embryogrowth (version 8.0)

STRN: Estimate the parameters that best describe the sexualisation thermal reaction norm within the TSP

Description

Estimate the parameters that best describe the sexualisation thermal reaction norm within the TSP. The Temperatures parameter is a character string which can be:

• TimeWeighted.temperature.mean

• GrowthWeighted.temperature.mean

• GrowthRateWeighted.temperature.mean

• TSP.TimeWeighted.temperature.mean

• TSP.GrowthWeighted.temperature.mean

• TSP.GrowthRateWeighted.temperature.mean

• TSP.STRNWeighted.temperature.mean

• TSP.GrowthWeighted.STRNWeighted.temperature.mean

• TSP.GrowthRateWeighted.STRNWeighted.temperature.mean

• MiddleThird.TimeWeighted.temperature.mean

• MiddleThird.GrowthWeighted.temperature.mean

• MiddleThird.GrowthRateWeighted.temperature.mean

If information for sex is not known for some timeseries, set NA for Sexed. Sexed, Males and Females must be vectors with names. The names must be the same as the names of timeseries of temperatures in EmbryoGrowthTRN. Only two of these 3 parameters are required: Males, Females and Sexed Note: four species have predefined embryo stages. embryo.stages parameter can take the values:

• Caretta caretta.SCL

• Chelonia mydas.SCL

• Emys orbicularis.SCL

• Emys orbicularis.mass

• Podocnemis expansa.SCL

• Generic.ProportionDevelopment

Usage

STRN(
  Initial_STRN = NULL,
  fixed.parameters = NULL,
  EmbryoGrowthTRN = stop("Embryo Growth Thermal Reaction Norm must be provided"),
  TSP.borders = NULL,
  embryo.stages = "Generic.ProportionDevelopment",
  TSP.begin = 0,
  TSP.end = 0.5,
  tsd = NULL,
  equation = "logistic",
  Sexed = NULL,
  Males = NULL,
  Females = NULL,
  Temperatures = "TSP.GrowthWeighted.STRNWeighted.temperature.mean",
  SE = TRUE,
  parallel = TRUE,
  itnmax = 1000,
  method = c("Nelder-Mead", "BFGS"),
  control = list(trace = 1, REPORT = 10),
  zero = 1e-09
)

Arguments

Initial_STRN

Values for initial model of Sexualisation Thermal Reaction Norm

fixed.parameters

Value for Sexualisation Thermal Reaction Norm model that will not be changed

EmbryoGrowthTRN

The Embryo Growth Thermal Reaction Norm obtained with searchR()

TSP.borders

The limits of TSP in stages. See embryo.stages parameter.

embryo.stages

The embryo stages. At least TSP.borders stages must be provided to estimate TSP borders. See note.

TSP.begin

Where TSP begin during the stage of beginning? In relative proportion of the stage.

TSP.end

Where TSP begin during the stage of ending? In relative proportion of the stage.

tsd

The model used to predict sex ratio, obtained from tsd()

equation

If tsd parameter is not provided, equation and parameters for tsd model must be provided.

Sexed

The number of sexed embryos with names identifying timeseries

Males

The number of males embryos with names identifying timeseries

Females

The number of females embryos with names identifying timeseries

Temperatures

The temperature from out of info.nests to be used

SE

Should standard error of parameters and Hessian matrix be estimated ? TRUE or FALSE

parallel

Should parallel computing for info.nests() be used

itnmax

Maximum number of iterations for each method

method

Methods to be used with optimx

control

List for control parameters for optimx

zero

The value to replace a null sex ratio

Value

The list with object return by optim()

Details

STRN estimates the parameters that best describe the sexualisation thermal reaction norm within the TSP

Examples

# NOT RUN {
library(embryogrowth)
MedIncubation_Cc <- subset(DatabaseTSD, Species=="Caretta caretta" & 
RMU=="Mediterranean" & Sexed!=0)
Med_Cc <- with(MedIncubation_Cc, tsd(males=Males, females=Females, 
 temperatures=Incubation.temperature, par=c(P=29.5, S=-0.01)))
plot(Med_Cc, xlim=c(25, 35))
males <- c(7, 0, 0, 0, 0, 5, 6, 3, 5, 3, 2, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0)
names(males) <- rev(rev(names(resultNest_4p_SSM4p$data))[-(1:2)])
sexed <- rep(10, length(males))
names(sexed) <- rev(rev(names(resultNest_4p_SSM4p$data))[-(1:2)])
Initial_STRN <- resultNest_4p_SSM4p$par[c("DHA_STRN", "DHH_STRN", "T12H_STRN")]
Initial_STRN <- structure(c(582.567096666926, 2194.0806711639, 3475.28414940385), 
                          .Names = c("DHA_STRN", "DHH_STRN", "T12H_STRN"))
fp <- c(Rho25_STRN=100)
fitSTRN <- STRN(Initial_STRN=Initial_STRN, 
                EmbryoGrowthTRN=resultNest_4p_SSM4p, tsd=Med_Cc, 
                embryo.stages="Caretta caretta.SCL", 
                Sexed=sexed, Males=males, 
                fixed.parameters=fp, 
                SE=TRUE, 
                Temperatures="TSP.GrowthWeighted.STRNWeighted.temperature.mean")
plotR(fitSTRN, curves ="ML quantiles", ylim=c(0,2))
CTE <- info.nests(NestsResult=resultNest_4p_SSM4p, 
                  SexualisationTRN=fitSTRN,
                  SexualisationTRN.CI="Hessian",
                  embryo.stages="Caretta caretta.SCL", 
                  CI="Hessian", 
                  replicate.CI=100, 
                  progress=TRUE, 
                  warnings=TRUE, 
                  out="summary")$summary
# CTE with growth-weighted temperature average
plot(Med_Cc, xlim=c(25, 35))
points(x=CTE$TSP.GrowthWeighted.temperature.mean, y=males/sexed, 
         col="red", pch=19)
legend("topright", legend=c("CTE with growth-weighted TRN"), 
         pch=19, col=c("red"))
# CTE with sexualisation TRN and growth-weighted temperature average
plot(Med_Cc, xlim=c(25, 35))
points(x=CTE$TSP.GrowthWeighted.STRNWeighted.temperature.mean, y=males/sexed, 
         col="red", pch=19)
legend("topright", legend=c("CTE with growth-weighted TRN and Sex. TRN"), 
       pch=19, col=c("red"))
xx <- seq(from=20, to=35, by=0.1)
plot(x=xx, 
         y=log10(getFromNamespace(".SSM", ns="embryogrowth")(xx, 
                            c(fitSTRN$par, fitSTRN$fixed.parameters))[[1]]), 
         type="l", bty="n", xlim=c(20, 35), ylim=c(-20, 20), 
         xlab="Temperature", ylab="Sexualisation thermal reaction norm (log10)")
         
# Using only the sexualisation thermal reaction norm within TSP to calculate CTE

Initial_STRN <- resultNest_4p_SSM4p$par[c("DHA_STRN", "DHH_STRN", "T12H_STRN")]
Initial_STRN <- structure(c(3678.94960547096, -301.436485427701, 912.595953854977), 
                          .Names = c("DHA_STRN", "DHH_STRN", "T12H_STRN"))
fp <- c(Rho25_STRN=100)
fitSTRN_2 <- STRN(Initial_STRN=Initial_STRN, 
                EmbryoGrowthTRN=resultNest_4p_SSM4p, tsd=Med_Cc, 
                embryo.stages="Caretta caretta.SCL", 
                Sexed=sexed, Males=males, 
                fixed.parameters=fp,  
                Temperatures="TSP.STRNWeighted.temperature.mean")
CTE <- info.nests(NestsResult=resultNest_4p_SSM4p, 
                  SexualisationTRN=fitSTRN_2,
                  SexualisationTRN.CI="Hessian",
                  embryo.stages="Caretta caretta.SCL", 
                  CI="Hessian", 
                  replicate.CI=100, 
                  progress=TRUE, 
                  warnings=TRUE, 
                  out="summary")$summary
# CTE with sexualisation TRN
plot(Med_Cc, xlim=c(25, 35))
points(x=CTE$TSP.STRNWeighted.temperature.mean, y=males/sexed, 
         col="red", pch=19)
legend("topright", legend=c("CTE with Sexualisation TRN"), 
       pch=19, col=c("red"))
xx <- seq(from=20, to=35, by=0.1)
plot(x=xx, 
         y=getFromNamespace(".SSM", ns="embryogrowth")(xx, 
                            c(fitSTRN$par, fitSTRN$fixed.parameters))[[1]], 
         type="l", bty="n", xlim=c(20, 35), ylim=c(0, 1E-18), 
         xlab="Temperature", ylab="Sexualisation thermal reaction norm")
# }