Merge pull request #548 from aloctavodia/reformulas

Use reformulas for formula processing functions

Author: aloctavodia

DESCRIPTION

@@ -56,7 +56,8 @@ Imports:
     MASS,
     ordinal,
     nnet,
-    mclogit
+    mclogit,
+    reformulas,
 Suggests:
     ggrepel,
     ggfortify,

NEWS.md

@@ -9,7 +9,7 @@ If you read this from a place other than <https://mc-stan.org/projpred/news/inde
 * Added support for censored observations when using the latent projection (with response-scale analyses). This makes it possible, e.g., to use the latent projection for time-to-event models (also known as models for survival analysis). Due to this new feature, the function passed to argument `latent_ll_oscale` of `extend_family()` now needs to have an argument `cens`. See `?extend_family` (section "Latent projection") as well as the latent-projection vignette (section ["Censored observations (survival analysis)"](https://mc-stan.org/projpred/articles/latent.html#cens)) for more information and examples. Note that only the performance statistics `"elpd"`, `"mlpd"`, and `"gmpd"` take censoring into account (on response scale). (GitHub: #528)
 
 ## Minor changes
-
+* Use `reformulas` package directly for formula processing functions. This package is already a dependency of `lme4` >= v1.1-38.
 
 ## Bug fixes
 

R/divergence_minimizers.R

@@ -52,7 +52,7 @@ divmin <- function(
     sdivmin <- fit_glmer_callback
     if (getOption("projpred.PQL", FALSE)) {
       # Split up the formula into a fixed and a random part (note: we could also
-      # use lme4::nobars() and lme4::findbars() here):
+      # use reformulas::nobars() and reformulas::findbars() here):
       formula_random <- split_formula_random_gamm4(formula)
       projpred_formulas_no_random <- validate_response_formula(
         formula_random$formula
@@ -1342,11 +1342,11 @@ empty_intersection <- function(x, el_nm = "new") {
 # "GPL (>=2)" (see <https://CRAN.R-project.org/package=lme4>).
 mkNewReTrms_man <- function(re.form, newdata, xlevels, re, D = NULL) {
   stopifnot(!is.null(newdata))
-  tt <- terms(lme4::subbars(re.form))
+  tt <- terms(reformulas::subbars(re.form))
   rfd <- suppressWarnings(
     model.frame(tt, newdata, na.action = na.pass, xlev = xlevels)
   )
-  ReTrms <- lme4::mkReTrms(lme4::findbars(re.form[[2]]), rfd)
+  ReTrms <- reformulas::mkReTrms(reformulas::findbars(re.form[[2]]), rfd)
   ns.re <- names(re)
   nRnms <- names(Rcnms <- ReTrms$cnms)
   if (!all(nRnms %in% ns.re)) {

tests/testthat/test_refmodel.R

@@ -260,20 +260,17 @@ test_that(paste(
 
     # Without `ynew`:
     expect_warning(
-      predref_resp <- withCallingHandlers(
-        predict(refmods[[tstsetup]], dat,
-                weightsnew = wobs_crr,
-                offsetnew = offs_crr,
-                type = "response"),
+      withCallingHandlers(
+        predref_resp <- predict(refmods[[tstsetup]], dat, weightsnew = wobs_crr,
+                                offsetnew = offs_crr, type = "response"),
         warning = function(w) {
-          if (grepl("nobars.*reformulas", conditionMessage(w))) {
+          if (grepl("(nobars|subbars|findbars|mkReTrms).*reformulas", conditionMessage(w))) {
             invokeRestart("muffleWarning")
           }
         }
       ),
-      get_warn_wrhs_orhs(tstsetup,
-                        weightsnew = wobs_crr,
-                        offsetnew = offs_crr),
+      get_warn_wrhs_orhs(tstsetup, weightsnew = wobs_crr,
+                         offsetnew = offs_crr),
       info = tstsetup
     )