Tools to Manage a Parametric Function that Describes Phenology and More
Format a CMR dataset into a file that Tagloss_L can use.
Return the -log likelihood of a set of individuals under a model of ta...
Return a list with the number of days for different kinds of individua...
Run a shiny application for basic functions of phenology package
Create the data to be used with fitRMU() for a summary(phenology).
Print information on a phenologymap object.
Print the result information from a result object.
Transform a set of parameters from Begin End to LengthB LengthE.
Extract the parameters from a set of parameters to be used with anothe...
Run the Metropolis-Hastings algorithm for RMU.data
Create a new dataset or add a timeserie to a previous dataset.
Add standard error for a fixed parameter.
Automatic fit for phenology and tests
Return a posterior remigration interval.
Generate a likelihood map varying Phi and Delta.
Calculate the confidence interval of the results of fitRMU()
Calculate a table of probabilities of ECF and OCF.
Calculate a table of probabilities of ECF and OCF.
Non-biased exponential regression
Generates set of parameters to be used with fitRMU_MHmcmc()
Extract the set of parameters from a result object.
Fit the phenology parameters to timeseries of counts.
Generate set of parameters to be used with fitCF_MHmcmc()
Run the Metropolis-Hastings algorithm for ECFOCF data
Fit a model of Clutch Frequency for marine turtles.
Adjust incomplete timeseries with various constraints.
Generate a set of fixed parameters for series with only 0 counts
Generate a set of data to test Clutch Frequency for marine turtles.
Fit a model of Internesting Period for marine turtles.
Estimates the pattern of internesting intervals for a set of parameter...
Predict the possible clutch number based on observed Internesting Peri...
Transform a set of parameters from Length format to LengthB LengthE
Transform a set of parameters from LengthB LengthE to Begin End.
Transform a set of parameters from LengthB LengthE format to Length
Estimate the likelihood of timeseries based on a set of parameters.
Calculate the -log likelihood of data within a model.
Return a remigration interval.
Return Log Likelihood of a fit done using fitCF
Return Log Likelihood of a fit generated by fitRMU
Return Log Likelihood of a fit generated by fit_phenology
Return Log Likelihood of a fit generated by Tagloss_fit
Transform a set of parameters from MinB and MinE to Min
Calculate initial set of parameters.
Transform a set of parameters from Year to global effect, or reverse
Generates set of parameters to be used with phenology_MHmcmc()
Run the Metropolis-Hastings algorithm for data
Tools to Manage a Parametric Function that Describes Phenology and Mor...
Plot a likelihood lineplot obtained after map_phenology.
Plot the best likelihood for fixed Phi value.
Plot a result of clutch frequency fit.
Plot the synthesis of RMU fit.
Plot a result of Internesting Period fit or data.
Plot the phenology from a result.
Plot a likelihood map with Delta and Phi varying.
Plot the remigration intervals.
Plot a TableECFOCF dataset.
Plot the daily rate of tag loss.
Plot data used for tagloss analysis.
Print the result information from a result x.
Print information on a phenologymap object.
Print the result information from a IP object.
Print the information from a ouput x.
Removes site information from a set of parameters.
Return an expected remigration interval.
Calculate Breeding Proportion from Remigration Interval.
Shift sinusoid information.
Print the summary information from a ouput object.
Format a CMR dataset into a file that fitCF can use.
Return the cumulative rate of tag loss.
Return the maximum number of days an individual has been observed in a...
fit a model of tag loss using a CMR database.
Generates set of parameters to be used with Tagloss_mcmc()
Bayesian model of tag loss using a CMR database.
Return the daily rate of tag loss.
Return a list with the number of days different kinds of individuals a...
Transform a set of parameters from Min, MinB or MinE to PMin, PminB or...
Functions used to fit and test the phenology of species based on counts. Based on Girondot, M. (2010) <doi:10.3354/esr00292> for the phenology function, Girondot, M. (2017) <doi:10.1016/j.ecolind.2017.05.063> for the convolution of negative binomial, Girondot, M. and Rizzo, A. (2015) <doi:10.2993/etbi-35-02-337-353.1> for Bayesian estimate, Pfaller JB, ..., Girondot M (2019) <doi:10.1007/s00227-019-3545-x> for tag-loss estimate, Hancock J, ..., Girondot M (2019) <doi:10.1016/j.ecolmodel.2019.04.013> for nesting history, Laloe J-O, ..., Girondot M, Hays GC (2020) <doi:10.1007/s00227-020-03686-x> for aggregating several seasons.