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embryogrowth (version 6.3)

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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Version

Install

install.packages('embryogrowth')

Monthly Downloads

291

Version

6.3

License

GPL-2

Maintainer

Marc Girondot

Last Published

July 18th, 2016

Functions in embryogrowth (6.3)

FormatNests

Create a dataset of class Nests to be used with searchR
dydt.exponential

Return the derivative of the exponential function
GenerateAnchor

Generate a set of anchored parameters
dydt.linear

Return the derivative of the linear function
GenerateConstInc

Generate a data.frame with constant incubation temperature and incubation duration
dydt.Gompertz

Return the derivative of the Gompertz function
DatabaseNestingArea

Database of RMU for marine turtles
DatabaseTSD

Database of TSD information for reptiles
ChangeSSM

Generate set of parameters for Schoolfield-Sharpe-Magnuson model
embryogrowth-package

The package embryogrowth
MovingIncubation

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

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

Timeseries of temperatures for nests
GenerateTest

Generate a data.frame that can be used as test value for searchR()
likelihoodR

Estimate the likelihood of a set of parameters for nest incubation data
logLik.NestsResult

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

Return Log Likelihood of a fit generated by tsd
hist.NestsResult

Show the histogram of temperatures with set of nests
hist.Nests

Show the histogram of temperatures with set of nests
info.nests

Calculte statistics about nests
plot.NestsResult

Plot the embryo growth
plot.tsd

Plot results of tsd() that best describe temperature-dependent sex determination
plot_transition

Show fonction used for transition
predict.tsd

Estimate sex ratio according to constant incubation temperature
result_mcmc_4p_weight

Result of the mcmc using the nest database
result_mcmc_6p

Result of the mcmc using the nest database
result_mcmc_newp

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

Shows the histogram of temperatures with set of nests and the R function superimpose
result_mcmc_4p

Result of the mcmc using the nest database
plotR

Show the fitted growth rate dependent on temperature
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
resultNest_newp

Fit using the nest database with anchored parameters
resultNest_4p

Fit using the nest database
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_6p

Fit using the nest database
searchR

Fit the parameters that best represent nest incubation data.
resultNest_4p_transition

Result of the fit using the nest database using transition
resultNest_4p_weight

Fit using the nest database with weight
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_MHmcmc

Metropolis-Hastings algorithm for Sex ratio
tsd

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

Search for the weights of the nests which maximize the entropy of nest temperatures distribution
switch.transition

Add a transition parameter on a set of parameters or remove it
tempConst

Timeseries of constant temperatures for nests
tsd_MHmcmc_p

Generates set of parameters to be used with tsd_MHmcmc()