Tools to manage a parametric function that describes phenology

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Documentation for package ‘phenology’ version 3.63

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phenology-package The package 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 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
compare_AIC Compares the AIC of several outputs
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
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.
L_to_LBLE Transform a set of parameters from Length format to LengthB LengthE
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()
phenology_swot Fit a nesting season of marine turtles
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 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