Functions used to fit and test the phenology of species based on counts.

Author | Marc Girondot |

Date of publication | 2016-10-01 14:58:08 |

Maintainer | Marc Girondot <marc.girondot@u-psud.fr> |

License | GPL-2 |

Version | 5.3 |

http://max2.ese.u-psud.fr/epc/conservation/Girondot/Publications/Marine_Turtles_Nesting_Season.html |

**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_SD:** Add SD for a fixed parameter.

**BE_to_LBLE:** Transform a set of parameters from Begin End to LengthB...

**extract_result:** Extract the set of parameters from a result object.

**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()

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

**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...

**logLik.fitRMU:** Return Log Likelihood of a fit generated by fitRMU

**logLik.phenology:** Return Log Likelihood of a fit generated by fit_phenology

**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.

**MinBMinE_to_Min:** Transform a set of parameters from MinB and MinE to Min

**par_init:** Calculate initial set of parameters.

**phenology:** Run a shiny application for basic functions of phenology...

**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.fitRMU:** Plot the synthesis of RMU fit.

**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.

**print.phenology:** Print the result information from a result object.

**print.phenologymap:** Print information on a phenologymap object.

**print.phenologyout:** Print the information from a ouput object.

**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

**shift_sinusoid:** Shift sinusoid information.

**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.

**toggle_Min_PMin:** Transform a set of parameters from Min, MinB or MinE to PMin,...

phenology

phenology/inst

phenology/inst/shiny

phenology/inst/shiny/ui.R

phenology/inst/shiny/server.R

phenology/inst/shiny/www

phenology/inst/shiny/www/fr.png

phenology/inst/shiny/www/gb.png

phenology/inst/shiny/www/sp.png

phenology/inst/shiny/www/logo.png

phenology/inst/shiny/www/PDF.png

phenology/inst/shiny/www/logoRASTOMA.png

phenology/inst/shiny/www/pt.png

phenology/inst/shiny/www/logoSWOT.png

phenology/inst/shiny/babel.Rdata

phenology/NAMESPACE

phenology/NEWS

phenology/data

phenology/data/result_Gratiot_Flat.rda

phenology/data/result_Gratiot2.rda

phenology/data/result_Gratiot1.rda

phenology/data/result_Gratiot.rda

phenology/data/map_Gratiot.rda

phenology/data/Gratiot.rda

phenology/data/result_Gratiot_mcmc.rda

phenology/R

phenology/R/Likelihood_phenology.R
phenology/R/par_init.R
phenology/R/fitRMU.R
phenology/R/format_par.R
phenology/R/result_Gratiot.R
phenology/R/result_Gratiot2.R
phenology/R/onAttach.R
phenology/R/Lnegbin.R
phenology/R/add_phenology.R
phenology/R/summary.phenologymap.R
phenology/R/logLik.phenology.R
phenology/R/plot.fitRMU.R
phenology/R/adapt_parameters.R
phenology/R/plot_delta.R
phenology/R/print.phenologyout.R
phenology/R/phenology-package.R
phenology/R/Gratiot.R
phenology/R/phenology_MHmcmc.R
phenology/R/map_Gratiot.R
phenology/R/LBLE_to_BE.R
phenology/R/phenology.R
phenology/R/MinBMinE_to_Min.R
phenology/R/summary.phenology.R
phenology/R/fitRMU_MHmcmc.R
phenology/R/add_SD.R
phenology/R/shift_sinusoid.R
phenology/R/plot.phenology.R
phenology/R/plot.phenologymap.R
phenology/R/toggle_Min_PMin.R
phenology/R/phenology_MHmcmc_p.R
phenology/R/fitRMU_MHmcmc_p.R
phenology/R/result_Gratiot_mcmc.R
phenology/R/plot_phi.R
phenology/R/result_Gratiot_Flat.R
phenology/R/LBLE_to_L.R
phenology/R/fit_phenology.R
phenology/R/result_Gratiot1.R
phenology/R/print.phenologymap.R
phenology/R/LikelihoodRMU.R
phenology/R/extract_result.R
phenology/R/map_phenology.R
phenology/R/summary.phenologyout.R
phenology/R/read_phenology.R
phenology/R/remove_site.R
phenology/R/L_to_LBLE.R
phenology/R/daily_count.R
phenology/R/print.phenology.R
phenology/R/logLik.fitRMU.R
phenology/R/BE_to_LBLE.R
phenology/MD5

phenology/DESCRIPTION

phenology/man

phenology/man/map_Gratiot.Rd
phenology/man/fitRMU.Rd
phenology/man/plot_phi.Rd
phenology/man/L_to_LBLE.Rd
phenology/man/plot.fitRMU.Rd
phenology/man/adapt_parameters.Rd
phenology/man/BE_to_LBLE.Rd
phenology/man/print.phenologymap.Rd
phenology/man/phenology.Rd
phenology/man/print.phenologyout.Rd
phenology/man/map_phenology.Rd
phenology/man/LBLE_to_L.Rd
phenology/man/result_Gratiot.Rd
phenology/man/toggle_Min_PMin.Rd
phenology/man/plot_delta.Rd
phenology/man/add_SD.Rd
phenology/man/remove_site.Rd
phenology/man/likelihood_phenology.Rd
phenology/man/Gratiot.Rd
phenology/man/shift_sinusoid.Rd
phenology/man/MinBMinE_to_Min.Rd
phenology/man/add_phenology.Rd
phenology/man/fitRMU_MHmcmc.Rd
phenology/man/LBLE_to_BE.Rd
phenology/man/result_Gratiot1.Rd
phenology/man/summary.phenologyout.Rd
phenology/man/plot.phenology.Rd
phenology/man/summary.phenology.Rd
phenology/man/par_init.Rd
phenology/man/print.phenology.Rd
phenology/man/logLik.phenology.Rd
phenology/man/phenology_MHmcmc.Rd
phenology/man/phenology_MHmcmc_p.Rd
phenology/man/extract_result.Rd
phenology/man/result_Gratiot_Flat.Rd
phenology/man/plot.phenologymap.Rd
phenology/man/result_Gratiot2.Rd
phenology/man/fitRMU_MHmcmc_p.Rd
phenology/man/phenology-package.Rd
phenology/man/summary.phenologymap.Rd
phenology/man/result_Gratiot_mcmc.Rd
phenology/man/logLik.fitRMU.Rd
phenology/man/fit_phenology.Rd
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