Tools to Manage a Parametric Function that Describes Phenology

Documentation for package ‘phenology’ version 4.0.4

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phenology-package	Tools to Manage a Parametric Function that Describes Phenology
adapt_parameters	Extract the parameters from a set of parameters to be used with another dataset.
add_phenology	Create a new dataset or add a timeserie to a previous dataset.
add_SD	Add SD for a fixed parameter.
as.mcmc.mcmcComposite	Extract mcmc object from the result of phenology_MHmcmc to be used with coda package
as.par.mcmcComposite	Extract parameters at maximum likelihood from the result of MHmcmc
asc	Return the codes (in UTF-8) of a string
barplot_errbar	Plot a barplot graph with error bar on y
BE_to_LBLE	Transform a set of parameters from Begin End to LengthB LengthE.
ChangeCoordinate	Return a value in a changed coordinate
chr	Return the characters defined by the codes
clean.knitr	Delete temporary files created during knitr compile
compare_AIC	Compares the AIC of several outputs
compassRose2	Display a compass rose
convert.tz	Convert one Date-Time from one timezone to another
extract_result	Extract the set of parameters from a result object.
fit_phenology	Fit the phenology parameters to timeseries of counts.
getTide	Annual tide calendar for one particular location
Gratiot	Leatherback nest counts from Gratiot et al. (2006) Figure 1
growlnotify	Send growl notification for MacOs X system.
ind_long_lat	Return or the index in ncdf object from lat/longitude or inverse
insidesearch	Search a string within files of a folder #'
LBLE_to_BE	Transform a set of parameters from LengthB LengthE to Begin End.
LBLE_to_L	Transform a set of parameters from LengthB LengthE format to Length
likelihood_phenology	Estimate the likelihood of timeseries based on a set of parameters.
local.search	Return path of file searched for in local disk based on its file name
logLik.phenology	Return Log Likelihood of a fit generated by fit_phenology
L_to_LBLE	Transform a set of parameters from Length format to LengthB LengthE
map.scale2	Add Scale to Existing Unprojected Map
map_Gratiot	Likelihood map of Leatherback nest counts
map_phenology	Generate a likelihood map varying Phi and Delta.
MinBMinE_to_Min	Transform a set of parameters from MinB and MinE to Min
moon_phase	Moon phase based on a date
par_init	Calculate initial set of parameters.
phenology	Run a shiny application for basic functions of phenology
phenology_MHmcmc	Run the Metropolis-Hastings algorithm for data
phenology_MHmcmc_p	Generates set of parameters to be used with phenology_MHmcmc()
plot.mcmcComposite	Plot the result of a MCMC search
plot.phenology	Plot the phenology from a result.
plot.phenologymap	Plot a likelihood map with Delta and Phi varying.
plot_add	Add a plot to a previous one
plot_delta	Plot a likelihood lineplot obtained after map_phenology.
plot_errbar	Plot a xy graph with error bar on x and/or y
plot_phi	Plot the best likelihood for fixed Phi value.
print.phenology	Print the result information from a result object.
print.phenologymap	Print information on a phenologymap object.
print.phenologyout	Print the information from a ouput object.
read_folder	Reads all files present in a folder and creates a list with the content of these files
remove_site	Removes site information from a set of parameters.
result_Gratiot	Result of the fit of Leatherback nest counts
result_Gratiot1	Result of the fit of Leatherback nest counts
result_Gratiot2	Result of the fit of Leatherback nest counts
result_Gratiot_Flat	Result of the fit of Leatherback nest counts
result_Gratiot_mcmc	Result of the mcmc for Leatherback nest counts
ScalePreviousPlot	Return the scale of the previous plot
shift_sinusoid	Shift sinusoid information.
summary.mcmcComposite	Summarize the result of a MCMC search
summary.phenology	Print the result information from a result object.
summary.phenologymap	Print information on a phenologymap object.
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