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phenology (version 9.1)

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

250

Version

9.1

License

GPL-2

Maintainer

Marc Girondot

Last Published

October 16th, 2023

Functions in phenology (9.1)

Fit a model of Internesting Period for marine turtles.

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

Calculate a table of probabilities of ECF and OCF.

Calculate the confidence interval of the results of fitRMU()

ExponentialRegression

Non-biased exponential regression

AutoFitPhenology

Automatic fit for phenology and tests

Bayesian.remigration

Return a posterior remigration interval.

Calculate a table of probabilities of ECF and OCF.

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

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

MinBMinE_to_Min

Transform a set of parameters from MinB and MinE to Min

Parameter_Global_Year

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

Return the cumulative rate of tag loss.

Predict the possible clutch number based on observed Internesting Period.

Bayesian model of tag loss using a CMR database.

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

Generates set of parameters to be used with Tagloss_mcmc()

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

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.

Add standard error for a fixed parameter.

adapt_parameters

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

Return an expected remigration interval.

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

phenology_MHmcmc_p

Generates set of parameters to be used with phenology_MHmcmc()

Plot a result of clutch frequency fit.

Return a remigration interval.

Generate set of parameters to be used with fitCF_MHmcmc()

Return Log Likelihood of a fit done using fitCF

Calculate the -log likelihood of data within a model.

Adjust incomplete timeseries with various constraints.

phenology2fitRMU

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

plot.TableECFOCF

Plot a TableECFOCF dataset.

phenology_MHmcmc

Run the Metropolis-Hastings algorithm for data

plot.phenologymap

Plot a likelihood map with Delta and Phi varying.

Plot the phenology from a result.

Run the Metropolis-Hastings algorithm for ECFOCF data

Fit a model of Clutch Frequency for marine turtles.

Transform a set of parameters from LengthB LengthE format to Length

Transform a set of parameters from Length format to LengthB LengthE

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

fit a model of tag loss using a CMR database.

fitRMU_MHmcmc_p

Generates set of parameters to be used with fitRMU_MHmcmc()

Run the Metropolis-Hastings algorithm for RMU.data

Plot the daily rate of tag loss.

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

MarineTurtles_2002

Database of tagged marine turtles in 2002

Tagloss_simulate

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

likelihood_phenology

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

Return the daily rate of tag loss.

Return Log Likelihood of a fit generated by Tagloss_fit

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

Generate a likelihood map varying Phi and Delta.

print.phenologyout

Print the information from a ouput x.

summary.phenologyout

Print the summary information from a ouput object.

summary.phenologymap

Print information on a phenologymap object.

Removes site information from a set of parameters.

logLik.phenology

Return Log Likelihood of a fit generated by fit_phenology

Shift sinusoid information.

Likelihood map of Leatherback nest counts

result_Gratiot_mcmc

Result of the mcmc for Leatherback nest counts

Print the result information from a IP object.

Extract the set of parameters from a result object.

Model of tagloss based on Rivalan data

print.phenology

Print the result information from a result x.

Return Log Likelihood of a fit generated by fitRMU

Fit the phenology parameters to timeseries of counts.

Plot a likelihood lineplot obtained after map_phenology.

fixed.parameters0

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

print.phenologymap

Print information on a phenologymap object.

Plot the best likelihood for fixed Phi value.

result_Gratiot2

Result of the fit of Leatherback nest counts

toggle_Min_PMin

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

result_Gratiot_Flat

Result of the fit of Leatherback nest counts

summary.phenology

Print the result information from a result object.

phenology-package

Tools to Manage a Parametric Function that Describes Phenology and More

Calculate initial set of parameters.

Database of leatherback CMR in French Guiana

plot.TaglossData

Plot data used for tagloss analysis.

Plot the synthesis of RMU fit.

Run a shiny application for basic functions of phenology package

plot.Remigration

Plot the remigration intervals.

Plot a result of Internesting Period fit or data.

Result of the fit of Leatherback nest counts

result_Gratiot1

Result of the fit of Leatherback nest counts