REsolving merge conflict

Author: juliettelimozin

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # R specific hooks: https://github.com/lorenzwalthert/precommit
 repos:
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.3.9003
+    rev: v0.4.3.9007
     hooks:
     -   id: style-files
         args: [--style_pkg=styler, --style_fun=tidyverse_style, --ignore-start="^# Generated by using Rcpp"]

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: TrialEmulation
 Title: Causal Analysis of Observational Time-to-Event Data
-Version: 0.0.4.3
+Version: 0.0.4.4
 Authors@R: c(
     person("Isaac", "Gravestock", , "isaac.gravestock@roche.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0283-2065")),
@@ -57,6 +57,11 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2.9000
 Collate: 
     'RcppExports.R'
+<<<<<<< HEAD
+=======
+    'lr_utils.R'
+    'utils.R'
+>>>>>>> 3893af84c0c2b9fe7ae5f4b4c1bc91716d3b27e1
     'bootstrap.R'
     'calculate_weights.R'
     'data.R'
@@ -68,7 +73,6 @@ Collate:
     'expand_trials.R'
     'generics.R'
     'initiators.R'
-    'lr_utils.R'
     'te_model_fitter.R'
     'te_outcome_model.R'
     'te_datastore.R'
@@ -85,5 +89,4 @@ Collate:
     'te_datastore_duckdb.R'
     'te_parsnip.R'
     'te_stats_glm_logit.R'
-    'utils.R'
     'weighting.R'

NEWS.md

@@ -1,4 +1,4 @@
-# TrialEmulation 0.0.4.3
+# TrialEmulation 0.0.4.4
 
 * Update tests for duckdb 1.2.0 changes to sampling.
 

R/trial_sequence.R

@@ -514,7 +514,12 @@ setMethod(
       period = as_formula(trial_period_terms, add = collection),
       stabilised = as_formula(get_stabilised_weights_terms(object), add = collection)
     )
-    adjustment <- unique(c(all.vars(formula_list$adjustment), all.vars(formula_list$stabilised)))
+    treatment <- all.vars(formula_list$treatment)
+    adjustment <- setdiff(
+      unique(c(all.vars(formula_list$adjustment), all.vars(formula_list$stabilised))),
+      treatment
+    )
+
     assert_names(
       adjustment,
       subset.of = colnames(object@data@data),
@@ -619,6 +624,7 @@ get_stabilised_weights_terms <- function(object) {
   stabilised_terms
 }
 
+# Update outcome model (formulas generally and variables in stabilised models)
 update_outcome_formula <- function(object) {
   assert_class(object, "trial_sequence")
 
@@ -638,7 +644,7 @@ update_outcome_formula <- function(object) {
   object@outcome_model@formula <- outcome_formula
 
   object@outcome_model@adjustment_vars <- unique(
-    c(all.vars(formula_list$adjustment), all.vars(formula_list$stabilised))
+    c(object@outcome_model@adjustment_vars, all.vars(formula_list$stabilised))
   )
 
   object

man/weight_func_bootstrap.Rd

@@ -500,7 +500,29 @@ test_that("stabilised weight terms are included in outcome model", {
   )
 })
 
-# Expand
+
+test_that("interaction terms work as expected", {
+  result <- trial_sequence("PP") |>
+    set_data(data_censored) |>
+    set_outcome_model(adjustment_terms = ~ assigned_treatment * x2)
+
+  expect_equal(
+    result@outcome_model@formula,
+    outcome ~ assigned_treatment + x2 + followup_time + I(followup_time^2) +
+      trial_period + I(trial_period^2) + assigned_treatment:x2,
+    ignore_formula_env = TRUE
+  )
+  expect_equal(result@outcome_model@treatment_var, "assigned_treatment")
+  expect_equal(result@outcome_model@adjustment_vars, "x2") # shouldn't include treatment
+  expect_equal(
+    result@outcome_model@adjustment_terms, # can include treatment
+    ~ assigned_treatment * x2,
+    ignore_formula_env = TRUE
+  )
+})
+
+# Expand ---
+
 test_that("weights are 1 when not calculated by calculate_weights", {
   trial_ex <- TrialEmulation::trial_example