plot_sd: Creates plot of model results (uncertainties optional)

In cvasi: Calibration, Validation, and Simulation of TKTD Models

Creates plot of model results (uncertainties optional)

Description

All parameter combinations and exposure patterns are simulated and the mean of predictions is derived for a single study. The uncertainty is passed to the function due to computation time. Results are displayed by plotting the time series including the uncertainty interval. Observation data can be optionally displayed. Data should be provided in long format. Function plots the time (column 1) and the predictions (column 2, can be changed by the user plot_col)

Usage

plot_sd(
  model_base,
  treatments,
  rs_mean,
  rs_range = NULL,
  obs_mean = NULL,
  obs_full = NULL,
  x_breaks = NULL,
  y_lim = NULL,
  grid_labels = NULL,
  grid_ncol = 2,
  plot_col = 2,
  y_title = NULL,
  ...
)

Arguments

model_base	effect scenario object with mean parameters
treatments	treatments exposure levels as data frame
rs_mean	data.frame, model results best fit params
rs_range	data.frame, uncertainties as data frame
obs_mean	data.frame, observation data with means per treatment level
obs_full	data.frame, full set including results for replicates
x_breaks	optional vector of breaks of x-axis
y_lim	optional vector containing limits of y-axis
grid_labels	optional labels of grid headers
grid_ncol	optional number of grid columns
plot_col	output column which should be plotted
y_title	optional title of y-axis
...	any additional parameters

Value

a ggplot2 plot object

Examples

set.seed(124)
exposure <- data.frame(
  time = 0:21,
  conc = rnorm(n = 22, mean = 0.1, sd = 0.06),
  trial = "T1"
)
forcings <- list(temp = 12, rad = 15000)
param <- list(EC50 = 0.3, b = 4.16, P_up = 0.0054)
inits <- list(BM = 0.0012, E = 1, M_int = 0)

scenario <- Lemna_Schmitt() %>%
  set_forcings(forcings) %>%
  set_param(param) %>%
  set_init(inits)

sim_result <- simulate_batch(
  model_base = scenario,
  treatments = exposure,
  param_sample = NULL
)

plot_sd(
  model_base = scenario,
  treatments = exposure,
  rs_mean = sim_result
)

cvasi documentation built on Sept. 23, 2024, 9:08 a.m.