stressaddition (version 3.1.0)

lc: Lethal Concentrations

Description

Estimate the concentration to reach a certain mortality relative to the control.

Usage

lc(model, response_name, response_level, reference, warn = TRUE)

Arguments

model

This can be one of three types of objects: Either the output of ecxsys or the output of predict_ecxsys or a data frame with a "concentration" column and a response_name column. In the case of the data frame the first row is assumed to be the control. See the examples.

response_name

The name of the survival or stress for which you want to calculate the LC.

response_level

The desired response level as a percentage between 0 and 100. For example with the value 10 the function will return the LC10, i.e. the concentration where the response falls below 90 % of the control response. In other words: where a mortality of 10 % relative to the control is reached.

reference

The reference value of the response, usually the control at concentration 0. This argument is optional. If it is missing, the first value of the response is used as control. This value determines what number response_level actually corresponds to. For example if response_level is 10 and reference is 45, then the function returns the concentration where the curve is reduced by 10% relative to 45 = 40.5.

warn

Logical. Should the function emit a warning if the calculation of the lethal concentration is not possible?

Value

A list containing the lethal concentration and the corresponding survival. The survival will be NA if its calculation is impossible using the supplied data.

Details

If the response level occurs multiple times because of hormesis, which may happen for low values of response_level, then the occurrence with the smallest concentration is returned.

This function only makes sense for curves which generally go down with increasing concentration, i.e. all survival_* curves and also sys_tox and sys_tox_env. Others are untested and may give unexpected results, if any.

Examples

# NOT RUN {
# Calculate the LC10, the concentration where the survival falls
# below 90% of the survival in the control.

model <- ecxsys(
    concentration = c(0, 0.05, 0.5, 5, 30),
    hormesis_concentration = 0.5,
    survival_tox_observed = c(90, 81, 92, 28, 0)
)

# using the ecxsys() output or the curves therein directly:
lc(model, "survival_tox_sys", 10)
lc(model$curves, "survival_tox_sys", 10)

# using the output of predict_ecxsys() with custom concentrations:
conc <- 10^seq(-9, 1, length.out = 1000)
curves <- predict_ecxsys(model, conc)
lc(curves, "survival_tox_sys", 10)

# using a custom data frame:
df_custom <- data.frame(
    concentration = curves$concentration,
    foo = curves$survival_tox_sys
)
lc(df_custom, "foo", 10)

# Calculate the LC50 relative to an survival of 100
# instead of relative to the control:
lc(model, "survival_tox_sys", 50, reference = 100)

# }