Tools to Manage a Parametric Function that Describes Phenology and More

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Documentation for package ‘phenology’ version 9.1

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phenology-package Tools to Manage a Parametric Function that Describes Phenology and More
adapt_parameters Extract the parameters from a set of parameters to be used with another dataset.
add_phenology Create a new dataset or add a timeserie to a previous dataset.
add_SE Add standard error for a fixed parameter.
AutoFitPhenology Automatic fit for phenology and tests
Bayesian.remigration Return a posterior remigration interval.
BE_to_LBLE Transform a set of parameters from Begin End to LengthB LengthE.
CI.RMU Calculate the confidence interval of the results of fitRMU()
ECFOCF_f Calculate a table of probabilities of ECF and OCF.
ECFOCF_full Calculate a table of probabilities of ECF and OCF.
ExponentialRegression Non-biased exponential regression
extract_result Extract the set of parameters from a result object.
fitCF Fit a model of Clutch Frequency for marine turtles.
fitCF_MHmcmc Run the Metropolis-Hastings algorithm for ECFOCF data
fitCF_MHmcmc_p Generate set of parameters to be used with fitCF_MHmcmc()
fitRMU Adjust incomplete timeseries with various constraints.
fitRMU_MHmcmc Run the Metropolis-Hastings algorithm for RMU.data
fitRMU_MHmcmc_p Generates set of parameters to be used with fitRMU_MHmcmc()
fit_phenology Fit the phenology parameters to timeseries of counts.
fixed.parameters0 Generate a set of fixed parameters for series with only 0 counts
generateCF Generate a set of data to test Clutch Frequency for marine turtles.
Gratiot Leatherback nest counts from Gratiot et al. (2006) Figure 1
IPFit Fit a model of Internesting Period for marine turtles.
IPModel Estimates the pattern of internesting intervals for a set of parameters.
IPPredict Predict the possible clutch number based on observed Internesting Period.
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
likelihood_phenology Estimate the likelihood of timeseries based on a set of parameters.
lnLCF Calculate the -log likelihood of data within a model.
LnRI_norm Return a remigration interval.
logLik.ECFOCF Return Log Likelihood of a fit done using fitCF
logLik.fitRMU Return Log Likelihood of a fit generated by fitRMU
logLik.phenology Return Log Likelihood of a fit generated by fit_phenology
logLik.Tagloss Return Log Likelihood of a fit generated by Tagloss_fit
L_to_LBLE Transform a set of parameters from Length format to LengthB LengthE
map_Gratiot Likelihood map of Leatherback nest counts
map_phenology Generate a likelihood map varying Phi and Delta.
MarineTurtles_2002 Database of tagged marine turtles in 2002
MinBMinE_to_Min Transform a set of parameters from MinB and MinE to Min
outLR Database of leatherback CMR in French Guiana
o_4p_p1p2 Model of tagloss based on Rivalan data
Parameter_Global_Year Transform a set of parameters from Year to global effect, or reverse
par_init Calculate initial set of parameters.
phenology Run a shiny application for basic functions of phenology package
phenology2fitRMU Create the data to be used with fitRMU() for a summary(phenology).
phenology_MHmcmc Run the Metropolis-Hastings algorithm for data
phenology_MHmcmc_p Generates set of parameters to be used with phenology_MHmcmc()
plot.ECFOCF Plot a result of clutch frequency fit.
plot.fitRMU Plot the synthesis of RMU fit.
plot.IP Plot a result of Internesting Period fit or data.
plot.phenology Plot the phenology from a result.
plot.phenologymap Plot a likelihood map with Delta and Phi varying.
plot.Remigration Plot the remigration intervals.
plot.TableECFOCF Plot a TableECFOCF dataset.
plot.Tagloss Plot the daily rate of tag loss.
plot.TaglossData Plot data used for tagloss analysis.
plot_delta Plot a likelihood lineplot obtained after map_phenology.
plot_phi Plot the best likelihood for fixed Phi value.
print.phenology Print the result information from a result x.
print.phenologymap Print information on a phenologymap object.
print.phenologyout Print the information from a ouput x.
remove_site Removes site information from a set of parameters.
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
result_Gratiot_Flat Result of the fit of Leatherback nest counts
result_Gratiot_mcmc Result of the mcmc for Leatherback nest counts
RI Return an expected remigration interval.
shift_sinusoid Shift sinusoid information.
summary.IP Print the result information from a IP object.
summary.phenology Print the result information from a result object.
summary.phenologymap Print information on a phenologymap object.
summary.phenologyout Print the summary information from a ouput object.
TableECFOCF Format a CMR dataset into a file that fitCF can use.
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_fit fit a model of tag loss using a CMR database.
Tagloss_format Format a CMR dataset into a file that Tagloss_L can use.
Tagloss_L Return the -log likelihood of a set of individuals under a model of tagloss.
Tagloss_LengthObs Return a list with the number of days for different kinds of individuals are seen.
Tagloss_mcmc Bayesian model of tag loss using a CMR database.
Tagloss_mcmc_p Generates set of parameters to be used with Tagloss_mcmc()
Tagloss_model Return the daily rate of tag loss.
Tagloss_simulate Return a list with the number of days different kinds of individuals are seen.
toggle_Min_PMin Transform a set of parameters from Min, MinB or MinE to PMin, PminB or PminE, or reverse