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Added ci = FALSE to svyquantile function#88

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Added ci = FALSE to svyquantile function#88
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@chipmanj

@chipmanj chipmanj commented Jan 21, 2022

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Hi Kazuki,

I too came across issue #83. As noted by, @docvock, the source of the problem is that survey updated the default output of the svyquantile function. Here's further elaboration:

The previous default input for svyquantile was ci=FALSE. Now it is ci=TRUE.

survey(version 4.0): https://www.rdocumentation.org/packages/survey/versions/4.0/topics/svyquantile
survey(version 4.1): https://rdrr.io/cran/survey/man/svyquantile.html

Under survey (v4.1), svyQuant (within tableone) returns a quantile, 95% ci, and standard error (a numeric vector of size 4) for each variable. Previously, svyQuant only returned a quantile (singleton) for each variable.

As a downstream effect, the error regarding rounding occurs when updating the class of the result object (created within svyCreateContTable). I was not able to track down why this particular error occurred. However, the proposed pull request resolves the original problem by setting ci = FALSE when calling svyquantile (within tableone::svyQuant).

I tested the updates using the NHANES example within ?svyCreateTableOne.

I hope you are well and best wishes,

Jonathan Chipman

@kaz-yos

kaz-yos commented Feb 3, 2022

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Thanks for tracking this down! I'm investigating the R-CMD-check issue with ubuntu devel.

@chipmanj

chipmanj commented Feb 4, 2022

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You're welcome!!!

@kaz-yos

kaz-yos commented Feb 24, 2022

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TODO: Figure out the following error:

Run options(crayon.enabled = TRUE)
[2](https://github.com/kaz-yos/tableone/runs/5058870960?check_suite_focus=true#step:9:2)
  options(crayon.enabled = TRUE)
[3](https://github.com/kaz-yos/tableone/runs/5058870960?check_suite_focus=true#step:9:3)
  rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
[4](https://github.com/kaz-yos/tableone/runs/5058870960?check_suite_focus=true#step:9:4)
  shell: /usr/local/bin/Rscript {0}
[5](https://github.com/kaz-yos/tableone/runs/5058870960?check_suite_focus=true#step:9:5)
  env:
[6](https://github.com/kaz-yos/tableone/runs/5058870960?check_suite_focus=true#step:9:6)
    R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
[7](https://github.com/kaz-yos/tableone/runs/5058870960?check_suite_focus=true#step:9:7)
    RSPM: https://packagemanager.rstudio.com/cran/__linux__/focal/latest
[8](https://github.com/kaz-yos/tableone/runs/5058870960?check_suite_focus=true#step:9:8)
    GITHUB_PAT: ***
[9](https://github.com/kaz-yos/tableone/runs/5058870960?check_suite_focus=true#step:9:9)
    R_LIBS_USER: /home/runner/work/_temp/Library
[10](https://github.com/kaz-yos/tableone/runs/5058870960?check_suite_focus=true#step:9:10)
    TZ: UTC
[11](https://github.com/kaz-yos/tableone/runs/5058870960?check_suite_focus=true#step:9:11)
    _R_CHECK_SYSTEM_CLOCK_: FALSE
[12](https://github.com/kaz-yos/tableone/runs/5058870960?check_suite_focus=true#step:9:12)
    NOT_CRAN: true
[13](https://github.com/kaz-yos/tableone/runs/5058870960?check_suite_focus=true#step:9:13)
    _R_CHECK_CRAN_INCOMING_REMOTE_: false
[14](https://github.com/kaz-yos/tableone/runs/5058870960?check_suite_focus=true#step:9:14)
Error: Error in loadNamespace(x) : there is no package called ‘rcmdcheck’
[15](https://github.com/kaz-yos/tableone/runs/5058870960?check_suite_focus=true#step:9:15)
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
[16](https://github.com/kaz-yos/tableone/runs/5058870960?check_suite_focus=true#step:9:16)
Execution halted
[17](https://github.com/kaz-yos/tableone/runs/5058870960?check_suite_focus=true#step:9:17)
Error: Process completed with exit code 1.

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@chipmanj @kaz-yos