| STRN {embryogrowth} | R Documentation |
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.meanSex ratio based on average temperature during the TSP -
TSP.GrowthWeighted.sexratio.meanSex ratio based on average temperature weighted by the actual growth during the TSP -
TSP.TimeWeighted.GrowthRateWeighted.sexratio.meanSex ratio based on average temperature weighted by the growth rate during the TSP -
TSP.TimeWeighted.STRNWeighted.sexratio.meanSex ratio based on average temperature weighted by the thermal reaction norm of sexualization during the TSP -
TSP.GrowthWeighted.STRNWeighted.sexratio.meanSex ratio based on average temperature weighted by the actual growth and thermal reaction norm of sexualization during the TSP -
TSP.TimeWeighted.GrowthRateWeighted.STRNWeighted.sexratio.meanSex ratio based on average temperature weighted by the growth rate and the thermal reaction norm of sexualization during the TSP -
MiddleThird.TimeWeighted.sexratio.meanSex ratio based on average temperature during the middle third incubation -
MiddleThird.GrowthWeighted.sexratio.meanSex ratio based on average temperature weighted by actual growth during the middle third incubation -
MiddleThird.TimeWeighted.GrowthRateWeighted.sexratio.meanSex ratio based on average temperature weighted by growth rate during the middle third incubation -
TimeWeighted.sexratio.meanSex ratio based on average temperature during all incubation -
GrowthWeighted.sexratio.meanSex ratio based on average temperature weighted by actual growth during all incubation -
TimeWeighted.GrowthRateWeighted.sexratio.meanSex ratio based on average temperature weighted by growth rate during all incubation -
TSP.PM.TimeWeighted.meanAverage sex ratio based on temperature during the TSP -
TSP.PM.GrowthWeighted.meanAverage sex ratio based on temperature weighted by the actual growth during the TSP -
TSP.PM.TimeWeighted.GrowthRateWeighted.meanAverage 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 marc.girondot@gmail.com
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)