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phenology (version 3.43)

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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Version

Install

install.packages('phenology')

Monthly Downloads

295

Version

3.43

License

GPL-2

Maintainer

Marc Girondot

Last Published

January 3rd, 2013

Functions in phenology (3.43)

phenology_swot

Fit a nesting season of marine turtles

likelihood_phenology

Estimate the likelihood of timeseries based on a set of parameters.

print.phenologymap

Print information on a phenologymap object.

map_Gratiot

Likelihood map of Leatherback nest counts

remove_site

Removes site information from a set of parameters.

phenology-package

The package phenology

LBLE_to_L

Transform a set of parameters from LengthB LengthE format to Length

result_Gratiot1

Result of the fit of Leatherback nest counts

extract_result

Extract the set of parameters from a result object.

phenology_MHmcmc_p

Generates set of parameters to be used with phenology_MHmcmc()

result_Gratiot2

Result of the fit of Leatherback nest counts

plot_map

Plot a likelihood map with Delta and Phi varying.

print.phenologyout

Print the information from a ouput object.

adapt_parameters

Extract the parameters from a set of parameters ton conform on a dataset.

summary.phenologyout

Print the summary information from a ouput object.

growlnotify

Send growl notification for MacOs X system.

L_to_LBLE

Transform a set of parameters from Length format to LengthB LengthE

BE_to_LBLE

Transform a set of parameters from Begin End to LengthB LengthE.

moon_phase

Moon phase based on a date

par_init

Calculate initial set of parameters.

plot.mcmcComposite

Plot the result of a MCMC search

result_Gratiot

Result of the fit of Leatherback nest counts

print.phenology

Print the result information from a result object.

map_phenology

Generate a likelihood map varying Phi and Delta.

result_Gratiot_mcmc

Result of the mcmc for Leatherback nest counts

plot_phi

Plot the best likelihood for fixed Phi value.

read_folder

Open all file present in a folder and create a list with these files

LBLE_to_BE

Transform a set of parameters from LengthB LengthE to Begin End.

phenology

Help for phenology package.

Gratiot

Leatherback nest counts from Gratiot et al. (2006) Figure 1

compare_AIC

Compares the AIC of several outputs

phenology_MHmcmc

Run the Metropolis-Hastings algorithm for data

shift_sinusoid

Shift sinusoid information.

fit_phenology

Fit the phenology parameters to timeseries of counts.

add_SD

Add SD for a fixed parameter.

plot.phenologymap

Plot a likelihood map with Delta and Phi varying.

summary.mcmcComposite

Summarize the result of a MCMC search

plot_phenology

Plot the phenology from a result.

summary.phenologymap

Print information on a phenologymap object.

summary.phenology

Print the result information from a result object.

plot.phenology

Plot the phenology from a result.

plot_delta

Plot a likelihood lineplot obtained after map_phenology.

add_phenology

Create a new dataset or add a timeserie to a previous dataset.

result_Gratiot_Flat

Result of the fit of Leatherback nest counts