AutoFitPhenology        Automatic fit for phenology and tests
BE_to_LBLE              Transform a set of parameters from Begin End to
                        LengthB LengthE.
Gratiot                 Leatherback nest counts from Gratiot et al.
                        (2006) Figure 1
LBLE_to_BE              Transform a set of parameters from LengthB
                        LengthE to Begin End.
LBLE_to_L               Transform a set of parameters from LengthB
                        LengthE format to Length
L_to_LBLE               Transform a set of parameters from Length
                        format to LengthB LengthE
MinBMinE_to_Min         Transform a set of parameters from MinB and
                        MinE to Min
Tagloss_L               Return the -log likelihood of a set of
                        individuals under a model of tagloss.
Tagloss_LengthObs       Return a list with the number of days different
                        kinds of individuals are seen.
Tagloss_daymax          Return the maximum number of days an individual
                        has been observed in a dataset.
Tagloss_fit             fit a model of tag loss using a CMR database.
Tagloss_format          Format a CMR dataset into a file that Tagloss_L
                        can use.
Tagloss_model           Return the daily rate of tag loss.
Tagloss_simulate        Return a list with the number of days different
                        kinds of individuals are seen.
adapt_parameters        Extract the parameters from a set of parameters
                        to be used with another dataset.
add_SD                  Add SD for a fixed parameter.
add_phenology           Create a new dataset or add a timeserie to a
                        previous dataset.
extract_result          Extract the set of parameters from a result
                        object.
fitRMU                  Adjust incomplete timeseries with various
                        constraints.
fitRMU_MHmcmc           Run the Metropolis-Hastings algorithm for
                        RMU.data
fitRMU_MHmcmc_p         Generates set of parameters to be used with
                        fitRMU_MHmcmc()
fit_phenology           Fit the phenology parameters to timeseries of
                        counts.
likelihood_phenology    Estimate the likelihood of timeseries based on
                        a set of parameters.
logLik.Tagloss          Return Log Likelihood of a fit generated by
                        Tagloss_fit
logLik.fitRMU           Return Log Likelihood of a fit generated by
                        fitRMU
logLik.phenology        Return Log Likelihood of a fit generated by
                        fit_phenology
map_Gratiot             Likelihood map of Leatherback nest counts
map_phenology           Generate a likelihood map varying Phi and
                        Delta.
outLR                   Database of leatherback CMR in French Guiana
par_init                Calculate initial set of parameters.
phenology               Run a shiny application for basic functions of
                        phenology package
phenology-package       Tools to Manage a Parametric Function that
                        Describes Phenology
phenology_MHmcmc        Run the Metropolis-Hastings algorithm for data
phenology_MHmcmc_p      Generates set of parameters to be used with
                        phenology_MHmcmc()
plot.Tagloss            Plot the daily rate of tag loss.
plot.fitRMU             Plot the synthesis of RMU fit.
plot.phenology          Plot the phenology from a result.
plot.phenologymap       Plot a likelihood map with Delta and Phi
                        varying.
plot_delta              Plot a likelihood lineplot obtained after
                        map_phenology.
plot_phi                Plot the best likelihood for fixed Phi value.
print.phenology         Print the result information from a result x.
print.phenologymap      Print information on a phenologymap object.
print.phenologyout      Print the information from a ouput x.
remove_site             Removes site information from a set of
                        parameters.
result_Gratiot          Result of the fit of Leatherback nest counts
result_Gratiot1         Result of the fit of Leatherback nest counts
result_Gratiot2         Result of the fit of Leatherback nest counts
result_Gratiot_Flat     Result of the fit of Leatherback nest counts
result_Gratiot_mcmc     Result of the mcmc for Leatherback nest counts
shift_sinusoid          Shift sinusoid information.
summary.phenology       Print the result information from a result
                        object.
summary.phenologymap    Print information on a phenologymap object.
summary.phenologyout    Print the summary information from a ouput
                        object.
toggle_Min_PMin         Transform a set of parameters from Min, MinB or
                        MinE to PMin, PminB or PminE, or reverse
