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phenology (version 3.72)

Tools to manage a parametric function that describes phenology

Description

Functions to fit and test the phenology of species based on counts. The package includes also several useful more general functions.

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Version

Install

install.packages('phenology')

Monthly Downloads

295

Version

3.72

License

GPL-2

Maintainer

Marc Girondot

Last Published

August 25th, 2014

Functions in phenology (3.72)

plot.phenology

Plot the phenology from a result.
ScalePreviousPlot

Return the scale of the previous plot
print.phenologyout

Print the information from a ouput object.
compare_AIC

Compares the AIC of several outputs
phenology_swot

Fit a nesting season of marine turtles
getTide

Annual tide calendar for one particular location
summary.phenologymap

Print information on a phenologymap object.
result_Gratiot_mcmc

Result of the mcmc for Leatherback nest counts
ind_long_lat

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

Convert one Date-Time from one timezone to another
print.phenology

Print the result information from a result object.
summary.phenologyout

Print the summary information from a ouput object.
LBLE_to_BE

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

Generates set of parameters to be used with phenology_MHmcmc()
add_phenology

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

Likelihood map of Leatherback nest counts
result_Gratiot2

Result of the fit of Leatherback nest counts
growlnotify

Send growl notification for MacOs X system.
result_Gratiot

Result of the fit of Leatherback nest counts
map_phenology

Generate a likelihood map varying Phi and Delta.
remove_site

Removes site information from a set of parameters.
compassRose2

Display a compass rose
as.mcmc.mcmcComposite

Extract mcmc object from the result of phenology_MHmcmc to be used with coda package
plot.phenologymap

Plot a likelihood map with Delta and Phi varying.
toggle_Min_PMin

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

Print the result information from a result object.
adapt_parameters

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

Add SD for a fixed parameter.
phenology_MHmcmc

Run the Metropolis-Hastings algorithm for data
L_to_LBLE

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

Return a value in a changed coordinate
shift_sinusoid

Shift sinusoid information.
local.search

Return path of file searched for in local disk based on its file name
read_folder

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

The package phenology
par_init

Calculate initial set of parameters.
likelihood_phenology

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

Return Log Likelihood of a fit generated by fit_phenology
phenology

Run a shiny application for basic functions of phenology
chr

Return the characters defined by the codes
as.par.mcmcComposite

Extract parameters at maximum likelihood from the result of MHmcmc
extract_result

Extract the set of parameters from a result object.
print.phenologymap

Print information on a phenologymap object.
plot_phi

Plot the best likelihood for fixed Phi value.
plot_delta

Plot a likelihood lineplot obtained after map_phenology.
summary.mcmcComposite

Summarize the result of a MCMC search
plot_errbar

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

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

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

Plot a barplot graph with error bar on y
asc

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

Fit the phenology parameters to timeseries of counts.
result_Gratiot_Flat

Result of the fit of Leatherback nest counts
plot.mcmcComposite

Plot the result of a MCMC search
moon_phase

Moon phase based on a date
result_Gratiot1

Result of the fit of Leatherback nest counts
clean.knitr

Delete temporary files created during knitr compile
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
plot_add

Add a plot to a previous one
map.scale2

Add Scale to Existing Unprojected Map