Tools to Analyze the Thermal Reaction Norm of Embryo Growth

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Documentation for package ‘embryogrowth’ version 10.2

• DESCRIPTION file.
• Package NEWS.

Help Pages

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
HeterogeneityNests	Model heterogeneity of temperatures.
hist.Nests2	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.Nests2	Show the plot of temperatures with set of nests
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
ROSIE	Database of TSD information for turtles
ROSIE.version	Version of database of TSD information for reptiles
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.Nests2	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
UpdateNests	Create a dataset of class Nests2 from an object of class Nests
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