supporting multiple effect sizes in effectsize::effectsize for htest objects

[IndrajeetPatil]

As mentioned in easystats/parameters#354 (comment), creating a separate issue to see if it will be possible to support multiple effect sizes in effectsize::effectsize for htest objects

[mattansb]

Added type argument to

• htest:
  • chisq.test
  • oneway.test
• BFBayesfactor
  • contingencyTableBF
• aov / anova / aovlist

[mattansb]

Closing this in favor of #211 and #224

[IndrajeetPatil]

I am not sure if either of #211 or #224 cover this, but this is yet to be supported:

library(effectsize)
Ts <- t.test(1:10, y = c(7:20))
effectsize(Ts, type = "g")
#>     d |         95% CI
#> ----------------------
#> -2.32 | [-3.38, -1.22]

^{Created on 2020-12-30 by the reprex package (v0.3.0)}

[mattansb]

Fixed (:

library(effectsize)
Ts <- t.test(1:10, y = c(7:20))
effectsize(Ts, type = "g")
#> Hedge's g |         95% CI
#> --------------------------
#>     -2.12 | [-3.17, -1.15]
#> 
#> - Estimated using un-pooled SD.
#> - Bias corrected using Hedges and Olkin's method.

^{Created on 2020-12-30 by the reprex package (v0.3.0)}

[IndrajeetPatil]

Did something change with effectsize? I can no longer seem to get Hedge's g:

as.data.frame(effectsize::effectsize(
  t.test(extra ~ group, data = sleep),
  type = "cohens_d"
))
#> Warning in effectsize.htest(t.test(extra ~ group, data = sleep), type =
#> "cohens_d"): Unable to retrieve data from htest object. Using t_to_d()
#> approximation.
#>            d   CI    CI_low   CI_high
#> 1 -0.8826937 0.95 -1.844756 0.1018923

as.data.frame(effectsize::effectsize(
  t.test(extra ~ group, data = sleep),
  type = "hedges_g"
))
#> Warning in effectsize.htest(t.test(extra ~ group, data = sleep), type =
#> "hedges_g"): Unable to retrieve data from htest object. Using t_to_d()
#> approximation.
#>            d   CI    CI_low   CI_high
#> 1 -0.8826937 0.95 -1.844756 0.1018923

^{Created on 2021-01-03 by the reprex package (v0.3.0.9001)}

Discovered this while working on easystats/parameters#386.

Session info

sessioninfo::session_info()
#> - Session info ---------------------------------------------------------------
#>  setting  value                                             
#>  version  R Under development (unstable) (2020-12-28 r79717)
#>  os       Windows 10 x64                                    
#>  system   x86_64, mingw32                                   
#>  ui       RTerm                                             
#>  language (EN)                                              
#>  collate  English_United States.1252                        
#>  ctype    English_United States.1252                        
#>  tz       Europe/Berlin                                     
#>  date     2021-01-03                                        
#> 
#> - Packages -------------------------------------------------------------------
#>  package     * version    date       lib source                               
#>  assertthat    0.2.1      2019-03-21 [1] CRAN (R 4.1.0)                       
#>  backports     1.2.1      2020-12-09 [1] CRAN (R 4.1.0)                       
#>  bayestestR    0.8.0.1    2021-01-03 [1] Github (easystats/bayestestR@8b13219)
#>  cli           2.2.0      2020-11-20 [1] CRAN (R 4.1.0)                       
#>  crayon        1.3.4      2017-09-16 [1] CRAN (R 4.1.0)                       
#>  digest        0.6.27     2020-10-24 [1] CRAN (R 4.1.0)                       
#>  effectsize    0.4.1.2    2021-01-03 [1] Github (easystats/effectsize@946f9cb)
#>  ellipsis      0.3.1      2020-05-15 [1] CRAN (R 4.1.0)                       
#>  evaluate      0.14       2019-05-28 [1] CRAN (R 4.1.0)                       
#>  fansi         0.4.1      2020-01-08 [1] CRAN (R 4.1.0)                       
#>  fs            1.5.0      2020-07-31 [1] CRAN (R 4.1.0)                       
#>  glue          1.4.2      2020-08-27 [1] CRAN (R 4.1.0)                       
#>  highr         0.8        2019-03-20 [1] CRAN (R 4.1.0)                       
#>  htmltools     0.5.0      2020-06-16 [1] CRAN (R 4.1.0)                       
#>  insight       0.11.1.1   2021-01-03 [1] Github (easystats/insight@f4749fc)   
#>  knitr         1.30       2020-09-22 [1] CRAN (R 4.1.0)                       
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#>  magrittr      2.0.1      2020-11-17 [1] CRAN (R 4.1.0)                       
#>  parameters    0.10.1.1   2021-01-03 [1] local                                
#>  pillar        1.4.7      2020-11-20 [1] CRAN (R 4.1.0)                       
#>  pkgconfig     2.0.3      2019-09-22 [1] CRAN (R 4.1.0)                       
#>  purrr         0.3.4      2020-04-17 [1] CRAN (R 4.1.0)                       
#>  reprex        0.3.0.9001 2020-08-15 [1] Github (tidyverse/reprex@23a3462)    
#>  rlang         0.4.10     2020-12-30 [1] CRAN (R 4.1.0)                       
#>  rmarkdown     2.6        2020-12-14 [1] CRAN (R 4.1.0)                       
#>  rstudioapi    0.13       2020-11-12 [1] CRAN (R 4.1.0)                       
#>  sessioninfo   1.1.1      2018-11-05 [1] CRAN (R 4.1.0)                       
#>  stringi       1.5.3      2020-09-09 [1] CRAN (R 4.1.0)                       
#>  stringr       1.4.0      2019-02-10 [1] CRAN (R 4.1.0)                       
#>  styler        1.3.2.9000 2021-01-03 [1] Github (r-lib/styler@e1688f5)        
#>  tibble        3.0.4      2020-10-12 [1] CRAN (R 4.1.0)                       
#>  vctrs         0.3.6      2020-12-17 [1] CRAN (R 4.1.0)                       
#>  withr         2.3.0      2020-09-22 [1] CRAN (R 4.1.0)                       
#>  xfun          0.19       2020-10-30 [1] CRAN (R 4.1.0)                       
#>  yaml          2.2.1      2020-02-01 [1] CRAN (R 4.1.0)                       
#> 
#> [1] C:/Users/inp099/Documents/R/win-library/4.1
#> [2] C:/Program Files/R/R-devel/library

[mattansb]

insight::get_data.htest cannot retrieve data from objects with a formula and data = <something>.

# yup
insight::get_data(
  t.test(sleep$extra[sleep$group==1], sleep$extra[sleep$group==2])
)
#>       x    y
#> 1   0.7  1.9
#> 2  -1.6  0.8
#> 3  -0.2  1.1
#> 4  -1.2  0.1
#> 5  -0.1 -0.1
#> 6   3.4  4.4
#> 7   3.7  5.5
#> 8   0.8  1.6
#> 9   0.0  4.6
#> 10  2.0  3.4

# yup
insight::get_data(
  t.test(sleep$extra ~ sleep$group)
)
#>       x y
#> 1   0.7 1
#> 2  -1.6 1
#> 3  -0.2 1
#> 4  -1.2 1
#> 5  -0.1 1
#> 6   3.4 1
#> 7   3.7 1
#> 8   0.8 1
#> 9   0.0 1
#> 10  2.0 1
#> 11  1.9 2
#> 12  0.8 2
#> 13  1.1 2
#> 14  0.1 2
#> 15 -0.1 2
#> 16  4.4 2
#> 17  5.5 2
#> 18  1.6 2
#> 19  4.6 2
#> 20  3.4 2

# nope
insight::get_data(
  t.test(extra ~ group, data = sleep)
)
#> NULL

^{Created on 2021-01-03 by the reprex package (v0.3.0)}

[IndrajeetPatil]

Thanks!

So when data is not found, effectsize::effectsize uses an approximation here:

#> Warning in effectsize.htest(t.test(extra ~ group, data = sleep), type =
#> "hedges_g"): Unable to retrieve data from htest object. Using t_to_d()
#> approximation.

I am wondering if effectsize::effectsize can use a similar trick for computing Cohen's g for McNemar' test when data is not found (easystats/insight#276)?

I see effectsize::chisq_to_cramers_v, but no effectsize::chisq_to_cohens_g, so I am guessing not?

[mattansb]

I see effectsize::chisq_to_cramers_v, but no effectsize::chisq_to_cohens_g, so I am guessing not?

Correct - need the raw data for Cohen's g 🤷‍♂️