LCX: Predict X% Lethal Concentration at the maximum time point...

In morse: Modelling Reproduction and Survival Data in Ecotoxicology

Predict X% Lethal Concentration at the maximum time point (default).

Description

Predict median and 95% credible interval of the x% Lethal Concentration.

The function LCx, x% Lethal Concentration (LC_x), is use to compute the dose required to kill x% of the members of a tested population after a specified test duration (time_LCx) (default is the maximum time point of the experiment).

Mathematical definition of x% Lethal Concentration at time t, denoted LC(x,t), is:

S(LC(x,t), t) = S(0, t)*(1- x/100),

where S(LC(x,t), t) is the survival probability at concentration LC(x,t) at time t, and S(0,t) is the survival probability at no concentration (i.e. concentration is 0) at time t which reflect the background mortality h_b:

S(0, t) = exp(-hb* t).

In the function LCx, we use the median of S(0,t) to rescale the x% Lethal Concentration at time t.

Usage

LCx(object, ...)

## S3 method for class 'survFit'
LCx(object, X, time_LCx = NULL, conc_range = NULL, npoints = 100, ...)

Arguments

object	An object of class survFit
...	Further arguments to be passed to generic methods
X	Percentage of individuals dying (e.g., 50 for LC_{50}, 10 for LC_{10}, ...)
time_LCx	A number giving the time at which LC_{x} has to be estimated. If NULL, the latest time point of the experiment is used.
conc_range	A vector of length 2 with minimal and maximal value of the range of concentration. If NULL, the range is define between 0 and the highest tested concentration of the experiment.
npoints	Number of time point in conc_range between 0 and the maximal concentration. 100 by default.

Details

When class of object is survFit, see LCx.survFit.

Value

returns an object of class LCx.

The function returns an object of class LCx, which is a list with the following information:

X_prop	Survival probability of individuals surviving considering the median of the background mortality (i.e. S(0, t)*(1- x/100))
X_prop_provided	Survival probability of individuals surviving as provided in arguments (i.e. (100-X)/100)
time_LCx	A number giving the time at which LC_{x} has to be estimated as provided in arguments or if NULL, the latest time point of the experiment is used.
df_LCx	A data.frame with quantiles (median, 2.5% and 97.5%) of LC_{X} at time time_LCx for X% of individuals
df_dose	A data.frame with four columns: concentration, and median q50 and 95% credible interval (qinf95 and qsup95) of the survival probability at time time_LCx

Examples

# (1) Load the data
data("propiconazole")

# (2) Create an object of class 'survData'
dataset <- survData(propiconazole)


# (3) Run the survFit function with model_type SD (or IT)
out_SD <- survFit(dataset, model_type = "SD")

# (4) estimate LC50 at time 4
LCx(out_SD, X = 50, time_LCx = 4)

morse documentation built on Oct. 29, 2022, 1:14 a.m.