R: Pharmacometric and Pharmacokinetic Toolkit

# Pharmacometric and Pharmacokinetic Toolkit

## Documentation for package ‘pmxTools’ version 1.5

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

## Help Pages

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.