# A Pharmacometrics Data Transformation and Analysis Tool

## Documentation for package ‘ruminate’ version 0.3.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

ruminate-package | ruminate: Shiny app and module to facilitate pharamacometrics analysis
apply_route_map | Applies Route Mapping to Dataset
CTS_add_covariate | Add Covariate to Elemetnt
CTS_add_rule | Add Rule to Element
CTS_append_report | Append Report Elements
CTS_change_source_model | Change the Source Model
CTS_del_current_element | Deletes Current cohort
CTS_fetch_code | Fetch Module Code
CTS_fetch_current_element | Fetches Current cohort
CTS_fetch_ds | Fetch Clinical Trial Simulator Module Datasets
CTS_fetch_sc_meta | Fetches Simulation Parameter Meta Information
CTS_fetch_state | Fetch Clinical Trial Simulator State
CTS_init_element_model | Initializes Cohort When Model Changes
CTS_init_state | Initialize CTS Module State
CTS_mk_preload | Make List of Current CTS State
CTS_new_element | New Clinical Trial Simulation Cohort
CTS_plot_element | Plots the Specified Element
CTS_preload | Preload Data for CTS Module
CTS_Server | Clinical Trial Simulator State Server
CTS_set_current_element | Sets the Value for the Current cohort
CTS_simulate_element | Simulates the Specified Element
CTS_sim_isgood | Checks Simulation in Element for Goodness
CTS_test_mksession | Populate Session Data for Module Testing
CTS_update_checksum | Updates CTS Module Checksum
dose_records_builder | Builds Dose Records Dataframe
fetch_rxinfo | Fetches Information from an rxode2 Object
fetch_rxtc | Extracts Timecourse and Merges Covariates
MB_append_report | Append Report Elements
MB_build_code | Build Code to Generate Model
MB_del_current_element | Deletes Current model
MB_fetch_appends | Fetches List of Available Models
MB_fetch_catalog | Fetches List of Available Models
MB_fetch_code | Fetch Module Code
MB_fetch_component | Fetch Selected Current Model Component
MB_fetch_current_element | Fetches Current model
MB_fetch_mdl | Fetch Model Builder Module Models
MB_fetch_state | Fetch Model Builder State
MB_init_state | Initialize MB Module State
MB_mk_preload | Make List of Current MB State
MB_new_element | New Model Building Model
MB_preload | Preload Data for MB Module
MB_Server | Model Builder State Server
MB_set_current_element | Sets the Value for the Current model
MB_test_catalog | Tests the Model Catalog
MB_test_mksession | Populate Session Data for Module Testing
MB_update_checksum | Update MB Module Checksum
MB_update_model | Updates Current Element with rxode2 Model
mk_figure_ind_obs | Creates Figures of Individual Observations from PKNCA Result
mk_rx_obj | Makes an rxode2 Object
mk_subjects | Fetches Information from an rxode2 Object
mk_table_ind_obs | Creates Tables of Individual Observations from PKNCA Result
mk_table_nca_params | Create Tabular Output from PKNCA Results
NCA_add_int | Adds Analysis Interval to Current Analysis
NCA_append_report | Append Report Elements
nca_builder | Builds NCA Code from ui Elements
NCA_fetch_ana_ds | Fetch Analysis Dataset
NCA_fetch_ana_pknca | Fetch PKNCA Results Object
NCA_fetch_code | Fetch Module Code
NCA_fetch_current_ana | Fetches Current Analysis
NCA_fetch_current_obj | Fetches the Current Analysis Object
NCA_fetch_data_format | Fetches Details About Data Requirements
NCA_fetch_ds | Fetch Module Datasets
NCA_fetch_np_meta | Fetches NCA Parameter Meta Information
NCA_fetch_PKNCA_meta | Fetches PKNCA Metadata
NCA_fetch_state | Fetch ruminate State
NCA_find_col | Determines Default Column Name
NCA_init_state | Initialize NCA Module State
NCA_load_scenario | Loads Pre-Defined Scenario
NCA_mkactive_ana | Fetch PKNCA Results Object
NCA_mk_preload | Make List of Current NCA State
NCA_new_ana | Initialize New Analysis
NCA_preload | Preload Data for NCA Module
NCA_process_current_ana | Processes Current Analysis to be Run
NCA_Server | Fetch Non-Compartmental Analysis State
NCA_set_current_ana | Sets Current Analysis
NCA_test_mksession | Populate Session Data for Module Testing
plot_sr_ev | Plots Timecourse of Rules Simulations
plot_sr_tc | Plots Timecourse of Rules Simulations
ruminate | ruminate: Shiny app and module to facilitate pharamacometrics analysis
ruminate_check | Checks 'ruminate' Dependencies
run_nca_components | Runs NCA for the Current Analysis
rx2other | Converts an rxode2 Object Into Specified Model Format
simulate_rules | Rule-Based simulates