ecotox (version 1.4.1)

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 = NULL, weights = NULL,
          subset = NULL, log_base = NULL, log_x = TRUE, het_sig = NULL,
          conf_level = NULL, long_output = TRUE)

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_logit 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 wanted specify by creating a vector. LT values can be calculated down to the 1e-16 of a percentage (e.g. LT99.99).However, the tibble produced can and will round to nearest whole number.

weights

vector of 'prior weights' to be used in the fitting process. Should be a numeric vector and is required for analysis.

subset

allows for the data to be subseted if desired. Default set to NULL.

log_base

default is 10 and will be used to calculate results using the anti of log10() given that the x variable has been log10 tranformed. If FALSE results will not be back transformed.

log_x

default is TRUE and will calculate results using the antilog of determined by log_base given that the x variable has been log() tranformed. If FALSE results will not be back transformed.

het_sig

significance level from person's chi sqaure goodness-of-fit test that is used to decide if a heterogeneity factor is used. NULL is set to 0.15.

conf_level

Adjust confidence level as necessary or NULL set at 0.95.

long_output

default is TRUE which will return a tibble with all 19 variabless. If FALSE the tibble returned will consist of the p level, n, the predicted LC for given p level, lower and upper confidence limits and their distances.

Value

Returns a tibble 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 chi sqaure goodness-of-fit test (pgof), 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(lamprey_time)

results <- LT_logit((response / total) ~ log10(hour),
p = c(50, 99),
weights = total,
data = lamprey_time,
subset = c(month == "May"))

# 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'

# }