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phenology (version 2025.11.12)

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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Install

install.packages('phenology')

Monthly Downloads

405

Version

2025.11.12

License

GPL-2

Maintainer

Marc Girondot

Last Published

November 12th, 2025

Functions in phenology (2025.11.12)

ECFOCF_f

Calculate a table of probabilities of ECF and OCF.
Gratiot

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

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

Calculate a table of probabilities of ECF and OCF.
BE_to_LBLE

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

Non-biased exponential regression
AutoFitPhenology

Automatic fit for phenology and tests
Bayesian.remigration

Return a posterior remigration interval.
CI.RMU

Calculate the confidence interval of the results of fitRMU()
IPFit

Fit a model of Internesting Period for marine turtles.
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
RI2BP

Calculate Breeding Proportion from Remigration Interval.
RI

Return an expected remigration interval.
IPPredict

Predict the possible clutch number based on observed Internesting Period.
MarineTurtles_2002

Database of tagged marine turtles in 2002
MinBMinE_to_Min

Transform a set of parameters from MinB and MinE to Min
LnRI_norm

Return a remigration interval.
Parameter_Global_Year

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

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

Generates set of parameters to be used with Tagloss_mcmc()
Tagloss_model

Return the daily rate of tag loss.
Tagloss_LengthObs

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

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

fit a model of tag loss using a CMR database.
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_L

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

Bayesian model of tag loss using a CMR database.
extract_result

Extract the set of parameters from a result object.
fitRMU_MHmcmc

Run the Metropolis-Hastings algorithm for RMU.data
fitCF_MHmcmc

Run the Metropolis-Hastings algorithm for ECFOCF data
add_phenology

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

Fit a model of Clutch Frequency for marine turtles.
fitRMU

Adjust incomplete timeseries with various constraints.
fitCF_MHmcmc_p

Generate set of parameters to be used with fitCF_MHmcmc()
logLik.ECFOCF

Return Log Likelihood of a fit done using fitCF
logLik.fitRMU

Return Log Likelihood of a fit generated by fitRMU
logLik.Tagloss

Return Log Likelihood of a fit generated by Tagloss_fit
generateCF

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

Calculate the -log likelihood of data within a model.
fitRMU_MHmcmc_p

Generates set of parameters to be used with fitRMU_MHmcmc()
likelihood_phenology

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

Fit the phenology parameters to timeseries of counts.
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
phenology_MHmcmc

Run the Metropolis-Hastings algorithm for data
map_Gratiot

Likelihood map of Leatherback nest counts
phenology2fitRMU

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

Run a shiny application for basic functions of phenology package
phenology_MHmcmc_p

Generates set of parameters to be used with phenology_MHmcmc()
par_init

Calculate initial set of parameters.
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
phenology-package

Tools to Manage a Parametric Function that Describes Phenology and More
plot.Remigration

Plot the remigration intervals.
plot.phenology

Plot the phenology from a result.
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.phenologymap

Plot a likelihood map with Delta and Phi varying.
plot.ECFOCF

Plot a result of clutch frequency fit.
plot_delta

Plot a likelihood lineplot obtained after map_phenology.
plot.IP

Plot a result of Internesting Period fit or data.
print.phenology

Print the result information from a result x.
result_Gratiot_Flat

Result of the fit of Leatherback nest counts
shift_sinusoid

Shift sinusoid information.
remove_site

Removes site information from a set of parameters.
print.phenologymap

Print information on a phenologymap object.
plot_phi

Plot the best likelihood for fixed Phi value.
print.phenologyout

Print the information from a ouput x.
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
summary.IP

Print the result information from a IP object.
summary.phenology

Print the result information from a result object.
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.
summary.phenologyout

Print the summary information from a ouput object.