Merge master into add-cwres-foce

Resolves conflicts in R/calc_residuals.R and R/get_map_estimates.R
where master removed `...` while this branch added new explicit
parameters and used `...` to forward to the new CWRES code.

Resolution: accept master's intent (drop `...` from the public
signatures and all downstream sim_ode calls) while keeping the new
explicit `nonfixed`, `as_eta`, `steady_state_analytic`, and
`weight_prior_var` parameters of calc_residuals(). Also drop `...`
from calc_cwres()/simulate_with_etas() since nothing flows in any
more.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: roninsightrx

R/calc_cwres.R

@@ -42,7 +42,6 @@
 #'   Used to scale omega in the FOCE Hessian computation to match the
 #'   estimation objective. CWRES uses the unscaled omega (model diagnostic).
 #' @param delta perturbation size for finite differences
-#' @param ... additional arguments passed to PKPDsim::sim_ode
 #'
 #' @return list with components:
 #'   \item{cwres}{numeric vector of CWRES values}
@@ -73,8 +72,7 @@ calc_cwres <- function(
     t_init = 0,
     steady_state_analytic = NULL,
     weight_prior_var = 1,
-    delta = 1e-4,
-    ...
+    delta = 1e-4
 ) {
   n_obs <- length(y)
   n_eta <- length(eta_hat)
@@ -98,13 +96,13 @@ calc_cwres <- function(
       eta_plus, parameters_population, nonfixed, as_eta,
       model, covariates, regimen, lagtime, t_obs, obs_type_sim,
       int_step_size, iov_bins, A_init, t_init,
-      steady_state_analytic, ...
+      steady_state_analytic
     )
     pred_minus <- simulate_with_etas(
       eta_minus, parameters_population, nonfixed, as_eta,
       model, covariates, regimen, lagtime, t_obs, obs_type_sim,
       int_step_size, iov_bins, A_init, t_init,
-      steady_state_analytic, ...
+      steady_state_analytic
     )
 
     F_matrix[, j] <- (transf(pred_plus) - transf(pred_minus)) / (2 * delta)
@@ -194,8 +192,7 @@ simulate_with_etas <- function(
     iov_bins,
     A_init,
     t_init,
-    steady_state_analytic,
-    ...
+    steady_state_analytic
 ) {
   # Compute individual parameters from etas
   par <- parameters_population
@@ -242,8 +239,7 @@ simulate_with_etas <- function(
       A_init = a_init,
       iov_bins = iov_bins,
       t_init = t_init,
-      lagtime = lagtime,
-      ...
+      lagtime = lagtime
     )
   })
 

R/calc_residuals.R

@@ -13,6 +13,8 @@
 #' @param nonfixed character vector of non-fixed parameter names
 #' @param as_eta character vector of parameters estimated directly as eta
 #' @param steady_state_analytic steady state settings (or NULL)
+#' @param weight_prior_var prior weight variance scaling factor (default 1).
+#'   Forwarded to `calc_cwres()` to scale omega in the FOCE Hessian.
 #'
 calc_residuals <- function(
   obj,
@@ -39,8 +41,7 @@ calc_residuals <- function(
   nonfixed = NULL,
   as_eta = c(),
   steady_state_analytic = NULL,
-  weight_prior_var = 1,
-  ...
+  weight_prior_var = 1
 ) {
 
   ## Observation vectors
@@ -68,8 +69,7 @@ calc_residuals <- function(
       iov_bins = iov_bins,
       output_include = output_include,
       t_init = t_init,
-      lagtime = lagtime,
-      ...
+      lagtime = lagtime
     )
   })
   suppressMessages({
@@ -88,8 +88,7 @@ calc_residuals <- function(
       iov_bins = iov_bins,
       A_init = A_init_population,
       t_init = t_init,
-      lagtime = lagtime,
-      ...
+      lagtime = lagtime
     )
   })
 
@@ -140,8 +139,7 @@ calc_residuals <- function(
         A_init = A_init_individual,
         t_init = t_init,
         steady_state_analytic = steady_state_analytic,
-        weight_prior_var = weight_prior_var,
-        ...
+        weight_prior_var = weight_prior_var
       ),
       error = function(e) {
         warning("CWRES computation failed: ", e$message)

R/get_map_estimates.R

@@ -61,8 +61,7 @@
 #'option is `TRUE`.
 #' @param skip_hessian skip calculation of Hessian
 #' @param verbose show more output
-#' @param ... parameters passed on to `sim_ode()` function
-#' 
+#'
 #' @examples
 #' \dontrun{
 #' ## define parameters
@@ -134,8 +133,7 @@ get_map_estimates <- function(
                       verbose = FALSE,
                       A_init = NULL,
                       skip_hessian = FALSE,
-                      output_include = list(covariates = FALSE, parameters = FALSE),
-                      ...) {
+                      output_include = list(covariates = FALSE, parameters = FALSE)) {
 
   ## get prior weight for scaling of variance term
   weight_prior_var <- parse_weight_prior(weight_prior, type)
@@ -232,8 +230,7 @@ get_map_estimates <- function(
       t_max = tail(t_obs, 1) + t_init + 1,
       iov_bins = iov_bins,
       return_design = TRUE,
-      t_init = t_init,
-      ...
+      t_init = t_init
     )
   })
 
@@ -434,8 +431,7 @@ get_map_estimates <- function(
       nonfixed = omega$nonfixed,
       as_eta = as_eta,
       steady_state_analytic = steady_state_analytic,
-      weight_prior_var = weight_prior_var,
-      ...
+      weight_prior_var = weight_prior_var
     )
   }