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embryogrowth (version 8.0)
Tools to Analyze the Thermal Reaction Norm of Embryo Growth
Description
Tools to analyze the embryo growth and the sexualisation thermal reaction norms.
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Install
install.packages('embryogrowth')
Monthly Downloads
355
Version
8.0
License
GPL-2
Maintainer
Marc Girondot
Last Published
October 22nd, 2020
Functions in embryogrowth (8.0)
Search all functions
GenerateAnchor
Generate a set of anchored parameters
HatchingSuccess.model
Return the hatching success according the set of parameters and temperatures
HatchingSuccess.lnL
Return -log likelihood of the data and the parameters
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
hist.NestsResult
Show the histogram of temperatures with set of nests
likelihoodR
Estimate the likelihood of a set of parameters for nest incubation data
logLik.HatchingSuccess
Return -log L of a fit
nobs.NestsResult
Return number of observations of a fit
info.nests
Calculte statistics about nests
logLik.NestsResult
Return Log Likelihood of a fit generated by searchR
TRN_MHmcmc_p
Generates set of parameters to be used with GRTRN_MHmcmc() or STRN_MHmcmc()
TSP.list
Database of thermosensitive period of development for sex determination
embryogrowth-package
The package embryogrowth
HatchingSuccess.MHmcmc_p
Generates set of parameters to be used with HatchingSuccess.MHmcmc()
logLik.STRN
Return Log Likelihood of a fit generated by STRN
HatchingSuccess.fit
Fit a hatching success model to data using maximum likelihood
plot.HatchingSuccess
Plot results of HatchingSuccess.fit() that best describe hatching success
plot.tsd
Plot results of tsd() that best describe temperature-dependent sex determination
plot.NestsResult
Plot the embryo growth
resultNest_4p_normal
Result of the fit using the nest database using asymmetric normal function
predict.HatchingSuccess
Return prediction based on a model fitted with HatchingSuccess.fit()
resultNest_4p_transition
Result of the fit using the nest database using transition
resultNest_6p_SSM6p
Fit using the nest database
dydt.exponential
Return the derivative of the exponential function
dydt.linear
Return the derivative of the linear function
resultNest_mcmc_4p_SSM4p
Result of the mcmc using the nest database
web.tsd
Run a shiny application for basic functions of tsd function
MovingIncubation
Simulate incubation of a nest with the beginning of incubation varying
nobs.HatchingSuccess
Return number of observations of a fit
nest
Timeseries of temperatures for nests
tsd_MHmcmc_p
Generates set of parameters to be used with tsd_MHmcmc()
uncertainty.datalogger
Uncertainty of average temperatures obtained using temperature data logger
P_TRT
Estimate the transitional range of temperatures based on a set of parameters
weightmaxentropy
Search for the weights of the nests which maximize the entropy of nest temperatures distribution
dydt.Gompertz
Return the derivative of the Gompertz function
calibrate.datalogger
Calibrate data loggers and correct time series of temperatures
predict.tsd
Estimate sex ratio according to constant incubation temperature
logLik.tsd
Return Log Likelihood of a fit generated by tsd
movement
Analyze movement recorded within a nest with an accelerometer datalogger
plotR
Show the fitted growth rate dependent on temperature and its density
hist.Nests
Show the histogram of temperatures with set of nests
plot_transition
Show fonction used for transition
resultNest_3p_Weibull
Result of the fit using the nest database using Weibull function
resultNest_3p_Dallwitz
Fit using the nest database
resultNest_4p_SSM4p
Fit using the nest database
resultNest_4p_SSM
Fit using the nest database
resultNest_newp
Fit using the nest database with anchored parameters
summary.Nests
Summarize the information from a Nests object.
resultNest_4p_weight
Fit using the nest database with weight
resultNest_4p_trigo
Result of the fit using the nest database using trigonometric function
searchR
Fit the parameters that best represent nest incubation data.
result_mcmc_newp
Result of the mcmc using the nest database with anchored parameters
stages
Database of of embryonic development and thermosensitive period of development for sex determination
test.parallel
Estimate the likelihood of a set of parameters for nest incubation data with or without parallel computing option
tempConst
Timeseries of constant temperatures for nests
resultNest_5p_Dallwitz
Fit using the nest database
tsd
Estimate the parameters that best describe temperature-dependent sex determination
tsd_MHmcmc
Metropolis-Hastings algorithm for Sex ratio
resultNest_6p_SSM
Fit using the nest database
switch.transition
Add a transition parameter on a set of parameters or remove it
GRTRN_MHmcmc
Metropolis-Hastings algorithm for Embryo Growth Rate Thermal Reaction Norm
GenerateTest
Generate a data.frame that can be used as test 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
FormatNests
Create a dataset of class Nests to be used with searchR
ChangeSSM
Generate set of parameters for different forms of thermal norm of reaction
DatabaseTSD
Database of TSD information for reptiles
HatchingSuccess.MHmcmc
Metropolis-Hastings algorithm for hatching success
DatabaseNestingArea
Database of RMU for marine turtles