Added print methods for bbi_nonmem_summary and babylon_process objects. The bbi_nonmem_summary object should print nicely in the console, and also look good in .Rmd chunks with the option results = 'asis'. (#298 and #294)
The bbi_nonmem_summary object now contains the absolute_model_path and we have added the following methods to work on that object (these previously only worked on bbi_nonmem_model objects): get_model_id(), get_model_path(), get_output_dir(), get_yaml_path(), check_grd(), check_ext(). (#297)
For developers, there are now scripts in data-raw which regenerate the test reference files and re-run the test models. All test references and example files have now been consolidated in inst as well. Users will see these files in extdata, model, and test-refs when the package is installed. (#289)
Also for developers, we are now using pkgr and renv to isolate dependencies when developing. The README has been updated with instructions for how to use this when developing. (#276)
Previously replace_model_field(), which is called under the hood by replace_tag() and replace_note() did not modify the YAML file as it should have. That has been fixed. (#281)
Previously the add_summary() function would error if all the model summaries errored. Now it will return, passing through the model summary errors to the tibble, as it should. (#282)
Deprecated replace_tags(), replace_bbi_args(), and replace_based_on() and replaced them with replace_all_ variants. These functions will warn about this for two more releases and then begin to error for two more releases before being removed altogether. (#264)
Added replace_tag() (singular) which replaces a single tag with a new tag. replace_note() (mentioned below) functions the same way. (#264)
Added collapse_to_string() which collapses a list column in a tibble to a character column containing a string representation of the column’s previous contents. For list columns containing character, numeric, or logical vectors, this means collapsing with paste(collapse = ', '). For other types dput() is used. (#260)
Added run column to all bbi_log_df tibbles. This is always the second column and is equivalent to basename(absolute_model_path). While, absolute_model_path remains the primary key for the tibble, run is useful for displaying tables when absolute_model_path becomes long and difficult to look at. (#259)
Added notes field to model object (and bbi_run_log_df) and associated helpers add_notes(), replace_note(), replace_all_notes(), remove_notes(). This will replace decisions, to reflect the fact that users will want to use this field throughout the modeling process, not only at the end once some “decisions” have been reached. add_decisions() and replace_decisions() now print a warning telling the user that they will be deprecated in the future and encouraging use of their _notes counterparts. (#258)
.description is no longer a required argument for new_model() or copy_model_from(), nor is it a required element of a model object or YAML file. The helper function add_description() has been added to fill the description field. (#267)
The .update_model_file argument to copy_model_from() no longer updates the $PROB in the new control stream with the .description argument. Instead it puts the following in $PROB: From rbabylon: see {get_model_id(.new_model)}.yaml for details (#265)
Added remove_tags(), remove_notes(), and remove_based_on() functions for removing specific strings from the relevant model object field. (#252)
submit_models() correctly handles the case where bbi arguments are neither present in the YAML file nor passed at runtime (#248).
config_log() and add_config() are supposed to warn a user if models are found that do not have a corresponding bbi_config.json file (i.e. have not yet been run, or did not finish successfully). However, if there is no output directory at all for a given model (it has never been run) then these functions would error. Now they correctly warn in that scenario. (#253)
.base_dir becomes a required argument to config_log(), run_log(), and summary_log() (#227).
The .directory argument is removed from copy_model_from(), model_summaries(), model_summary(), new_model(), read_model(), submit_model(), and submit_models() (#217, #222, #224, #225, #226).
The .new_model argument to copy_model_from() can be either an absolute path or relative to the location of .parent_mod (previously, the path was constructed with .directory) (#222).
The .yaml_path argument to new_model() becomes .path, and the .model_path argument is removed, to reflect that a single path identifies the output directory and the model and YAML files (without extension). new_model() and read_model() throw an error if a model file is not found at .path plus any relevant file extension, e.g., ctl or mod for NONMEM (#213, #217).
The default value of the .config_path argument to submit_model() and submit_models() changes to NULL, in which case the function will look for a babylon.yaml in the same directory as the model file (#228).
get_model_directory() and set_model_directory() have been removed because the rbabylon.model_directory option is no longer used (#229).
as_model() has been removed because it was not used (#194).
The character and numeric methods for copy_model_from(), model_summaries(), model_summary(), submit_model(), and submit_models() have been removed because they created an unnecessarily complicated interface (#188).
get_path_from_object() has been removed and replaced by equivalent functionality, e.g., get_model_path() (#195).
yml_ext() has been removed because support for the yml file extension has been removed (#211).
get_model_path(), get_output_dir(), get_yaml_path() return the paths to the model file, the output directory, and the model YAML file, respectively, replacing get_path_from_object() (#195).
The object returned by each of add_config(), add_summary(), config_log(), run_log(), and summary_log() inherits from abstract class bbi_log_df. get_model_path(), get_output_dir(), and get_yaml_path() gain methods for this new class (#192).
Added vignette demonstrating new summary_log() functionality.
Added shrinkage column to the tibble output from param_estimates.bbi_nonmem_summary().
Changed the column name containing the names of the parameters, in the table output from param_estimates.bbi_nonmem_summary(), from names to parameter_names to avoid confusion.
param_estimates.bbi_nonmem_summary() now errors with a “not implemented” error for models where the final estimation method is Bayesian.
Added a NEWS.md file to track changes to the package.
The minimum compatible version of babylon is increased to 2.3.0.
The list of arguments that can be passed via .bbi_args is updated to reflect the possible values as of babylon 2.3.0. Only arguments for bbi nonmem run, arguments for bbi nonmem summary, and global arguments are included. Also, print_nonmem_args() is renamed to print_bbi_args() to better reflect its purpose (#123).
config_log() returns the versions of babylon and NONMEM (#115).
config_log() indicates whether the model file or the data file has changed since the model was last run (#30). Updated “Using the based_on field” vignette to reflect the new feature and its usage.
Model summaries no longer include information about covariance or correlation, because bbi nonmem summary no longer parses the relevant files (#128).
Model summary logs, as obtained from summary_log() or add_summary(), include the condition number, whether a PRDERR file was created, and whether any p-value is less than 0.05. In addition, the objective function value is now included without the constant (#122).
New function summary_log() combines summaries of multiple models, as obtained from model_summaries(). Its companion add_summary() adds the summary information to an existing run log (#67).
Multiple models can be summarized with a call to model_summaries() (#53).