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 distribution on y when residual
                        variability is added
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 functions
advan_process_infusion_doses
                        Add column RATEALL to ADVAN-style dataset to
                        handle infusions
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
calc_auc_analytic       Convenience function to calculate the AUC based
                        on PK model parameters at any given moment, for
                        linear iv models.
calc_dydP               Calculate derivative
calc_ss_analytic        Returns the state of a linear PK system at
                        steady state (trough) using analytics equations
                        (so for linear PK systems only).
calculate_parameters    Calculate model-specific variables using a
                        dummy call to sim_ode()
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
cv_to_omega             Create lower-diagonal omega matrix from CV for
                        parameter estimates
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++ code for model
get_parameters_from_code
                        Get model parameters from code
get_var_y               Get expected variance/sd/ci of dependent
                        variable based on PKPDsim model, parameters,
                        and regimen
ifelse0                 ifelse function but then based on whether value
                        is NULL or not
install_default_literature_model
                        Install default literature model
is_positive_definite    Is matrix positive definite
join_cov_and_par        Combines covariates and parameters into a
                        single list, useful for reparametrization of
                        the model.
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 used by nlmixr
nm_to_regimen           Create a regimen from NONMEM data
pkdata                  PK dataset
pkpdsim_to_nlmixr       Convert a model generated with PKPDsim to an
                        object for nlmixr
pop_regimen             Remove n doses (from tail) of PKPDsim regimen
print_list              Return a list in R syntax
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 defined within the model.
search_replace_in_file
                        Find string and replace in file
shift_regimen           Remove n doses (from start) of PKPDsim regimen
sim                     Simulate ODE or analytical equation
sim_core                Only core function of the simulation function,
                        always just returns observations. Mostly useful
                        for estimations / optimal design. Has no checks
                        (for speed)!
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
translate_ode           Translate a model from/to various PKPD
                        simulators
triangle_to_full        Convert triangle omega matrix to full omega
                        matrix
