AutoFitPhenology        Automatic fit for phenology and tests
BE_to_LBLE              Transform a set of parameters from Begin End to
                        LengthB LengthE.
Bayesian.remigration    Return a posterior remigration interval.
CI.RMU                  Calculate the confidence interval of the
                        results of fitRMU()
ECFOCF_f                Calculate a table of probabilities of ECF and
                        OCF.
ECFOCF_full             Calculate a table of probabilities of ECF and
                        OCF.
ExponentialRegression   Non-biased exponential regression
Gratiot                 Leatherback nest counts from Gratiot et al.
                        (2006) Figure 1
IPFit                   Fit a model of Internesting Period for marine
                        turtles.
IPModel                 Estimates the pattern of internesting intervals
                        for a set of parameters.
IPPredict               Predict the possible clutch number based on
                        observed Internesting Period.
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
LnRI_norm               Return a remigration interval.
MarineTurtles_2002      Database of tagged marine turtles in 2002
MinBMinE_to_Min         Transform a set of parameters from MinB and
                        MinE to Min
Parameter_Global_Year   Transform a set of parameters from Year to
                        global effect, or reverse
RI                      Return an expected remigration interval.
RI2BP                   Calculate Breeding Proportion from Remigration
                        Interval.
TableECFOCF             Format a CMR dataset into a file that fitCF can
                        use.
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 for
                        different kinds of individuals are seen.
Tagloss_cumul           Return the cumulative rate of tag loss.
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_mcmc            Bayesian model of tag loss using a CMR
                        database.
Tagloss_mcmc_p          Generates set of parameters to be used with
                        Tagloss_mcmc()
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_SE                  Add standard error 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.
fitCF                   Fit a model of Clutch Frequency for marine
                        turtles.
fitCF_MHmcmc            Run the Metropolis-Hastings algorithm for
                        ECFOCF data
fitCF_MHmcmc_p          Generate set of parameters to be used with
                        fitCF_MHmcmc()
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.
fixed.parameters0       Generate a set of fixed parameters for series
                        with only 0 counts
generateCF              Generate a set of data to test Clutch Frequency
                        for marine turtles.
likelihood_phenology    Estimate the likelihood of timeseries based on
                        a set of parameters.
lnLCF                   Calculate the -log likelihood of data within a
                        model.
logLik.ECFOCF           Return Log Likelihood of a fit done using fitCF
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.
o_4p_p1p2               Model of tagloss based on Rivalan data
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 and More
phenology2fitRMU        Create the data to be used with fitRMU() for a
                        summary(phenology).
phenology_MHmcmc        Run the Metropolis-Hastings algorithm for data
phenology_MHmcmc_p      Generates set of parameters to be used with
                        phenology_MHmcmc()
plot.ECFOCF             Plot a result of clutch frequency fit.
plot.IP                 Plot a result of Internesting Period fit or
                        data.
plot.Remigration        Plot the remigration intervals.
plot.TableECFOCF        Plot a TableECFOCF dataset.
plot.Tagloss            Plot the daily rate of tag loss.
plot.TaglossData        Plot data used for tagloss analysis.
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
shift_sinusoid          Shift sinusoid information.
summary.IP              Print the result information from a IP object.
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
