P_TRT: Estimate the transitional range of temperatures based on a...

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

Estimate the transitional range of temperatures based on a set of parameters

Description

Estimate the parameters that best describe the thermal reaction norm for sex ratio when temperature-dependent sex determination occurs.
It can be used also to evaluate the relationship between incubation duration and sex ratio.
The parameter l was defined in Girondot (1999). The TRT is defined from the difference between the two boundary temperatures giving sex ratios of l and 1 - l.
In Girondot (1999), l was 0.05 and then the TRT was defined as being the range of temperatures producing from 5 If l is null, TRT is not estimated and only sex ratio is estimated.
if replicate.CI is null or 0, no replicate is used and only point estimate is done.
Standard error is calculated using resampling based on the Hessian matrix with Cholesky decomposition or using MCMC chain if resultmcmc is provided. In the former case, a replicate.CI random sample of the MCMC results will be used.

Usage

P_TRT(
  x = NULL,
  resultmcmc = NULL,
  fixed.parameters = NULL,
  chain = 1,
  equation = NULL,
  l = 0.05,
  replicate.CI = NULL,
  temperatures = NULL,
  durations = NULL,
  SD.temperatures = NULL,
  SD.durations = NULL,
  probs = c(0.025, 0.5, 0.975),
  warn = TRUE
)

Arguments

x	Set of parameters or a result of tsd()
resultmcmc	A result of tsd_MHmcmc()
fixed.parameters	Set of fixed parameters
chain	What chain to be used if resultmcmc is provided
equation	What equation should be used. Must be provided if x is not a result of tsd()
l	Sex ratio limits to define TRT are l and 1-l. If NULL, TRT is not estimated.
replicate.CI	If a result of tsd() is provided, use replicate.CI replicates from the hessian matrix to estimate CI
temperatures	If provided returns the sex ratio and its quantiles for each temperature
durations	If provided returns the sex ratio and its quantiles for each duration
SD.temperatures	SD of temperatures
SD.durations	SD of durations
probs	Probabilities used to estimate quantiles
warn	Do the warnings must be shown ? TRUE or FALSE

Details

P_TRT estimates the transitional range of temperatures based on a set of parameters

Value

A list with a P_TRT object containing a matrix with lower and higher bounds for TRT, TRT and P and a P_TRT_quantiles object with quantiles for each and a sexratio_quantiles object

Author(s)

Marc Girondot [e-mail]

References

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.

See Also

Other Functions for temperature-dependent sex determination: DatabaseTSD.version(), DatabaseTSD, TSP.list, plot.tsd(), predict.tsd(), stages, tsd_MHmcmc_p(), tsd_MHmcmc(), tsd()

Examples

## Not run: 
library("embryogrowth")
CC_AtlanticSW <- subset(DatabaseTSD, RMU=="Atlantic, SW" & 
                          Species=="Caretta caretta" & Sexed!=0)
tsdL <- with (CC_AtlanticSW, tsd(males=Males, females=Females, 
                                 temperatures=Incubation.temperature-Correction.factor, 
                                 equation="logistic"))
P_TRT(tsdL)
P_TRT(tsdL, replicate.CI=1000)
P_TRT(tsdL, replicate.CI=1000, temperatures=20:35)
P_TRT_out <- P_TRT(tsdL, replicate.CI=1000, temperatures=c(T1=20, T2=35))
attributes(P_TRT_out$sexratio_quantiles)$temperatures
P_TRT(tsdL$par, equation="logistic")
pMCMC <- tsd_MHmcmc_p(tsdL, accept=TRUE)
# Take care, it can be very long
result_mcmc_tsd <- tsd_MHmcmc(result=tsdL, 
		parametersMCMC=pMCMC, n.iter=10000, n.chains = 1,  
		n.adapt = 0, thin=1, trace=FALSE, adaptive=TRUE)
P_TRT(result_mcmc_tsd, equation="logistic")

## End(Not run)

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