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phenology (version 9.0)

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

474

Version

9.0

License

GPL-2

Maintainer

Marc Girondot

Last Published

April 1st, 2023

Functions in phenology (9.0)

AutoFitPhenology

Automatic fit for phenology and tests

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

Bayesian.remigration

Return a posterior remigration interval.

Fit a model of Internesting Period for marine turtles.

Calculate a table of probabilities of ECF and OCF.

ExponentialRegression

Non-biased exponential regression

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

Calculate a table of probabilities of ECF and OCF.

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

Calculate the confidence interval of the results of fitRMU()

Parameter_Global_Year

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

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

Predict the possible clutch number based on observed Internesting Period.

Return an expected remigration interval.

MinBMinE_to_Min

Transform a set of parameters from MinB and MinE to Min

MarineTurtles_2002

Database of tagged marine turtles in 2002

Transform a set of parameters from LengthB LengthE format to Length

Return a remigration interval.

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

Transform a set of parameters from Length format to LengthB LengthE

Return the cumulative rate of tag loss.

Bayesian model of tag loss using a CMR database.

Generates set of parameters to be used with Tagloss_mcmc()

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

Tagloss_LengthObs

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

Tagloss_simulate

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

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

Return the daily rate of tag loss.

fit a model of tag loss using a CMR database.

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

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

fitRMU_MHmcmc_p

Generates set of parameters to be used with fitRMU_MHmcmc()

Run the Metropolis-Hastings algorithm for RMU.data

Generate set of parameters to be used with fitCF_MHmcmc()

Fit a model of Clutch Frequency for marine turtles.

Add standard error for a fixed parameter.

adapt_parameters

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

Run the Metropolis-Hastings algorithm for ECFOCF data

Adjust incomplete timeseries with various constraints.

Extract the set of parameters from a result object.

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

Calculate the -log likelihood of data within a model.

Return Log Likelihood of a fit done using fitCF

likelihood_phenology

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

Return Log Likelihood of a fit generated by fitRMU

Fit the phenology parameters to timeseries of counts.

fixed.parameters0

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

Return Log Likelihood of a fit generated by Tagloss_fit

Likelihood map of Leatherback nest counts

logLik.phenology

Return Log Likelihood of a fit generated by fit_phenology

Database of leatherback CMR in French Guiana

phenology2fitRMU

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

Generate a likelihood map varying Phi and Delta.

Calculate initial set of parameters.

phenology_MHmcmc

Run the Metropolis-Hastings algorithm for data

phenology_MHmcmc_p

Generates set of parameters to be used with phenology_MHmcmc()

Plot a result of clutch frequency fit.

Run a shiny application for basic functions of phenology package

Model of tagloss based on Rivalan data

phenology-package

Tools to Manage a Parametric Function that Describes Phenology and More

Plot the synthesis of RMU fit.

Plot the best likelihood for fixed Phi value.

Plot a likelihood lineplot obtained after map_phenology.

plot.TableECFOCF

Plot a TableECFOCF dataset.

plot.TaglossData

Plot data used for tagloss analysis.

Plot the daily rate of tag loss.

plot.Remigration

Plot the remigration intervals.

Plot a result of Internesting Period fit or data.

Plot the phenology from a result.

plot.phenologymap

Plot a likelihood map with Delta and Phi varying.

Result of the fit of Leatherback nest counts

print.phenologyout

Print the information from a ouput x.

Shift sinusoid information.

result_Gratiot2

Result of the fit of Leatherback nest counts

result_Gratiot_Flat

Result of the fit of Leatherback nest counts

print.phenology

Print the result information from a result x.

Removes site information from a set of parameters.

print.phenologymap

Print information on a phenologymap object.

result_Gratiot1

Result of the fit of Leatherback nest counts

result_Gratiot_mcmc

Result of the mcmc for Leatherback nest counts

Print the result information from a IP object.

toggle_Min_PMin

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

summary.phenologyout

Print the summary information from a ouput object.

summary.phenologymap

Print information on a phenologymap object.

summary.phenology

Print the result information from a result object.