Tools to Analyze the Thermal Reaction Norm of Embryo Growth


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Documentation for package ‘embryogrowth’ version 9.1

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embryogrowth-package The package embryogrowth
calibrate.datalogger Calibrate data loggers and correct time series of temperatures
ChangeSSM Generate set of parameters for different forms of thermal norm of reaction
DatabaseNestingArea Database of RMU for marine turtles
DatabaseTSD Database of TSD information for reptiles
DatabaseTSD.version Version of database of TSD information for reptiles
dydt.exponential Return the derivative of the exponential function
dydt.Gompertz Return the derivative of the Gompertz function
dydt.linear Return the derivative of the linear function
FormatNests Create a dataset of class Nests to be used with searchR
GenerateAnchor Generate a set of anchored parameters
GenerateConstInc Generate a data.frame with constant incubation temperature and incubation duration
Generate_hatchling_metric Generate a data.frame that can be used as hatchling.metric value for searchR()
GRTRN_MHmcmc Metropolis-Hastings algorithm for Embryo Growth Rate Thermal Reaction Norm
HatchingSuccess.fit Fit a hatching success model to data using maximum likelihood
HatchingSuccess.lnL Return -log likelihood of the data and the parameters
HatchingSuccess.MHmcmc Metropolis-Hastings algorithm for hatching success
HatchingSuccess.MHmcmc_p Generates set of parameters to be used with HatchingSuccess.MHmcmc()
HatchingSuccess.model Return the hatching success according the set of parameters and temperatures
hist.Nests Show the histogram of temperatures with set of nests
hist.NestsResult Show the histogram of temperatures with set of nests
info.nests Calculte statistics about nests
integral.exponential Return the derivative of the exponential function
integral.Gompertz Return the result of the Gompertz function
integral.linear Return the linear function
likelihoodR Estimate the likelihood of a set of parameters for nest incubation data
logLik.HatchingSuccess Return -log L of a fit
logLik.NestsResult Return Log Likelihood of a fit generated by searchR
logLik.STRN Return Log Likelihood of a fit generated by STRN
logLik.tsd Return Log Likelihood of a fit generated by tsd
movement Analyze movement recorded within a nest with an accelerometer datalogger
MovingIncubation Simulate incubation of a nest with the beginning of incubation varying
nest Timeseries of temperatures for nests
nobs.HatchingSuccess Return number of observations of a fit
nobs.NestsResult Return number of observations of a fit
plot.HatchingSuccess Plot results of HatchingSuccess.fit() that best describe hatching success
plot.NestsResult Plot the embryo growth
plot.tsd Plot results of tsd() that best describe temperature-dependent sex determination
plotR Plot the fitted growth rate dependent on temperature and its density
plot_transition Show fonction used for transition
predict.HatchingSuccess Return prediction based on a model fitted with HatchingSuccess.fit()
predict.tsd Estimate sex ratio according to constant incubation temperature
P_TRT Estimate the transitional range of temperatures based on a set of parameters
resultNest_3p_Dallwitz Fit using the nest database
resultNest_3p_Weibull Result of the fit using the nest database using Weibull function
resultNest_4p_normal Result of the fit using the nest database using asymmetric normal function
resultNest_4p_SSM Fit using the nest database
resultNest_4p_SSM_Linear Fit using the nest database
resultNest_4p_transition Result of the fit using the nest database using transition
resultNest_4p_trigo Result of the fit using the nest database using trigonometric function
resultNest_4p_weight Fit using the nest database with weight
resultNest_5p_Dallwitz Fit using the nest database
resultNest_6p_SSM Fit using the nest database
resultNest_mcmc_4p_SSM Result of the mcmc using the nest database
resultNest_mcmc_4p_SSM_Linear Result of the mcmc using the nest database
resultNest_mcmc_6p_SSM Result of the mcmc using the nest database
resultNest_mcmc_newp Result of the mcmc using the nest database with anchored parameters
resultNest_newp Fit using the nest database with anchored parameters
searchR Fit the parameters that best represent nest incubation data.
stages Database of of embryonic development and thermosensitive period of development for sex determination
STRN Estimate the parameters that best describe the sexualisation thermal reaction norm within the TSP
STRN_MHmcmc Metropolis-Hastings algorithm for Sexualisation Thermal Reaction Norm
summary.Nests Summarize the information from a Nests object.
switch.transition Add a transition parameter on a set of parameters or remove it
tempConst Timeseries of constant temperatures for nests
test.parallel Estimate the likelihood of a set of parameters for nest incubation data with or without parallel computing option
TRN_MHmcmc_p Generates set of parameters to be used with GRTRN_MHmcmc() or STRN_MHmcmc()
tsd Estimate the parameters that best describe temperature-dependent sex determination
tsd_MHmcmc Metropolis-Hastings algorithm for Sex ratio
tsd_MHmcmc_p Generates set of parameters to be used with tsd_MHmcmc()
TSP.list Database of thermosensitive period of development for sex determination
uncertainty.datalogger Uncertainty of average temperatures obtained using temperature data logger
web.tsd Run a shiny application for basic functions of tsd function
weightmaxentropy Search for the weights of the nests which maximize the entropy of nest temperatures distribution