Removed reshape2 imports and replaced with tidyr v1.0.0.
Added check_installation for users to be able to
verify installations (fixes #18).
All closed form ADVAN/TRANS combinations added to the code library. Modified $ERROR so that log transformed DV and M3 models can be obtained by uncommenting lines.
The run monitor addin now uses object highlighting - useful for
when objects are not in .GlobalEnv (e.g. they’re in a
data.frame).
Changed run_nm() to have threads
argument and make use of a job_time_spacing option to
stagger multiple jobs and prevent overloading of a server (resolves
#28).
Reorders arguments for decision so that auto
decisions can be specified without explicitly referring to
arguments
Removed future package from suggests and async
arguments from nm_render*() functions.
Manual edits can now be performed on vector nm objects
Included *map*_nm() functions as equivalents to
purrr::*map*_*() functions. These return
nm_list objects.
Improvements to the subroutine() function and
included package tests.
Added path argument to write_ctl() so
control file can be written to other locations.
Added package hex sticker.
Added covariance_matrix() for extracting covariance
matrices.
Added completed_nm() for handling completed nonmem
runs.
Added sge_parallel_execute_batch for SGE cluster
environments.
Added support for “name [unit] :trans” type parameter comments.
Fixed resolve manual edit failure when directory change was responsible for failure.
RANMETHOD=3S2 changed to RANMETHOD=3S2P in code library and examples to improve parallel processing consistency of runs.
Replaced caching mechanism of nm_render() and
nm_list_render() with xfun.
Fixed bug when OMEGAS have same names as THETAS.
Added ability to use NMproject-specific code completion snippets
setup_code_completion(). Typing new_nm will
set up parent object, child will set up child
object.
fixed bug in Windows where R markdown templates weren’t being produced.
fixed minor windows bug where addins were executing models.
run_nm() checks for psn installation in first use of
R session
clean_tempfiles() replaces
clean_run()
Fixed failing CRAN checks in macOS systems.
Added run monitor RStudio Addin.
Revamped the manual edit interface. This is backwards incompatible. merge conflicts will now be flagged.
Resolve manual edit ‘addin’ for handling merge conflicts in manual edits (#17)
view_patch() prints to console instead of opening
window
Better instructions on RStudio Addin usage.
Fixed bug were nm_create_analysis_project would fail
in windows if using the home directory due to a mismatch between how ‘~’
is interpreted by R and usethis.
The first post CRAN release
Revamped the NMproject project creation template and
nm_create_analysis_project() for greater customisability
ability and removed dependence on options() which was
causing strange behaviour.
Expanded analysis README template for new NMprojects to run analysis level tests on build. Useful for compliance checking.
Added nm_pre_commit_hook() and
nm_pre_commit_hook() for custom NMproject analysis
projects
Expanded model diagnostic rmarkdown template to include more ‘xpose’ plots.
Included an experimental %f>% pipe for applying
functions elementwise to vector valued nm objects.
Included is_nmproject_dir(), intended for package
owners of dependent packages
Renamed nm_default_dir() to
nm_dir()
Removed nm.cmd_default option in favour of the more
flexible nm_default_fields. See
?nm_default_fields() for help.
decision() uses usethis::ui_yeah() for
prompting rather than readline().
stage() has find_replace_dir_names
argument to handle custom NMproject directory structures.
Made run_id argument mandatory in
child().
Added example code for first object creation in code library dialog boxes when a model file is imported
new_nm() will now fail if user tries to use a run
based on one in the Models. This is for safety as the Models directory
should only contain NMproject generated code.
The code library will not display .Rroj or
README files.
preview() is now deprecated and removed in favour of
the code library ‘Addin’
nm_default_dir is now deprecated
This is the first CRAN release of NMproject. Here are the major changes here relative to 0.5.1:
Removal and deprecation of tidyproject as an NMproject dependency.
Project libraries are now handled with
renv.
Analysis project creation has been moved from tidyproject to
NMproject with light wrappers around usethis project
creation functionality and RStudio project templates. Analysis projects
have a package-like structure.
Expanded demo based on a theophylline pharmacometric analysis and new vignette based around same demo.
The code library has been moved to NMproject. New shiny interface to code library available via RStudio ‘Addins’. The code library has been restructured to match NMproject analysis directory structure.
new_nm() function to create parent
nm_list objects. This is mostly for creation of your first
model. Subsequent models are generated with the child()
function.
New manual edit interface via RStudio ‘Addins’. NMproject is now the only NONMEM interface (known to the author) that tracks manual edits to NONMEM code in the form of reusable patches.
Fully vectorised functions and compatibility of
nm_list objects with dplyr.
Custom NMproject implementations of PsN’s bootstrap, cross-validation, stepwise covariate selection, simulation-re-estimation, and PPCs have been added.
“overwrite behaviour” RStudio ‘Addin’ has been created to allow different behaviours when modifying and rerunning a previously executed run. The default is to ask for confirmation.
This is the last version of NMproject to be developed at AZ. It has is a developmental version of the newer “beta”” interface.
This is the last release of the alpha interface developed at AZ.