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phenology (version 2026.8.24)

Tools to Manage a Parametric Function that Describes Phenology and More

Description

Functions used to fit and test the phenology of species based on counts. Based on Girondot, M. (2010) for the phenology function, Girondot, M. (2017) for the convolution of negative binomial, Girondot, M. and Rizzo, A. (2015) for Bayesian estimate, Pfaller JB, ..., Girondot M (2019) for tag-loss estimate, Hancock J, ..., Girondot M (2019) for nesting history, Laloe J-O, ..., Girondot M, Hays GC (2020) for aggregating several seasons.

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Version

Install

install.packages('phenology')

Monthly Downloads

362

Version

2026.8.24

License

GPL-2

Maintainer

Marc Girondot

Last Published

August 24th, 2026

Functions in phenology (2026.8.24)

Leatherback nest counts from Gratiot et al. (2006) Figure 1

Calculate the confidence interval of the results of fitRMU()

ExponentialRegression

Non-biased exponential regression

AutoFitPhenology

Automatic fit for phenology and tests

Transform a set of parameters from Begin End to LengthB LengthE.

Calculate a table of probabilities of ECF and OCF.

Bayesian.remigration

Return a posterior remigration interval.

Estimates the pattern of internesting intervals for a set of parameters.

Calculate a table of probabilities of ECF and OCF.

Fit a model of Internesting Period for marine turtles.

Predict the possible clutch number based on observed Internesting Period.

MinBMinE_to_Min

Transform a set of parameters from MinB and MinE to Min

Return a remigration interval.

MarineTurtles_2002

Database of tagged marine turtles in 2002

Parameter_Global_Year

Transform a set of parameters from Year to global effect, or reverse

Transform a set of parameters from Length format to LengthB LengthE

Transform a set of parameters from LengthB LengthE to Begin End.

Transform a set of parameters from LengthB LengthE format to Length

Return an expected remigration interval.

Calculate Breeding Proportion from Remigration Interval.

Return the maximum number of days an individual has been observed in a dataset.

Return the cumulative rate of tag loss.

Bayesian model of tag loss using a CMR database.

Tagloss_LengthObs

Return a list with the number of days for different kinds of individuals are seen.

fit a model of tag loss using a CMR database.

Return the -log likelihood of a set of individuals under a model of tagloss.

Sea_Turtles_Bayesian

R code for Girondot, M., & Guillon, J.-M. (2026) Book chapter

Generates set of parameters to be used with Tagloss_mcmc()

Format a CMR dataset into a file that Tagloss_L can use.

Format a CMR dataset into a file that fitCF can use.

Extract the set of parameters from a result object.

Return the daily rate of tag loss.

Fit a model of Clutch Frequency for marine turtles.

Create a new dataset or add a timeserie to a previous dataset.

Run the Metropolis-Hastings algorithm for ECFOCF data

adapt_parameters

Extract the parameters from a set of parameters to be used with another dataset.

Adjust incomplete timeseries with various constraints.

Generate set of parameters to be used with fitCF_MHmcmc()

Add standard error for a fixed parameter.

Tagloss_simulate

Return a list with the number of days different kinds of individuals are seen.

Return Log Likelihood of a fit generated by fitRMU

Return Log Likelihood of a fit done using fitCF

Return Log Likelihood of a fit generated by Tagloss_fit

Run the Metropolis-Hastings algorithm for RMU.data

Generate a set of data to test Clutch Frequency for marine turtles.

fitRMU_MHmcmc_p

Generates set of parameters to be used with fitRMU_MHmcmc()

Fit the phenology parameters to timeseries of counts.

likelihood_phenology

Estimate the likelihood of timeseries based on a set of parameters.

Calculate the -log likelihood of data within a model.

fixed.parameters0

Generate a set of fixed parameters for series with only 0 counts

logLik.phenology

Return Log Likelihood of a fit generated by fit_phenology

phenology2fitRMU

Create the data to be used with fitRMU() for a summary(phenology).

Database of leatherback CMR in French Guiana

phenology_MHmcmc

Run the Metropolis-Hastings algorithm for data

Generate a likelihood map varying Phi and Delta.

Run a shiny application for basic functions of phenology package

Calculate initial set of parameters.

Likelihood map of Leatherback nest counts

Model of tagloss based on Rivalan data

phenology-package

Tools to Manage a Parametric Function that Describes Phenology and More

plot.phenologydata

Plot the phenology from a add_phenology().

Plot the phenology from a result.

phenology_MHmcmc_p

Generates set of parameters to be used with phenology_MHmcmc()

Plot a result of clutch frequency fit.

plot.TaglossData

Plot data used for tagloss analysis.

Plot the synthesis of RMU fit.

Plot the daily rate of tag loss.

Plot a result of Internesting Period fit or data.

plot.Remigration

Plot the remigration intervals.

plot.TableECFOCF

Plot a TableECFOCF dataset.

result_Gratiot2

Result of the fit of Leatherback nest counts

Plot the best likelihood for fixed Phi value.

print.phenologyout

Print the information from a ouput x.

print.phenology

Print the result information from a result x.

Plot a likelihood lineplot obtained after map_phenology.

print.phenologymap

Print information on a phenologymap object.

Removes site information from a set of parameters.

plot.phenologymap

Plot a likelihood map with Delta and Phi varying.

Result of the fit of Leatherback nest counts

result_Gratiot1

Result of the fit of Leatherback nest counts

summary.phenologymap

Print information on a phenologymap object.

summary.phenologyout

Print the summary information from a ouput object.

summary.phenology

Print the result information from a result object.

result_Gratiot_Flat

Result of the fit of Leatherback nest counts

Shift sinusoid information.

toggle_Min_PMin

Transform a set of parameters from Min, MinB or MinE to PMin, PminB or PminE, or reverse

Print the result information from a IP object.