phenology: Tools to Manage a Parametric Function that Describes Phenology
Version 5.4

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

AuthorMarc Girondot
Date of publication2017-03-10 11:49:52
MaintainerMarc Girondot <marc.girondot@u-psud.fr>
LicenseGPL-2
Version5.4
URL http://max2.ese.u-psud.fr/epc/conservation/Girondot/Publications/Marine_Turtles_Nesting_Season.html
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("phenology")

Getting started

Package overview

Popular man pages

Gratiot: Leatherback nest counts from Gratiot et al. (2006) Figure 1
L_to_LBLE: Transform a set of parameters from Length format to LengthB...
phenology: Run a shiny application for basic functions of phenology...
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.phenology: Plot the phenology from a result.
See all...

All man pages Function index File listing

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.
AutoFitPhenology: Automatic fit for phenology and tests
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 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
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,...

Functions

AutoFitPhenology Man page Source code
BE_to_LBLE Man page Source code
Gratiot Man page
LBLE_to_BE Man page Source code
LBLE_to_L Man page Source code
L_to_LBLE Man page Source code
MinBMinE_to_Min Man page Source code
adapt_parameters Man page Source code
add_SD Man page Source code
add_phenology Man page Source code
daily_count Source code
extract_result Man page Source code
fitRMU Man page Source code
fitRMU_MHmcmc Man page Source code
fitRMU_MHmcmc_p Man page Source code
fit_phenology Man page Source code
format_par Source code
ikelihoodRMU Source code
likelihood_phenology Man page Source code
logLik.fitRMU Man page Source code
logLik.phenology Man page Source code
map_Gratiot Man page
map_phenology Man page Source code
negbin Source code
nv.p.multinomial Source code
onAttach Source code
p.multinomial Source code
par_init Man page Source code
phenology Man page Source code
phenology-package Man page
phenology_MHmcmc Man page Source code
phenology_MHmcmc_p Man page Source code
plot.fitRMU Man page Source code
plot.phenology Man page Source code
plot.phenologymap Man page Source code
plot_delta Man page Source code
plot_phi Man page Source code
print.phenology Man page Source code
print.phenologymap Man page Source code
print.phenologyout Man page Source code
read_phenology Source code
remove_site Man page Source code
repeat_last Source code
result_Gratiot Man page
result_Gratiot1 Man page
result_Gratiot2 Man page
result_Gratiot_Flat Man page
result_Gratiot_mcmc Man page
shift_sinusoid Man page Source code
summary.phenology Man page Source code
summary.phenologymap Man page Source code
summary.phenologyout Man page Source code
toggle_Min_PMin Man page Source code
wrapperLnegbin Source code

Files

inst
inst/shiny
inst/shiny/ui.R
inst/shiny/server.R
inst/shiny/www
inst/shiny/www/fr.png
inst/shiny/www/gb.png
inst/shiny/www/sp.png
inst/shiny/www/logo.png
inst/shiny/www/PDF.png
inst/shiny/www/spinner.gif
inst/shiny/www/logoRASTOMA.png
inst/shiny/www/pt.png
inst/shiny/www/logoSWOT.png
inst/shiny/babel.Rdata
NAMESPACE
NEWS
data
data/result_Gratiot_Flat.rda
data/result_Gratiot2.rda
data/result_Gratiot1.rda
data/result_Gratiot.rda
data/map_Gratiot.rda
data/Gratiot.rda
data/result_Gratiot_mcmc.rda
R
R/Likelihood_phenology.R
R/par_init.R
R/fitRMU.R
R/format_par.R
R/result_Gratiot.R
R/result_Gratiot2.R
R/onAttach.R
R/Lnegbin.R
R/add_phenology.R
R/summary.phenologymap.R
R/logLik.phenology.R
R/plot.fitRMU.R
R/adapt_parameters.R
R/plot_delta.R
R/print.phenologyout.R
R/phenology-package.R
R/Gratiot.R
R/phenology_MHmcmc.R
R/map_Gratiot.R
R/LBLE_to_BE.R
R/phenology.R
R/MinBMinE_to_Min.R
R/summary.phenology.R
R/fitRMU_MHmcmc.R
R/AutoFitPhenology.R
R/add_SD.R
R/shift_sinusoid.R
R/plot.phenology.R
R/plot.phenologymap.R
R/toggle_Min_PMin.R
R/phenology_MHmcmc_p.R
R/repeat_last.R
R/fitRMU_MHmcmc_p.R
R/result_Gratiot_mcmc.R
R/plot_phi.R
R/result_Gratiot_Flat.R
R/LBLE_to_L.R
R/fit_phenology.R
R/result_Gratiot1.R
R/print.phenologymap.R
R/LikelihoodRMU.R
R/extract_result.R
R/map_phenology.R
R/summary.phenologyout.R
R/read_phenology.R
R/remove_site.R
R/L_to_LBLE.R
R/daily_count.R
R/print.phenology.R
R/logLik.fitRMU.R
R/BE_to_LBLE.R
MD5
DESCRIPTION
man
man/map_Gratiot.Rd
man/fitRMU.Rd
man/plot_phi.Rd
man/L_to_LBLE.Rd
man/plot.fitRMU.Rd
man/adapt_parameters.Rd
man/BE_to_LBLE.Rd
man/print.phenologymap.Rd
man/phenology.Rd
man/print.phenologyout.Rd
man/map_phenology.Rd
man/LBLE_to_L.Rd
man/result_Gratiot.Rd
man/toggle_Min_PMin.Rd
man/plot_delta.Rd
man/add_SD.Rd
man/AutoFitPhenology.Rd
man/remove_site.Rd
man/likelihood_phenology.Rd
man/Gratiot.Rd
man/shift_sinusoid.Rd
man/MinBMinE_to_Min.Rd
man/add_phenology.Rd
man/fitRMU_MHmcmc.Rd
man/LBLE_to_BE.Rd
man/result_Gratiot1.Rd
man/summary.phenologyout.Rd
man/plot.phenology.Rd
man/summary.phenology.Rd
man/par_init.Rd
man/print.phenology.Rd
man/logLik.phenology.Rd
man/phenology_MHmcmc.Rd
man/phenology_MHmcmc_p.Rd
man/extract_result.Rd
man/result_Gratiot_Flat.Rd
man/plot.phenologymap.Rd
man/result_Gratiot2.Rd
man/fitRMU_MHmcmc_p.Rd
man/phenology-package.Rd
man/summary.phenologymap.Rd
man/result_Gratiot_mcmc.Rd
man/logLik.fitRMU.Rd
man/fit_phenology.Rd
phenology documentation built on May 20, 2017, 3:10 a.m.

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