAN a new package called 'eha', which
stands for 'Event History Analysis'. Its main focus is on proportional
hazards modeling in survival analysis, and in that respect eha can
be regarded as a complement and an extension to the 'survival'
package. In fact eha requires survival. Eha contains three functions
for proportional hazards
2006 May 07
1
model selection, stepAIC(), and coxph() (fwd)
Hello,
My question concerns model selection, stepAIC(), add1(), and coxph().
In Venables and Ripley (3rd Ed) pp389-390 there is an example of using
stepAIC() for the automated selection of a coxph model for VA lung cancer
data.
A statistics question: Can partial likelihoods be interpreted in the same
manner as likelihoods with respect to information based criterion and
likelihood ratio tests?
2007 Oct 01
3
Apparently Conflicting Results with coxph
Dear List:
I have a data frame prepared in the couting process style for including
a binary time-dependent covariate. The first few rows look like this.
PtNo Start End Status Imp
1 1 0 608.0 0 0
2 2 0 513.0 0 0
3 2 513 887.0 0 1
4 3 0 57.0 0 0
5 3 57 604.0 0 1
6 4 0 150.0 1 0
The outcome
2007 Dec 06
0
coxme() random effect syntax
Hello:
I would like to run a Cox proportional hazards regression on crayfish
dislodgement at different water velocities by crayfish size class and
substrate (rock) type. Additionally, there is a covariate variable, rock
movement that may be influencing crayfish dislodgment. So...
I have crayfish size class (CFSZCL) and substrate type (SUBSZ) as fixed
factors influencing the dislodgment of
2011 Jun 09
0
Help on survival analysis
Hi,
I need a help in a survival analysis using survreg function with weibull
distribution from survival package.
Look the data sample:
########## Start of script
dados <- structure(list(TFD = c(20L, 34L, 1L, 2L, 3L, 3L, 50L, 26L, 1L,
50L, 21L, 3L, 13L, 11L, 22L, 50L, 50L, 1L, 50L, 9L, 50L, 1L,
13L, 50L, 50L, 1L, 6L, 50L, 50L, 50L, 36L, 3L, 46L, 10L, 50L,
1L, 18L, 3L, 36L, 37L, 50L, 7L, 1L,
2003 Oct 27
1
Bioassays Yielding concentration-Mortality data
Dear all,
I'm trying reproduce an example of bioassays Yielding Concentration-Mortality Data particularly control - adjustment model from book Bioassay of Entomopathogenic Microbes and Nematodes chapter 7 with R.
I used glm with family=binomial and link=probit, but I do not know how to implement parameter gamma (control mortality - mortality of the untreated control insect in this exaple)
2008 Mar 13
1
How to set type of censored data in coxph regression
Dear R users,
I tried to analysis the hazard function of some data by coxph function
in survival package.
The type of the data include "left-censored", "right-censored", "both
right-censored and
left-censored" (btw, does this has a technical term?), and "complete" ones.
I noticed that event (one parameter in "Surv()") might be an indicator
for the
2006 Oct 06
0
Bivariate Weibull distribution -- Copula
"Jenny Stadt" <jennystadt at yahoo.ca> asked:
>
> I am struggling in a bivariate Weibull distribution although I
> searched R-Site-Help and found suggestion with Copula. Seems the
> maximum likelihood estimate is beyond what I can understand.
>
> My case is: given two known marginal distribution (both are Weibull),
> and the correlation between them. How can I