plot.td2pLL_mod: Plot interactive td2pLL models

In jcduda/td2pLL: Fitting a time-dose two-parameter log-logistic model to time-dose-response data

Plot interactive td2pLL models

Description

plot.td2pLL_mod is the plot method for the S3 class td2pLL_mod. Model fits generated with the fit_td2pLL() function are of class c("td2pLL_mod", "nls") and can therefore be used for this plot method. If no fitted model but a through parameters pre-specified td2pLL model shall be plotted, this can be done via the plot_td2pLL. For details on the td2pLL model, see fit_td2pLL(). If the TDR() function is used which performs the two-step modeling pipeline, one can apply plot.td2pLL_mod() to the fit list entry of the object returned by TDR(), if fitting a td2pLL model was chosen in accordance to the anova pre-test (see td2pLL_anova()) calculated in TDR().

Usage

## S3 method for class 'td2pLL_mod'
plot(
  x = NULL,
  dose_lim = NULL,
  time_lim = NULL,
  add_model_data = TRUE,
  add_ext_data = NULL,
  n_grid = 100,
  title = NULL,
  xaxis_scale = "log",
  yaxis_scale = "-",
  xaxis_title = "Dose",
  yaxis_title = "Time",
  zaxis_title = "Response",
  add_ED50_line = TRUE,
  ED50_line_col = "red",
  ED50_line_width = 6,
  ...
)

Arguments

x	(td2pLL_mod object) A td2pLL_mod object generatet via fit_td2pLL. If not provided, alternatively, td2pLL_coefs can be provided.
dose_lim	(numeric(2)) Boundaries of the doses (xaxis) for plotting. Note: If xaxis_scale = "log" (default), then dose_lim cannot include 0. If dose_lim shall include the 0, set xaxis_scale = "linear".
time_lim	(numeric(2)) Boundaries for the time (yaxis) for plotting.
add_model_data	(logical(1)) By default the original data used for the fit are added to the plot.
add_ext_data	(data.frame()) Optional numeric data.frame to add data points to the surface plot. Must include columns dose, time and resp.
n_grid	(integer(1)) n_grid*n_grid is the dose*time grid for surface evaluations that will be interpolated. Increase n_grid for a smoother plot.
title	(character(1)) Optional plot title.
xaxis_scale	(character(1) in c("log", "linear", "-") Scale of x-axis (dose-axis). If "-" is set, then plot_ly() tries to guess which scale to use.
yaxis_scale	(character(1) in c("log", "linear", "-") Scale of y-axis (time-axis). If "-" is set, then plot_ly() tries to guess which scale to use.
xaxis_title, yaxis_title, zaxis_title	(character(1)) Title for dose-axis, time-axis and response-axis.
add_ED50_line	(logical(1)) Indicates if the line of ED50 values shall be annotated (=TRUE).
ED50_line_col	(character(1)) Color for optionally added ED50 line.
ED50_line_width	(numeric(1)) Width for optionally added ED50 line.
...	any Not used.

Details

For further details on the td2pLL model, check fit_td2pLL(). For details on the ANOVA used, see td2pLL_anova(). More over, the entire procedure is explained in duda et al. (2021). For plotting, the plot_ly function of package plotly is used.

Examples

data(cytotox)
data_subset <- cytotox[cytotox$compound == "ASP", c("expo", "dose", "resp")]
colnames(data_subset)[1] <- "time"
fit <- fit_td2pLL(data = data_subset)
plot(fit)
plot(fit, xaxis_scale = "linear")
plot(fit, title = "td2pLL model of Compound ASP", dose_lim = c(0.01, 100))
plot(fit, xaxis_scale = "linear", dose_lim = c(0, 15))
# If you want to see how the model looks like for certain parameters,
# use [plot_td2pLL]
plot_td2pLL(td2pLL_coefs = c(h = 2, delta = 3, gamma = 1.5, c0 = 1),
 dose_lim = c(0.01, 10), time_lim = c(1, 5))

jcduda/td2pLL documentation built on May 14, 2022, 6:48 p.m.