Package 'pharmax.viz'

pharmax color palette

Description

pharmax color palette

Usage

px_colors(n = 8)

Arguments

n	Number of colors.

Value

Character vector of hex colors.

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Forest plot for estimates and intervals

Description

Forest plot for estimates and intervals

Usage

px_forest(
  data,
  term = "term",
  estimate = "estimate",
  lower = "lower",
  upper = "upper",
  reference = 0,
  mode = "light"
)

Arguments

data	Data frame with estimate and interval columns.
term	Term label column.
estimate	Estimate column.
lower	Lower interval column.
upper	Upper interval column.
reference	Reference line value.
mode	Theme mode passed to theme_pharmax().

Value

A ggplot2 object.

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Goodness-of-fit diagnostic panel

Description

Creates a four-panel diagnostic plot: DV vs PRED, DV vs IPRED, CWRES vs TIME, and CWRES vs PRED.

Usage

px_gof(data, log_scale = TRUE, mode = "light")

Arguments

data	Data frame with at least DV and PRED columns.
log_scale	Use log10 axes for observed-vs-predicted panels.
mode	Theme mode passed to theme_pharmax().

Value

A patchwork plot object.

---

NPDE diagnostic panel

Description

NPDE diagnostic panel

Usage

px_npde(
  data,
  npde = "NPDE",
  time = "TIME",
  prediction = "PRED",
  mode = "light"
)

Arguments

data	Data frame containing an NPDE-like column.
npde	NPDE column name.
time	Optional time column.
prediction	Optional prediction column.
mode	Theme mode passed to theme_pharmax().

Value

A patchwork plot object.

---

Compose pharmax plots

Description

Compose pharmax plots

Usage

px_plot_grid(
  ...,
  ncol = 2,
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  mode = "light"
)

Arguments

...	ggplot2 or patchwork plots, or a single list of plots.
ncol	Number of columns.
title	Optional grid title.
subtitle	Optional grid subtitle.
caption	Optional grid caption.
mode	Theme mode passed to theme_pharmax().

Value

A patchwork plot object.

---

Residual diagnostic panel

Description

Creates residual-vs-time, residual-vs-prediction, histogram, and QQ panels.

Usage

px_residuals(
  data,
  residual = NULL,
  time = "TIME",
  prediction = "PRED",
  mode = "light"
)

Arguments

data	Data frame containing residual columns.
residual	Residual column. Auto-detects CWRES, IWRES, then RES.
time	Time column used for residual-vs-time when available.
prediction	Prediction column used for residual-vs-prediction when available.
mode	Theme mode passed to theme_pharmax().

Value

A patchwork plot object.

---

Save a pharmax plot

Description

Save a pharmax plot

Usage

px_save(plot, filename, width = 8, height = 6, dpi = 300, ...)

Arguments

plot	A ggplot2 or patchwork plot.
filename	Output filename.
width	Width in inches.
height	Height in inches.
dpi	Resolution.
...	Additional arguments passed to ggplot2::ggsave().

Value

The input filename, invisibly.

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Individual PK concentration-time profiles

Description

Individual PK concentration-time profiles

Usage

px_spaghetti(
  data,
  group = NULL,
  log_y = FALSE,
  facet_by = NULL,
  highlight_ids = NULL,
  mode = "light"
)

Arguments

data	Data frame with ID, TIME, and DV columns.
group	Optional grouping variable for color.
log_y	Use a log10 y-axis.
facet_by	Optional column to facet by.
highlight_ids	Optional vector of subject IDs to highlight.
mode	Theme mode passed to theme_pharmax().

Value

A ggplot2 object.

---

Lightweight visual predictive check

Description

Lightweight visual predictive check

Usage

px_vpc(
  data,
  time = "TIME",
  observed = "DV",
  simulated = "SIM",
  bins = NULL,
  probs = c(0.05, 0.5, 0.95),
  mode = "light"
)

Arguments

data	Data frame with observed and simulated values.
time	Time column.
observed	Observed concentration column.
simulated	Simulated concentration column.
bins	Number of time bins. If NULL, exact time values are used.
probs	Quantiles to show for observed and simulated values.
mode	Theme mode passed to theme_pharmax().

Value

A ggplot2 object.

---

pharmax color scale for ggplot2

Description

pharmax color scale for ggplot2

Usage

scale_color_pharmax(...)

scale_fill_pharmax(...)

Arguments

...	Arguments passed to ggplot2::discrete_scale().

---

The pharmax ggplot2 theme

Description

A clean, publication-ready theme for pharmacometric graphics.

Usage

theme_pharmax(base_size = 12, base_family = "", mode = c("light", "dark"))

Arguments

base_size	Base font size.
base_family	Base font family.
mode	Theme mode, either "light" or "dark".

Value

A ggplot2 theme object.

Examples

library(ggplot2)
ggplot(mtcars, aes(wt, mpg)) +
  geom_point() +
  theme_pharmax()

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