LD50: Estimate the parameters that best describe LD50

In HelpersMG: Tools for Environmental Analyses, Ecotoxicology and Various R Functions

Estimate the parameters that best describe LD50

Description

Estimate the parameters that best describe LD50
Logistic and logit models are the same but with different parametrization:
logistic = 1/(1+exp((1/S)(P-d)))
logit = 1/(1+exp(P+dS))
See these publications for the description of equations:
Girondot, M. 1999. Statistical description of temperature-dependent sex determination using maximum likelihood. Evolutionary Ecology Research, 1, 479-486.
Godfrey, M.H., Delmas, V., Girondot, M., 2003. Assessment of patterns of temperature-dependent sex determination using maximum likelihood model selection. Ecoscience 10, 265-272.
Hulin, V., Delmas, V., Girondot, M., Godfrey, M.H., Guillon, J.-M., 2009. Temperature-dependent sex determination and global change: are some species at greater risk? Oecologia 160, 493-506.
The flexit equation is not still published :

if dose < P then (1 + (2^K1 - 1) * exp(4 * S1 * (P - x)))^(-1/K1)

if dose > P then 1-((1 + (2^K2 - 1) * exp(4 * S2 * (x - P)))^(-1/K2)

with:

S1 = S/((4/K1)*(2^(-K1))^(1/K1+1)*(2^K1-1))

S2 = S/((4/K2)*(2^(-K2))^(1/K2+1)*(2^K2-1))

Usage

LD50(
  df = NULL,
  alive = NULL,
  dead = NULL,
  N = NULL,
  doses = NULL,
  l = 0.05,
  parameters.initial = NULL,
  fixed.parameters = NULL,
  SE = NULL,
  equation = "logistic",
  replicates = 1000,
  range.CI = 0.95,
  limit.low.TRD.minimum = 5,
  limit.high.TRD.maximum = 1000,
  print = TRUE,
  doses.plot = seq(from = 0, to = 1000, by = 0.1)
)

Arguments

df	A dataframe with at least two columns named alive, dead or N and doses columns
alive	A vector with alive individuals at the end of experiment
dead	A vector with dead individuals at the end of experiment
N	A vector with total numbers of tested individuals
doses	The doses
l	The limit to define TRD (see Girondot, 1999)
parameters.initial	Initial values for P, S or K search as a vector, ex. c(P=29, S=-0.3)
fixed.parameters	Parameters that will not be changed during fit
SE	Standard errors for parameters
equation	Could be "logistic", "logit", "probit", Hill", "Richards", "Hulin", "flexit" or "Double-Richards"
replicates	Number of replicates to estimate confidence intervals
range.CI	The range of confidence interval for estimation, default=0.95
limit.low.TRD.minimum	Minimum lower limit for TRD
limit.high.TRD.maximum	Maximum higher limit for TRD
print	Do the results must be printed at screen? TRUE (default) or FALSE
doses.plot	Sequences of doses that will be used for plotting. If NULL, does not estimate them

Details

LD50 estimates the parameters that best describe LD50

Value

A list with the LD50, Transitional Range of Doses and their SE

Author(s)

Marc Girondot [e-mail]

See Also

Other LD50 functions: LD50_MHmcmc(), LD50_MHmcmc_p(), logLik.LD50(), plot.LD50(), predict.LD50()

Examples

## Not run: 
library("HelpersMG")
data <- data.frame(Doses=c(80, 120, 150, 150, 180, 200),
Alive=c(10, 12, 8, 6, 2, 1),
Dead=c(0, 1, 5, 6, 9, 15))
LD50_logistic <- LD50(data, equation="logistic")
predict(LD50_logistic, doses=c(140, 170))
plot(LD50_logistic, xlim=c(0, 300), at=seq(from=0, to=300, by=50))
LD50_probit <- LD50(data, equation="probit")
predict(LD50_probit, doses=c(140, 170))
plot(LD50_probit)
LD50_logit <- LD50(data, equation="logit")
predict(LD50_logit, doses=c(140, 170))
plot(LD50_logit)
LD50_hill <- LD50(data, equation="hill")
predict(LD50_hill, doses=c(140, 170))
plot(LD50_hill)
LD50_Richards <- LD50(data, equation="Richards")
predict(LD50_Richards, doses=c(140, 170))
plot(LD50_Richards)
LD50_Hulin <- LD50(data, equation="Hulin")
predict(LD50_Hulin, doses=c(140, 170))
plot(LD50_Hulin)
LD50_DoubleRichards <- LD50(data, equation="Double-Richards")
predict(LD50_DoubleRichards, doses=c(140, 170))
plot(LD50_DoubleRichards)
LD50_flexit <- LD50(data, equation="flexit")
predict(LD50_flexit, doses=c(140, 170))
plot(LD50_flexit)

## End(Not run)

HelpersMG documentation built on Sept. 12, 2024, 9:35 a.m.