SurvFit {morseTKTD} | R Documentation |
Fits a TKTD model for survival analysis using Bayesian inference
Description
This function estimates the parameters of a TKTD model ('SD' or 'IT') for survival analysis using Bayesian inference. In this model, the survival rate of individuals is modeled as a function of the chemical compound concentration with a mechanistic description of the effects on survival over time.
The function returns the parameter estimates of
Toxicokinetic-toxicodynamic (TKTD) models
SD
for 'Stochastic Death' or IT
fo 'Individual Tolerance'.
TKTD models, and particularly the General Unified Threshold model of
Survival (GUTS), provide a consistent process-based
framework to analyse both time and concentration dependent datasets.
In GUTS-SD, all organisms are assumed to have the same internal concentration
threshold (denoted z
), and, once exceeded, the instantaneous probability
to die increases linearly with the internal concentration.
In GUTS-IT, the threshold concentration is distributed among all the organisms, and once
exceeded in one individual, this individual dies immediately.
This is the generic plot
S3 method for the SurvFit
class. It
plots concentration-response fit under target time survival analysis.
Usage
fit(data, model_type, hb_value, ...)
## S3 method for class 'SurvDataCstExp'
fit(data, model_type, hb_value = NULL, ...)
## S3 method for class 'SurvDataVarExp'
fit(data, model_type, hb_value = NULL, ...)
## S3 method for class 'SurvFit'
plot(
x,
xlab = "Time",
ylab = "Number of Survival",
main = NULL,
add_data = TRUE,
add_legend = FALSE,
...
)
Arguments
data |
An object of class |
model_type |
Can be |
hb_value |
If |
... |
Further arguments to be passed to generic methods using argument of sampling function. |
x |
a |
xlab |
label of the x-axis, default is "Time", |
ylab |
label of the y-axis, default is "Number of Survival" |
main |
title of the plot, defaul is |
add_data |
to add original data to the plot. Default ir |
add_legend |
add legend to the plot, default is |
Value
An object of class stanfit
returned by rstan::sampling
an object of class ggplot
, see function ggplot
References
Jager, T., Albert, C., Preuss, T. G. and Ashauer, R. (2011) General unified threshold model of survival-a toxicokinetic-toxicodynamic framework for ecotoxicology, Environmental Science and Technology, 45, 2529-2540. 303-314.