polyserial correlations not working in correlation()

[shirdekel]

library(correlation)

d <- data.frame(
  x = sample(1:5, 20, TRUE),
  y = as.ordered(sample(letters[1:5], 20, TRUE))
)

# Works

cor_test(d, "x", "y", method = "polychoric")
#> Parameter1 | Parameter2 |  rho |        95% CI | t(18) |     p
#> --------------------------------------------------------------
#> x          |          y | 0.11 | [-0.35, 0.53] |  0.48 | 0.640
#> 
#> Observations: 20

# Doesn't work

correlation(d, method = "polychoric")
#> Warning: It seems like there is not enough continuous variables in your data.
#> Maybe you want to include the factors? We're setting `include_factors=TRUE` for
#> you.
#> Error: No random effects terms specified in formula

^{Created on 2022-09-12 by the reprex package (v2.0.1)}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.2.1 (2022-06-23)
#>  os       macOS Big Sur ... 10.16
#>  system   x86_64, darwin17.0
#>  ui       X11
#>  language (EN)
#>  collate  en_AU.UTF-8
#>  ctype    en_AU.UTF-8
#>  tz       Australia/Sydney
#>  date     2022-09-12
#>  pandoc   2.19 @ /usr/local/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
#>  admisc        0.29    2022-06-20 [1] CRAN (R 4.2.0)
#>  bayestestR    0.12.1  2022-05-02 [1] CRAN (R 4.2.0)
#>  boot          1.3-28  2021-05-03 [1] CRAN (R 4.2.1)
#>  cli           3.3.0   2022-04-25 [1] CRAN (R 4.2.0)
#>  correlation * 0.8.2   2022-08-09 [1] CRAN (R 4.2.0)
#>  datawizard    0.5.1   2022-08-17 [1] CRAN (R 4.2.0)
#>  digest        0.6.29  2021-12-01 [1] CRAN (R 4.2.0)
#>  evaluate      0.16    2022-08-09 [1] CRAN (R 4.2.0)
#>  fansi         1.0.3   2022-03-24 [1] CRAN (R 4.2.0)
#>  fastmap       1.1.0   2021-01-25 [1] CRAN (R 4.2.0)
#>  fs            1.5.2   2021-12-08 [1] CRAN (R 4.2.0)
#>  glue          1.6.2   2022-02-24 [1] CRAN (R 4.2.0)
#>  highr         0.9     2021-04-16 [1] CRAN (R 4.2.0)
#>  htmltools     0.5.3   2022-07-18 [1] CRAN (R 4.2.0)
#>  insight       0.18.2  2022-08-10 [1] CRAN (R 4.2.0)
#>  knitr         1.39    2022-04-26 [1] CRAN (R 4.2.0)
#>  lattice       0.20-45 2021-09-22 [1] CRAN (R 4.2.1)
#>  lifecycle     1.0.1   2021-09-24 [1] CRAN (R 4.2.0)
#>  lme4          1.1-30  2022-07-08 [1] CRAN (R 4.2.0)
#>  magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.2.0)
#>  MASS          7.3-57  2022-04-22 [1] CRAN (R 4.2.1)
#>  Matrix        1.4-1   2022-03-23 [1] CRAN (R 4.2.1)
#>  minqa         1.2.4   2014-10-09 [1] CRAN (R 4.2.0)
#>  mnormt        2.1.0   2022-06-07 [1] CRAN (R 4.2.0)
#>  nlme          3.1-157 2022-03-25 [1] CRAN (R 4.2.1)
#>  nloptr        2.0.3   2022-05-26 [1] CRAN (R 4.2.0)
#>  pillar        1.8.1   2022-08-19 [1] CRAN (R 4.2.0)
#>  pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.2.0)
#>  polycor       0.8-1   2022-01-11 [1] CRAN (R 4.2.0)
#>  psych         2.2.5   2022-05-10 [1] CRAN (R 4.2.0)
#>  purrr         0.3.4   2020-04-17 [1] CRAN (R 4.2.0)
#>  R.cache       0.16.0  2022-07-21 [1] CRAN (R 4.2.0)
#>  R.methodsS3   1.8.2   2022-06-13 [1] CRAN (R 4.2.0)
#>  R.oo          1.25.0  2022-06-12 [1] CRAN (R 4.2.0)
#>  R.utils       2.12.0  2022-06-28 [1] CRAN (R 4.2.0)
#>  Rcpp          1.0.9   2022-07-08 [1] CRAN (R 4.2.0)
#>  reprex        2.0.1   2021-08-05 [1] CRAN (R 4.2.0)
#>  rlang         1.0.4   2022-07-12 [1] CRAN (R 4.2.0)
#>  rmarkdown     2.14    2022-04-25 [1] CRAN (R 4.2.0)
#>  sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.2.0)
#>  stringi       1.7.8   2022-07-11 [1] CRAN (R 4.2.0)
#>  stringr       1.4.0   2019-02-10 [1] CRAN (R 4.2.0)
#>  styler        1.7.0   2022-03-13 [1] CRAN (R 4.2.0)
#>  tibble        3.1.8   2022-07-22 [1] CRAN (R 4.2.0)
#>  utf8          1.2.2   2021-07-24 [1] CRAN (R 4.2.0)
#>  vctrs         0.4.1   2022-04-13 [1] CRAN (R 4.2.0)
#>  withr         2.5.0   2022-03-03 [1] CRAN (R 4.2.0)
#>  xfun          0.31    2022-05-10 [1] CRAN (R 4.2.0)
#>  yaml          2.3.5   2022-02-21 [1] CRAN (R 4.2.0)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

Less important but perhaps related, why do I need to set include_factors=TRUE for correlation() and not for cor_test()?

[briana-new]

Has this issue been addressed? I am also experiencing issues with the polyserial calculation using correlation(). Not sure if it is a me issue or a bug

[mattansb]

This issue has not yet been addressed - a major update to the package is in the works for this coming year (that will also address this issue) and all efforts are going towards that.

[jmgirard]

Would be great to revisit this.

set.seed(2024)

o <-
  sample(
    LETTERS[1:4],
    size = 100,
    replace = TRUE
  ) |>
  factor(
    levels = LETTERS[1:4],
    ordered = TRUE
  )

x <- rnorm(100)

d <- data.frame(o, x)

correlation::correlation(d, include_factors = TRUE, method = "auto")
#> For i = 2 j = 1  A cell entry of 0 was replaced with correct =  0.5.  Check your data!
#> For i = 2 j = 1  A cell entry of 0 was replaced with correct =  0.5.  Check your data!
#> For i = 2 j = 1  A cell entry of 0 was replaced with correct =  0.5.  Check your data!
#> For i = 2 j = 1  A cell entry of 0 was replaced with correct =  0.5.  Check your data!
#> For i = 2 j = 1  A cell entry of 0 was replaced with correct =  0.5.  Check your data!
#> For i = 2 j = 1  A cell entry of 0 was replaced with correct =  0.5.  Check your data!
#> # Correlation Matrix (auto-method)
#> 
#> Parameter1 | Parameter2 |       rho |         95% CI |  t(98) |         p
#> -------------------------------------------------------------------------
#> o.A        |        o.B |     -0.75 | [-0.82, -0.64] | -11.09 | < .001***
#> o.A        |        o.C |     -0.72 | [-0.80, -0.61] | -10.32 | < .001***
#> o.A        |        o.D |     -0.81 | [-0.87, -0.72] | -13.50 | < .001***
#> o.A        |          x |      0.02 | [-0.17,  0.22] |   0.24 | > .999   
#> o.B        |        o.C |     -0.59 | [-0.71, -0.45] |  -7.28 | < .001***
#> o.B        |        o.D |     -0.69 | [-0.78, -0.57] |  -9.41 | < .001***
#> o.B        |          x | -9.54e-03 | [-0.21,  0.19] |  -0.09 | > .999   
#> o.C        |        o.D |     -0.66 | [-0.76, -0.54] |  -8.78 | < .001***
#> o.C        |          x |     -0.01 | [-0.21,  0.18] |  -0.12 | > .999   
#> o.D        |          x | -6.68e-03 | [-0.20,  0.19] |  -0.07 | > .999   
#> 
#> p-value adjustment method: Holm (1979)
#> Observations: 100

polycor::polyserial(x, o)
#> [1] -0.02025863

^{Created on 2024-08-15 with reprex v2.1.1}