Man pages for PKPDsim
Tools for Performing Pharmacokinetic-Pharmacodynamic Simulations
| add_quotes | Put vector values in quotes |
| add_ruv | Add residual variability to the dependent variable |
| add_ruv_to_quantile | Calculate the increase in a specific quantile for a... |
| adherence_binomial | Binomial adherence |
| adherence_markov | Markov adherence model |
| advan | ADVAN-style functions to calculate linear PK systems |
| advan_create_data | Create ADVAN-style dataset |
| advan_parse_output | Internal function to parse the raw output from ADVAN-style... |
| advan_process_infusion_doses | Add column RATEALL to ADVAN-style dataset to handle infusions |
| analytical_eqn_wrapper | Wrapper for using analytical equations with PKPD regimens |
| apply_duration_scale | Apply infusion duration scale to a regimen |
| apply_lagtime | Apply lagtime to a regimen |
| available_default_literature_models | See models from the literature available for installation |
| bioavailability_to_R_code | Transforms bioavailability specs into appropriate R code |
| calc_auc_analytic | Convenience function to calculate the AUC based on PK model... |
| calc_dydP | Calculate derivative |
| calc_ss_analytic | Returns the state of a linear PK system at steady state... |
| calculate_parameters | Calculate model-specific variables using a dummy call to... |
| check_iov_specification | Checks that IOV was specified appropriately |
| check_mixture_model | Check that mixture model is specified in right format and... |
| check_obs_input | Checks obs input for valid combinations of cmt, var, scale |
| compile_sim_cpp | Compile ODE model to c++ function |
| covariate_last_obs_only | Use only last observed covariate values |
| covariates_table_to_list | Convert covariate table specified as data.frame |
| create_event_table | Create an event table |
| create_obs_data | Create obs data |
| cv_to_omega | Create lower-diagonal omega matrix from CV for parameter... |
| define_tdm_init_model | defines C code for TDM before dose conditions |
| detect_ode_syntax | Auto-detect the syntax for the ODE code |
| f_cov | covariate function builder |
| get_fixed_parameters | Get fixed parameters from model definition. |
| get_model_info | Functions for getting information about a model |
| get_ode_model_size | Get the number of states in the ODE from the code code C++... |
| get_parameters_from_code | Get model parameters from code |
| get_t_obs_from_regimen | Extract sensible default observation times from a specified... |
| get_var_y | Get expected variance/sd/ci of dependent variable based on... |
| ifelse0 | ifelse function but then based on whether value is NULL or... |
| install_default_literature_model | Install default literature model |
| is_newer_package | Check if package number is different from currently... |
| is_positive_definite | Is matrix positive definite |
| join_cov_and_par | Combines covariates and parameters into a single list, useful... |
| join_regimen | Join two dosing regimens |
| lower_triangle_mat_size | Size of the lower triangle of the matrix |
| merge_regimen | Merge two regimens together. |
| model_from_api | Load model definition from API, and compile to R library |
| model_library | Model library |
| mvrnorm2 | More powerful multivariate normal sampling function |
| na_locf | Fill in NAs with the previous non-missing value |
| new_adherence | Probabilistically model adherence |
| new_covariate | New covariate |
| new_covariate_model | covariate model function |
| new_ode_model | Create new ODE model |
| new_regimen | Dose regimen for sim_ode |
| nlmixr_parse_parameters | Function to parse parameters for a model into a structure... |
| nm_to_regimen | Create a regimen from NONMEM data |
| now_utc | Current time in UTC |
| OneCompIVbolus | ADVAN-style equations |
| OneCompIVinfusion | IV infusion- 1 compartment |
| OneCompOral | first-order absorption 1 compartment |
| parse_obs_types | Parse observation types to simulation code |
| pkdata | PK dataset |
| PKPDsim-package | PKPDsim package |
| pkpdsim_to_nlmixr | Convert a model generated with PKPDsim to an object for... |
| pop_regimen | Remove n doses (from tail) of PKPDsim regimen |
| print.covariate | Print function for PKPDsim covariate object |
| print_list | Return a list in R syntax |
| print.PKPDsim | Print function for PKPDsim simulation function |
| print.regimen | Print function for PKPDsim regimen |
| read_model_json | Read model definition from JSON |
| regimen_to_nm | Convert PKPDsim regimen to NONMEM table (doses only) |
| reparametrize | Reparametrize model parameters using a reparametrization... |
| search_replace_in_file | Find string and replace in file |
| shift_regimen | Remove n doses (from start) of PKPDsim regimen |
| shift_state_indices | R starts counting vector indices at 1, c++ starts at 0, so... |
| sim | Simulate ODE or analytical equation |
| sim_core | Only core function of the simulation function, always just... |
| sim_ode | Deprecated function, renamed to 'sim()' |
| sim_ode_shiny | Simulate ODE and create a Shiny app |
| table_to_list | Convert a table to a list |
| test_model | Test a model |
| test_pointer | Test if model still in memory |
| ThreeCompIVbolus | IV bolus- 3 compartment |
| ThreeCompIVinfusion | IV infusion- 3 compartment |
| ThreeCompIVinfusionMetab | 3-compartment IV infusion with first-order metabolite... |
| ThreeCompOral | first-order absorption- 3 compartment |
| ThreeCompOralMetab | first-order absorption- 3 compartment-Metabolite |
| translate_ode | Translate a model from/to various PKPD simulators |
| triangle_to_full | Convert triangle omega matrix to full omega matrix |
| TwoCompIVbolus | IV bolus- 2 compartment |
| TwoCompIVinfusion | IV infusion- 2 compartment |
| TwoCompOral | First-order absorption- 2 compartment |
| vector_to_R_code | Transform a vector into a string that evaluates to the same... |
