# Script Based 'NONMEM' Model Development

## Documentation for package ‘NMproject’ version 0.6.7

- DESCRIPTION file.

## Help Pages

A B C D E F G I J L M N O P R S T U W misc

## -- 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 --

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
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_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 --

gsub_ctl | Pattern replacement for control file contents

## -- I --

ignore | Get/set ignore statement from control file contents
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

## -- 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

## -- 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_dir | Get a default directory
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
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
run_nm_batch | 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
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
system_nm_intern | Convenience function for system_nm

## -- 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