indiv_plot: Generate Individual Plots

In certara/ggcertara: A ggplot2 theme for Certara CSC-iDD

Generate Individual Plots

Description

Observations (DV), individual predictions (IPRED), and population predictions (PRED) plotted against the independent variable for each individual.

Usage

indiv_plot(
  data,
  x,
  y,
  ipred,
  pred,
  labels = gof_labels(),
  ip_ncol = 4,
  ip_nrow = 4,
  scale_facet = "fixed",
  labelfacet = "label_value",
  strati1 = id,
  strati2 = NULL,
  color_color = c(dv = ggcertara::certara_pal()[1], outliers =
    ggcertara::certara_pal()[2], ipred = ggcertara::certara_pal()[4], pred =
    ggcertara::certara_pal()[7]),
  fill_fill = c(ipred = ggcertara::certara_pal()[4]),
  alpha_fill = 0.5,
  line_linetype = c(dv = "blank", outliers = "blank", ipred = "solid", pred = "dashed"),
  line_size = 1,
  shape_shape = c(dv = 16, outliers = 10, ipred = NA, pred = NA),
  shape_size = 1,
  cwres.outliers = FALSE,
  limit.outliers = 5,
  uncertainty = FALSE,
  uncert.ci = 0.95,
  ...
)

Arguments

data	A data.frame containing the dataset.
x	The name of the independent variable column. Default value is "time".
y	The name of the dependent variable column. Default value is "dv".
ipred	The name of the individual prediction variable column. Default value is "ipred".
pred	The name of the population prediction variable column. Default value is "pred".
labels	A named list of labels for plot annotations. Default values are provided by gof_labels().
ip_ncol	Number of columns per plot. Default is 4. Adjust if encountering issues with incomplete first rows on the last page due to ggforce::facet_wrap_paginate.
ip_nrow	Number of rows per plot. Default is 4. Adjust similarly to ip_ncol for pagination issues.
strati1	The variable used to stratify the plots. Default is "id".
strati2	An optional variable for an additional layer of stratification. Default is NULL.
color_color	A named vector specifying colors for different elements (dv, ipred, pred, outliers). Should be a vector of 4 colors.
fill_fill	A named vector specifying fill colors for elements when uncertainty is plotted. Specifically for 'ipred' when uncertainty is TRUE.
alpha_fill	Transparency level for the filled area representing the confidence interval, when uncertainty is TRUE.
line_linetype	A named vector specifying line types for different elements (dv, outliers, ipred, pred).
line_size	Line width for the line layer. Default is 1.
shape_shape	A named vector specifying shapes for different elements. When not specified, defaults are used.
shape_size	Size for the shape layer. Default is 1.
cwres.outliers	If TRUE, only profiles of individuals with outlier observations are displayed. Default is FALSE.
limit.outliers	Threshold for CWRES to identify outliers. Default is 5.
uncertainty	If TRUE, plots a confidence interval around individual predictions. Default is FALSE.
uncert.ci	Confidence interval level when uncertainty is TRUE. Default is 0.95.
...	Additional arguments passed to lower-level functions.

Examples

## Not run: 
indiv_plot(data = dat,
           x = "time",
           y = "dv",
           ipred = "ipred",
           pred = "pred",
           strati1 = "id",
           ip_ncol = 3,
           ip_nrow = 4,
           uncertainty = FALSE)

## End(Not run)

# Example with individuals with high cwres values
## Not run: 
indiv_plot(data = dat,
           x = "time",
           y = "dv",
           ipred = "ipred",
           pred = "pred",
           strati1 = "id",
           cwres.outliers = TRUE,
           limit.outliers = 5,
           ip_ncol = 3,
           ip_nrow = 4,
           uncertainty = FALSE)

## End(Not run)

# Example to apply layers with the ampersand sign & (example to change legend.position)
## Not run: 
indiv_plot(data = dat,
           x = "time",
           y = "dv",
           ipred = "ipred",
           pred = "pred",
           strati1 = "id") &
theme(legend.position = "bottom")

## End(Not run)

certara/ggcertara documentation built on Feb. 28, 2024, 5:01 a.m.