ecotox

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Overview

‘ecotox’ was created as simple approach to using either probit or logit analysis to calculate lethal concentration (LC) or time (LT) and the appropriate fiducial confidence limits desired for selected LC or LT for ecotoxicology studies (Finney 1971; Wheeler et al. 2006; Robertson et al. 2007). The simplicity of ‘ecotox’ comes from the syntax it implies within its functions which are similar to functions like glm() and lm(). In addition to the simplicity of the syntax, a comprehensive data frame is produced which gives the user a predicted LC or LT value for the desired level and a suite of parameters such as fiducial confidence limits, z-value, and slope. ‘ecotox’ was built for and is published in Hlina et al. In Preparation.

Installation

You can install the CRAN released version of ‘ecotox’ from CRAN with:

install.packages("ecotox")

You can install the developer version of ‘ecotox’ from github with:

install.packages("devtools")
devtools::install_github("benjaminhlina/ecotox")

Example

This is an example which uses the LC_probit function to calculate a LC50 and LC99 for a probit analysis :

## Calculate LC50 and LC99
head(lampreytox)

## within the dataframe used, control dose, unless produced a value
## during experimentation, are removed from the dataframe,
## as glm cannot handle values of infinite. Other statistical programs
## make note of the control dose but do not include within analysis. 

## calculate LC50 and LC99 for May

m <- LC_probit((response / total) ~ log10(dose),
                p = c(50, 99),
                weights = total,
                data = lampreytox,
                subset = c(month == "May"))

## view calculated LC50 and LC99 for seasonal toxicity of a pisicide,
## 3-trifluoromethyl-4-nitrophenol (TFM) to lamprey in 2011

m

References

Citation