embryogrowth (version 8.0)

likelihoodR: Estimate the likelihood of a set of parameters for nest incubation data

Description

Estimate the likelihood of a set of parameters for nest incubation data

Usage

likelihoodR(
  result = NULL,
  parameters = NULL,
  fixed.parameters = NULL,
  temperatures = NULL,
  derivate = NULL,
  test = NULL,
  M0 = NULL,
  hessian = FALSE,
  weight = NULL,
  parallel = TRUE,
  echo = TRUE
)

Arguments

result

A object obtained after searchR or likelihoodR

parameters

A set of parameters

fixed.parameters

A set of parameters that will not be changed

temperatures

Timeseries of temperatures

derivate

Function used to fit embryo growth: dydt.Gompertz, dydt.exponential or dydt.linear

test

Mean and SD of size of hatchlings

M0

Measure of hatchling size or mass proxi at laying date

hessian

If TRUE, the hessian matrix is estimated and the SE of parameters estimated.

weight

A named vector of the weight for each nest for likelihood estimation

parallel

If true, try to use several cores using parallel computing.

echo

If FALSE, does not display the result.

Value

A result object

Details

likelihoodR estimates the likelihood of a set of parameters for nest incubation data

Examples

# NOT RUN {
library(embryogrowth)
data(nest)
formated <- FormatNests(nest)
# The initial parameters value can be:
# "T12H", "DHA",  "DHH", "Rho25"
# Or
# "T12L", "DT", "DHA",  "DHH", "DHL", "Rho25"
# K for Gompertz must be set as fixed parameter or being a constant K  
# or relative to the hatchling size rK
x <- structure(c(118.768297442004, 475.750095909406, 306.243694918151, 
116.055824800264), .Names = c("DHA", "DHH", "T12H", "Rho25"))
# pfixed <- c(K=82.33) or rK=82.33/39.33
pfixed <- c(rK=2.093313)
# K or rK are not used for dydt.linear or dydt.exponential
LresultNest_4p <- likelihoodR(parameters=x, fixed.parameters=pfixed,  
	temperatures=formated, derivate=dydt.Gompertz, M0=1.7,  
	test=c(Mean=39.33, SD=1.92))
data(resultNest_4p_SSM4p)
LresultNest_4p <- likelihoodR(result=resultNest_4p_SSM4p)
# }