summary_log: Create a tibble from 'model_summaries()' data

In metrumresearchgroup/rbabylon: R package for bbi

Create a tibble from model_summaries() data

Description

Runs model_summaries() on all models in the input and returns a subset of the each resulting summary as a tibble.

Usage

summary_log(.base_dir, .recurse = FALSE, .include = NULL, ...)

add_summary(.log_df, ...)

Arguments

.base_dir	Base directory to look in for models.
.recurse	If FALSE, the default, only include models in .base_dir but not subdirectories. This is passed through to fs::dir_ls() – If TRUE recurse fully, if a positive number the number of levels to recurse.
.include	A character vector specifying which runs or model tags to include in the run log.
...	Arguments passed through to model_summaries()
.log_df	a bbi_run_log_df tibble (the output of run_log())

Details

The following fields from bbi_nonmem_summary (the output of model_summary()) are extracted and included by default. If you would like more fields from the summary object, you can extract them manually from the bbi_summary list column.

• error_msg – Error message from model_summary(). If NULL the call succeeded. If not NULL, the rest of the fields will be NULL.

• needed_fail_flags – Logical for whether the call initially failed, but passed with the inclusion of .fail_flags. See model_summaries() docs for more details.

• bbi_summary – The full bbi_nonmem_summary object for each row. This can be queried further by extracting it as a list, or by using dplyr::mutate() etc.

• ofv – Objective function value with no constant from the final estimation method. The constant, and the value with the constant can be found in ⁠$ofv⁠.

• param_count – Count of (non-fixed) parameters estimated in final estimation method.

• estimation_method – Character vector of estimation method(s) used. Extracted from ⁠$run_details⁠.

• problem_text – Character vector of text from ⁠$PROB⁠. Extracted from ⁠$run_details⁠.

• number_of_subjects – Count of unique subjects in the input data set, extracted from ⁠$run_details⁠.

• number_of_obs – Total count of observations in the input data set, extracted from ⁠$run_details⁠.

• condition_number – The condition number for the final estimation method, if present.

• any_heuristics – Logical indicating whether any of the columns extracted from ⁠$run_heuristics⁠ are TRUE. Duplicative information, but helpful for filtering.

• ⁠$run_heuristics⁠ columns – One logical column for each element extracted from ⁠$run_heuristics⁠. These are named and described in the model_summary() docs.

Value

An object of class bbi_summary_log_df, which includes the fields described below. If all model summaries fail, the returned tibble will only contain the absolute_model_path, run, and error_msg columns.

summary_log() creates a new tibble with one row per model found in .base_dir (and subdirectories, if .recurse = TRUE).

add_summary() adds these fields to the tibble passed to .log_df.

See Also

run_log(), config_log(), model_summary(), model_summaries()

metrumresearchgroup/rbabylon documentation built on April 21, 2024, 3:26 a.m.