Man pages for NMproject
Script Based 'NONMEM' Model Development

add_mixed_paramAdd a mixed effect parameter to $PK (or $PRED)
add_remove_covsAdd/remove a covariate to a NONMEM model
append_nonmem_varInclude NONMEM variables in output table
apply_manual_editApply a manual edit patch
as_nm_genericConvert nm object to nm_generic
as_nm_listCoerce object into nm_list
based_onUse file to set control file contents in nm object
bind_covariate_resultsAdd run results into a covariate tibble
block-omega-sigmaCreate or remove $OMEGA/$SIGMA BLOCKs
boot_to_csvSave bootstrap datasets to disk
change_parentChange parent object
childMake child nm object from parent
code_libraryCode Library
coef_widelongExtract parameter values
comment_linesComment and uncomment lines of control file
cond_numCondition number of run
convert_to_simulationConvert a NONMEM run to a simulation
covariance_plotPlot $COV matrix
covariate_step_tibblePrepare forward covariate step
cov_cov_plotPlot correlation between two covariates
cov_forest_dataProduce dataset for covariate forest plotting
cov_forest_plotPlot covariate forest plots
ctl_characterConstructor/converter to ctl_character
ctl_contentsGet/set control file contents
ctl_listConstructor/converter to ctl_list
ctl_pathGet and set path to NONMEM control file
data_filter_charGet filter statement
data_ignore_charGet ignore statement
data_pathGet/set path to dataset
decisionMake decision point
delete_dollarDelete a NONMEM subroutine from control file contents
dollarGet/set existing subroutine
dollar_subroutineGet/set $SUBROUTINE values in control file
exclude_rowsExclude rows of NONMEM dataset
fill_inputFill $INPUT
find_nonmemFind location of NONMEM installation
gen_sim_pathGenerate paths for simulation runs
git_cmd_availableCheck if git is available on command line
git_hooksGit hooks
grapes-f-greater-than-grapesFunction pipe for nm objects
gsub_ctlPattern replacement for control file contents
ignoreGet/set ignore statement from control file contents
importImport staged files into project
info_scriptsList information about scripts
init_thetaGet/set initial parameters
input_dataRead input dataset of an nm object
insert_dollarInsert a new subroutine into control file_contents
is_finishedTests if job is finished
is_full_pathTest if full path
is_nmTest if object is an nm coercible object
is_nmproject_dirIs the directory an NMproject directory
is_rstudioLogical flag for detecting if R session is on RStudio
is_successfulTest if NONMEM ran without errors
job_infoGet job information (if it exists)
job_statsGet job stats for a completed NONMEM run
kill_jobKill cluster job
list_dirsList directories
ls_code_libraryList files in code library
ls_scriptsList scripts
make_boot_datasetsPrepare a bootstrap tibble
make_OCC_every_doseMake an OCC column for NONMEM IOV use
make_xv_datasetsWrite (bootstrap) cross validation datasets
new_nmCreate a new (parent) nm object
nmCreate core NM object
nm_create_analysis_projectCreate analysis project
nm_default_dirGet a default directory
nm_default_dirsSetup analysis subdirectories
nm_default_fieldsSetup default nm object fields
nm_diffCompute diff between two NONMEM runs
nm_dirGet a directory name
nm_getsettersFunctions to access and modify fields of nm objects
nm_getsetters_executionExecution related functions to access and modify fields of nm...
nm_list_gatherGet all nm_list objects
nm_outputGet NONMEM output tables
nm_output_pathFind an output file associated with a run
NMproject-packageNMproject: Script Based 'NONMEM' Model Development
nm_read_tableFast read of NONMEM output table
nm_renderCreate run reports
nm_rowConvert nm objects to a row-wise tibble/data.frame
nmsaveSave plots in results_dir
nm_summaryGenerate a summary of NONMEM results
nm_tranRun NMTRAN step of a NONMEM job
nm_tran_commandGet/set nm_tran_command
nm_treeMake data.tree object
nonmem_code_to_rConvert NONMEM code to R ready
NONMEM_versionNONMEM version info
ofvGet Objective Function Value (OFV)
omega_matrixGet OMEGA matrix from run
output_tableReads all $TABLE outputs and merge with input dataset
overwrite_behaviourOverwrite behaviour of NMproject
parallel_executeGeneric execute command for parallelised runs
param_cov_diagPlot relationship between a parameter and covariate
parent_runGet parent object of nm object
pipePipe operator
plot_iterPlot iterations vs parameters/OBJ
plot_iter_dataGet data for iterations vs parameters/OBJ plots
plot_iter_dygraphPlot iterations vs parameters/OBJ with dygraphs
plot_iter_ggplotPlot iterations vs parameters/OBJ (ggplot2)
ppcPPC functions: process data from simulation and plot
psn_availableTest if psn is available locally
psn_checkTests if psn is accessible
psn_style_scmPsN style stepwise covariate method
read_derived_dataRead derived data
reexportsObjects exported from other packages
relative_pathCompute path relative to reference
remove_parameterRemove parameter from NONMEM control file
rename_parameterRename a parameter in NONMEM control stream
rmd_to_vignettesConvert R markdown scripts to vignettes
rrRun record
run_all_scriptsRun all project scripts sequentially
run_dir_pathGet path to run_dir
run_nmRun NONMEM jobs
search_rawSearch for files matching raw text search
setup_code_completionSet up code completion for NMproject
setup_nm_demoSetup demo in current directory
sge_parallel_executeGeneric execute command for SGE grids
shiny_nmRun monitor & summary app
show_ctlShow an uneditable version of the control file
show_outShow an uneditable version of the lst file
simple_fieldInterface for getting and setting your own simple fields in...
stageStage files in project staging area ready for import
start_manual_editStart manual edit
statusGet status of NONMEM runs
status_tableGet status of multiple runs in form of table
subroutineSubroutine
system_cmdSystem/shell command wrapper
system_nmSystem command for NONMEM execution
system_nm_availableTest integrity of system_nm
system_nm_defaultDefault system_nm function
system_nm_internConvenience function for system_nm
tail_lstTail of lst file
targetTarget part of control object for further modification
temp_filesRemove temporary NONMEM files
test_relationsGenerate tibble of covariate relations to test
update_parametersUpdate initial estimates to final estimates
valid_package_namePackage name validator from 'usethis'
view_patchView a patch
wait_finishWait for runs to finish
wait_forWait for statement to be TRUE
wipe_runWipe previous run files
write_ctlWrite control file to disk
write_derived_dataWrite derived data file
NMproject documentation built on Oct. 18, 2021, 1:08 a.m.