phenology: Tools to Manage a Parametric Function that Describes Phenology

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
URLs

View on CRAN

Man pages

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,...

Files in this package

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