Learn R Programming
⚠️There's a newer version (2025.11.12) of this package.Take me there.

phenology (version 3.63)

Tools to manage a parametric function that describes phenology

Description

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

Copy Link

Version

Install

install.packages('phenology')

Monthly Downloads

250

Version

3.63

License

GPL-2

Maintainer

Marc Girondot

Last Published

April 7th, 2014

Functions in phenology (3.63)

ChangeCoordinate

Return a value in a changed coordinate
moon_phase

Moon phase based on a date
asc

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

Add SD for a fixed parameter.
chr

Return the characters defined by the codes
growlnotify

Send growl notification for MacOs X system.
as.mcmc.mcmcComposite

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

Print the information from a ouput object.
shift_sinusoid

Shift sinusoid information.
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, PminB or PminE, or reverse
plot_errbar

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

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

Extract the set of parameters from a result object.
result_Gratiot2

Result of the fit of Leatherback nest counts
ScalePreviousPlot

Return the scale of the previous plot
as.par.mcmcComposite

Extract parameters at maximum likelihood from the result of MHmcmc
summary.phenologymap

Print information on a phenologymap object.
phenology

Run a shiny application for basic functions of phenology
LBLE_to_BE

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

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

Annual tide calendar for one particular location
phenology_MHmcmc_p

Generates set of parameters to be used with phenology_MHmcmc()
plot.phenologymap

Plot a likelihood map with Delta and Phi varying.
phenology_MHmcmc

Run the Metropolis-Hastings algorithm for data
read_folder

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

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

Plot a likelihood lineplot obtained after map_phenology.
result_Gratiot_mcmc

Result of the mcmc for Leatherback nest counts
fit_phenology

Fit the phenology parameters to timeseries of counts.
result_Gratiot_Flat

Result of the fit of Leatherback nest counts
LBLE_to_L

Transform a set of parameters from LengthB LengthE format to Length
MinBMinE_to_Min

Transform a set of parameters from MinB and MinE to Min
print.phenologymap

Print information on a phenologymap object.
L_to_LBLE

Transform a set of parameters from Length format to LengthB LengthE
likelihood_phenology

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

Calculate initial set of parameters.
plot.mcmcComposite

Plot the result of a MCMC search
summary.mcmcComposite

Summarize the result of a MCMC search
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
BE_to_LBLE

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

Fit a nesting season of marine turtles
Gratiot

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

Removes site information from a set of parameters.
map_Gratiot

Likelihood map of Leatherback nest counts
print.phenology

Print the result information from a result object.
compare_AIC

Compares the AIC of several outputs
map_phenology

Generate a likelihood map varying Phi and Delta.
plot.phenology

Plot the phenology from a result.
phenology-package

The package phenology
result_Gratiot

Result of the fit of Leatherback nest counts
plot_phi

Plot the best likelihood for fixed Phi value.
plot_add

Add a plot to a previous one