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

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Tools to analyze the embryo growth and the sexualisation thermal reaction norms.

Author
Marc Girondot <marc.girondot@u-psud.fr>
Date of publication
2016-10-02 10:12:28
Maintainer
Marc Girondot <marc.girondot@u-psud.fr>
License
GPL-2
Version
6.4

View on CRAN

Man pages

ChangeSSM
Generate set of parameters for Schoolfield-Sharpe-Magnuson...
DatabaseNestingArea
Database of RMU for marine turtles
DatabaseTSD
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
embryogrowth-package
The package embryogrowth
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...
GenerateTest
Generate a data.frame that can be used as test value for...
GRTRN_MHmcmc
Metropolis-Hastings algorithm for Embryo Growth Rate Thermal...
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
likelihoodR
Estimate the likelihood of a set of parameters for nest...
logLik.NestsResult
Return Log Likelihood of a fit generated by searchR
logLik.tsd
Return Log Likelihood of a fit generated by tsd
MovingIncubation
Simulate incubation of a nest with the beginning of...
nest
Timeseries of temperatures for nests
plot.NestsResult
Plot the embryo growth
plotR
Show the fitted growth rate dependent on temperature
plotR_hist
Shows the histogram of temperatures with set of nests and the...
plot_transition
Show fonction used for transition
plot.tsd
Plot results of tsd() that best describe...
predict.tsd
Estimate sex ratio according to constant incubation...
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
result_mcmc_newp
Result of the mcmc using the nest database with anchored...
resultNest_4p
Fit using the nest database
resultNest_4p_transition
Result of the fit using the nest database using transition
resultNest_4p_weight
Fit using the nest database with weight
resultNest_6p
Fit using the nest database
resultNest_newp
Fit using the nest database with anchored parameters
searchR
Fit the parameters that best represent nest incubation data.
SEforR
Estimate the standard error for a set of parameters
stages
Database of of embryonic development and thermosensitive...
STRN
Estimate the parameters that best describe the sexualisation...
STRN_MHmcmc
Metropolis-Hastings algorithm for Sexualisation Thermal...
summary.Nests
Summarize the information from a Nests object.
switch.transition
Add a transition parameter on a set of parameters or remove...
tempConst
Timeseries of constant temperatures for nests
TestParallel
Estimate the likelihood of a set of parameters for nest...
TRN_MHmcmc_p
Generates set of parameters to be used with GRTRN_MHmcmc() or...
tsd
Estimate the parameters that best describe...
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...
web.tsd
Run a shiny application for basic functions of tsd function
weightmaxentropy
Search for the weights of the nests which maximize the...

Files in this package

embryogrowth
embryogrowth/inst
embryogrowth/inst/shiny
embryogrowth/inst/shiny/ui.R
embryogrowth/inst/shiny/server.R
embryogrowth/inst/shiny/www
embryogrowth/inst/shiny/www/PDF.png
embryogrowth/NAMESPACE
embryogrowth/NEWS
embryogrowth/data
embryogrowth/data/resultNest_6p.rda
embryogrowth/data/nest.rda
embryogrowth/data/resultNest_4p_weight.rda
embryogrowth/data/stages.rda
embryogrowth/data/resultNest_4p_transition.rda
embryogrowth/data/resultNest_newp.rda
embryogrowth/data/result_mcmc_4p_weight.rda
embryogrowth/data/result_mcmc_6p.rda
embryogrowth/data/DatabaseNestingArea.rda
embryogrowth/data/result_mcmc_newp.rda
embryogrowth/data/resultNest_4p.rda
embryogrowth/data/DatabaseTSD.rda
embryogrowth/data/result_mcmc_4p.rda
embryogrowth/data/tempConst.rda
embryogrowth/data/TSP.list.rda
embryogrowth/R
embryogrowth/R/result_mcmc_4p.R
embryogrowth/R/resultNest_4p_transition.R
embryogrowth/R/fonctiontsdMCMC.R
embryogrowth/R/TestParallel.R
embryogrowth/R/DatabaseTSD.R
embryogrowth/R/Linear.R
embryogrowth/R/GenerateTest.R
embryogrowth/R/searchR.R
embryogrowth/R/fitSSM.R
embryogrowth/R/SEforR.R
embryogrowth/R/predict.tsd.R
embryogrowth/R/plot.NestsResult.R
embryogrowth/R/web.tsd.R
embryogrowth/R/tempConst.R
embryogrowth/R/resultNest_4p_weight.R
embryogrowth/R/result_mcmc_6p.R
embryogrowth/R/plot_transition.R
embryogrowth/R/embryogrowth-package.R
embryogrowth/R/FormatNests.R
embryogrowth/R/Gompertz.R
embryogrowth/R/tsd.R
embryogrowth/R/summary.Nests.R
embryogrowth/R/STRN_MHmcmc.R
embryogrowth/R/nest.R
embryogrowth/R/result_mcmc_newp.R
embryogrowth/R/tsd_MHmcmc.R
embryogrowth/R/logLik.tsd.R
embryogrowth/R/DatabaseNestingArea.R
embryogrowth/R/gradientRichardson.R
embryogrowth/R/modelTSD.R
embryogrowth/R/weightmaxentropy.R
embryogrowth/R/logLik.NestsResult.R
embryogrowth/R/SSM.R
embryogrowth/R/plotR.R
embryogrowth/R/resultNest_newp.R
embryogrowth/R/hessianRichardson.R
embryogrowth/R/TRN_MHmcmc_p.R
embryogrowth/R/stages.R
embryogrowth/R/likelihoodR.R
embryogrowth/R/weightmaxentropy_fit.R
embryogrowth/R/hist.NestsResult.R
embryogrowth/R/GenerateConstInc.R
embryogrowth/R/hist.Nests.R
embryogrowth/R/resultNest_4p.R
embryogrowth/R/plot.tsd.R
embryogrowth/R/STRN.R
embryogrowth/R/MovingIncubation.R
embryogrowth/R/TSP.list.R
embryogrowth/R/result_mcmc_4p_weight.R
embryogrowth/R/switch.transition.R
embryogrowth/R/tsd_MHmcmc_p.R
embryogrowth/R/fonctionSTRNMCMC.R
embryogrowth/R/ChangeSSM.R
embryogrowth/R/resultNest_6p.R
embryogrowth/R/plotR_hist.R
embryogrowth/R/tsd_fit.R
embryogrowth/R/GenerateAnchor.R
embryogrowth/R/GRTRN_MHmcmc.R
embryogrowth/R/STRN_fit.R
embryogrowth/R/info.nests.R
embryogrowth/R/Exponential.R
embryogrowth/MD5
embryogrowth/DESCRIPTION
embryogrowth/man
embryogrowth/man/logLik.tsd.Rd
embryogrowth/man/weightmaxentropy.Rd
embryogrowth/man/tsd.Rd
embryogrowth/man/resultNest_4p_weight.Rd
embryogrowth/man/GenerateAnchor.Rd
embryogrowth/man/result_mcmc_newp.Rd
embryogrowth/man/hist.Nests.Rd
embryogrowth/man/GenerateConstInc.Rd
embryogrowth/man/embryogrowth-package.Rd
embryogrowth/man/ChangeSSM.Rd
embryogrowth/man/result_mcmc_4p_weight.Rd
embryogrowth/man/plotR_hist.Rd
embryogrowth/man/resultNest_6p.Rd
embryogrowth/man/tsd_MHmcmc.Rd
embryogrowth/man/tsd_MHmcmc_p.Rd
embryogrowth/man/hist.NestsResult.Rd
embryogrowth/man/logLik.NestsResult.Rd
embryogrowth/man/likelihoodR.Rd
embryogrowth/man/predict.tsd.Rd
embryogrowth/man/info.nests.Rd
embryogrowth/man/nest.Rd
embryogrowth/man/dydt.exponential.Rd
embryogrowth/man/switch.transition.Rd
embryogrowth/man/summary.Nests.Rd
embryogrowth/man/resultNest_newp.Rd
embryogrowth/man/dydt.Gompertz.Rd
embryogrowth/man/TestParallel.Rd
embryogrowth/man/plot.tsd.Rd
embryogrowth/man/MovingIncubation.Rd
embryogrowth/man/resultNest_4p_transition.Rd
embryogrowth/man/resultNest_4p.Rd
embryogrowth/man/result_mcmc_6p.Rd
embryogrowth/man/plot.NestsResult.Rd
embryogrowth/man/DatabaseNestingArea.Rd
embryogrowth/man/GenerateTest.Rd
embryogrowth/man/STRN.Rd
embryogrowth/man/web.tsd.Rd
embryogrowth/man/tempConst.Rd
embryogrowth/man/plotR.Rd
embryogrowth/man/result_mcmc_4p.Rd
embryogrowth/man/TRN_MHmcmc_p.Rd
embryogrowth/man/dydt.linear.Rd
embryogrowth/man/SEforR.Rd
embryogrowth/man/TSP.list.Rd
embryogrowth/man/plot_transition.Rd
embryogrowth/man/searchR.Rd
embryogrowth/man/FormatNests.Rd
embryogrowth/man/GRTRN_MHmcmc.Rd
embryogrowth/man/STRN_MHmcmc.Rd
embryogrowth/man/DatabaseTSD.Rd
embryogrowth/man/stages.Rd