embryogrowth (version 9.5)

HatchingSuccess.lnL: Return -log likelihood of the data and the parameters

Description

Set of functions to study the hatching success.

Usage

HatchingSuccess.lnL(
  par,
  data,
  fixed.parameters = NULL,
  column.Incubation.temperature = "Incubation.temperature",
  column.Hatched = "Hatched",
  column.NotHatched = "NotHatched"
)

Value

Return -log likelihood of the data and the parameters

Arguments

par

A set of parameters.

data

A dataset in a data.frame with a least three columns: Incubation.temperature, Hatched and NotHatched

fixed.parameters

A set of parameters that must not be fitted.

column.Incubation.temperature

Name of the column with incubation temperatures

column.Hatched

Name of the column with hatched number

column.NotHatched

Name of the column with not hatched number

Author

Marc Girondot

Details

HatchingSuccess.lnL return -log likelihood of the data and the parameters

See Also

Other Hatching success: HatchingSuccess.MHmcmc(), HatchingSuccess.MHmcmc_p(), HatchingSuccess.fit(), HatchingSuccess.model(), logLik.HatchingSuccess(), nobs.HatchingSuccess(), predict.HatchingSuccess()

Examples

if (FALSE) {
library(embryogrowth)
totalIncubation_Cc <- subset(DatabaseTSD, 
                             Species=="Caretta caretta" & 
                               Note != "Sinusoidal pattern" & 
                               !is.na(Total) & Total != 0 & 
                               !is.na(NotHatched) & !is.na(Hatched))

par <- c(S.low=0.5, S.high=0.3, 
         P.low=25, deltaP=10, MaxHS=0.8)
         
HatchingSuccess.lnL(par=par, data=totalIncubation_Cc)

g <- HatchingSuccess.fit(par=par, data=totalIncubation_Cc)

HatchingSuccess.lnL(par=g$par, data=totalIncubation_Cc)

t <- seq(from=20, to=40, by=0.1)
CIq <- predict(g, temperature=t)

par(mar=c(4, 4, 1, 1), +0.4)
plot(g)
}