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embryogrowth (version 10.2)

Tools to Analyze the Thermal Reaction Norm of Embryo Growth

Description

Tools to analyze the embryo growth and the sexualisation thermal reaction norms. See for tsd functions; see for thermal reaction norm of embryo growth.

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Version

Install

install.packages('embryogrowth')

Monthly Downloads

580

Version

10.2

License

GPL-2

Maintainer

Marc Girondot

Last Published

June 16th, 2025

Functions in embryogrowth (10.2)

P_TRT

Estimate the transitional range of temperatures based on a set of parameters
ROSIE

Database of TSD information for turtles
HatchingSuccess.lnL

Return -log likelihood of the data and the parameters
HatchingSuccess.model

Return the hatching success according the set of parameters and temperatures
STRN_MHmcmc

Metropolis-Hastings algorithm for Sexualisation Thermal Reaction Norm
HeterogeneityNests

Model heterogeneity of temperatures.
MovingIncubation

Simulate incubation of a nest with the beginning of incubation varying
TRN_MHmcmc_p

Generates set of parameters to be used with GRTRN_MHmcmc() or STRN_MHmcmc()
HatchingSuccess.MHmcmc_p

Generates set of parameters to be used with HatchingSuccess.MHmcmc()
embryogrowth-package

The package embryogrowth
hist.Nests2

Show the histogram of temperatures with set of nests
HatchingSuccess.fit

Fit a hatching success model to data using maximum likelihood
dydt.exponential

Return the derivative of the exponential function
ROSIE.version

Version of database of TSD information for reptiles
STRN

Estimate the parameters that best describe the sexualisation thermal reaction norm within the TSP
integral.linear

Return the linear function
integral.exponential

Return the derivative of the exponential function
integral.Gompertz

Return the result of the Gompertz function
dydt.linear

Return the derivative of the linear function
calibrate.datalogger

Calibrate data loggers and correct time series of temperatures
plot.Nests2

Show the plot of temperatures with set of nests
nobs.HatchingSuccess

Return number of observations of a fit
hist.NestsResult

Show the histogram of temperatures with set of nests
plot.HatchingSuccess

Plot results of HatchingSuccess.fit() that best describe hatching success
dydt.Gompertz

Return the derivative of the Gompertz function
UpdateNests

Create a dataset of class Nests2 from an object of class Nests
TSP.list

Database of thermosensitive period of development for sex determination
resultNest_3p_Dallwitz

Fit using the nest database
nobs.NestsResult

Return number of observations of a fit
likelihoodR

Estimate the likelihood of a set of parameters for nest incubation data
resultNest_3p_Weibull

Result of the fit using the nest database using Weibull function
logLik.HatchingSuccess

Return -log L of a fit
info.nests

Calculte statistics about nests
logLik.NestsResult

Return Log Likelihood of a fit generated by searchR
logLik.STRN

Return Log Likelihood of a fit generated by STRN
resultNest_4p_normal

Result of the fit using the nest database using asymmetric normal function
logLik.tsd

Return Log Likelihood of a fit generated by tsd
movement

Analyze movement recorded within a nest with an accelerometer datalogger
plotR

Plot the fitted growth rate dependent on temperature and its density
nest

Timeseries of temperatures for nests
resultNest_4p_transition

Result of the fit using the nest database using transition
switch.transition

Add a transition parameter on a set of parameters or remove it
summary.Nests2

Summarize the information from a Nests object.
resultNest_newp

Fit using the nest database with anchored parameters
stages

Database of of embryonic development and thermosensitive period of development for sex determination
weightmaxentropy

Search for the weights of the nests which maximize the entropy of nest temperatures distribution
searchR

Fit the parameters that best represent nest incubation data.
resultNest_mcmc_6p_SSM

Result of the mcmc using the nest database
resultNest_4p_SSM

Fit using the nest database
test.parallel

Estimate the likelihood of a set of parameters for nest incubation data with or without parallel computing option
plot_transition

Show fonction used for transition
resultNest_mcmc_newp

Result of the mcmc using the nest database with anchored parameters
resultNest_4p_trigo

Result of the fit using the nest database using trigonometric function
resultNest_4p_weight

Fit using the nest database with weight
plot.NestsResult

Plot the embryo growth
plot.tsd

Plot results of tsd() that best describe temperature-dependent sex determination
predict.HatchingSuccess

Return prediction based on a model fitted with HatchingSuccess.fit()
resultNest_5p_Dallwitz

Fit using the nest database
tsd_MHmcmc

Metropolis-Hastings algorithm for Sex ratio
predict.tsd

Estimate sex ratio according to constant incubation temperature
tsd

Estimate the parameters that best describe temperature-dependent sex determination
resultNest_6p_SSM

Fit using the nest database
tsd_MHmcmc_p

Generates set of parameters to be used with tsd_MHmcmc()
resultNest_4p_SSM_Linear

Fit using the nest database
tempConst

Timeseries of constant temperatures for nests
uncertainty.datalogger

Uncertainty of average temperatures obtained using temperature data logger
web.tsd

Run a shiny application for basic functions of tsd function
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
ChangeSSM

Generate set of parameters for different forms of thermal norm of reaction
Generate_hatchling_metric

Generate a data.frame that can be used as hatchling.metric value for searchR()
DatabaseTSD.version

Version of database of TSD information for reptiles
GenerateConstInc

Generate a data.frame with constant incubation temperature and incubation duration
DatabaseTSD

Database of TSD information for reptiles
FormatNests

Create a dataset of class Nests to be used with searchR
GRTRN_MHmcmc

Metropolis-Hastings algorithm for Embryo Growth Rate Thermal Reaction Norm
GenerateAnchor

Generate a set of anchored parameters
HatchingSuccess.MHmcmc

Metropolis-Hastings algorithm for hatching success
DatabaseNestingArea

Database of RMU for marine turtles