Learn R Programming

phenology (version 10.1)

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.

Copy Link

Version

Install

install.packages('phenology')

Monthly Downloads

568

Version

10.1

License

GPL-2

Maintainer

Last Published

August 23rd, 2024

Functions in phenology (10.1)

Predict the possible clutch number based on observed Internesting Period.

Return a remigration interval.

Parameter_Global_Year

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

MinBMinE_to_Min

Transform a set of parameters from MinB and MinE to Min

MarineTurtles_2002

Database of tagged marine turtles in 2002

Return an expected remigration interval.

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

Transform a set of parameters from Length format to LengthB LengthE

Transform a set of parameters from LengthB LengthE format to Length

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

Generates set of parameters to be used with Tagloss_mcmc()

Tagloss_simulate

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

Bayesian model of tag loss using a CMR database.

Return the daily rate of tag loss.

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

Return the cumulative rate of tag loss.

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

fit a 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.

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

Add standard error for a fixed parameter.

adapt_parameters

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

Generate set of parameters to be used with fitCF_MHmcmc()

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

Fit a model of Clutch Frequency for marine turtles.

Run the Metropolis-Hastings algorithm for RMU.data

Adjust incomplete timeseries with various constraints.

Extract the set of parameters from a result object.

Run the Metropolis-Hastings algorithm for ECFOCF data

fitRMU_MHmcmc_p

Generates set of parameters to be used with fitRMU_MHmcmc()

Return Log Likelihood of a fit generated by Tagloss_fit

logLik.phenology

Return Log Likelihood of a fit generated by fit_phenology

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

Calculate the -log likelihood of data within a model.

Likelihood map of Leatherback nest counts

fixed.parameters0

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

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 generated by fitRMU

phenology_MHmcmc_p

Generates set of parameters to be used with phenology_MHmcmc()

phenology_MHmcmc

Run the Metropolis-Hastings algorithm for data

phenology2fitRMU

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

Generate a likelihood map varying Phi and Delta.

Model of tagloss based on Rivalan data

phenology-package

Tools to Manage a Parametric Function that Describes Phenology and More

Run a shiny application for basic functions of phenology package

Calculate initial set of parameters.

Return Log Likelihood of a fit done using fitCF

Database of leatherback CMR in French Guiana

Plot the synthesis of RMU fit.

plot.TaglossData

Plot data used for tagloss analysis.

plot.TableECFOCF

Plot a TableECFOCF dataset.

Plot the daily rate of tag loss.

Plot a result of clutch frequency fit.

Plot the best likelihood for fixed Phi value.

Plot a likelihood lineplot obtained after map_phenology.

Plot a result of Internesting Period fit or data.

plot.Remigration

Plot the remigration intervals.

result_Gratiot2

Result of the fit of Leatherback nest counts

Removes site information from a set of parameters.

print.phenologyout

Print the information from a ouput x.

toggle_Min_PMin

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

print.phenologymap

Print information on a phenologymap object.

print.phenology

Print the result information from a result x.

Print the result information from a IP object.

result_Gratiot_mcmc

Result of the mcmc for Leatherback nest counts

summary.phenology

Print the result information from a result object.

Shift sinusoid information.

Plot the phenology from a result.

plot.phenologymap

Plot a likelihood map with Delta and Phi varying.

summary.phenologymap

Print information on a phenologymap object.

result_Gratiot1

Result of the fit of Leatherback nest counts

Result of the fit of Leatherback nest counts

result_Gratiot_Flat

Result of the fit of Leatherback nest counts

summary.phenologyout

Print the summary information from a ouput object.

Bayesian.remigration

Return a posterior remigration interval.

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

Calculate a table of probabilities of ECF and OCF.

Fit a model of Internesting Period for marine turtles.

ExponentialRegression

Non-biased exponential regression

AutoFitPhenology

Automatic fit for phenology and tests

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

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()