Script Based 'NONMEM' Model Development

Documentation for package ‘NMproject’ version 0.6.9

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-- A --

add_cov	Add/remove a covariate to a NONMEM model
add_mixed_param	Add a mixed effect parameter to $PK (or $PRED)
add_remove_covs	Add/remove a covariate to a NONMEM model
advan	Get/set $SUBROUTINE values in control file
append_nonmem_var	Include NONMEM variables in output table
apply_manual_edit	Apply a manual edit patch

-- B --

bind_covariate_results	Add run results into a covariate tibble
block	Create or remove $OMEGA/$SIGMA BLOCKs
block-omega-sigma	Create or remove $OMEGA/$SIGMA BLOCKs

-- C --

check_installation	Check NMproject installation
child	Make child nm object from parent
clean_run	Remove temporary NONMEM files
clean_tempfiles	Remove temporary NONMEM files
cmd	Functions to access and modify fields of nm objects
code_library	Code Library
coef_long	Extract parameter values
coef_wide	Extract parameter values
coef_widelong	Extract parameter values
comment_lines	Comment and uncomment lines of control file
comment_out	Comment and uncomment lines of control file
completed_nm	Create an nm object from an already completed PsN run
cond_num	Condition number of run
convert_to_simulation	Convert a NONMEM run to a simulation
cores	Execution related functions to access and modify fields of nm objects
covariance_matrix	Get covariance matrix
covariance_plot	Plot $COV matrix
covariate_step_tibble	Prepare forward covariate step
cov_cov_plot	Plot correlation between two covariates
cov_forest_data	Produce dataset for covariate forest plotting
cov_forest_plot	Plot covariate forest plots
ctl_contents	Get/set control file contents
ctl_name	Functions to access and modify fields of nm objects
ctl_path	Get and set path to NONMEM control file

-- D --

data_path	Get/set path to dataset
decision	Make decision point
delete_dollar	Delete a NONMEM subroutine from control file contents
dollar	Get/set existing subroutine
dollar_subroutine	Get/set $SUBROUTINE values in control file

-- E --

exclude_rows	Exclude rows of NONMEM dataset
executed	Execution related functions to access and modify fields of nm objects

-- F --

fill_input	Fill $INPUT
find_nm_install_path	Find location of NONMEM installation
find_nm_tran_path	Find location of NONMEM installation
find_nonmem	Find location of NONMEM installation

-- G --

Pattern replacement for control file contents

-- I --

ignore	Get/set ignore statement from control file contents
imap_nm	A purrr-like looping function over nm objects
import	Import staged files into project
init_omega	Get/set initial parameters
init_sigma	Get/set initial parameters
init_theta	Get/set initial parameters
input_data	Read input dataset of an nm object
insert_dollar	Insert a new subroutine into control file_contents
is_finished	Tests if job is finished
is_nm	Test if object is an nm coercible object
is_nmproject_dir	Is the directory an NMproject directory
is_nm_generic	Test if object is an nm coercible object
is_nm_list	Test if object is an nm coercible object
is_successful	Test if NONMEM ran without errors

-- J --

job_stats	Get job stats for a completed NONMEM run
job_time_spacing	Setup default job_time_spacing option

-- L --

lst_path	Functions to access and modify fields of nm objects
ls_code_library	List files in code library
ls_scripts	List scripts
ls_tempfiles	Remove temporary NONMEM files

-- M --

make_boot_datasets	Prepare a bootstrap tibble
make_OCC_every_dose	Make an OCC column for NONMEM IOV use
make_xv_datasets	Write (bootstrap) cross validation datasets
map2_nm	A purrr-like looping function over nm objects
map_nm	A purrr-like looping function over nm objects

-- N --

new_nm	Create a new (parent) nm object
nmsave	Save plots in results_dir
nmsave_plot	Save plots in results_dir
nmsave_table	Save plots in results_dir
nm_create_analysis_project	Create analysis project
nm_default_dirs	Setup analysis subdirectories
nm_default_fields	Setup default nm object fields
nm_diff	Compute diff between two NONMEM runs
nm_dir	Get a directory name
nm_getsetters	Functions to access and modify fields of nm objects
nm_getsetters_execution	Execution related functions to access and modify fields of nm objects
nm_list_gather	Get all nm_list objects
nm_list_render	Create run reports
nm_output_path	Find an output file associated with a run
nm_read_table	Fast read of NONMEM output table
nm_render	Create run reports
nm_summary	Generate a summary of NONMEM results
nm_tran	Run NMTRAN step of a NONMEM job
nm_tran_command	Get/set nm_tran_command
nm_tree	Make data.tree object
NONMEM_version	NONMEM version info

-- O --

ofv	Get Objective Function Value (OFV)
omega_matrix	Get OMEGA matrix from run
output_table	Reads all $TABLE outputs and merge with input dataset
output_table_first	Reads all $TABLE outputs and merge with input dataset
overwrite_behaviour	Overwrite behaviour of NMproject

-- P --

parafile	Execution related functions to access and modify fields of nm objects
parallel_execute	Generic execute command for parallelised runs
param_cov_diag	Plot relationship between a parameter and covariate
parent_ctl_name	Functions to access and modify fields of nm objects
parent_results_dir	Functions to access and modify fields of nm objects
parent_run	Get parent object of nm object
parent_run_id	Functions to access and modify fields of nm objects
parent_run_in	Functions to access and modify fields of nm objects
plot_iter	Plot iterations vs parameters/OBJ
pmap_nm	A purrr-like looping function over nm objects
ppc	PPC functions: process data from simulation and plot
ppc_data	PPC functions: process data from simulation and plot
ppc_histogram_plot	PPC functions: process data from simulation and plot
ppc_whisker_plot	PPC functions: process data from simulation and plot
psn_style_scm	PsN style stepwise covariate method

-- R --

read_derived_data	Read derived data
remove_cov	Add/remove a covariate to a NONMEM model
remove_parameter	Remove parameter from NONMEM control file
rename_parameter	Rename a parameter in NONMEM control stream
results_dir	Functions to access and modify fields of nm objects
result_files	Functions to access and modify fields of nm objects
rmd_to_vignettes	Convert R markdown scripts to vignettes
rr	Run record
run_all_scripts	Run all project scripts sequentially
run_dir	Functions to access and modify fields of nm objects
run_dir_path	Get path to run_dir
run_id	Functions to access and modify fields of nm objects
run_in	Functions to access and modify fields of nm objects
run_nm	Run NONMEM jobs

-- S --

search_raw	Search for files matching raw text search
setup_code_completion	Set up code completion for NMproject
setup_nm_demo	Setup demo in current directory
sge_parallel_execute	Generic execute command for SGE grids
sge_parallel_execute2	Generic execute command for SGE grids
sge_parallel_execute_batch	Generic execute command for SGE grids
shiny_nm	Run monitor & summary app
show_ctl	Show an uneditable version of the control file
show_out	Show an uneditable version of the lst file
simple_field	Interface for getting and setting your own simple fields in nm objects
stage	Stage files in project staging area ready for import
status	Get status of NONMEM runs
status_table	Get status of multiple runs in form of table
subroutine	Subroutine
summary_long	Generate a summary of NONMEM results
summary_wide	Generate a summary of NONMEM results
system_cmd	System/shell command wrapper
system_nm	System command for NONMEM execution

-- T --

temp_files	Remove temporary NONMEM files
test_relations	Generate tibble of covariate relations to test
tol	Get/set $SUBROUTINE values in control file
trans	Get/set $SUBROUTINE values in control file
type	Functions to access and modify fields of nm objects

-- U --

unblock	Create or remove $OMEGA/$SIGMA BLOCKs
uncomment	Comment and uncomment lines of control file
unique_id	Functions to access and modify fields of nm objects
update_parameters	Update initial estimates to final estimates

-- W --

wait_finish	Wait for runs to finish
wait_for	Wait for statement to be TRUE
walltime	Execution related functions to access and modify fields of nm objects
wipe_run	Wipe previous run files
write_derived_data	Write derived data file

-- misc --

%f>%	Function pipe for nm objects