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phenology (version 3.57)

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

250

Version

3.57

License

GPL-2

Maintainer

Marc Girondot

Last Published

February 25th, 2014

Functions in phenology (3.57)

ChangeCoordinate

Return a value in a changed coordinate

LBLE_to_L

Transform a set of parameters from LengthB LengthE format to Length

extract_result

Extract the set of parameters from a result object.

BE_to_LBLE

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

fit_phenology

Fit the phenology parameters to timeseries of counts.

as.mcmc.mcmcComposite

Extract mcmc object from the result of MHmcmc to be used with coda package

L_to_LBLE

Transform a set of parameters from Length format to LengthB LengthE

adapt_parameters

Extract the parameters from a set of parameters to be used with another dataset.

map_phenology

Generate a likelihood map varying Phi and Delta.

ind_long_lat

Return or the index in ncdf object from lat/longitude or inverse

barplot_errbar

Plot a barplot graph with error bar on y

par_init

Calculate initial set of parameters.

plot.phenologymap

Plot a likelihood map with Delta and Phi varying.

add_phenology

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

asc

Return the codes (in UTF-8) of a string

print.phenologymap

Print information on a phenologymap object.

compare_AIC

Compares the AIC of several outputs

plot.phenology

Plot the phenology from a result.

ScalePreviousPlot

Return the scale of the previous plot

summary.phenology

Print the result information from a result object.

print.phenologyout

Print the information from a ouput object.

moon_phase

Moon phase based on a date

LBLE_to_BE

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

toggle_Min_PMin

Transform a set of parameters from Min, MinB or MinE to PMin, PminB or PminE, or reverse

add_SD

Add SD for a fixed parameter.

remove_site

Removes site information from a set of parameters.

summary.mcmcComposite

Summarize the result of a MCMC search

shift_sinusoid

Shift sinusoid information.

print.phenology

Print the result information from a result object.

summary.phenologymap

Print information on a phenologymap object.

map_Gratiot

Likelihood map of Leatherback nest counts

as.par.mcmcComposite

Extract parameters at maximum likelihood from the result of MHmcmc

plot_phi

Plot the best likelihood for fixed Phi value.

result_Gratiot

Result of the fit of Leatherback nest counts

phenology-package

The package phenology

chr

Return the characters defined by the codes

phenology

Help for phenology package.

Gratiot

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

likelihood_phenology

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

read_folder

Reads all files present in a folder and creates a list with the the content of these files

phenology_MHmcmc

Run the Metropolis-Hastings algorithm for data

phenology_swot

Fit a nesting season of marine turtles

result_Gratiot_mcmc

Result of the mcmc for Leatherback nest counts

plot_delta

Plot a likelihood lineplot obtained after map_phenology.

result_Gratiot1

Result of the fit of Leatherback nest counts

plot_errbar

Plot a xy graph with error bar on x and/or y

result_Gratiot_Flat

Result of the fit of Leatherback nest counts

MinBMinE_to_Min

Transform a set of parameters from MinB and MinE to Min

growlnotify

Send growl notification for MacOs X system.

result_Gratiot2

Result of the fit of Leatherback nest counts

phenology_MHmcmc_p

Generates set of parameters to be used with phenology_MHmcmc()

plot.mcmcComposite

Plot the result of a MCMC search

plot_add

Add a plot to a previous one

summary.phenologyout

Print the summary information from a ouput object.