Hi Love, I have finally had a chance to look at this more closely. I think that the following link:
https://cran.r-project.org/web/packages/survival/vignettes/adjcurve.pdf may be useful. See section 4.2. This is not my area of expertise, but it seems to be a known problem. Perhaps by posting to the: R-SGI-Epi mailing list you will get responses from specialists in the field. Jim On Tue, Feb 1, 2022 at 9:02 PM Love Umesi <yugoh...@gmail.com> wrote: > > I am new in using R, and I need to run a multilevel analysis (two-phase > design on two levels) using Cox frailty survival model on a survey data > (Nigeria Demographic and Health 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/cluster= > v021 individual-level weight= wt1_1 cluster-level weigh= wt2_1 strata/stratum= > v022 > > Please can someone help me with the survey design (svydesign) code and how > to include it and the weights in a model. > > I understand I have to use svycoxph in the model. Please how do I include > survey design and account for the 2 weights (individual-level and > cluster-level weights) in the gamma frailty model below? > > Frailty1 <- coxph (Surv(study_time, died) ~ factor(v024) + factor(mat_edu) > + v025 + frailty(v021,distribution="gamma"), data=rcom2018) > > Really looking forward to your help as my project is hanging on this. > > Many thanks. > > > library(survival)#> Warning: package 'survival' was built under R version > 4.0.5 > library(frailtypack)#> Warning: package 'frailtypack' was built under > R version 4.0.5#> Loading required package: boot#> #> Attaching > package: 'boot'#> The following object is masked from > 'package:survival':#> #> aml#> Loading required package: MASS#> > Loading required package: survC1#> Warning: package 'survC1' was built > under R version 4.0.5#> Loading required package: doBy#> Warning: > package 'doBy' was built under R version 4.0.5#> #> Attaching package: > 'frailtypack'#> The following object is masked from > 'package:survival':#> #> cluster > > > rcom1 <- data.frame( > 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, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, > 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, > 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, > 93, 94, 95, 96, 97, 98, 99, 100 > ), > 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, 53, 5, 28, 13, 37, 0, 23, 33, 27, 36, 20, > 24, 58, 34, 12, 44, 3, 34, 14, 5, 10, 40, 12, 36, 19, 58, 17, > 40, 39, 58, 53, 53, 1, 50, 2, 28, 24, 13, 13, 50, 46, 46, 19, 6, > 32, 59, 9, 30, 30, 43 > ), > 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, 0, 1, 0, 0, 0, 1, 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, 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, 4, 4, 4, 4, 4, 4, 4, > 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, > 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, > 6 > ), > 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", "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", "2", "2", "2", "2", "2", "2", "2", > "2", "2", "2" > ), > 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, 33, 39, 38, 38, 38, 38, 24, 27, > 35, 40, 22, 38, 38, 21, 30, 30, 30, 39, 43, 18, 23, 23, 25, 25, > 30, 45, 26, 26, 35, 35, 35, 35, 32, 32, 40, 25, 27, 30, 30, 30, > 28, 28, 18, 27, 30, 30, 27, 21, 21, 30 > ), > 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, 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, > 631.818176269531, 631.818176269531, 631.818176269531, > 631.818176269531, 631.818176269531, 631.818176269531, 631.818176269531, > 631.818176269531, 631.818176269531, 631.818176269531 > ), > 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, 1.06203985214233, 1.06203985214233, 1.06203985214233, > 1.06203985214233, 1.06203985214233, 1.06203985214233, > 1.06203985214233, 1.06203985214233, 1.06203985214233, 1.06203985214233, > 1.06203985214233, 1.06203985214233, 1.06203985214233, > 1.06203985214233, 1.06203985214233, 1.06203985214233, 1.06203985214233, > 2.80098295211792, 2.80098295211792, 2.80098295211792, > 2.80098295211792, 2.80098295211792, 2.80098295211792, 2.80098295211792, > 2.80098295211792, 2.80098295211792, 2.80098295211792, > 2.80098295211792, 2.80098295211792, 2.80098295211792, 2.80098295211792, > 2.80098295211792, 2.80098295211792, 2.80098295211792, > 2.80098295211792, 2.80098295211792, 2.80098295211792, 2.80098295211792, > 2.80098295211792, 2.80098295211792, 1.24210178852081, > 1.24210178852081, 1.24210178852081, 1.24210178852081, 1.24210178852081, > 1.24210178852081, 1.24210178852081, 1.24210178852081, > 1.24210178852081, 1.24210178852081 > ), > 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", "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", "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", "2", "2", "2", "2", "2", "2", "2", > "2", "2", "2" > ), > 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", "5", "5", "5", "5", "5", "5", "5", "4", "5", > "5", "4", "5", "5", "3", "4", "4", "5", "3", "1", "3", "3", "3", > "1", "3", "2", "1", "3", "3", "4", "4", "0", "0", "2", "2", > "1", "0", "4", "4", "4", "4", "0", "0", "3", "4", "2", "2", "3", > "3", "3", "0" > ) > )) > > [[alternative HTML version deleted]] > > ______________________________________________ > 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