Merge pull request #718 from metrumresearchgroup/release/1.12.0

Release 1.12.0

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: bbr
 Title: R package for bbi
-Version: 1.11.0
+Version: 1.12.0
 Authors@R: 
     c(person(given = "Seth",
              family = "Green",

NEWS.md

@@ -1,3 +1,40 @@
+# bbr 1.12.0
+
+## New features and changes
+
+* New model tree feature: `bbr` now allows you to visualize any `run_log()` as
+  an interactive model tree diagram via `model_tree()`. This function allows 
+  users to easily visualize and track the modeling process for a given project 
+  and display any information available in a `run_log()`, such as model summary
+  information, configuration options, and more. See the vignette 
+  [here](https://metrumresearchgroup.github.io/bbr/articles/model-tree.html) (#673).
+
+* New `run_nmtran()` function for running `NM-TRAN` on a model object to validate
+  its control stream for correct coding before submission. The `NM-TRAN` dataset
+  (`FDATA`) and other `NONMEM` artifacts can be further inspected by keeping the
+  run directory around (#705).
+
+* `nm_data()` now has a `filter` argument, allowing the user to filter data based
+  on `IGNORE LIST` or `ACCEPT LIST` options defined in the `$DATA` record of a
+  `NONMEM` control stream file (#711).
+
+* `setup_bootstrap_run()` now has a `data` argument, allowing users to provide
+  their own starting dataset to resample from. This defaults to `NULL`, which
+  will use the output from `nm_data(.boot_run, filter = TRUE)` (#707, #711).
+
+## Bugs addressed
+
+* Bootstrap adjustment: previously `setup_bootstrap_run()` assumed a `NUM` column
+  was present in the input dataset (the default `.join_col` in `nm_join()`). 
+  `nm_join()` was being used in the back-end to create the starting dataset to
+  resample from; the intention being to only include subjects that entered the
+  original problem. Given the `nm_join()` use, this also required that the original
+  model had finished executing before bootstrapping. Rather than using `nm_join()`
+  by default, we now use `nm_data(.boot_run, filter = TRUE)`. This both fixes the
+  aforementioned bug and removes the requirement that the base model (model being
+  bootstrapped) has been executed. If the model has been executed, however, we will
+  check the number of records to ensure the filtering was done correctly (#707, #711).
+
 # bbr 1.11.0
 
 ## New features and changes

R/bootstrap-model.R

@@ -86,7 +86,7 @@ new_bootstrap_run <- function(
 #' @param seed A numeric seed to set prior to resampling the data; use `NULL` to
 #'   avoid setting a seed.
 #' @param data A dataset to resample from. Defaults to `NULL`, which will use
-#'   the _filtered_ output from `nm_data(.mod, filter = TRUE)`. If provided,
+#'   the _filtered_ output from `nm_data(.boot_run, filter = TRUE)`. If provided,
 #'   must include the same column names as what's returned from `nm_data(.mod)`.
 #' @param .bbi_args Named list passed to `model_summary(orig_mod, .bbi_args)`,
 #'   where `orig_mod` is the model `.boot_run` is based on. See
@@ -212,7 +212,7 @@ setup_bootstrap_run <- function(
           cli::cli_abort(
             c(
               "!" = "The filtered dataset does not have the same number of records as the original model:",
-              "*" = "{.code nm_data(orig_mod, filter = TRUE)} returned {.val {nrec_f}} records",
+              "*" = "{.code nm_data(.boot_run, filter = TRUE)} returned {.val {nrec_f}} records",
               "*" = "{.code model_summary(orig_mod)} returned {.val {nrec}} records",
               "i" = "where {.code orig_mod <- read_model(get_based_on(.boot_run))}",
               "i" = "Try providing a starting dataset (e.g., {.code setup_bootstrap_run(.boot_run, data = nm_join(orig_mod))})"