Reference

Automatic import of run output

Import tables and output files from a NLME run to R.

xpose_data()

Import NONMEM output into R

Manual import of run output

Manually import tables and output files from a NLME run to R.

read_nm_files()

NONMEM output file import function

read_nm_model()

NONMEM model file parser

manual_nm_import()

Manually define nonmem tables to be imported

list_nm_tables()

List NONMEM output tables

read_nm_tables()

NONMEM output table import function

xpdb examples

Example of xpose_data

xpdb_ex_pk

xpose_data examples

Data summary

Summarize the xpdb content or the run

print(<xpose_data>)

Print an xpose_data object

summary(<xpose_data>)

Summarizing xpose_data

prm_table()

Display a parameter estimates to the console

list_vars()

List available variables

list_data() list_files() list_special()

List available datasets

Edit xpdb content

Edit data, index or files within an xpdb

filter(<xpose_data>) slice(<xpose_data>) distinct(<xpose_data>)

Subset datasets in an xpdb

mutate(<xpose_data>) select(<xpose_data>) rename(<xpose_data>)

Add, remove or rename variables in an xpdb

group_by(<xpose_data>) ungroup(<xpose_data>) summarise(<xpose_data>) summarize(<xpose_data>)

Group/ungroup and summarize variables in an xpdb

irep()

Add simulation counter

set_var_types() set_var_labels() set_var_units()

Set variable type, label or units

Access data from an xpdb

Access code, data, files or summary from an xpdb object

get_code()

Access model code

get_data()

Access model output table data

get_file()

Access model output file data

get_prm()

Access model parameters

get_special()

Access special model data

get_summary()

Access model summary data

Basic gof

Basic goodness-of-fit plots.

res_vs_idv() absval_res_vs_idv()

Residuals plotted against the independent variable

res_vs_pred() absval_res_vs_pred()

Residuals plotted against population predictions

dv_vs_ipred() dv_vs_pred()

Observations plotted against model predictions

dv_vs_idv() ipred_vs_idv() pred_vs_idv() dv_preds_vs_idv()

Observations and model predictions plotted against the independent variable

Indiviudal plots

Indiviudal observations and model predictions profiles by the independent variable

ind_plots()

Observations, individual predictions and population predictions plotted against the independent variable for every individual

Visual predictive checks

Visual predictive checks data and plot generation

vpc_data()

Visual predictive checks data

vpc_opt()

Generate a list of options for VPC data generation

vpc()

Visual predictive checks

Distribution plots

Covariate, parameters, etas and residuals distribution plots

prm_distrib() eta_distrib() res_distrib() cov_distrib()

Distribution plots of ETA and parameters

QQ plots

Covariate, parameters, etas and residuals QQ plots

prm_qq() eta_qq() res_qq() cov_qq()

QQ plots of ETA and residuals

Kinetic plots

Plots of compartments’ amount

amt_vs_idv()

Compartment kinetics

Minimization diagnostics

Graphics to evaluate the estimation step

prm_vs_iteration() grd_vs_iteration()

Parameter value or gradient vs. iterations

General plotting functions

Functions to manually create customized plots from an xpose_data object.

xplot_distrib()

Default xpose distribution plot function

xplot_qq()

Default xpose QQ plot function

xplot_scatter()

Default xpose scatter plot function

data_opt()

Create options for data import

Customize plots

Add, customize themes or template titles.

template_titles

Template titles

update_themes()

Create xpose theme

theme_bw2() theme_readable()

An additional set of themes for ggplot2

theme_xp_default() theme_xp_xpose4()

A set of xpose themes

Print plots to the console or save them into a file.

print(<xpose_plot>)

Draw an xpose_plot object

xpose_save()

Save xpose plot