Awareness of contrasts for ordered factors

[wlandau]

When AVISIT is an ordered factor and I manually set contrasts, my custom contrasts seem to be ignored:

library(mmrm)
packageVersion("mmrm")
#> [1] '0.3.12.9000'
packageDescription("mmrm")$GithubSHA1
#> [1] "b06da426f04eb6bb4edbc17a9159c89020030fca"
data("fev_data", package = "mmrm")
fev_data$AVISIT <- ordered(fev_data$AVISIT)
contrasts(fev_data$AVISIT) <- contr.treatment(n = 4)
coef(lm(FEV1 ~ AVISIT, data = fev_data))
#> (Intercept)     AVISIT2     AVISIT3     AVISIT4 
#>   34.605646    5.159606   10.237350   15.572446
coef(mmrm(FEV1 ~ AVISIT + us(AVISIT | USUBJID), data = fev_data))
#> (Intercept)    AVISIT.L    AVISIT.Q    AVISIT.C 
#>  42.3854364  11.5452671   0.5005517   0.1479297

^{Created on 2024-07-09 with reprex v2.1.0}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.4.0 (2024-04-24)
#>  os       macOS Sonoma 14.5
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/Indiana/Indianapolis
#>  date     2024-07-09
#>  pandoc   3.1.11 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version     date (UTC) lib source
#>  backports     1.4.1       2021-12-13 [1] CRAN (R 4.4.0)
#>  checkmate     2.3.1       2023-12-04 [1] CRAN (R 4.4.0)
#>  cli           3.6.2       2023-12-11 [1] CRAN (R 4.4.0)
#>  digest        0.6.35      2024-03-11 [1] CRAN (R 4.4.0)
#>  evaluate      0.23        2023-11-01 [1] CRAN (R 4.4.0)
#>  fansi         1.0.6       2023-12-08 [1] CRAN (R 4.4.0)
#>  fastmap       1.2.0       2024-05-15 [1] CRAN (R 4.4.0)
#>  fs            1.6.4       2024-04-25 [1] CRAN (R 4.4.0)
#>  generics      0.1.3       2022-07-05 [1] CRAN (R 4.4.0)
#>  glue          1.7.0       2024-01-09 [1] CRAN (R 4.4.0)
#>  htmltools     0.5.8.1     2024-04-04 [1] CRAN (R 4.4.0)
#>  knitr         1.46        2024-04-06 [1] CRAN (R 4.4.0)
#>  lattice       0.22-6      2024-03-20 [1] CRAN (R 4.4.0)
#>  lifecycle     1.0.4       2023-11-07 [1] CRAN (R 4.4.0)
#>  magrittr      2.0.3       2022-03-30 [1] CRAN (R 4.4.0)
#>  Matrix        1.7-0       2024-03-22 [1] CRAN (R 4.4.0)
#>  mmrm        * 0.3.12.9000 2024-07-09 [1] Github (openpharma/mmrm@b06da42)
#>  nlme          3.1-164     2023-11-27 [1] CRAN (R 4.4.0)
#>  pillar        1.9.0       2023-03-22 [1] CRAN (R 4.4.0)
#>  pkgconfig     2.0.3       2019-09-22 [1] CRAN (R 4.4.0)
#>  purrr         1.0.2       2023-08-10 [1] CRAN (R 4.4.0)
#>  R.cache       0.16.0      2022-07-21 [1] CRAN (R 4.4.0)
#>  R.methodsS3   1.8.2       2022-06-13 [1] CRAN (R 4.4.0)
#>  R.oo          1.26.0      2024-01-24 [1] CRAN (R 4.4.0)
#>  R.utils       2.12.3      2023-11-18 [1] CRAN (R 4.4.0)
#>  rbibutils     2.2.16      2023-10-25 [1] CRAN (R 4.4.0)
#>  Rcpp          1.0.12      2024-01-09 [1] CRAN (R 4.4.0)
#>  Rdpack        2.6         2023-11-08 [1] CRAN (R 4.4.0)
#>  reprex        2.1.0       2024-01-11 [1] CRAN (R 4.4.0)
#>  rlang         1.1.4       2024-06-04 [1] CRAN (R 4.4.0)
#>  rmarkdown     2.26        2024-03-05 [1] CRAN (R 4.4.0)
#>  rstudioapi    0.16.0      2024-03-24 [1] CRAN (R 4.4.0)
#>  sessioninfo   1.2.2       2021-12-06 [1] CRAN (R 4.4.0)
#>  stringi       1.8.4       2024-05-06 [1] CRAN (R 4.4.0)
#>  stringr       1.5.1       2023-11-14 [1] CRAN (R 4.4.0)
#>  styler        1.10.3      2024-04-07 [1] CRAN (R 4.4.0)
#>  tibble        3.2.1       2023-03-20 [1] CRAN (R 4.4.0)
#>  TMB           1.9.14      2024-07-03 [1] CRAN (R 4.4.0)
#>  utf8          1.2.4       2023-10-22 [1] CRAN (R 4.4.0)
#>  vctrs         0.6.5       2023-12-01 [1] CRAN (R 4.4.0)
#>  withr         3.0.0       2024-01-16 [1] CRAN (R 4.4.0)
#>  xfun          0.43        2024-03-25 [1] CRAN (R 4.4.0)
#>  yaml          2.3.8       2023-12-11 [1] CRAN (R 4.4.0)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

I would like to handle time as an ordered factor because the ordering of the levels is important for ARMA correlation structures. Unfortunately, R uses contr.poly() on ordered factors by default, which is usually counterintuitive and often statistically inappropriate. Would it be reasonable for mmrm to respect user-defined contrasts so users like me can work around the strange defaults in base R?

[danielinteractive]

Thanks @wlandau for the question! Good one, so far we did not play around with custom contrasts too much as far as I am aware. @clarkliming any thoughts?

[clarkliming]

yes we did not use custom contrasts at all, but it could be improved i believe

[clarkliming]

and actually we always use the factor levels to decide the order (similar to a ordered vector?)