Analysis of Ecotoxicology

A simple approach to using a 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 important parameters such as fiducial confidence limits and slope. Finney, D.J. (1971, ISBN: 052108041X); Wheeler, M.W., Park, R.M., and Bailer, A.J. (2006) ; Robertson, J.L., Savin, N.E., Russell, R.M., and Preisler, H.K. (2007, ISBN: 0849323312).


Build Status AppVeyor Build Status CRAN statusCoverage status

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
 
## several new features include 1) being able to change the output length 
## 2) you can indicate whether the x variable has been log10 transformed or 
## not if it has the output will take that into consideration
 
m_2 <- LC_probit((response / total) ~ dose,
                  p = c(50, 99),
                  weights = total,
                  data = lampreytox,
                  subset = c(month == "May"), 
                  log_x = FALSE, 
                  long_output = FALSE)
                  
## view calculated LC50 and LC99 for seasonal toxicity of a pisicide,
## 3-trifluoromethyl-4-nitrophenol (TFM) to lamprey in 2011.
 
m_2
 

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: 0849323312

Citation

  • When using this package please cite the following publication:

    Hlina, B.L., Birceanu, O., Robinson, C.S., Thackeray, N., Tessier, L.R., Muhametsafina, A., Bragg, L.M., Servos, M.R., Wilkie, M.P. In Preparation. Changes in the sensitivity of piscicide in an invasive species. Environmental Science & Technology.

  • version 1.3.2 written by Benjamin L. Hlina, Carleton University, Ottawa, Ontario, Canada. Written in 'Programming Language R', 3.5.1 (2018-07-02) -- "Feather Spray". Run on a PC with Intel® Core™ I7 - Q820 CPU, 1.73 GHz processor, 8.0 GB RAM, and Microsoft Windows 7 Professional operating system, 2009 Service Pack 1. Source code is available at 'ecotox' or by contacting Benjamin L. Hlina at [email protected]

News

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("ecotox")

1.4.0 by Benjamin L Hlina, 25 days ago


Browse source code at https://github.com/cran/ecotox


Authors: Benjamin L Hlina [aut, cre]


Documentation:   PDF Manual  


GPL-3 | file LICENSE license


Imports ggplot2, stats, tibble

Suggests covr, dplyr, Hmisc, readr, testthat, tidyr, xlsx


See at CRAN