plot.pk {invivoPKfit}R Documentation

Plot a [pk()] object.

Description

Plot data and model fits from a [pk()] object.

Usage

## S3 method for class 'pk'
plot(
  x,
  newdata = NULL,
  model = NULL,
  method = NULL,
  use_scale_conc = FALSE,
  time_trans = FALSE,
  log10_C = NULL,
  plot_data_aes = NULL,
  plot_point_aes = NULL,
  facet_fun = NULL,
  facet_fun_args = NULL,
  drop_nonDetect = FALSE,
  plot_fit_aes = NULL,
  n_interp = 10,
  fit_limits = NULL,
  print_out = FALSE,
  best_fit = FALSE,
  ...
)

Arguments

x

A [pk()] object. In this case 'x' is used to align with generic method.

newdata

Optional: A 'data.frame' containing new data to plot. Must contain at least variables 'Chemical', 'Species', 'Route', 'Media', 'Dose', 'Time', 'Time.Units', 'Conc', 'Detect', 'Conc_SD'. Default 'NULL', to use the data in 'obj$data'.

model

Character: One or more of the models fitted. Curve fits will be plotted for these models. Default 'NULL' to plot fits for all models in 'x$stat_model'.

method

Character: One or more of the [optimx::optimx()] methods used. Default 'NULL' to plot fits for all methods in 'x$settings_optimx$method'.

use_scale_conc

Possible values: 'TRUE', 'FALSE', or a named list with elements 'dose_norm' and 'log10_trans' which themselves should be either 'TRUE' or 'FALSE'. If 'use_scale_conc = FALSE' (the default for this function), then the data and fits will be plotted without any dose-normalization or log-transformation. If 'use_scale_conc = TRUE' , then the concentration scaling/transformations in 'x' will be applied to the y-axis (concentration axis). If 'use_scale_conc = list(dose_norm = ..., log10_trans = ...)', then the specified dose normalization and/or log10-transformation will be applied to the y-axis (concentration axis) of the plots.

time_trans

Default 'FALSE'. Determines whether time values will be transformed.

log10_C

Default 'NULL'. Determines whether y-axis (concentration) should be log10 transformed. Takes 'TRUE' or 'FALSE' values. Otherwise it defaults to the value determined from 'use_scale_conc'.

plot_data_aes

Optional: Aesthetic mapping for the plot layer that visualizes the data. Default 'NULL', in which case a default mapping will be used based on the value of 'use_scale_conc'.

plot_point_aes

Optional: Aesthetic mappings for geom_point layer that determines the fill of the points. Defaults to 'NULL'.

facet_fun

Default '"facet_grid"'. Optional: The name of the 'ggplot2' faceting function to use: [ggplot2::facet_grid()], [ggplot2::facet_wrap()], or ''none'' to do no faceting. Default 'NULL', in which case a default faceting will be applied based on the value of 'use_scale_conc'.

facet_fun_args

A named list of arguments to the faceting function in 'facet_fun' (if any). Default: “' list(rows = ggplot2::vars(Route), cols= ggplot2::vars(Media), scales = "free_y", labeller = "label_both") “'

drop_nonDetect

Default 'FALSE'. Whether to eliminate observations below the level of quantification (LOQ).

plot_fit_aes

Optional: Aesthetic mapping for the plot layer that visualizes the fitted curves. Default 'NULL', in which case a default mapping will be used based on the value of 'use_scale_conc'.

n_interp

For plotting: the number of time points to interpolate between each observed time point. Default 10.

fit_limits

Default 'NULL'. c(Upper Bound, Lower Bound). Supply a numeric vector. These values filter the predicted values for fits to not exceed 2.25x of the maximum observed concentration values for each 'data_group' in the 'pk' object. When there is a log10 transformation of concentration values, it limits predicted values to 1/20th of the minimum observed concentration values and 5 times the maximum value.

print_out

For plotting: whether the output of the function should be the list of plots. Default 'FALSE'.

best_fit

Default FALSE. Determines whether fit plot outputs only the best fit from 'get_winning_model()'

...

Additional arguments not in use.

Details

If the [pk()] object has not been fitted, then only the data will be plotted (because no curve fits exist).

Value

A [ggplot2::ggplot()]-class plot object.

Author(s)

Caroline Ring, Gilberto Padilla Mercado


[Package invivoPKfit version 2.0.1 Index]