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conf.int values for random effects do not depend on scales argument in tidy() #94

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joelgautschi opened this issue Apr 28, 2020 · 0 comments

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@joelgautschi
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if I use scales = "vcov" to set scales for random effects terms to variances and covariances instead of the default "sd-cor" in broom.mixed::tidy(), the random effects' confidence interval reported remain on the scale "sd-cor" and not the scale of my random effects "vcov"`. Is this a bug or by design?

library(lme4)
library(broom.mixed)
fm1 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)

tidy(fm1,
     effects = "ran_pars",
     conf.int = TRUE,
     conf.method = "profile")
#> Computing profile confidence intervals ...
#> # A tibble: 4 x 6
#>   effect   group    term                  estimate conf.low conf.high
#>   <chr>    <chr>    <chr>                    <dbl>    <dbl>     <dbl>
#> 1 ran_pars Subject  sd__(Intercept)        24.7      14.4      37.7  
#> 2 ran_pars Subject  cor__(Intercept).Days   0.0656   -0.482     0.685
#> 3 ran_pars Subject  sd__Days                5.92      3.80      8.75 
#> 4 ran_pars Residual sd__Observation        25.6      22.9      28.9

# set scales for random effects terms to variances and covariances
tidy(fm1,
     effects = "ran_pars",
     scales = "vcov",
     conf.int = TRUE,
     conf.method = "profile")
#> Computing profile confidence intervals ...
#> # A tibble: 4 x 6
#>   effect   group    term                  estimate conf.low conf.high
#>   <chr>    <chr>    <chr>                    <dbl>    <dbl>     <dbl>
#> 1 ran_pars Subject  var__(Intercept)        612.     14.4      37.7  
#> 2 ran_pars Subject  cov__(Intercept).Days     9.60   -0.482     0.685
#> 3 ran_pars Subject  var__Days                35.1     3.80      8.75 
#> 4 ran_pars Residual var__Observation        655.     22.9      28.9

Created on 2020-04-28 by the reprex package (v0.3.0)

Session info
devtools::session_info()
#> - Session info ---------------------------------------------------------------
#>  setting  value                       
#>  version  R version 3.6.3 (2020-02-29)
#>  os       Windows 10 x64              
#>  system   x86_64, mingw32             
#>  ui       RTerm                       
#>  language (EN)                        
#>  collate  German_Switzerland.1252     
#>  ctype    German_Switzerland.1252     
#>  tz       Europe/Berlin               
#>  date     2020-04-28                  
#> 
#> - Packages -------------------------------------------------------------------
#>  ! package     * version  date       lib source                              
#>    assertthat    0.2.1    2019-03-21 [1] CRAN (R 3.6.3)                      
#>    backports     1.1.6    2020-04-05 [1] CRAN (R 3.6.3)                      
#>    boot          1.3-24   2019-12-20 [1] CRAN (R 3.6.3)                      
#>    broom         0.5.6    2020-04-20 [1] CRAN (R 3.6.3)                      
#>    broom.mixed * 0.2.5    2020-04-28 [1] Github (bbolker/broom.mixed@7b16240)
#>    callr         3.4.3    2020-03-28 [1] CRAN (R 3.6.3)                      
#>    cli           2.0.2    2020-02-28 [1] CRAN (R 3.6.3)                      
#>    coda          0.19-3   2019-07-05 [1] CRAN (R 3.6.3)                      
#>    crayon        1.3.4    2017-09-16 [1] CRAN (R 3.6.3)                      
#>    desc          1.2.0    2018-05-01 [1] CRAN (R 3.6.3)                      
#>    devtools      2.3.0    2020-04-10 [1] CRAN (R 3.6.3)                      
#>    digest        0.6.25   2020-02-23 [1] CRAN (R 3.6.3)                      
#>    dplyr         0.8.5    2020-03-07 [1] CRAN (R 3.6.3)                      
#>    ellipsis      0.3.0    2019-09-20 [1] CRAN (R 3.6.3)                      
#>    evaluate      0.14     2019-05-28 [1] CRAN (R 3.6.3)                      
#>    fansi         0.4.1    2020-01-08 [1] CRAN (R 3.6.3)                      
#>    fs            1.4.1    2020-04-04 [1] CRAN (R 3.6.3)                      
#>    generics      0.0.2    2018-11-29 [1] CRAN (R 3.6.3)                      
#>    glue          1.4.0    2020-04-03 [1] CRAN (R 3.6.3)                      
#>    highr         0.8      2019-03-20 [1] CRAN (R 3.6.3)                      
#>    htmltools     0.4.0    2019-10-04 [1] CRAN (R 3.6.3)                      
#>    knitr         1.28     2020-02-06 [1] CRAN (R 3.6.3)                      
#>    lattice       0.20-41  2020-04-02 [1] CRAN (R 3.6.3)                      
#>    lifecycle     0.2.0    2020-03-06 [1] CRAN (R 3.6.3)                      
#>    lme4        * 1.1-23   2020-04-07 [1] CRAN (R 3.6.3)                      
#>    magrittr      1.5      2014-11-22 [1] CRAN (R 3.6.3)                      
#>    MASS          7.3-51.5 2019-12-20 [1] CRAN (R 3.6.3)                      
#>    Matrix      * 1.2-18   2019-11-27 [1] CRAN (R 3.6.3)                      
#>    memoise       1.1.0    2017-04-21 [1] CRAN (R 3.6.3)                      
#>    minqa         1.2.4    2014-10-09 [1] CRAN (R 3.6.3)                      
#>    nlme          3.1-147  2020-04-13 [1] CRAN (R 3.6.3)                      
#>    nloptr        1.2.2.1  2020-03-11 [1] CRAN (R 3.6.3)                      
#>    pillar        1.4.3    2019-12-20 [1] CRAN (R 3.6.3)                      
#>    pkgbuild      1.0.6    2019-10-09 [1] CRAN (R 3.6.3)                      
#>    pkgconfig     2.0.3    2019-09-22 [1] CRAN (R 3.6.3)                      
#>    pkgload       1.0.2    2018-10-29 [1] CRAN (R 3.6.3)                      
#>    plyr          1.8.6    2020-03-03 [1] CRAN (R 3.6.3)                      
#>    prettyunits   1.1.1    2020-01-24 [1] CRAN (R 3.6.3)                      
#>    processx      3.4.2    2020-02-09 [1] CRAN (R 3.6.3)                      
#>    ps            1.3.2    2020-02-13 [1] CRAN (R 3.6.3)                      
#>    purrr         0.3.4    2020-04-17 [1] CRAN (R 3.6.3)                      
#>    R6            2.4.1    2019-11-12 [1] CRAN (R 3.6.3)                      
#>    Rcpp          1.0.4.6  2020-04-09 [1] CRAN (R 3.6.3)                      
#>    remotes       2.1.1    2020-02-15 [1] CRAN (R 3.6.3)                      
#>    reshape2      1.4.4    2020-04-09 [1] CRAN (R 3.6.3)                      
#>    rlang         0.4.5    2020-03-01 [1] CRAN (R 3.6.3)                      
#>    rmarkdown     2.1      2020-01-20 [1] CRAN (R 3.6.3)                      
#>    rprojroot     1.3-2    2018-01-03 [1] CRAN (R 3.6.3)                      
#>    sessioninfo   1.1.1    2018-11-05 [1] CRAN (R 3.6.3)                      
#>    statmod       1.4.34   2020-02-17 [1] CRAN (R 3.6.3)                      
#>    stringi       1.4.6    2020-02-17 [1] CRAN (R 3.6.2)                      
#>    stringr       1.4.0    2019-02-10 [1] CRAN (R 3.6.3)                      
#>    testthat      2.3.2    2020-03-02 [1] CRAN (R 3.6.3)                      
#>    tibble        3.0.1    2020-04-20 [1] CRAN (R 3.6.3)                      
#>    tidyr         1.0.2    2020-01-24 [1] CRAN (R 3.6.3)                      
#>    tidyselect    1.0.0    2020-01-27 [1] CRAN (R 3.6.3)                      
#>  D TMB           1.7.16   2020-01-15 [1] CRAN (R 3.6.3)                      
#>    usethis       1.6.0    2020-04-09 [1] CRAN (R 3.6.3)                      
#>    utf8          1.1.4    2018-05-24 [1] CRAN (R 3.6.3)                      
#>    vctrs         0.2.4    2020-03-10 [1] CRAN (R 3.6.3)                      
#>    withr         2.2.0    2020-04-20 [1] CRAN (R 3.6.3)                      
#>    xfun          0.13     2020-04-13 [1] CRAN (R 3.6.3)                      
#>    yaml          2.2.1    2020-02-01 [1] CRAN (R 3.6.2)                      
#> 
#> [1] C:/R/R-3.6.3/library
#> 
#>  D -- DLL MD5 mismatch, broken installation.
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