Pharmacometric and Pharmacokinetic Toolkit

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Documentation for package ‘pmxTools’ version 1.3

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blq_log_trans A transform for ggplot2 with data that may be below the lower limit of quantification
blq_trans A transform for ggplot2 with data that may be below the lower limit of quantification
breaks_blq_general Generate breaks for measurements below the limit of quantification
calc_derived Calculate derived pharmacokinetic parameters for a 1-, 2-, or 3-compartment linear model.
calc_derived_1cpt Calculate derived pharmacokinetic parameters for a 1-, 2-, or 3-compartment linear model.
calc_derived_2cpt Calculate derived pharmacokinetic parameters for a 1-, 2-, or 3-compartment linear model.
calc_derived_3cpt Calculate derived pharmacokinetic parameters for a 1-, 2-, or 3-compartment linear model.
calc_sd_1cmt Calculate C(t) for a 1-compartment linear model
calc_sd_1cmt_linear_bolus Calculate C(t) for a 1-compartment linear model
calc_sd_1cmt_linear_infusion Calculate C(t) for a 1-compartment linear model
calc_sd_1cmt_linear_oral_0 Calculate C(t) for a 1-compartment linear model
calc_sd_1cmt_linear_oral_0_lag Calculate C(t) for a 1-compartment linear model
calc_sd_1cmt_linear_oral_1 Calculate C(t) for a 1-compartment linear model
calc_sd_1cmt_linear_oral_1_lag Calculate C(t) for a 1-compartment linear model
calc_sd_2cmt Calculate C(t) for a 2-compartment linear model
calc_sd_2cmt_linear_bolus Calculate C(t) for a 2-compartment linear model
calc_sd_2cmt_linear_infusion Calculate C(t) for a 2-compartment linear model
calc_sd_2cmt_linear_oral_0 Calculate C(t) for a 2-compartment linear model
calc_sd_2cmt_linear_oral_0_lag Calculate C(t) for a 2-compartment linear model
calc_sd_2cmt_linear_oral_1 Calculate C(t) for a 2-compartment linear model
calc_sd_2cmt_linear_oral_1_lag Calculate C(t) for a 2-compartment linear model
calc_sd_3cmt Calculate C(t) for a 3-compartment linear model
calc_sd_3cmt_linear_bolus Calculate C(t) for a 3-compartment linear model
calc_sd_3cmt_linear_infusion Calculate C(t) for a 3-compartment linear model
calc_sd_3cmt_linear_oral_0 Calculate C(t) for a 3-compartment linear model
calc_sd_3cmt_linear_oral_0_lag Calculate C(t) for a 3-compartment linear model
calc_sd_3cmt_linear_oral_1 Calculate C(t) for a 3-compartment linear model
calc_sd_3cmt_linear_oral_1_lag Calculate C(t) for a 3-compartment linear model
calc_ss_1cmt Calculate C(t) for a 1-compartment linear model at steady-state
calc_ss_1cmt_linear_bolus Calculate C(t) for a 1-compartment linear model at steady-state
calc_ss_1cmt_linear_infusion Calculate C(t) for a 1-compartment linear model at steady-state
calc_ss_1cmt_linear_oral_0 Calculate C(t) for a 1-compartment linear model at steady-state
calc_ss_1cmt_linear_oral_0_lag Calculate C(t) for a 1-compartment linear model at steady-state
calc_ss_1cmt_linear_oral_1 Calculate C(t) for a 1-compartment linear model at steady-state
calc_ss_1cmt_linear_oral_1_lag Calculate C(t) for a 1-compartment linear model at steady-state
calc_ss_2cmt Calculate C(t) for a 2-compartment linear model at steady-state
calc_ss_2cmt_linear_bolus Calculate C(t) for a 2-compartment linear model at steady-state
calc_ss_2cmt_linear_infusion Calculate C(t) for a 2-compartment linear model at steady-state
calc_ss_2cmt_linear_oral_0 Calculate C(t) for a 2-compartment linear model at steady-state
calc_ss_2cmt_linear_oral_0_lag Calculate C(t) for a 2-compartment linear model at steady-state
calc_ss_2cmt_linear_oral_1 Calculate C(t) for a 2-compartment linear model at steady-state
calc_ss_2cmt_linear_oral_1_lag Calculate C(t) for a 2-compartment linear model at steady-state
calc_ss_3cmt Calculate C(t) for a 3-compartment linear model at steady-state
calc_ss_3cmt_linear_bolus Calculate C(t) for a 3-compartment linear model at steady-state
calc_ss_3cmt_linear_infusion Calculate C(t) for a 3-compartment linear model at steady-state
calc_ss_3cmt_linear_oral_0 Calculate C(t) for a 3-compartment linear model at steady-state
calc_ss_3cmt_linear_oral_0_lag Calculate C(t) for a 3-compartment linear model at steady-state
calc_ss_3cmt_linear_oral_1 Calculate C(t) for a 3-compartment linear model at steady-state
calc_ss_3cmt_linear_oral_1_lag Calculate C(t) for a 3-compartment linear model at steady-state
count_na Count the number of NA values in a vector.
dgr_table Generate a summary table of descriptive data for every individual in a dataset suitable for tabulation in a report.
estimate_lloq Estimate the lower limit of quantification (LLOQ) from a vector
fmt_signif Format a number with the correct number of significant digits and trailing zeroes.
ftrans_blq_linear Forward transformation for linear BLQ data
ftrans_blq_log Forward transformation for linear BLQ data
gcv Calculate a geometric coefficient of variation.
gcv_convert Convert geometric variance or standard deviation to a geometric coefficient of variation
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_probinfo Extract problem and estimation information 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
itrans_blq_linear Inverse transformation for linear BLQ data
itrans_blq_log Inverse transformation for linear BLQ data
label_blq Label axes with censoring labels for BLQ
pcv Calculate percentage coefficient of variation
pk_curve Provide concentration-time curves.
plot_dist Plot a distribution as a hybrid containing a halfeye, a boxplot and jittered points.
plot_nmprogress Plot NONMEM parameter estimation by iteration.
plot_scm Visualize PsN SCM output.
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_nm_all Read all NONMEM files for a single NONMEM run.
read_nm_multi_table Read (single or) multiple NONMEM tables from a single file
read_nm_std_ext Read a standard NONMEM extension file
read_scm Read PsN SCM output into a format suitable for further use.
rnm Read NONMEM 7.2+ output into an R object.
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.