STRN: Estimate the parameters that best describe the sexualisation...

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

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 sexratio parameter is a character string which can be:

• TSP.TimeWeighted.sexratio.mean Sex ratio based on average temperature during the TSP

• TSP.GrowthWeighted.sexratio.mean Sex ratio based on average temperature weighted by the actual growth during the TSP

• TSP.TimeWeighted.GrowthRateWeighted.sexratio.mean Sex ratio based on average temperature weighted by the growth rate during the TSP

• TSP.TimeWeighted.STRNWeighted.sexratio.mean Sex ratio based on average temperature weighted by the thermal reaction norm of sexualization during the TSP

• TSP.GrowthWeighted.STRNWeighted.sexratio.mean Sex ratio based on average temperature weighted by the actual growth and thermal reaction norm of sexualization during the TSP

• TSP.TimeWeighted.GrowthRateWeighted.STRNWeighted.sexratio.mean Sex ratio based on average temperature weighted by the growth rate and the thermal reaction norm of sexualization during the TSP

• MiddleThird.TimeWeighted.sexratio.mean Sex ratio based on average temperature during the middle third incubation

• MiddleThird.GrowthWeighted.sexratio.mean Sex ratio based on average temperature weighted by actual growth during the middle third incubation

• MiddleThird.TimeWeighted.GrowthRateWeighted.sexratio.mean Sex ratio based on average temperature weighted by growth rate during the middle third incubation

• TimeWeighted.sexratio.mean Sex ratio based on average temperature during all incubation

• GrowthWeighted.sexratio.mean Sex ratio based on average temperature weighted by actual growth during all incubation

• TimeWeighted.GrowthRateWeighted.sexratio.mean Sex ratio based on average temperature weighted by growth rate during all incubation

• TSP.PM.TimeWeighted.mean Average sex ratio based on temperature during the TSP

• TSP.PM.GrowthWeighted.mean Average sex ratio based on temperature weighted by the actual growth during the TSP

• TSP.PM.TimeWeighted.GrowthRateWeighted.mean Average sex ratio based on temperature weighted by the growth rate during the TSP

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

• Lepidochelys olivacea.SCL

• Generic.ProportionDevelopment

A fifth name fitted must be used when limits of TSP are fitted using BeginTSP and EndTSP parameters.
The parameters that can be used in STRN are:
BeginTSP, EndTSP are the logit of the proportion of development;
To ensure that BeginTSP < EndTSP, it is better to use:
BeginTSP, LengthTSP and then EndTSP is estimated using BeginTSP + abs(LengthTSP)
DHA, DHH, T12H are the SSM parameters of sexualisation thermal reaction norm;
dbeta_mu, dbeta_v are the beta mean and variance of the impact of sexualisation according to TSP progress.
Or any parameter that can be used in a TSD model.

Usage

STRN(
  EmbryoGrowthTRN = stop("Embryo Growth Thermal Reaction Norm must be provided"),
  Initial_STRN = NULL,
  fixed.parameters = NULL,
  TSP.borders = NULL,
  embryo.stages = NULL,
  TSP.begin = 0,
  TSP.end = 0.5,
  tsd = NULL,
  equation = "logistic",
  Sexed = NULL,
  Males = NULL,
  Females = NULL,
  sexratio = "TSP.TimeWeighted.GrowthRateWeighted.STRNWeighted.sexratio.mean",
  fill = 60,
  parallel = TRUE,
  itnmax = 1000,
  method = c("Nelder-Mead", "BFGS"),
  control = list(trace = 1, REPORT = 10),
  zero = 1e-09,
  verbose = FALSE,
  hessian = TRUE
)

Arguments

EmbryoGrowthTRN	The Embryo Growth Thermal Reaction Norm obtained with searchR()
Initial_STRN	Values for initial model of Sexualisation Thermal Reaction Norm or tsd model
fixed.parameters	Value for Sexualisation Thermal Reaction Norm or tsd model that will not be changed
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 in Initial_STRN 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
sexratio	The sex ratio to be used
fill	See info.nests()
parallel	Should parallel computing for info.nests() be used
itnmax	Maximum number of iterations for each method; if 0, just return the likelihood
method	Methods to be used with optimx
control	List for control parameters for optimx
zero	The value to replace a null sex ratio
verbose	If TRUE, will show all intermediate parameters during fit
hessian	If TRUE, the Hessian approximation is estimated atthe end of the fit.

Details

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

Value

The list with object return by optim()

Author(s)

Marc Girondot [e-mail]

Examples

## Not run: 
library(embryogrowth)
MedIncubation_Cc <- subset(DatabaseTSD, Species=="Caretta caretta" & 
RMU=="Mediterranean" & Sexed!=0)
Med_Cc <- tsd(males=MedIncubation_Cc$Males, 
             females=MedIncubation_Cc$Females, 
             temperatures=MedIncubation_Cc$Incubation.temperature, 
             par=c(P=29.5, S=-0.1))
plot(Med_Cc, xlim=c(25, 35))
males <- c(7, 0, 0, 0, 0, 5, 6, 3, 5, 3, 2, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0)
names(males) <- rev(rev(names(resultNest_4p_SSM$data))[-(1:2)])
sexed <- rep(10, length(males))
names(sexed) <- rev(rev(names(resultNest_4p_SSM$data))[-(1:2)])

Initial_STRN <- c('DHA' = 1174.6461503413307, 
                  'DHH' = 2001.0619192107047, 
                  'T12H' = 3731.353104743393)
fp <- c(Rho25=100)
fitSTRN <- STRN(Initial_STRN=Initial_STRN, 
                EmbryoGrowthTRN=resultNest_4p_SSM, 
                tsd=Med_Cc, 
                embryo.stages="Caretta caretta.SCL", 
                Sexed=sexed, Males=males, 
                fixed.parameters=fp, 
                sexratio="TSP.GrowthWeighted.STRNWeighted.sexratio.mean")
plotR(fitSTRN, curve ="ML", ylim=c(0,2))
plotR(fitSTRN)
out <- info.nests(NestsResult=resultNest_4p_SSM, 
                  SexualisationTRN=fitSTRN,
                  SexualisationTRN.CI="Hessian",
                  embryo.stages="Caretta caretta.SCL", 
                  GTRN.CI="Hessian", 
                  tsd=Med_Cc, 
                  tsd.CI="Hessian", 
                  replicate.CI=100, 
                  progressbar=TRUE, 
                  warnings=TRUE, 
                  out="summary")$summary
# CTE with growth-weighted temperature average
plot(Med_Cc, xlim=c(25, 35))
points(x=out[, "TSP.GrowthWeighted.STRNWeighted.temperature.mean"], y=males/sexed, 
         col="red", pch=19)
legend("topright", legend=c("CTE with growth-weighted and Sexualization TRN"), 
         pch=19, col=c("red"))
       
#  Fit the beginning and end of TSP

Initial_STRN <- c('BeginTSP' = invlogit(0.33), 
                  'EndTSP' = invlogit(0.66))
fp <- NULL
fitSTRN <- STRN(Initial_STRN=Initial_STRN, 
                EmbryoGrowthTRN=resultNest_4p_SSM, 
                tsd=Med_Cc, 
                embryo.stages="fitted", 
                Sexed=sexed, Males=males, 
                fixed.parameters=fp, 
                sexratio="TSP.TimeWeighted.GrowthRateWeighted.STRNWeighted.sexratio.mean")
invlogit(fitSTRN$par)
invlogit(fitSTRN$par-2*fitSTRN$SE)
invlogit(fitSTRN$par+2*fitSTRN$SE)

Initial_STRN <- c('dbeta_mu' = logit(0.5), 
                  'dbeta_v' = 1/12)
fp <- NULL
fitSTRN <- STRN(Initial_STRN=Initial_STRN, 
                EmbryoGrowthTRN=resultNest_4p_SSM, 
                tsd=Med_Cc, 
                embryo.stages="Caretta caretta.SCL", 
                Sexed=sexed, Males=males, 
                fixed.parameters=fp, 
                sexratio="TSP.TimeWeighted.GrowthRateWeighted.STRNWeighted.sexratio.mean")
                mu <- invlogit(fitSTRN$par["dbeta_mu"]), 
                v <- abs(fitSTRN$par["dbeta_v"])
                shape1 <- mu * (((mu * (1 - mu))/v) - 1)
                shape2 <- shape1 * (1 - mu)/mu
plot(seq(from=0, to=1, length.out=100), 
     dbeta(seq(from=0, to=1, length.out=100), 
               shape1=shape1, shape2=shape2), 
     type="l", xlab="Progress of TSP", 
     ylab="Force of sexualisation", bty="n", ylim=c(0, 6), las=1)
               
 Initial_STRN <- c('dbeta_mu' = 7.2194053298953236, 
                   'dbeta_v' = 0.00050390986089928467)
fp <- NULL
fitSTRN <- STRN(Initial_STRN=Initial_STRN                                                 , 
                EmbryoGrowthTRN=resultNest_4p_SSM                                         , 
                tsd=Med_Cc                                                                , 
                embryo.stages="Caretta caretta.SCL"                                       , 
                Sexed=sexed                                                               , 
                Males=males                                                               , 
                fixed.parameters=fp                                                       , 
                sexratio="TSP.TimeWeighted.GrowthRateWeighted.STRNWeighted.sexratio.mean" )
                
                mu <- invlogit(fitSTRN$par["dbeta_mu"]), 
                v <- abs(fitSTRN$par["dbeta_v"])
                shape1 <- mu * (((mu * (1 - mu))/v) - 1)
                shape2 <- shape1 * (1 - mu)/mu
                
plot(seq(from=0, to=1, length.out=100), 
     dbeta(seq(from=0, to=1, length.out=100), 
               shape1=shape1, shape2=shape2), 
     type="l", xlab="Progress of TSP", 
     ylab="Force of sexualisation", bty="n", ylim=c(0, 0.04), las=1)
               
Initial_STRN <- c('dbeta_mu' = logit(0.5), 
                  'dbeta_v' = 1/12)
L <- STRN(Initial_STRN=NULL                                                        , 
          fixed.parameters=Initial_STRN                                            , 
          EmbryoGrowthTRN=resultNest_4p_SSM                                        , 
          tsd=Med_Cc                                                               , 
          embryo.stages="Caretta caretta.SCL"                                                   , 
          Sexed=sexed                                                              ,
          Males=males                                                              , 
          sexratio="TSP.TimeWeighted.GrowthRateWeighted.STRNWeighted.sexratio.mean")
Initial_STRN <- c('dbeta_mu' = logit(0.6), 
                  'dbeta_v' = 1/12)
L <- STRN(Initial_STRN=NULL                                                        , 
          fixed.parameters=Initial_STRN                                            , 
          EmbryoGrowthTRN=resultNest_4p_SSM                                        , 
          tsd=Med_Cc                                                               , 
          embryo.stages="Caretta caretta.SCL"                                                   , 
          Sexed=sexed                                                              ,
          Males=males                                                              , 
          sexratio="TSP.TimeWeighted.GrowthRateWeighted.STRNWeighted.sexratio.mean")
 Initial_STRN <- c('dbeta_mu' = 7.2192972077000004, 
                    'dbeta_v' = 0.00050396969999999997)
L <- STRN(Initial_STRN=NULL                                                        , 
          fixed.parameters=Initial_STRN                                            , 
          EmbryoGrowthTRN=resultNest_4p_SSM                                        , 
          tsd=Med_Cc                                                               , 
          embryo.stages="Caretta caretta.SCL"                                      , 
          Sexed=sexed                                                              ,
          Males=males                                                              , 
          sexratio="TSP.TimeWeighted.GrowthRateWeighted.STRNWeighted.sexratio.mean")
                mu <- invlogit(fitSTRN$par["dbeta_mu"]), 
                v <- abs(fitSTRN$par["dbeta_v"])
                shape1 <- mu * (((mu * (1 - mu))/v) - 1)
                shape2 <- shape1 * (1 - mu)/mu
 
   tsp_progress <- seq(from=0, to=1, length.out=100)     
  plot(tsp_progress, 
     dbeta(tsp_progress, 
           shape1=shape1, shape2=shape2), 
       type="l", xlab="Progress of TSP", 
       ylab="Force of sexualisation", bty="n", ylim=c(0, 0.04), las=1)
 segments(x0=0, x1=1, y0=0, y1=0, lty=2)

## End(Not run)

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