ecotox (version 1.3.0)

LT_logit: Lethal Time Logit

Description

Calculates lethal time (LT) and its fiducial confidence limits (CL) using a logit analysis according to Finney 1971, Wheeler et al. 2006, and Robertson et al. 2007.

Usage

LT_logit(formula, data, p = seq(1, 99, 1),
weights = NULL, het_sig = NULL, conf_level = NULL)

Arguments

formula

an object of class formula or one that can be coerced to that class: a symbolic description of the model to be fitted.

data

an optional data frame, list or environment (or object coercible by as.data.frame to a data frame) containing the variables in the model. If not found in data, the variables are taken from environment(formula), typically the environment from which LT is called.

p

Lethal time (LT) values for given p, example will return a LT50 value if p equals 50. If more than one LT value desired specify by creating a vector.

weights

vector of 'prior weights' to be used in the fitting process. Should be a numeric vector, if set to NULL weights will not be used.

het_sig

signficance level from person's goodness-of-fit test that is used to decide if a hetrogentiy factor is used. NULL is set to 0.15.

conf_level

Adjust confidence level as necessary or NULL set at 0.95.

Value

Returns a data frame with predicted LT for given p level, lower CL (LCL), upper CL (UCL), LCL and UCL distance away from LT (LCL_dis & UCL_dis; important for creating a plot), Pearson's goodness-of-fit test, slope, intercept, slope and intercept p values and standard error, and LT variance.

References

Finney, D.J., 1971. Probit Analysis, Cambridge University Press, Cambridge, England, ISBN: 052108041X

Wheeler, M.W., Park, R.M., and Bailey, A.J., 2006. Comparing median lethal concentration values using confidence interval overlap or ratio tests, Environ. Toxic. Chem. 25(5), 1441-1444.10.1897/05-320R.1

Robertson, J.L., Savin, N.E., Russell, R.M. and Preisler, H.K., 2007. Bioassays with arthropods. CRC press. ISBN: 9780849323317

Examples

# NOT RUN {
head(lampreytime)

results <- LT_logit((dead/total) ~ log10(hour), p = c(50, 99),
weights = lampreytime[c(1:11), ]$total,
data = lampreytime[c(1:11), ])

#view calculated LT50 and LT99 for seasonal
#toxicity of a piscicide, 3-trifluoromethyl-4-nitrophenol, to lamprey in 2011

results

#dose-response curve can be plotted using 'ggplot2'
# }