Man pages for phenology
Tools to Manage a Parametric Function that Describes Phenology and More
| adapt_parameters | Extract the parameters from a set of parameters to be used... |
| add_phenology | Create a new dataset or add a timeserie to a previous... |
| 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... |
| 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() |
| fit_phenology | Fit the phenology parameters to timeseries of counts. |
| 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() |
| fixed.parameters0 | Generate a set of fixed parameters for series with only 0... |
| generateCF | Generate a set of data to test Clutch Frequency for marine... |
| 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... |
| IPPredict | Predict the possible clutch number based on observed... |
| LBLE_to_BE | Transform a set of parameters from LengthB LengthE to Begin... |
| LBLE_to_L | Transform a set of parameters from LengthB LengthE format to... |
| likelihood_phenology | Estimate the likelihood of timeseries based on a set of... |
| 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... |
| 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 |
| o_4p_p1p2 | Model of tagloss based on Rivalan data |
| outLR | Database of leatherback CMR in French Guiana |
| Parameter_Global_Year | Transform a set of parameters from Year to global effect, or... |
| par_init | Calculate initial set of parameters. |
| phenology | Run a shiny application for basic functions of phenology... |
| phenology2fitRMU | Create the data to be used with fitRMU() for a... |
| phenology_MHmcmc | Run the Metropolis-Hastings algorithm for data |
| phenology_MHmcmc_p | Generates set of parameters to be used with... |
| phenology-package | Tools to Manage a Parametric Function that Describes... |
| plot_delta | Plot a likelihood lineplot obtained after map_phenology. |
| 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_phi | Plot the best likelihood for fixed Phi value. |
| 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. |
| 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... |
| 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... |
| Tagloss_LengthObs | Return a list with the number of days for different kinds of... |
| 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... |
| toggle_Min_PMin | Transform a set of parameters from Min, MinB or MinE to PMin,... |
