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phenology (version 3.51)
Tools to manage a parametric function that describes phenology
Description
Functions to fit and test the phenology of species based on counts.
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2025.11.12
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Install
install.packages('phenology')
Monthly Downloads
250
Version
3.51
License
GPL-2
Maintainer
Marc Girondot
Last Published
July 11th, 2013
Functions in phenology (3.51)
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as.mcmc.mcmcComposite
Extract mcmc object from the result of MHmcmc to be used with coda package
BE_to_LBLE
Transform a set of parameters from Begin End to LengthB LengthE.
Gratiot
Leatherback nest counts from Gratiot et al. (2006) Figure 1
fit_phenology
Fit the phenology parameters to timeseries of counts.
as.par.mcmcComposite
Extract parameters at maximum likelihood from the result of MHmcmc
plot_errbar
Plot a xy graph with error bar on x and/or y
barplot_errbar
Plot a barplot graph with error bar on y
summary.phenology
Print the result information from a result object.
result_Gratiot1
Result of the fit of Leatherback nest counts
print.phenologyout
Print the information from a ouput object.
phenology_MHmcmc
Run the Metropolis-Hastings algorithm for data
phenology_MHmcmc_p
Generates set of parameters to be used with phenology_MHmcmc()
result_Gratiot_Flat
Result of the fit of Leatherback nest counts
moon_phase
Moon phase based on a date
plot.mcmcComposite
Plot the result of a MCMC search
compare_AIC
Compares the AIC of several outputs
plot.phenologymap
Plot a likelihood map with Delta and Phi varying.
print.phenologymap
Print information on a phenologymap object.
add_phenology
Create a new dataset or add a timeserie to a previous dataset.
result_Gratiot
Result of the fit of Leatherback nest counts
print.phenology
Print the result information from a result object.
ScalePreviousPlot
Return the scale of the previous plot
par_init
Calculate initial set of parameters.
shift_sinusoid
Shift sinusoid information.
plot_add
Add a plot to a previous one
result_Gratiot2
Result of the fit of Leatherback nest counts
map_Gratiot
Likelihood map of Leatherback nest counts
phenology-package
The package phenology
growlnotify
Send growl notification for MacOs X system.
read_folder
Open all file present in a folder and create a list with these files
LBLE_to_L
Transform a set of parameters from LengthB LengthE format to Length
add_SD
Add SD for a fixed parameter.
likelihood_phenology
Estimate the likelihood of timeseries based on a set of parameters.
summary.phenologymap
Print information on a phenologymap object.
summary.phenologyout
Print the summary information from a ouput object.
plot_delta
Plot a likelihood lineplot obtained after map_phenology.
result_Gratiot_mcmc
Result of the mcmc for Leatherback nest counts
L_to_LBLE
Transform a set of parameters from Length format to LengthB LengthE
adapt_parameters
Extract the parameters from a set of parameters ton conform on a dataset.
ChangeCoordinate
Return a value in a changed coordinate
plot.phenology
Plot the phenology from a result.
LBLE_to_BE
Transform a set of parameters from LengthB LengthE to Begin End.
extract_result
Extract the set of parameters from a result object.
phenology
Help for phenology package.
map_phenology
Generate a likelihood map varying Phi and Delta.
plot_phi
Plot the best likelihood for fixed Phi value.
remove_site
Removes site information from a set of parameters.
phenology_swot
Fit a nesting season of marine turtles
summary.mcmcComposite
Summarize the result of a MCMC search