Pharmacometric and Pharmacokinetic Toolkit

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Documentation for package ‘pmxTools’ version 0.1.1

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calc_derived_1cpt Calculate derived pharmacokinetic parameters for a 1-compartment linear model
calc_derived_2cpt Calculate derived pharmacokinetic parameters for a 2-compartment linear model
calc_derived_3cpt Calculate derived pharmacokinetic parameters for a 3-compartment linear model
calc_sd_1cmt_linear_bolus Calculate C(t) for a 1-compartment linear model after a single IV bolus dose
calc_sd_1cmt_linear_infusion Calculate C(t) for a 1-compartment linear model after a single infusion
calc_sd_1cmt_linear_oral_0 Calculate C(t) for a 1-compartment linear model with zero-order absorption after a single oral dose
calc_sd_1cmt_linear_oral_0_lag Calculate C(t) for a 1-compartment linear model with zero-order absorption after a single oral dose, with lag time
calc_sd_1cmt_linear_oral_1 Calculate C(t) for a 1-compartment linear model with first-order absorption after a single oral dose
calc_sd_1cmt_linear_oral_1_lag Calculate C(t) for a 1-compartment linear model with first-order absorption after a single oral dose, with lag time
calc_sd_2cmt_linear_bolus Calculate C(t) for a 2-compartment linear model after a single IV bolus dose
calc_sd_2cmt_linear_infusion Calculate C(t) for a 2-compartment linear model after a single infusion
calc_sd_2cmt_linear_oral_0 Calculate C(t) for a 2-compartment linear model after a single zero-order oral dose
calc_sd_2cmt_linear_oral_0_lag Calculate C(t) for a 2-compartment linear model after a single zero-order oral dose, with lag time
calc_sd_2cmt_linear_oral_1 Calculate C(t) for a 2-compartment linear model after a single first-order oral dose
calc_sd_2cmt_linear_oral_1_lag Calculate C(t) for a 2-compartment linear model after a single first-order oral dose with a lag time
calc_sd_3cmt_linear_bolus Calculate C(t) for a 3-compartment linear model after a single IV bolus dose
calc_sd_3cmt_linear_infusion Calculate C(t) for a 3-compartment linear model after a single IV infusion
calc_sd_3cmt_linear_oral_0 Calculate C(t) for a 3-compartment linear model after a single dose, with zero-order absorption
calc_sd_3cmt_linear_oral_0_lag Calculate C(t) for a 3-compartment linear model after a single dose, with zero-order absorption and a lag time
calc_sd_3cmt_linear_oral_1 Calculate C(t) for a 3-compartment linear model after a single oral dose
calc_sd_3cmt_linear_oral_1_lag Calculate C(t) for a 3-compartment linear model after a single oral dose
calc_ss_1cmt_linear_bolus Calculate C(t) for a 1-compartment linear model with IV bolus dosing at steady state
calc_ss_1cmt_linear_infusion Calculate C(t) for a 1-compartment linear model with infusion at steady state
calc_ss_1cmt_linear_oral_0 Calculate C(t) for a 1-compartment linear model with zero-order oral absorption at steady state
calc_ss_1cmt_linear_oral_0_lag Calculate C(t) for a 1-compartment linear model with zero-order oral absorption at steady state, with lag time
calc_ss_1cmt_linear_oral_1 Calculate C(t) for a 1-compartment linear model with first-order oral absorption at steady state
calc_ss_1cmt_linear_oral_1_lag Calculate C(t) for a 1-compartment linear model with first-order oral absorption at steady state, with lag time
calc_ss_2cmt_linear_bolus Calculate C(t) for a 2-compartment linear model with IV bolus dosing at steady-state
calc_ss_2cmt_linear_infusion Calculate C(t) for a 2-compartment linear model with infusion at steady state
calc_ss_2cmt_linear_oral_0 Calculate C(t) for a 2-compartment linear model at steady-state with zero-order oral dosing
calc_ss_2cmt_linear_oral_0_lag Calculate C(t) for a 2-compartment linear model at steady-state with zero-order oral dosing and a lag time
calc_ss_2cmt_linear_oral_1 Calculate C(t) for a 2-compartment linear model at steady-state with first-order oral dosing
calc_ss_2cmt_linear_oral_1_lag Calculate C(t) for a 2-compartment linear model at steady-state with first-order oral dosing
calc_ss_3cmt_linear_bolus Calculate C(t) for a 3-compartment linear model at steady state with IV bolus dosing
calc_ss_3cmt_linear_infusion Calculate C(t) for a 3-compartment linear model at steady state with IV infusions
calc_ss_3cmt_linear_oral_0 Calculate C(t) for a 3-compartment linear model at steady state, with zero-order absorption
calc_ss_3cmt_linear_oral_0_lag Calculate C(t) for a 3-compartment linear model at steady state, with zero-order absorption and lag time
calc_ss_3cmt_linear_oral_1 Calculate C(t) for a 3-compartment linear model at steady-state with first-order oral dosing
calc_ss_3cmt_linear_oral_1_lag Calculate C(t) for a 3-compartment linear model at steady-state with first-order oral dosing with a lag time
get_auc Calculate the area under the curve (AUC) for each subject over the time interval for dependent variables ('dv') using the trapezoidal rule.
get_est_table Create a table of model parameter estimates from a NONMEM output object.
get_omega Extract variability parameter estimates from a NONMEM output object.
get_shrinkage Extract shrinkage estimates from a NONMEM output object.
get_sigma Extract residual variability parameter estimates from a NONMEM output object.
get_theta Extract structural model parameter estimates and associated information from a NONMEM output object.
gm Calculate geometric mean
pcv Calculate percentage coefficient of variation
pk_curve Provide concentration-time curves.
plot_nmprogress Plot NONMEM parameter estimation by iteration.
read_nm Read NONMEM 7.2+ output into a list of lists.
read_nmcov Read in the NONMEM variance-covariance matrix.
read_nmext Read NONMEM output into a list.
read_nmtables Reads NONMEM output tables.
read_scm Read PsN SCM output into a format suitable for further use.
sample_omega Sample from the multivariate normal distribution using the OMEGA variance-covariance matrix to generate new sets of simulated ETAs from NONMEM output.
sample_sigma Sample from the multivariate normal distribution using the SIGMA variance-covariance matrix to generate new sets of simulated EPSILONs from NONMEM output.
sample_uncert Sample from the multivariate normal distribution to generate new sets of parameters from NONMEM output.
table_rtf Read NONMEM output into a list.