distrib_plot: Distribution plots of ETA and parameters

In xpose: Diagnostics for Pharmacometric Models

Distribution plots of ETA and parameters

Description

Histograms and density plots of the ETA and parameter values.

Usage

prm_distrib(
  xpdb,
  mapping = NULL,
  drop_fixed = TRUE,
  type = "hr",
  title = "Parameter distribution | @run",
  subtitle = "Based on @nind individuals",
  caption = "@dir",
  tag = NULL,
  log = NULL,
  guide = FALSE,
  facets,
  .problem,
  quiet,
  ...
)

eta_distrib(
  xpdb,
  mapping = NULL,
  drop_fixed = TRUE,
  type = "hr",
  title = "Eta distribution | @run",
  subtitle = "Based on @nind individuals, Eta shrink: @etashk",
  caption = "@dir",
  tag = NULL,
  log = NULL,
  guide = FALSE,
  facets,
  .problem,
  quiet,
  ...
)

res_distrib(
  xpdb,
  mapping = NULL,
  res = "CWRES",
  type = "hr",
  title = "@x distribution | @run",
  subtitle = "Based on @nobs observations",
  caption = "@dir",
  tag = NULL,
  log = NULL,
  guide = FALSE,
  facets,
  .problem,
  quiet,
  ...
)

cov_distrib(
  xpdb,
  mapping = NULL,
  drop_fixed = TRUE,
  type = "hr",
  title = "Continuous covariates distribution | @run",
  subtitle = "Based on @nind individuals",
  caption = "@dir",
  tag = NULL,
  log = NULL,
  guide = FALSE,
  facets,
  .problem,
  quiet,
  ...
)

Arguments

xpdb	An xpose database object.
mapping	List of aesthetics mappings to be used for the xpose plot (e.g. point_color).
drop_fixed	Should columns that only have a single unique value (i.e. fixed) be dropped.
type	String setting the type of plot to be used. Can be histogram 'h', density 'd', rug 'r' or any combination of the three.
title	Plot title. Use NULL to remove.
subtitle	Plot subtitle. Use NULL to remove.
caption	Page caption. Use NULL to remove.
tag	Plot identification tag. Use NULL to remove.
log	String assigning logarithmic scale to axes, can be either ”, 'x', y' or 'xy'.
guide	Should the guide (e.g. reference distribution) be displayed.
facets	Either a character string to use facet_wrap_paginate or a formula to use facet_grid_paginate.
.problem	The $problem number to be used. By default returns the last estimation problem.
quiet	Logical, if FALSE messages are printed to the console.
...	Any additional aesthetics to be passed on xplot_scatter.
res	Only used for res_distrib. Defines the type of residual to be used. Default is "CWRES".

Layers mapping

Plots can be customized by mapping arguments to specific layers. The naming convention is layer_option where layer is one of the names defined in the list below and option is any option supported by this layer e.g. histogram_fill = 'blue', rug_sides = 'b', etc.

• histogram: options to geom_histogram

• density: options to geom_density

• rug: options to geom_rug

• xscale: options to scale_x_continuous or scale_x_log10

• yscale: options to scale_y_continuous or scale_y_log10

Faceting

Every xpose plot function has built-in faceting functionalities. Faceting arguments are passed to the functions facet_wrap_paginate when the facets argument is a character string (e.g. facets = c('SEX', 'MED1')) or facet_grid_paginate when facets is a formula (e.g. facets = SEX~MED1). All xpose plot functions accept all the arguments for the facet_wrap_paginate and facet_grid_paginate functions e.g. dv_vs_ipred(xpdb_ex_pk, facets = SEX~MED1, ncol = 3, nrow = 3, page = 1, margins = TRUE, labeller = 'label_both').

Faceting options can either be defined in plot functions (e.g. dv_vs_ipred(xpdb_ex_pk, facets = 'SEX')) or assigned globally to an xpdb object via the xp_theme (e.g. xpdb <- update_themes(xpdb_ex_pk, xp_theme = list(facets = 'SEX'))). In the latter example all plots generate from this xpdb will automatically be stratified by 'SEX'.

By default, some plot functions use a custom stratifying variable named 'variable', e.g. eta_distrib(). When using the facets argument, 'variable' needs to be added manually e.g. facets = c('SEX', 'variable') or facets = c('SEX', 'variable'), but is optional, when using the facets argument in xp_theme variable is automatically added whenever needed.

Template titles

Template titles can be used to create highly informative diagnostics plots. They can be applied to any plot title, subtitle, caption and tag. Template titles are defined via a single string containing key variables staring with a '@' (e.g. '@ofv') which will be replaced by their actual value when rendering the plot. For example ''@run, @nobs observations in @nind subjects'' would become ''run001, 1022 observations in 74 subjects''. The available key variables are listed under template_titles.

See Also

xplot_distrib

Examples

# Histogram of parameters
prm_distrib(xpdb_ex_pk, type = 'h')

# Density plot of etas with a rug
eta_distrib(xpdb_ex_pk, type = 'dr')

# Histogram of different residuals
res_distrib(xpdb_ex_pk, type = 'hr', res = c('IWRES', 'CWRES'))

# Density plot of continuous covariates
cov_distrib(xpdb_ex_pk, type = 'd')

xpose documentation built on May 29, 2024, 5:12 a.m.