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

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

AuthorMarc Girondot <marc.girondot@u-psud.fr>
Date of publication2017-03-11 09:18:31
MaintainerMarc Girondot <marc.girondot@u-psud.fr>
LicenseGPL-2
Version6.5

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

nobs.NestsResult: Return number of observations of a fit

plot.NestsResult: Plot the embryo growth

plotR: Show the fitted growth rate dependent on temperature and its...

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...

P_TRT: Estimate the transitional range of temperatures based on a...

result_mcmc_4p_weight: Result of the mcmc using the nest database

result_mcmc_newp: Result of the mcmc using the nest database with anchored...

resultNest_3p_Weibull: Result of the fit using the nest database using Weibull...

resultNest_4p_normal: Result of the fit using the nest database using asymmetric...

resultNest_4p_SSM4p: Fit using the nest database

resultNest_4p_transition: Result of the fit using the nest database using transition

resultNest_4p_trigo: Result of the fit using the nest database using trigonometric...

resultNest_4p_weight: Fit using the nest database with weight

resultNest_6p_SSM6p: Fit using the nest database

resultNest_mcmc_3p_Weibull: Result of the fit using the nest database using Weibull...

resultNest_mcmc_4p_epsilon: Result of the mcmc using the nest database

resultNest_mcmc_4p_normal: Result of the fit using the nest database using asymmetric...

resultNest_mcmc_4p_SSM4p: Result of the mcmc using the nest database

resultNest_mcmc_4p_trigo: Result of the fit using the nest database using trigonometric...

resultNest_mcmc_6p_SSM6p: 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.

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...

Functions

ChangeSSM Man page
DatabaseNestingArea Man page
DatabaseTSD Man page
dydt.exponential Man page
dydt.Gompertz Man page
dydt.linear Man page
embryogrowth-package Man page
FormatNests Man page
GenerateAnchor Man page
GenerateConstInc Man page
GenerateTest Man page
GRTRN_MHmcmc Man page
hist.Nests Man page
hist.NestsResult Man page
info.nests Man page
likelihoodR Man page
logLik.NestsResult Man page
logLik.tsd Man page
MovingIncubation Man page
nest Man page
nobs.NestsResult Man page
plot.NestsResult Man page
plotR Man page
plot_transition Man page
plot.tsd Man page
predict.tsd Man page
P_TRT Man page
result_mcmc_4p_weight Man page
result_mcmc_newp Man page
resultNest_3p_Weibull Man page
resultNest_4p_normal Man page
resultNest_4p_SSM4p Man page
resultNest_4p_transition Man page
resultNest_4p_trigo Man page
resultNest_4p_weight Man page
resultNest_6p_SSM6p Man page
resultNest_mcmc_3p_Weibull Man page
resultNest_mcmc_4p_epsilon Man page
resultNest_mcmc_4p_normal Man page
resultNest_mcmc_4p_SSM4p Man page
resultNest_mcmc_4p_trigo Man page
resultNest_mcmc_6p_SSM6p Man page
resultNest_newp Man page
searchR Man page
stages Man page
STRN Man page
STRN_MHmcmc Man page
summary.Nests Man page
switch.transition Man page
tempConst Man page
TestParallel Man page
TRN_MHmcmc_p Man page
tsd Man page
tsd_MHmcmc Man page
tsd_MHmcmc_p Man page
TSP.list Man page
web.tsd Man page
weightmaxentropy Man page

Files

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_3p_Weibull.rda
embryogrowth/data/resultNest_4p_normal.rda
embryogrowth/data/resultNest_mcmc_4p_epsilon.rda
embryogrowth/data/nest.rda
embryogrowth/data/resultNest_mcmc_6p_SSM6p.rda
embryogrowth/data/resultNest_4p_trigo.rda
embryogrowth/data/resultNest_4p_weight.rda
embryogrowth/data/stages.rda
embryogrowth/data/resultNest_4p_transition.rda
embryogrowth/data/resultNest_6p_SSM6p.rda
embryogrowth/data/resultNest_newp.rda
embryogrowth/data/result_mcmc_4p_weight.rda
embryogrowth/data/DatabaseNestingArea.rda
embryogrowth/data/result_mcmc_newp.rda
embryogrowth/data/DatabaseTSD.rda
embryogrowth/data/datalist
embryogrowth/data/tempConst.rda
embryogrowth/data/resultNest_4p_SSM4p.rda
embryogrowth/data/TSP.list.rda
embryogrowth/data/resultNest_mcmc_4p_trigo.rda
embryogrowth/data/resultNest_mcmc_3p_Weibull.rda
embryogrowth/data/resultNest_mcmc_4p_normal.rda
embryogrowth/data/resultNest_mcmc_4p_SSM4p.rda
embryogrowth/R
embryogrowth/R/resultNest_4p_transition.R embryogrowth/R/resultNest_mcmc_4p_epsilon.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/predict.tsd.R embryogrowth/R/plot.NestsResult.R embryogrowth/R/resultNest_mcmc_4p_normal.R embryogrowth/R/resultNest_3p_Weibull.R embryogrowth/R/web.tsd.R embryogrowth/R/tempConst.R embryogrowth/R/resultNest_4p_weight.R embryogrowth/R/resultNest_mcmc_6p_SSM6p.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/resultNest_4p_trigo.R embryogrowth/R/STRN_MHmcmc.R embryogrowth/R/nobs.NestsResult.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/resultNest_6p_SSM6p.R embryogrowth/R/modelTSD.R embryogrowth/R/weightmaxentropy.R embryogrowth/R/resultNest_mcmc_4p_trigo.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/plot.tsd.R embryogrowth/R/resultNest_mcmc_3p_Weibull.R embryogrowth/R/resultNest_4p_SSM4p.R embryogrowth/R/STRN.R embryogrowth/R/MovingIncubation.R embryogrowth/R/TSP.list.R embryogrowth/R/result_mcmc_4p_weight.R embryogrowth/R/resultNest_mcmc_4p_SSM4p.R embryogrowth/R/switch.transition.R embryogrowth/R/tsd_MHmcmc_p.R embryogrowth/R/fonctionSTRNMCMC.R embryogrowth/R/ChangeSSM.R embryogrowth/R/tsd_fit.R embryogrowth/R/GenerateAnchor.R embryogrowth/R/resultNest_4p_normal.R embryogrowth/R/GRTRN_MHmcmc.R embryogrowth/R/STRN_fit.R embryogrowth/R/P_TRT.R embryogrowth/R/info.nests.R embryogrowth/R/Exponential.R
embryogrowth/MD5
embryogrowth/DESCRIPTION
embryogrowth/man
embryogrowth/man/nobs.NestsResult.Rd 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/resultNest_4p_SSM4p.Rd embryogrowth/man/tsd_MHmcmc.Rd embryogrowth/man/tsd_MHmcmc_p.Rd embryogrowth/man/P_TRT.Rd embryogrowth/man/hist.NestsResult.Rd embryogrowth/man/logLik.NestsResult.Rd embryogrowth/man/resultNest_6p_SSM6p.Rd embryogrowth/man/likelihoodR.Rd embryogrowth/man/predict.tsd.Rd embryogrowth/man/info.nests.Rd embryogrowth/man/resultNest_mcmc_4p_epsilon.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/resultNest_4p_normal.Rd embryogrowth/man/resultNest_mcmc_4p_normal.Rd embryogrowth/man/plot.tsd.Rd embryogrowth/man/MovingIncubation.Rd embryogrowth/man/resultNest_mcmc_3p_Weibull.Rd embryogrowth/man/resultNest_4p_transition.Rd embryogrowth/man/plot.NestsResult.Rd embryogrowth/man/DatabaseNestingArea.Rd embryogrowth/man/resultNest_mcmc_6p_SSM6p.Rd embryogrowth/man/GenerateTest.Rd embryogrowth/man/STRN.Rd embryogrowth/man/resultNest_4p_trigo.Rd embryogrowth/man/web.tsd.Rd embryogrowth/man/tempConst.Rd embryogrowth/man/plotR.Rd embryogrowth/man/TRN_MHmcmc_p.Rd embryogrowth/man/dydt.linear.Rd embryogrowth/man/TSP.list.Rd embryogrowth/man/resultNest_mcmc_4p_SSM4p.Rd embryogrowth/man/resultNest_mcmc_4p_trigo.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/resultNest_3p_Weibull.Rd embryogrowth/man/stages.Rd

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