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

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

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_nm_batch()

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

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

covariance_plot()

Plot $COV matrix

ofv()

Get Objective Function Value (OFV)

cond_num()

Condition number of run

omega_matrix()

Get OMEGA matrix from run

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