Frailty survival model using survey data

Ugonna · December 21, 2021, 2:11am

Hello,
I need to run a multilevel analysis (on two levels) using Cox frailty survival model on a survey data. My problem is how to write the design weight using the two weights needed and apply them to the analysis.

I have identified the needed variables for the survey design, which are; psu=~v021, level-1 weight=~wt1_1, level-2 weight=~wt2_1 ,strata=~v022.

Please can someone help me with the svydesign code and how to include it and the weights in a model.
For instance, how do I include them in the frailty model below

Thank you for the anticipated help.

williaml · December 21, 2021, 5:48am

Hi, it would make more sense if you could provide a reproducible example of your dataset.

FAQ: How to do a minimal reproducible example ( reprex ) for beginners Guides & FAQs

A minimal reproducible example consists of the following items: A minimal dataset, necessary to reproduce the issue The minimal runnable code necessary to reproduce the issue, which can be run on the given dataset, and including the necessary information on the used packages. Let's quickly go over each one of these with examples: Minimal Dataset (Sample Data) You need to provide a data frame that is small enough to be (reasonably) pasted on a post, but big enough to reproduce your issue. Let's say, as an example, that you are working with the iris data frame head(iris) #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.…

Ugonna · December 21, 2021, 8:25pm

Hi, thanks for your response.
Here is the reproducible example. Hoping I did the right thing.

library(survey)
#> Warning: package 'survey' was built under R version 4.0.5
#> Loading required package: grid
#> Loading required package: Matrix
#> Loading required package: survival
#> Warning: package 'survival' was built under R version 4.0.5
#> 
#> Attaching package: 'survey'
#> The following object is masked from 'package:graphics':
#> 
#>     dotchart
library(survival)


rcom1 <- data.frame(
                         pid = c(1,2,3,4,
                                 5,6,7,8,9,10,11,12,13,14,15,16,17,
                                 18,19,20,21,22,23,24,25,26,27,28,29,
                                 30,31,32,33,34,35,36,37,38,39,40,
                                 41,42,43,44,45,46,47,48,49,50),
                  study_time = c(13,9,17,
                                 31,39,22,24,0,23,12,9,35,18,20,60,
                                 18,5,46,26,54,37,51,31,55,27,15,39,6,
                                 29,0,9,40,23,12,35,56,14,40,57,42,
                                 5,42,39,39,54,19,52,42,7,28),
                        died = c(0,0,0,0,
                                 0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,
                                 0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,
                                 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0),
                        v021 = c(1,1,1,1,
                                 1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,
                                 2,2,2,2,2,2,2,2,2,2,2,2,2,2,3,
                                 3,3,3,3,3,3,3,3,3,3,3,3,3,4,4),
                        v022 = c("1","1",
                                 "1","1","1","1","1","1","1","1","1","1",
                                 "1","1","1","1","1","1","1","1","1",
                                 "1","1","1","1","1","1","1","1","1",
                                 "1","1","1","1","1","1","1","1","1","1",
                                 "1","1","1","1","1","1","1","1","1",
                                 "1"),
                        v012 = c(40,37,27,
                                 27,24,32,35,35,34,20,28,28,26,24,24,
                                 25,26,26,26,26,28,27,25,25,27,26,
                                 26,21,21,31,36,36,27,23,32,32,33,33,
                                 33,28,25,37,33,34,33,28,28,29,33,33),
                       wt2_1 = c(401.200012207031,401.200012207031,401.200012207031,
                                 401.200012207031,401.200012207031,
                                 401.200012207031,401.200012207031,401.200012207031,
                                 401.200012207031,401.200012207031,401.200012207031,
                                 401.200012207031,401.200012207031,
                                 401.200012207031,401.200012207031,401.200012207031,
                                 401.200012207031,401.200012207031,401.200012207031,
                                 401.200012207031,401.200012207031,
                                 401.200012207031,401.200012207031,401.200012207031,
                                 401.200012207031,401.200012207031,
                                 401.200012207031,401.200012207031,401.200012207031,
                                 401.200012207031,401.200012207031,401.200012207031,
                                 401.200012207031,401.200012207031,
                                 401.200012207031,401.200012207031,401.200012207031,
                                 401.200012207031,401.200012207031,
                                 401.200012207031,401.200012207031,401.200012207031,
                                 401.200012207031,401.200012207031,401.200012207031,
                                 401.200012207031,401.200012207031,
                                 401.200012207031,401.200012207031,401.200012207031),
                       wt1_1 = c(2.5074667930603,2.5074667930603,2.5074667930603,
                                 2.5074667930603,2.5074667930603,2.5074667930603,
                                 2.5074667930603,2.5074667930603,2.5074667930603,
                                 2.5074667930603,2.5074667930603,
                                 2.5074667930603,2.5074667930603,2.5074667930603,
                                 2.5074667930603,5.1194109916687,5.1194109916687,
                                 5.1194109916687,5.1194109916687,5.1194109916687,
                                 5.1194109916687,5.1194109916687,
                                 5.1194109916687,5.1194109916687,5.1194109916687,
                                 5.1194109916687,5.1194109916687,5.1194109916687,
                                 5.1194109916687,5.1194109916687,5.1194109916687,
                                 5.1194109916687,5.1194109916687,
                                 5.1194109916687,2.40910983085632,2.40910983085632,
                                 2.40910983085632,2.40910983085632,2.40910983085632,
                                 2.40910983085632,2.40910983085632,
                                 2.40910983085632,2.40910983085632,2.40910983085632,
                                 2.40910983085632,2.40910983085632,2.40910983085632,
                                 2.40910983085632,1.06203985214233,
                                 1.06203985214233),
                        v024 = c("1","1",
                                 "1","1","1","1","1","1","1","1","1","1",
                                 "1","1","1","1","1","1","1","1","1",
                                 "1","1","1","1","1","1","1","1","1",
                                 "1","1","1","1","1","1","1","1","1","1",
                                 "1","1","1","1","1","1","1","1","1",
                                 "1"),
                        v025 = c("1","1",
                                 "1","1","1","1","1","1","1","1","1","1",
                                 "1","1","1","1","1","1","1","1","1",
                                 "1","1","1","1","1","1","1","1","1",
                                 "1","1","1","1","1","1","1","1","1","1",
                                 "1","1","1","1","1","1","1","1","1",
                                 "1"),
                     mat_edu = c("5","5",
                                 "5","4","4","5","4","4","4","4","4","4",
                                 "5","5","5","5","5","5","4","4","5",
                                 "4","4","4","5","3","3","4","4","5",
                                 "5","5","5","4","2","2","0","0","0","5",
                                 "5","0","1","5","5","3","3","5","5",
                                 "5")
                )

Frailty1 <- coxph (Surv(study_time, died) ~ factor(v024) + factor(mat_edu) + v025 + frailty(v021,distribution="gamma"), data=rcom1)
#> Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]): contrasts can be applied only to factors with 2 or more levels

^{Created on 2022-01-07 by the reprex package (v2.0.1)}

williaml · December 22, 2021, 8:07am

Error in unique(x[!is.na(x)]) : object 'psu' not found

What is psu in here:

Model.frailty.gamma <- coxph (Surv(study_time, died) ~ factor(v024) + factor(mat_edu) + v025 + frailty(psu,distribution="gamma"), data=rcom2018)

Cleaner version of your code:

library(survey)
library(survival)

rcom2018 <- data.frame(
  pid = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10),
  study_time = c(13, 9, 17, 31, 39, 22, 24, 0, 23, 12),
  died = c(0, 0, 0, 0, 0, 0, 0, 1, 0, 0),
  v021 = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
  v022 = c("1", "1", "1", "1", "1", "1", "1", "1", "1", "1"),
  wt2_1 = c(401.200012207031,401.200012207031,
            401.200012207031,401.200012207031,401.200012207031,401.200012207031,
            401.200012207031,401.200012207031,401.200012207031,
            401.200012207031),
  wt1_1 = c(2.5074667930603,2.5074667930603,
            2.5074667930603,2.5074667930603,2.5074667930603,2.5074667930603,
            2.5074667930603,2.5074667930603,2.5074667930603,2.5074667930603),
  v024 = c("1", "1", "1", "1", "1", "1", "1", "1", "1", "1"),
  v025 = c("1", "1", "1", "1", "1", "1", "1", "1", "1", "1"),
  mat_edu = c("5", "5", "5", "4", "4", "5", "4", "4", "4", "4")
)

Model.frailty.gamma <- coxph(Surv(study_time, died) ~ factor(v024) + factor(mat_edu) + v025 + frailty(psu, distribution="gamma"), data=rcom2018)

Ugonna · December 22, 2021, 9:03am

I'm sorry about that. PSU is v021

Ugonna · January 2, 2022, 8:32pm

Please can you see if I have done the right thing in terms of bringing in the needed information.
I've corrected the 'psu' error, and extended the data.

I'm still new in R, and don't understand how to fix some of the error messages there.
My challenges are with writing the survey design (svy) code that recognizes the 2 weights, where psu=~v021, level-1 weight=~wt1_1, level-2 weight=~wt2_1 ,strata=~v022, and including them in the frailty model

Thank you

system · January 23, 2022, 8:33pm

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