similar to: Output predictions based on a Cox model

Hi useRs, Many studies of the link between red meat and colorectal cancer use Cox proportional hazards with (among other things) a gender covariate. If it is true that men eat more red meat, drink more alcohol and smoke more than women, and if it is also true that alcohol and tobacco are known risk factors then why does it make sense to "adjust" for gender? I would think that in this

Hi all: I finished cox analysis like this: fit_cox<-coxph(Surv(dat$Time, dat$death) ~ dat$CD4 + strata(dat$gender),data=dat); > fit_cox Call: coxph(formula = Surv(data_ori$Time, data_ori$death) ~ data_ori$drug + strata(data_ori$gender), data = data_ori) coef exp(coef) se(coef) z p data_ori$drugddI 0.216 1.24 0.146 1.47 0.14 Likelihood ratio test=2.17 on

Hello there, when using the function numSummary in Rcmdr and selecting more than one variable (without grouping), the grand mean across all variables is returned for each variable instead of the mean of each single variable. However, this happens only for the mean, and not for sd, quantiles and na. This is the output: > numSummary(dataset1 [,c("var1", "var2")],

Hello. I am attempting to duplicate a negative binomial regression in R. SAS uses generalized estimating equations for model fitting in the GENMOD procedure. proc genmod data=mydata (where=(gender='F')); by agegroup; class id gender type; model count = var1 var2 var3 /dist=NB link=log offset=lregtm; repeated subject=id /type=exch; run; Since my dataset has several observations for

Dear all, I have a table like this: > eds R.ID Region Gender Agegr Time nvisits 1 1 A F 60--64 1:00 1 2 2 O F 55--59 1:20 1 3 3 O F 55--59 3:45 3 4 4 S M 60--64 1:10 3 5 5 W F 55--59 12:30 1 6

Dear R users, Below I have written 4 functions CIT1, CIT2a and CIT2b and CIT3 which recode a variable CLD_ISCH into 3 new variables(T1 T2 T3), I wish to use T1, T2 and T3 based on the values of tf1 and tf2. (NOTE:- T2a is used to create T2 in a long winded manner due to my lack of programming experience) I then attach T1 T2 and T3 to a dataset KidneyT that contains other variables i wish to use

>Hello, I am hoping for assistance in regards to examining the contribution of stratified variables in a cox regression. A previous post by Terry Therneau noted that "That is the point of a strata; you are declaring a variable to NOT be proportional hazards, and thus there is no single "hazard ratio" that describes it". Given this purpose of stratification, in the

Hello all, thanks for your time and patience. I'm looking for a method in R to analyse the following data: Time to waking after anaesthetic for medical procedures repeated on the same individual. > str(mysurv) labelled [1:740, 1:2] 20 20 15 20 30+ 40+ 50 30 15 10 ... - attr(*, "dimnames")=List of 2 ..$ : NULL ..$ : chr [1:2] "time" "status" -

Lets say I have a linear model and I want to find the average expented value of the dependent variable. So let's assume that I'm studying the price I pay for coffee. Price = B0 + B1(weather) + B2(gender) + ... What I'm trying to find is the predicted price for every possible combination of values in the independent variables. So Expected price when: weather=1, gender=male weather=1,

Hi I am estimating the following coxph function with stratification and frailty?where each person had multiple events. m<-coxph(Surv(dtime1,status1)~gender+cage+uplf+strata(enum)+frailty(id),xmodel) ? > head(xmodel) id enum dtime status gender cage uplf 1 1008666 1 2259.1412037 1 MA 0.000 0 2 1008666 2 36.7495023 1 MA 2259.141 0 3 1008666

Dear all, I'm struggling with predicting "expected time until death" for a coxph and survreg model. I have two datasets. Dataset 1 includes a certain number of people for which I know a vector of covariates (age, gender, etc.) and their event times (i.e., I know whether they have died and when if death occurred prior to the end of the observation period). Dataset 2 includes another

Hello, I am hoping for some advice regarding warning/error messages I received when running a Cox regression # message 1 - obtained while creating a plot of residuals > plot (NV.zph, main = "groupNUSM - UNFIT", var= 'groupNUSM') Warning messages: 1: In approx(xx, xtime, seq(min(xx), max(xx), length.out = 17)[2 * : collapsing to unique 'x' values 2: In

Hi. I was wondering if anyone might have some suggestions about how I can overcome a problem of "iteration limit reached without convergence" when fitting a mixed effects model. In this study: Outcome is a measure of heart action Age is continuous (in weeks) Gender is Male or Female (0 or 1) Genotype is Wild type or knockout (0 or 1) Animal is the Animal ID as a factor

Dear R-user, I have a data like this below, age <- c("young","mid","old") married <- c("no","yes") income <- c("low","high","medium") gender <- c("female","male") I want to make some of combination data like these, age.income.dat <- expand.grid(age,

Dear R people, I am having a problem with modeling the following SAS code in R: Class ID Gr Hemi Region Gender Model Y = Gr Region Hemi Gender Gr*Hemi Gr*Region Hemi*Region Gender*Region Gender*Hemi Gr*Hemi*Region Gender*Hemi*Region Gr*Gender*Hemi*Region Random Intercept Region Hemi /Subject = ID (Gr Gender) I.e., ID is a random effect nested in Gr and Gender, leading to ID-specific

Hi everyone, I'm having some difficulty getting "simple effects" for the ols() function in the rms package. The example below illustrates my difficulty -- I'll be grateful for any help. #make up some data exD <- structure(list(Gender = structure(c(1L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 2L), .Label = c("F", "M"), class = "factor"),

dear all, I'm building new dataframes from bigger one's using e.g. columns F76, F83, F90: JJ<-data.frame( c( as.character(rep( gender,3))) , c( F76,6- F83, F90) ) Looking into JJ one has: c.as.character.rep.gender..8... c.6...F73..F78..F79..F82..6...F84..F94..F106..F109 1 w 2 2 w

Hello, I am trying to get the same values for the adjusted means and standard errors using R that are given in SAS for the following data. The model is Measurement ~ Age + Gender + Group. I can get the adusted means at the mean age by using predict. I do not know how to get the appropriate standard errors at the adjusted means for Gender using values from predict. So I attempted to get them

Hi, I've got a microarray dataset (Illumina) coming from a blood assay with a case-control factor of interest. I also have several other covariates (gender, weight, etc...). I know that the experimental design is highly unbalanced with respect to Gender: female male control 12 7 case 7 17 Therefore, if there is a Gender effect, then it really

Dear all, I am using R 3.4.3 on Windows 10. I am preparing some teaching materials and I'm having trouble matching the by-hand version with the R code. I have fitted a Cox model - let's use the ovarian data as an example: library(survival) data(ovarian) ova_mod <- coxph(Surv(futime,fustat)~age+rx,data=ovarian) If I want to make predict survival for a new set of individuals at 100