xpose0.4.18 package

Diagnostics for Pharmacometric Models

add_facet_var

Add faceting variable

aes_c

Set new default value for ggplot2 aesthetics

aes_filter

Convenience function to easily filter ggplot2 aesthetics

aes_rename

Convenience function to easily rename ggplot2 aesthetics

all_data_problem

Get all data problems

all_file_problem

Get all file problems

amt_vs_idv

Compartment kinetics

append_suffix

Append suffix contained in the xp_theme to titles

as.ctime

Time converter

as.nm.table.list

Convert an object to nm_table_list class

as.xpdb

Convert an object to xpose_data class

as.xpose.plot

Convert an object to xpose_plot class

as.xpose.theme

Convert an object to xpose_theme class

check_plot_type

Check plot type

check_problem

Check .problem, .subprob and .method

check_quo_vars

Check quoted variables

check_scales

Check plot scales

check_xpdb

Check xpdb

combine_tables

Combine tables

data_opt

Create options for data import

default_plot_problem

Get the default data problem to be plotted

distrib_plot

Distribution plots of ETA and parameters

drop_fixed_cols

Return names of columns having several unique values

dv_vs_pred

Observations plotted against model predictions

edit_xpose_data

Master xpdb editing function

fetch_data

Fetch data

file_path

Generate clean file paths

filter_xp_theme

Subset an xp_theme

get_code

Access model code

get_data

Access model output table data

get_extension

Get file extension

get_file

Access model output file data

get_prm

Access model parameters

get_prm_transformation_formulas

Generate default transformation formulas for parameters

get_special

Access special model data

get_summary

Access model summary data

gg_themes

An additional set of themes for ggplot2

grab_iter

Grab parameter for a given iteration number

ind_plots

Observations, individual predictions and population predictions plotte...

index_table

Index table columns

irep

Add simulation counter

is.formula

Test for formula class

is.nm.model

Test for nm_model class

is.nm.table.list

Test for nm_table_list class

is.xpdb

Test for xpose_data class

is.xpose.plot

Test for xpose_plot class

is.xpose.theme

Test for xpose_theme class

last_data_problem

Get last data problem

last_file_method

Get last file estimation method

last_file_problem

Get last file problem

last_file_subprob

Get last file subproblem

list_nm_tables

List NONMEM output tables

list_nm_tables_manual

Creates an nm_table_list from manually defined table name patterns

list_vars

List available variables

list_xpdb

List available datasets

make_extension

Generate extension string

manual_nm_import

Manually define nonmem tables to be imported

merge_firstonly

Merge firstonly table with full length tables

minimization_plots

Parameter value or gradient vs. iterations

modify_xpdb

Add, remove or rename variables in an xpdb

msg

Message function

only_distinct

Create functions for data deduplication

only_obs

Create functions to drop non observation records

parse_arg

Parse arguments from xpose to ggplot2 format

parse_nm_files

Parse NONMEM output files

parse_title

Parse keywords in string based on values contained in an xpdb

pred_vs_idv

Observations and model predictions plotted against the independent var...

print.ggplot

Import print ggplot method

print.xpose_data

Print an xpose_data object

print.xpose_plot

Draw an xpose_plot object

prm_table

Display a parameter estimates to the console

qq_plot

QQ plots of ETA and residuals

raw_to_tibble

Convert raw strings to tibble

read_args

Define data import arguments

read_funs

Define data import functions

read_nm_files

NONMEM output file import function

read_nm_model

NONMEM model file parser

read_nm_tables

NONMEM output table import function

reexports

Objects exported from other packages

reorder_factors

Reorder factors by numerical order

res_vs_idv

Residuals plotted against the independent variable

res_vs_pred

Residuals plotted against population predictions

set_vars

Set variable type, label or units

software

Get software from the xpdb

subset_xpdb

Subset datasets in an xpdb

summarise_xpdb

Group/ungroup and summarize variables in an xpdb

summary.xpose_data

Summarizing xpose_data

template_titles

Template titles

tidyr_new_interface

Check tidyr version

transform_prm

Mean and variance of tranformed parameters

update_args

Update xpose_geoms arguments

update_extension

Update file extension

update_themes

Create xpose theme

vpc

Visual predictive checks

vpc_data

Visual predictive checks data

vpc_opt

Generate a list of options for VPC data generation

xp_geoms

Generic ggplot2 layer for xpose_plots

xp_map

ggplot2 layer call

xp_themes

A set of xpose themes

xp_var

Access xpdb index information for a given variable or variable type

xpdb_index_update

Update data index

xplot_distrib

Default xpose distribution plot function

xplot_qq

Default xpose QQ plot function

xplot_scatter

Default xpose scatter plot function

xpose-package

xpose: graphical diagnostics for pharmacometric models

xpose_data

Import NONMEM output into R

xpose_panels

Generic panel function for xpose_plots

xpose_save

Save xpose plot

Diagnostics for non-linear mixed-effects (population) models from 'NONMEM' <https://www.iconplc.com/solutions/technologies/nonmem/>. 'xpose' facilitates data import, creation of numerical run summary and provide 'ggplot2'-based graphics for data exploration and model diagnostics.

  • Maintainer: Benjamin Guiastrennec
  • License: LGPL-3
  • Last published: 2024-02-01