embryogrowth-package |
The package embryogrowth |
calibrate.datalogger |
Calibrate data loggers and correct time series of temperatures |
ChangeSSM |
Generate set of parameters for different forms of thermal norm of reaction |
DatabaseNestingArea |
Database of RMU for marine turtles |
DatabaseTSD |
Database of TSD information for reptiles |
DatabaseTSD.version |
Version of 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 |
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 and incubation duration |
Generate_hatchling_metric |
Generate a data.frame that can be used as hatchling.metric value for searchR() |
GRTRN_MHmcmc |
Metropolis-Hastings algorithm for Embryo Growth Rate Thermal Reaction Norm |
HatchingSuccess.fit |
Fit a hatching success model to data using maximum likelihood |
HatchingSuccess.lnL |
Return -log likelihood of the data and the parameters |
HatchingSuccess.MHmcmc |
Metropolis-Hastings algorithm for hatching success |
HatchingSuccess.MHmcmc_p |
Generates set of parameters to be used with HatchingSuccess.MHmcmc() |
HatchingSuccess.model |
Return the hatching success according the set of parameters and temperatures |
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 |
integral.exponential |
Return the derivative of the exponential function |
integral.Gompertz |
Return the result of the Gompertz function |
integral.linear |
Return the linear function |
likelihoodR |
Estimate the likelihood of a set of parameters for nest incubation data |
logLik.HatchingSuccess |
Return -log L of a fit |
logLik.NestsResult |
Return Log Likelihood of a fit generated by searchR |
logLik.STRN |
Return Log Likelihood of a fit generated by STRN |
logLik.tsd |
Return Log Likelihood of a fit generated by tsd |
movement |
Analyze movement recorded within a nest with an accelerometer datalogger |
MovingIncubation |
Simulate incubation of a nest with the beginning of incubation varying |
nest |
Timeseries of temperatures for nests |
nobs.HatchingSuccess |
Return number of observations of a fit |
nobs.NestsResult |
Return number of observations of a fit |
plot.HatchingSuccess |
Plot results of HatchingSuccess.fit() that best describe hatching success |
plot.NestsResult |
Plot the embryo growth |
plot.tsd |
Plot results of tsd() that best describe temperature-dependent sex determination |
plotR |
Plot the fitted growth rate dependent on temperature and its density |
plot_transition |
Show fonction used for transition |
predict.HatchingSuccess |
Return prediction based on a model fitted with HatchingSuccess.fit() |
predict.tsd |
Estimate sex ratio according to constant incubation temperature |
P_TRT |
Estimate the transitional range of temperatures based on a set of parameters |
resultNest_3p_Dallwitz |
Fit using the nest database |
resultNest_3p_Weibull |
Result of the fit using the nest database using Weibull function |
resultNest_4p_normal |
Result of the fit using the nest database using asymmetric normal function |
resultNest_4p_SSM |
Fit using the nest database |
resultNest_4p_SSM_Linear |
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 function |
resultNest_4p_weight |
Fit using the nest database with weight |
resultNest_5p_Dallwitz |
Fit using the nest database |
resultNest_6p_SSM |
Fit using the nest database |
resultNest_mcmc_4p_SSM |
Result of the mcmc using the nest database |
resultNest_mcmc_4p_SSM_Linear |
Result of the mcmc using the nest database |
resultNest_mcmc_6p_SSM |
Result of the mcmc using the nest database |
resultNest_mcmc_newp |
Result of the mcmc using the nest database with anchored parameters |
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 period of development for sex determination |
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 |
summary.Nests |
Summarize the information from a Nests object. |
switch.transition |
Add a transition parameter on a set of parameters or remove it |
tempConst |
Timeseries of constant temperatures for nests |
test.parallel |
Estimate the likelihood of a set of parameters for nest incubation data with or without parallel computing option |
TRN_MHmcmc_p |
Generates set of parameters to be used with GRTRN_MHmcmc() or STRN_MHmcmc() |
tsd |
Estimate the parameters that best describe temperature-dependent sex determination |
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 determination |
uncertainty.datalogger |
Uncertainty of average temperatures obtained using temperature data logger |
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 |