Fix tidy_multgee's y.levels (Issue #260)

[jackmwolf]

• Defines y.levels in terms of the first J - 1 levels of the outcome instead of the last J - 1 levels.
• Updates relevant tests

I have ran devtools::test() on this fork and all seems to be working.

Reprex:

library(broom.helpers)
mod <- multgee::nomLORgee(
  y ~ factor(time) * sec,
  data = multgee::housing,
  id = id,
  repeated = time,
)
res <- mod %>% tidy_plus_plus()
#> ℹ multgee model detected.
#> ✔ `tidy_multgee()` used instead.
#> ℹ Add `tidy_fun = broom.helpers::tidy_multgee` to quiet these messages.

# Coefficients are for the 1st and 2nd factor levels (1 and 2) verus the
# reference level (3)
coef(summary(mod))
#>                      Estimate  san.se    san.z Pr(>|san.z|)
#> beta10                1.66073 0.25026  6.63594      0.00000
#> factor(time)6:1      -1.87010 0.31876 -5.86682      0.00000
#> factor(time)12:1     -2.92506 0.36829 -7.94235      0.00000
#> factor(time)24:1     -2.81359 0.34258 -8.21301      0.00000
#> sec:1                -0.53680 0.33704 -1.59271      0.11122
#> factor(time)6:sec:1  -1.18218 0.46036 -2.56797      0.01023
#> factor(time)12:sec:1  0.07916 0.48306  0.16386      0.86984
#> factor(time)24:sec:1  0.03273 0.46558  0.07030      0.94396
#> beta20                1.16643 0.26273  4.43974      0.00001
#> factor(time)6:2      -0.25454 0.30080 -0.84623      0.39742
#> factor(time)12:2     -0.57052 0.31176 -1.83000      0.06725
#> factor(time)24:2     -1.04101 0.30716 -3.38916      0.00070
#> sec:2                -0.10704 0.34759 -0.30796      0.75811
#> factor(time)6:sec:2  -1.62342 0.41349 -3.92613      0.00009
#> factor(time)12:sec:2 -2.04850 0.44543 -4.59898      0.00000
#> factor(time)24:sec:2 -1.04965 0.41831 -2.50925      0.01210

# Expect that values in res$y.level will correspond to the first 2 levels
# of the factor y and the corresponding names from coef(summary(mod))
res$y.level
#>  [1] "1" "1" "1" "1" "1" "1" "1" "1" "2" "2" "2" "2" "2" "2" "2" "2"
levels(factor(multgee::housing$y))
#> [1] "0" "1" "2"

^{Created on 2024-07-24 with reprex v2.1.0}

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 94.96%. Comparing base (b7fe7c7) to head (3e5f5b2).
Report is 2 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #261   +/-   ##
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  Coverage   94.96%   94.96%           
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  Files          43       43           
  Lines        2721     2721           
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  Hits         2584     2584           
  Misses        137      137           

Files	Coverage Δ
R/custom_tidiers.R	84.37% <100.00%> (ø)