# Tools to Manage a Parametric Function that Describes Phenology and More

## Documentation for package ‘phenology’ version 7.9

- DESCRIPTION file.
- Package NEWS.

## Help Pages

phenology-package | Tools to Manage a Parametric Function that Describes Phenology and More
adapt_parameters | Extract the parameters from a set of parameters to be used with another dataset.
add_phenology | Create a new dataset or add a timeserie to a previous dataset.
add_SE | Add standard error for a fixed parameter.
AutoFitPhenology | Automatic fit for phenology and tests
Bayesian.remigration | Return a posterior remigration interval.
BE_to_LBLE | Transform a set of parameters from Begin End to LengthB LengthE.
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
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.
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
likelihood_phenology | Estimate the likelihood of timeseries based on a set of parameters.
lnLCF | Calculate the -log likelihood of data within a model.
LnRI_norm | Return a remigration interval.
logLik.ECFOCF | Return Log Likelihood of a fit done using fitCF
logLik.fitRMU | Return Log Likelihood of a fit generated by fitRMU
logLik.phenology | Return Log Likelihood of a fit generated by fit_phenology
logLik.Tagloss | Return Log Likelihood of a fit generated by Tagloss_fit
L_to_LBLE | Transform a set of parameters from Length format to LengthB LengthE
map_Gratiot | Likelihood map of Leatherback nest counts
map_phenology | Generate a likelihood map varying Phi and Delta.
MarineTurtles_2002 | Database of tagged marine turtles in 2002
MinBMinE_to_Min | Transform a set of parameters from MinB and MinE to Min
outLR | Database of leatherback CMR in French Guiana
o_4p_p1p2 | Model of tagloss based on Rivalan data
Parameter_Global_Year | Transform a set of parameters from Year to global effect, or reverse
par_init | Calculate initial set of parameters.
phenology | Run a shiny application for basic functions of phenology package
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.fitRMU | Plot the synthesis of RMU fit.
plot.IP | Plot a result of Internesting Period fit or data.
plot.phenology | Plot the phenology from a result.
plot.phenologymap | Plot a likelihood map with Delta and Phi varying.
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_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
RI | Return an expected remigration interval.
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.
TableECFOCF | Format a CMR dataset into a file that fitCF can use.
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_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_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.
toggle_Min_PMin | Transform a set of parameters from Min, MinB or MinE to PMin, PminB or PminE, or reverse