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phenology (version 10.3)

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

305

Version

10.3

License

GPL-2

Maintainer

Marc Girondot

Last Published

June 17th, 2025

Functions in phenology (10.3)

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

Fit a model of Internesting Period for marine turtles.

Bayesian.remigration

Return a posterior remigration interval.

AutoFitPhenology

Automatic fit for phenology and tests

Calculate a table of probabilities of ECF and OCF.

Calculate the confidence interval of the results of fitRMU()

Calculate a table of probabilities of ECF and OCF.

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

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

Return an expected remigration interval.

Return a remigration interval.

MinBMinE_to_Min

Transform a set of parameters from MinB and MinE to Min

Transform a set of parameters from LengthB LengthE format to Length

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

Predict the possible clutch number based on observed Internesting Period.

Parameter_Global_Year

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

Calculate Breeding Proportion from Remigration Interval.

Transform a set of parameters from Length format to LengthB LengthE

MarineTurtles_2002

Database of tagged marine turtles in 2002

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

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

Return the cumulative rate of tag loss.

Tagloss_LengthObs

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

Bayesian model of tag loss using a CMR database.

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

Generates set of parameters to be used with Tagloss_mcmc()

Return the daily rate of tag loss.

fit a model of tag loss using a CMR database.

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

Tagloss_simulate

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

Extract the set of parameters from a result object.

Add standard error for a fixed parameter.

Run the Metropolis-Hastings algorithm for RMU.data

Run the Metropolis-Hastings algorithm for ECFOCF data

Generate set of parameters to be used with fitCF_MHmcmc()

Adjust incomplete timeseries with various constraints.

adapt_parameters

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

Fit a model of Clutch Frequency for marine turtles.

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

Fit the phenology parameters to timeseries of counts.

likelihood_phenology

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

Return Log Likelihood of a fit done using fitCF

logLik.phenology

Return Log Likelihood of a fit generated by fit_phenology

fitRMU_MHmcmc_p

Generates set of parameters to be used with fitRMU_MHmcmc()

fixed.parameters0

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

Return Log Likelihood of a fit generated by Tagloss_fit

Return Log Likelihood of a fit generated by fitRMU

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

Calculate the -log likelihood of data within a model.

phenology_MHmcmc

Run the Metropolis-Hastings algorithm for data

phenology_MHmcmc_p

Generates set of parameters to be used with phenology_MHmcmc()

Model of tagloss based on Rivalan data

Database of leatherback CMR in French Guiana

phenology-package

Tools to Manage a Parametric Function that Describes Phenology and More

Calculate initial set of parameters.

Generate a likelihood map varying Phi and Delta.

Likelihood map of Leatherback nest counts

Plot the phenology from a result.

Plot a result of clutch frequency fit.

plot.Remigration

Plot the remigration intervals.

plot.TableECFOCF

Plot a TableECFOCF dataset.

phenology2fitRMU

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

Plot the synthesis of RMU fit.

Run a shiny application for basic functions of phenology package

Plot a result of Internesting Period fit or data.

plot.TaglossData

Plot data used for tagloss analysis.

Plot the daily rate of tag loss.

plot.phenologymap

Plot a likelihood map with Delta and Phi varying.

Plot a likelihood lineplot obtained after map_phenology.

result_Gratiot1

Result of the fit of Leatherback nest counts

print.phenologymap

Print information on a phenologymap object.

print.phenologyout

Print the information from a ouput x.

Removes site information from a set of parameters.

Result of the fit of Leatherback nest counts

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

summary.phenologymap

Print information on a phenologymap object.

result_Gratiot2

Result of the fit of Leatherback nest counts

print.phenology

Print the result information from a result x.

Plot the best likelihood for fixed Phi value.

summary.phenologyout

Print the summary information from a ouput object.

Print the result information from a IP object.

summary.phenology

Print the result information from a result object.

ExponentialRegression

Non-biased exponential regression