likelihoodR: Estimate the likelihood of a set of parameters for nest...

In embryogrowth: Tools to Analyze the Thermal Reaction Norm of Embryo Growth

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,
  integral = NULL,
  derivate = NULL,
  hatchling.metric = 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
integral	Function used to fit embryo growth: integral.Gompertz, integral.exponential or integral.linear
derivate	Function used to fit embryo growth: dydt.Gompertz, dydt.exponential or dydt.linear. It will replace the one in NestsResult.
hatchling.metric	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.

Details

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

Value

A result object

Author(s)

Marc Girondot [e-mail]

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 integral.linear or integral.exponential
LresultNest_4p <- likelihoodR(parameters=x, fixed.parameters=pfixed,  
	temperatures=formated, integral=integral.Gompertz, M0=1.7,  
	hatchling.metric=c(Mean=39.33, SD=1.92))
data(resultNest_4p_SSM)
LresultNest_4p <- likelihoodR(result=resultNest_4p_SSM)

## End(Not run)

embryogrowth documentation built on Oct. 24, 2023, 5:07 p.m.