[R] Survey design for multilevel analysis

Jim Lemon drj|m|emon @end|ng |rom gm@||@com
Tue Feb 1 23:19:35 CET 2022


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 <yugohlav using 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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