phenology: Tools to Manage a Parametric Function that Describes Phenology

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

AuthorMarc Girondot
Date of publication2016-10-01 14:58:08
MaintainerMarc Girondot <marc.girondot@u-psud.fr>
LicenseGPL-2
Version5.3
http://max2.ese.u-psud.fr/epc/conservation/Girondot/Publications/Marine_Turtles_Nesting_Season.html

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,...

Functions

adapt_parameters Man page
add_phenology Man page
add_SD Man page
BE_to_LBLE Man page
extract_result Man page
fit_phenology Man page
fitRMU Man page
fitRMU_MHmcmc Man page
fitRMU_MHmcmc_p Man page
Gratiot Man page
LBLE_to_BE Man page
LBLE_to_L Man page
likelihood_phenology Man page
logLik.fitRMU Man page
logLik.phenology Man page
L_to_LBLE Man page
map_Gratiot Man page
map_phenology Man page
MinBMinE_to_Min Man page
par_init Man page
phenology Man page
phenology_MHmcmc Man page
phenology_MHmcmc_p Man page
phenology-package Man page
plot_delta Man page
plot.fitRMU Man page
plot.phenology Man page
plot.phenologymap Man page
plot_phi Man page
print.phenology Man page
print.phenologymap Man page
print.phenologyout Man page
remove_site Man page
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
summary.phenology Man page
summary.phenologymap Man page
summary.phenologyout Man page
toggle_Min_PMin Man page

Files

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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