method = "auto" not working for ordinal variables #260
Description
I assumed that if I use method = "auto" for ordinal variables I'd get a polychoric correlation, but instead I get the following:
library(correlation)
d <- data.frame(
x = as.ordered(sample(1:5, 20, TRUE)),
y = as.ordered(sample(letters[1:5], 20, TRUE))
)
# Expected
correlation(d, method = "polychoric", include_factors = TRUE)
#> # Correlation Matrix (polychoric-method)
#>
#> Parameter1 | Parameter2 | rho | 95% CI | t(18) | p
#> --------------------------------------------------------------
#> x | y | 0.10 | [-0.36, 0.52] | 0.41 | 0.688
#>
#> p-value adjustment method: Holm (1979)
#> Observations: 20
# Weird output
correlation(d, method = "auto", include_factors = TRUE)
#> 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!
#> 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!
#> 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!
#> 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!
#> 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!
#> 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(18) | p
#> ----------------------------------------------------------------------------
#> x.1 | x.2 | -0.38 | [-0.70, 0.08] | -1.72 | > .999
#> x.1 | x.3 | -0.38 | [-0.70, 0.08] | -1.72 | > .999
#> x.1 | x.4 | -0.38 | [-0.70, 0.08] | -1.72 | > .999
#> x.1 | x.5 | -0.27 | [-0.63, 0.20] | -1.17 | > .999
#> x.1 | y.a | -0.12 | [-0.53, 0.34] | -0.51 | > .999
#> x.1 | y.b | 0.16 | [-0.30, 0.56] | 0.69 | > .999
#> x.1 | y.c | -0.47 | [-0.75, -0.03] | -2.24 | > .999
#> x.1 | y.d | 0.16 | [-0.30, 0.56] | 0.69 | > .999
#> x.1 | y.e | 0.49 | [ 0.06, 0.76] | 2.36 | > .999
#> x.2 | x.3 | -0.29 | [-0.65, 0.18] | -1.26 | > .999
#> x.2 | x.4 | -0.29 | [-0.65, 0.18] | -1.26 | > .999
#> x.2 | x.5 | -0.18 | [-0.57, 0.29] | -0.76 | > .999
#> x.2 | y.a | 0.82 | [ 0.60, 0.93] | 6.15 | < .001***
#> x.2 | y.b | 0.27 | [-0.19, 0.64] | 1.20 | > .999
#> x.2 | y.c | -1.86e-05 | [-0.44, 0.44] | -7.90e-05 | > .999
#> x.2 | y.d | -0.18 | [-0.57, 0.29] | -0.76 | > .999
#> x.2 | y.e | -0.52 | [-0.79, -0.11] | -2.62 | 0.718
#> x.3 | x.4 | -0.29 | [-0.65, 0.18] | -1.26 | > .999
#> x.3 | x.5 | -0.18 | [-0.57, 0.29] | -0.76 | > .999
#> x.3 | y.a | -0.03 | [-0.47, 0.42] | -0.13 | > .999
#> x.3 | y.b | -0.18 | [-0.57, 0.29] | -0.76 | > .999
#> x.3 | y.c | 0.82 | [ 0.59, 0.93] | 6.06 | < .001***
#> x.3 | y.d | -0.18 | [-0.57, 0.29] | -0.76 | > .999
#> x.3 | y.e | -0.20 | [-0.59, 0.27] | -0.86 | > .999
#> x.4 | x.5 | -0.18 | [-0.57, 0.29] | -0.76 | > .999
#> x.4 | y.a | -0.03 | [-0.47, 0.42] | -0.13 | > .999
#> x.4 | y.b | -0.18 | [-0.57, 0.29] | -0.76 | > .999
#> x.4 | y.c | -1.86e-05 | [-0.44, 0.44] | -7.90e-05 | > .999
#> x.4 | y.d | 0.75 | [ 0.46, 0.90] | 4.84 | 0.006**
#> x.4 | y.e | -0.20 | [-0.59, 0.27] | -0.86 | > .999
#> x.5 | y.a | 0.07 | [-0.38, 0.50] | 0.31 | > .999
#> x.5 | y.b | 0.41 | [-0.04, 0.72] | 1.91 | > .999
#> x.5 | y.c | -0.27 | [-0.63, 0.20] | -1.17 | > .999
#> x.5 | y.d | -0.07 | [-0.49, 0.39] | -0.28 | > .999
#> x.5 | y.e | 0.50 | [ 0.07, 0.77] | 2.43 | > .999
#> y.a | y.b | 0.07 | [-0.38, 0.50] | 0.31 | > .999
#> y.a | y.c | -0.12 | [-0.53, 0.34] | -0.51 | > .999
#> y.a | y.d | 0.07 | [-0.38, 0.50] | 0.31 | > .999
#> y.a | y.e | -0.27 | [-0.64, 0.20] | -1.18 | > .999
#> y.b | y.c | -0.27 | [-0.63, 0.20] | -1.17 | > .999
#> y.b | y.d | -0.07 | [-0.49, 0.39] | -0.28 | > .999
#> y.b | y.e | -0.42 | [-0.72, 0.03] | -1.94 | > .999
#> y.c | y.d | -0.27 | [-0.63, 0.20] | -1.17 | > .999
#> y.c | y.e | -0.61 | [-0.83, -0.23] | -3.28 | 0.174
#> y.d | y.e | -0.42 | [-0.72, 0.03] | -1.94 | > .999
#>
#> p-value adjustment method: Holm (1979)
#> Observations: 20Created on 2022-09-09 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 2022-09-09
#> pandoc 2.19 @ /usr/local/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
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#>
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#>
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