Man pages for tsahota/NMproject
Script Based 'NONMEM' Model Development
| add_mixed_param | Add a mixed effect parameter to $PK (or $PRED) |
| add_remove_covs | Add/remove a covariate to a NONMEM model |
| append_nonmem_var | Include NONMEM variables in output table |
| apply_manual_edit | Apply a manual edit patch |
| as_nm_generic | Convert nm object to nm_generic |
| as_nm_list | Coerce object into nm_list |
| based_on | Use file to set control file contents in nm object |
| bind_covariate_results | Add run results into a covariate tibble |
| block-omega-sigma | Create or remove $OMEGA/$SIGMA BLOCKs |
| boot_to_csv | Save bootstrap datasets to disk |
| change_parent | Change parent object |
| check_installation | Check NMproject installation |
| child | Make child nm object from parent |
| code_library | Code Library |
| coef_widelong | Extract parameter values |
| comment_lines | 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 |
| 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_character | Constructor/converter to ctl_character |
| ctl_contents | Get/set control file contents |
| ctl_list | Constructor/converter to ctl_list |
| ctl_path | Get and set path to NONMEM control file |
| data_filter_char | Get filter statement |
| data_ignore_char | Get ignore statement |
| 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 |
| exclude_rows | Exclude rows of NONMEM dataset |
| fill_input | Fill $INPUT |
| find_nonmem | Find location of NONMEM installation |
| gen_sim_path | Generate paths for simulation runs |
| git_cmd_available | Check if git is available on command line |
| git_hooks | Git hooks |
| grapes-f-greater-than-grapes | Function pipe for nm objects |
| gsub_ctl | Pattern replacement for control file contents |
| ignore | Get/set ignore statement from control file contents |
| import | Import staged files into project |
| info_scripts | List information about scripts |
| 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_full_path | Test if full path |
| is_nm | Test if object is an nm coercible object |
| is_nmproject_dir | Is the directory an NMproject directory |
| is_rstudio | Logical flag for detecting if R session is on RStudio |
| is_successful | Test if NONMEM ran without errors |
| job_info | Get job information (if it exists) |
| job_stats | Get job stats for a completed NONMEM run |
| job_time_spacing | Setup default job_time_spacing option |
| kill_job | Kill cluster job |
| list_dirs | List directories |
| ls_code_library | List files in code library |
| ls_scripts | List scripts |
| 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 |
| map_nm | A purrr-like looping function over nm objects |
| new_nm | Create a new (parent) nm object |
| nm | Create core NM object |
| 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... |
| nm_list_gather | Get all nm_list objects |
| nm_output | Get NONMEM output tables |
| nm_output_path | Find an output file associated with a run |
| NMproject-package | NMproject: Script Based 'NONMEM' Model Development |
| nm_read_table | Fast read of NONMEM output table |
| nm_render | Create run reports |
| nm_row | Convert nm objects to a row-wise tibble/data.frame |
| nmsave | Save plots in results_dir |
| 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_code_to_r | Convert NONMEM code to R ready |
| NONMEM_version | NONMEM version info |
| ofv | Get Objective Function Value (OFV) |
| omega_matrix | Get OMEGA matrix from run |
| output_table | Reads all $TABLE outputs and merge with input dataset |
| overwrite_behaviour | Overwrite behaviour of NMproject |
| parallel_execute | Generic execute command for parallelised runs |
| param_cov_diag | Plot relationship between a parameter and covariate |
| parent_run | Get parent object of nm object |
| pipe | Pipe operator |
| plot_iter | Plot iterations vs parameters/OBJ |
| plot_iter_data | Get data for iterations vs parameters/OBJ plots |
| plot_iter_dygraph | Plot iterations vs parameters/OBJ with dygraphs |
| plot_iter_ggplot | Plot iterations vs parameters/OBJ (ggplot2) |
| ppc | PPC functions: process data from simulation and plot |
| psn_available | Test if psn is available locally |
| psn_check | Tests if psn is accessible |
| psn_style_scm | PsN style stepwise covariate method |
| read_derived_data | Read derived data |
| reexports | Objects exported from other packages |
| relative_path | Compute path relative to reference |
| remove_parameter | Remove parameter from NONMEM control file |
| rename_parameter | Rename a parameter in NONMEM control stream |
| rmd_to_vignettes | Convert R markdown scripts to vignettes |
| rr | Run record |
| run_all_scripts | Run all project scripts sequentially |
| run_dir_path | Get path to run_dir |
| run_nm | Run NONMEM jobs |
| run_nm_single | Run NONMEM jobs (single job) |
| 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... |
| stage | Stage files in project staging area ready for import |
| start_manual_edit | Start manual edit |
| status | Get status of NONMEM runs |
| status_table | Get status of multiple runs in form of table |
| subroutine | Subroutine |
| system_cmd | System/shell command wrapper |
| system_nm | System command for NONMEM execution |
| system_nm_available | Test integrity of system_nm |
| system_nm_default | Default system_nm function |
| system_nm_intern | Diagnostic test for system_nm |
| tail_lst | Tail of lst file |
| target | Target part of control object for further modification |
| temp_files | Remove temporary NONMEM files |
| test_relations | Generate tibble of covariate relations to test |
| update_parameters | Update initial estimates to final estimates |
| valid_package_name | Package name validator from 'usethis' |
| view_patch | View a patch |
| wait_finish | Wait for runs to finish |
| wait_for | Wait for statement to be TRUE |
| wipe_run | Wipe previous run files |
| write_ctl | Write control file to disk |
| write_derived_data | Write derived data file |
