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embryogrowth (version 6.4)
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
6.4
License
GPL-2
Maintainer
Marc Girondot
Last Published
October 2nd, 2016
Functions in embryogrowth (6.4)
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dydt.exponential
Return the derivative of the exponential function
DatabaseTSD
Database of TSD information for reptiles
DatabaseNestingArea
Database of RMU for marine turtles
dydt.linear
Return the derivative of the linear function
embryogrowth-package
The package embryogrowth
FormatNests
Create a dataset of class Nests to be used with searchR
ChangeSSM
Generate set of parameters for Schoolfield-Sharpe-Magnuson model
GenerateConstInc
Generate a data.frame with constant incubation temperature and incubation duration
GenerateAnchor
Generate a set of anchored parameters
dydt.Gompertz
Return the derivative of the Gompertz function
logLik.tsd
Return Log Likelihood of a fit generated by tsd
likelihoodR
Estimate the likelihood of a set of parameters for nest incubation data
MovingIncubation
Simulate incubation of a nest with the beginning of incubation varying
GenerateTest
Generate a data.frame that can be used as test value for searchR()
logLik.NestsResult
Return Log Likelihood of a fit generated by searchR
nest
Timeseries of temperatures for nests
hist.NestsResult
Show the histogram of temperatures with set of nests
GRTRN_MHmcmc
Metropolis-Hastings algorithm for Embryo Growth Rate Thermal Reaction Norm
info.nests
Calculte statistics about nests
hist.Nests
Show the histogram of temperatures with set of nests
plot.tsd
Plot results of tsd() that best describe temperature-dependent sex determination
plot.NestsResult
Plot the embryo growth
result_mcmc_newp
Result of the mcmc using the nest database with anchored parameters
plot_transition
Show fonction used for transition
plotR_hist
Shows the histogram of temperatures with set of nests and the R function superimpose
plotR
Show the fitted growth rate dependent on temperature
predict.tsd
Estimate sex ratio according to constant incubation temperature
result_mcmc_4p
Result of the mcmc using the nest database
result_mcmc_4p_weight
Result of the mcmc using the nest database
result_mcmc_6p
Result of the mcmc using the nest database
resultNest_newp
Fit using the nest database with anchored parameters
searchR
Fit the parameters that best represent nest incubation data.
STRN
Estimate the parameters that best describe the sexualisation thermal reaction norm within the TSP
resultNest_4p_transition
Result of the fit using the nest database using transition
SEforR
Estimate the standard error for a set of parameters
stages
Database of of embryonic development and thermosensitive period of development for sex determination
resultNest_4p
Fit using the nest database
resultNest_6p
Fit using the nest database
resultNest_4p_weight
Fit using the nest database with weight
STRN_MHmcmc
Metropolis-Hastings algorithm for Sexualisation Thermal Reaction Norm
TRN_MHmcmc_p
Generates set of parameters to be used with GRTRN_MHmcmc() or STRN_MHmcmc()
summary.Nests
Summarize the information from a Nests object.
TestParallel
Estimate the likelihood of a set of parameters for nest incubation data with or without parallel computing option
TSP.list
Database of thermosensitive period of development for sex determination
tsd
Estimate the parameters that best describe temperature-dependent sex determination
tsd_MHmcmc
Metropolis-Hastings algorithm for Sex ratio
switch.transition
Add a transition parameter on a set of parameters or remove it
tempConst
Timeseries of constant temperatures for 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
tsd_MHmcmc_p
Generates set of parameters to be used with tsd_MHmcmc()