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,... |

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