Function reference • NMproject

Configuration & setup
`check_installation()`	Check NMproject installation
`setup_code_completion()`	Set up code completion for NMproject
`nm_tran_command()`	Get/set nm_tran_command
`find_nm_install_path()` `find_nm_tran_path()`	Find location of NONMEM installation
`NONMEM_version()`	NONMEM version info
`nm_default_fields()`	Setup default nm object fields
`nm_default_dirs()`	Setup analysis subdirectories
`overwrite_behaviour()`	Overwrite behaviour of NMproject
`job_time_spacing()`	Setup default job_time_spacing option
Project directory management
`nm_create_analysis_project()`	Create analysis project
`setup_nm_demo()`	Setup demo in current directory
`run_all_scripts()`	Run all project scripts sequentially
`ls_tempfiles()` `clean_run()` `clean_tempfiles()`	Remove temporary NONMEM files
`rmd_to_vignettes()`	Convert R markdown scripts to vignettes
`nm_dir()`	Get a directory name
`is_nmproject_dir()`	Is the directory an NMproject directory
Importing code
`code_library()`	Code Library
`ls_code_library()`	List files in code library
`ls_scripts()`	List scripts
`stage()`	Stage files in project staging area ready for import
`import()`	Import staged files into project
`search_raw()`	Search for files matching raw text search
Data cleaning convenience functions
`read_derived_data()`	Read derived data
`write_derived_data()`	Write derived data file
`exclude_rows()`	Exclude rows of NONMEM dataset
`make_OCC_every_dose()`	Make an OCC column for NONMEM IOV use
Core object
`new_nm()`	Create a new (parent) nm object
`child()`	Make child nm object from parent
`run_dir()` `cmd()` `type()` `parent_run_id()` `parent_run_in()` `parent_ctl_name()` `parent_results_dir()` `unique_id()` `ctl_name()` `results_dir()` `run_in()` `run_id()` `result_files()` `lst_path()`	Functions to access and modify fields of nm objects
`data_path()`	Get/set path to dataset
`input_data()`	Read input dataset of an nm object
`nm_list_gather()`	Get all nm_list objects
`parent_run()`	Get parent object of nm object
`run_dir_path()`	Get path to run_dir
`ctl_path()`	Get and set path to NONMEM control file
`simple_field()`	Interface for getting and setting your own simple fields in nm objects
`map_nm()` `map2_nm()` `imap_nm()` `pmap_nm()`	A purrr-like looping function over nm objects
`is_nm_list()` `is_nm_generic()`	Test if object is an nm coercible object
`completed_nm()`	Create an nm object from an already completed PsN run
`%f>%`	Function pipe for nm objects
NONMEM code manipulation
`apply_manual_edit()`	Apply a manual edit patch
`nm_diff()`	Compute diff between two NONMEM runs
`show_ctl()`	Show an uneditable version of the control file
`dollar()`	Get/set existing subroutine
`fill_input()`	Fill $INPUT
`subroutine()`	Subroutine
`update_parameters()`	Update initial estimates to final estimates
`init_theta()` `init_omega()` `init_sigma()`	Get/set initial parameters
`block()` `unblock()`	Create or remove $OMEGA/$SIGMA BLOCKs
`gsub_ctl()`	Pattern replacement for control file contents
`comment_out()` `uncomment()`	Comment and uncomment lines of control file
`ignore()`	Get/set ignore statement from control file contents
`advan()` `trans()` `tol()`	Get/set $SUBROUTINE values in control file
`delete_dollar()`	Delete a NONMEM subroutine from control file contents
`insert_dollar()`	Insert a new subroutine into control file_contents
`add_mixed_param()`	Add a mixed effect parameter to $PK (or $PRED)
`remove_parameter()`	Remove parameter from NONMEM control file
`rename_parameter()`	Rename a parameter in NONMEM control stream
`target()` `untarget()`	Target part of control object for further modification
`ctl_contents()`	Get/set control file contents
Execution
`run_nm()`	Run NONMEM jobs
`nm_tran()`	Run NMTRAN step of a NONMEM job
`shiny_nm()`	Run monitor & summary app
`status()`	Get status of NONMEM runs
`status_table()`	Get status of multiple runs in form of table
`wait_finish()`	Wait for runs to finish
`wait_for()`	Wait for statement to be TRUE
`is_finished()`	Tests if job is finished
`is_successful()`	Test if NONMEM ran without errors
`parallel_execute`	Generic execute command for parallelised runs
`sge_parallel_execute` `sge_parallel_execute2` `sge_parallel_execute_batch`	Generic execute command for SGE grids
`system_nm()`	System command for NONMEM execution
`system_cmd()`	System/shell command wrapper
`kill_job()`	Kill cluster job
`wipe_run()`	Wipe previous run files
`cores()` `parafile()` `walltime()` `executed()`	Execution related functions to access and modify fields of nm objects
`job_stats()`	Get job stats for a completed NONMEM run
NONMEM postprocessing
`show_out()`	Show an uneditable version of the lst file
`nm_render()` `nm_list_render()`	Create run reports
`plot_iter()`	Plot iterations vs parameters/OBJ
`decision()`	Make decision point
`rr()`	Run record
`summary_wide()` `summary_long()`	Generate a summary of NONMEM results
`coef_wide()` `coef_long()`	Extract parameter values
`output_table()` `output_table_first()`	Reads all $TABLE outputs and merge with input dataset
`nm_read_table()`	Fast read of NONMEM output table
`nm_tree()`	Make data.tree object
`ofv()`	Get Objective Function Value (OFV)
`cond_num()`	Condition number of run
`omega_matrix()`	Get OMEGA matrix from run
`covariance_matrix()`	Get covariance matrix
`covariance_plot()`	Plot $COV matrix
`nmsave_plot()` `nmsave_table()`	Save plots in results_dir
`param_cov_diag()`	Plot relationship between a parameter and covariate
`nm_output_path()`	Find an output file associated with a run
Simulations
`convert_to_simulation()`	Convert a NONMEM run to a simulation
`ppc_data()` `ppc_whisker_plot()` `ppc_histogram_plot()`	PPC functions: process data from simulation and plot
Covariate modelling
`cov_cov_plot()`	Plot correlation between two covariates
`add_cov()` `remove_cov()`	Add/remove a covariate to a NONMEM model
`test_relations()`	Generate tibble of covariate relations to test
`covariate_step_tibble()`	Prepare forward covariate step
`bind_covariate_results()`	Add run results into a covariate tibble
`cov_forest_data()`	Produce dataset for covariate forest plotting
`cov_forest_plot()`	Plot covariate forest plots
`psn_style_scm()`	PsN style stepwise covariate method
`append_nonmem_var()`	Include NONMEM variables in output table
Bootstrap
`make_boot_datasets()`	Prepare a bootstrap tibble
`make_xv_datasets()`	Write (bootstrap) cross validation datasets

Reference

Configuration & setup

Project directory management

Importing code

Data cleaning convenience functions

Core object

NONMEM code manipulation

Execution

NONMEM postprocessing

Simulations

Covariate modelling

Bootstrap