This release adds a number of helper functions, primarily for use with NONMEM models.
Added nm_file(), nm_grd(), nm_tab(), nm_par_tab(), and nm_data() for reading in NONMEM files more easily. (#426)
Added nm_join(), nm_tables(), and nm_table_files() for reading in NONMEM tables more easily. Notably, nm_join() can be used to get a single tibble containing your NONMEM input data joined against all of your table outputs. (#429 and #430)
param_estimates_batch() for extracting a tibble of parameter estimates from a batch of NONMEM runs. Especially useful for large batches of runs created by something like a bootstrap. (#386)
cov_cor() and check_cor_threshold() for pulling in covariance and correlation matrices from NONMEM .cov and .cor files. (#414)
Passing the .new_model argument to copy_model_from() is now optional. By default, it now tries to increment to the next available integer in the destination directory (the directory containing the parent model). (#424)
update_model_id() for updating mentions of the parent model in the child model’s control stream. (#417)
Per guidance in bbr 1.0.0 release, replace_tags(), replace_bbi_args(), replace_based_on(), add_decisions(), and replace_decisions() have been removed.
Deprecated check_nonmem_table_output(), check_grd(), and check_ext() and replaced them with nm_file() variants. These functions will warn about this for two more releases and then begin to error for two more releases before being removed altogether. (#426)
Deprecated plot_nonmem_table_df(), plot_grd(), and plot_ext() in an effort to more tightly define the scope of bbr. These functions will warn about this for two more releases and then begin to error for two more releases before being removed altogether. (#426)
collapse_to_string() (#393)Fixed a bug where submitting multiple models in a loop with submit_model(.mode = "local", .wait = FALSE) would cause the models to never finish because the bbi processes would get killed by processx when the R objects were garbage collected. (#390)
bbr now checks for a valid configuration file before calling out to bbi to avoid the situation where .wait = FALSE and the “no config file” error from bbi is swallowed. Note, this check is skipped if .dry_run = TRUE. (#390)
Added options(bbr.bbi_exe_mode) for globally setting .mode argument to submit_model() and submit_models(). (#377)
Added .bbi_args argument to bbi_init() for passing through defaults to be stored in the created bbi.yaml file. (#378)
submit_models() (e.g. for bootstrapping) would hang indefinitely. This had something to do with a bug in processx. It was fixed (in bbr) by routing the stdout and stderr to a temp file and then reading from it when necessary, instead of relying on processx to poll the process. (#374)Added tags_diff() function for comparing the tags between different models. (#337)
Added model_diff() function for comparing the model files between different models. (#342)
Added check_up_to_date() function for checking whether the model file(s) and data file(s) associated with a model have changed since the model was run. (#338)
Added more documentation about the heuristics returned from model_summary.bbi_nonmem_model() (#343)
param_estimates() now correctly errors when a Bayesian method is used but is not the final method. (#344)bbi_model parent class to bbi_nonmem_model and bbi_nonmem_summary objects. Many of the helpers in get-path-from-object.R now dispatch on this class. This had been discussed in the past but was primarily done now in preparation for beginning development for Stan modeling, which will create bbi_stan_model and bbi_stan_summary objects that will also inherit from this parent class. (#332)This release is fairly small in terms of changes, but it increments to a new major release version primarily because of the name change which happened in bbr 0.12.0. The most significant change, from a user perspective, is to the default behavior of where bbr looks for bbi on the system. This change is described in issue #321 and a bit more detail is given below.
The 1.0.0 release also represents a stable feature set of basic NONMEM-related functionality. While there will be more features and development relevant to NONMEM in the future, for the immediate future we are shifting our attention towards building similar functionality to support Stan modeling with bbr.
The minimum compatible version of bbi is increased to 3.0.2. This is because there was a breaking change in bbi 3.0.2 which changed all references to "Patients" in the bbi nonmem summary output to "Patients" (discussed further below). Also because there was a bug where bbi could not parse the summary output from NONMEM 7.5 and this bug was fixed in bbi 3.0.1.
options("bbr.bbi_exe_path"), which tells bbr where to look for a bbi installation, now defaults to "bbi". This means that, by default, bbr will look for a bbi installation in the user’s $PATH. options("bbr.bbi_exe_path") can still be set manually by the user and, in fact, we encourage users to set this to an absolute path in their .Rprofile for their project because this explicitly guarantees the correct bbi installation is being used. (#322)
The use_bbi() installer function first tries to install to whatever path is set in options("bbr.bbi_exe_path"), falling back to the bbi in my $PATH (accessed via Sys.which("bbi")) and then an OS-dependent default, in that order. See ?use_bbi() for more details. (#322)
Added print method for bbi_nonmem_model object. Similar to the bbi_nonmem_summary object, the bbi_nonmem_model object should print nicely in the console, and also look good in .Rmd chunks with the option results = 'asis'. (#307)
Added get_data_path() helper function to extract the absolute path to the input data file from bbi_nonmem_model and bbi_nonmem_summary objects. (#314)
Added build_path_from_model() helper function to extract the absolute path to various output files from bbi_nonmem_model and bbi_nonmem_summary objects. (#314)
The output from model_summary() (and model_summaries() and summary_log()) will now refer to individuals in the data set as "Subjects" instead of "Patients", in accordance with the terminology widely used in scientific and medical literature. (#320)
Per guidance in rbabylon 0.10.0 release, replace_tags(), replace_bbi_args(), replace_based_on(), add_decisions(), and replace_decisions() will now error instead of warn about their impending deprecation. These functions will be removed entirely in two more releases.
We are no longer checking in either the .Rprofile or anything in the renv folder. As a result, the development workflow has changed slightly. This change is reflected in the README. (#307 and #308)
Added an option to suppress the minimum bbi version constraint. This is intended only for developers who want to try out development (unreleased) version of bbi while developing on bbr. (#305)
Our Drone CI system now uses a .drone.yml instead of .drone.jsonette. We have also switched the containers that we use for testing in CI to smaller containers which are more specialized for the purpose. (#309)
This package has been renamed to from rbabylon to bbr and the accompanying command-line tool has been renamed from babylon to bbi (which was already its alias, used throughout the package). Any mentions of babylon and rbabylon throughout the package have been renamed accordingly. Mentions of either in the older parts of this NEWS.md document were left as is for historical purposes.
Added print methods for bbi_nonmem_summary and bbi_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).