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phenology (version 5.1)
Tools to Manage a Parametric Function that Describes Phenology
Description
Functions used to fit and test the phenology of species based on counts.
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Install
install.packages('phenology')
Monthly Downloads
250
Version
5.1
License
GPL-2
Maintainer
Marc Girondot
Last Published
May 2nd, 2016
Functions in phenology (5.1)
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BE_to_LBLE
Transform a set of parameters from Begin End to LengthB LengthE.
map_Gratiot
Likelihood map of Leatherback nest counts
add_SD
Add SD for a fixed parameter.
phenology_MHmcmc
Run the Metropolis-Hastings algorithm for data
map_phenology
Generate a likelihood map varying Phi and Delta.
print.phenology
Print the result information from a result object.
phenology-package
Tools to Manage a Parametric Function that Describes Phenology
result_Gratiot_mcmc
Result of the mcmc for Leatherback nest counts
fitRMU_MHmcmc_p
Generates set of parameters to be used with fitRMU_MHmcmc()
LBLE_to_BE
Transform a set of parameters from LengthB LengthE to Begin End.
plot_phi
Plot the best likelihood for fixed Phi value.
add_phenology
Create a new dataset or add a timeserie to a previous dataset.
phenology_MHmcmc_p
Generates set of parameters to be used with phenology_MHmcmc()
extract_result
Extract the set of parameters from a result object.
logLik.fitRMU
Return Log Likelihood of a fit generated by fitRMU
plot.fitRMU
Plot the synthesis of RMU fit.
shift_sinusoid
Shift sinusoid information.
result_Gratiot
Result of the fit of Leatherback nest counts
Gratiot
Leatherback nest counts from Gratiot et al. (2006) Figure 1
logLik.phenology
Return Log Likelihood of a fit generated by fit_phenology
summary.phenology
Print the result information from a result object.
summary.phenologyout
Print the summary information from a ouput object.
result_Gratiot_Flat
Result of the fit of Leatherback nest counts
plot_delta
Plot a likelihood lineplot obtained after map_phenology.
print.phenologymap
Print information on a phenologymap object.
LBLE_to_L
Transform a set of parameters from LengthB LengthE format to Length
plot.phenology
Plot the phenology from a result.
remove_site
Removes site information from a set of parameters.
fitRMU_MHmcmc
Run the Metropolis-Hastings algorithm for RMU.data
L_to_LBLE
Transform a set of parameters from Length format to LengthB LengthE
plot.phenologymap
Plot a likelihood map with Delta and Phi varying.
fitRMU
Adjust incomplete timeseries with various constraints.
phenology
Run a shiny application for basic functions of phenology
MinBMinE_to_Min
Transform a set of parameters from MinB and MinE to Min
likelihood_phenology
Estimate the likelihood of timeseries based on a set of parameters.
summary.phenologymap
Print information on a phenologymap object.
print.phenologyout
Print the information from a ouput object.
adapt_parameters
Extract the parameters from a set of parameters to be used with another dataset.
fit_phenology
Fit the phenology parameters to timeseries of counts.
result_Gratiot2
Result of the fit of Leatherback nest counts
toggle_Min_PMin
Transform a set of parameters from Min, MinB or MinE to PMin, PminB or PminE, or reverse
par_init
Calculate initial set of parameters.
result_Gratiot1
Result of the fit of Leatherback nest counts