R: Tools to Analyze the Thermal Reaction Norm of Embryo Growth

# Tools to Analyze the Thermal Reaction Norm of Embryo Growth

## Documentation for package ‘embryogrowth’ version 9.1

- 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
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