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phenology (version 3.62)
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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Install
install.packages('phenology')
Monthly Downloads
530
Version
3.62
License
GPL-2
Maintainer
Marc Girondot
Last Published
March 15th, 2014
Functions in phenology (3.62)
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BE_to_LBLE
Transform a set of parameters from Begin End to LengthB LengthE.
extract_result
Extract the set of parameters from a result object.
L_to_LBLE
Transform a set of parameters from Length format to LengthB LengthE
add_phenology
Create a new dataset or add a timeserie to a previous dataset.
shift_sinusoid
Shift sinusoid information.
fit_phenology
Fit the phenology parameters to timeseries of counts.
plot_delta
Plot a likelihood lineplot obtained after map_phenology.
add_SD
Add SD for a fixed parameter.
moon_phase
Moon phase based on a date
phenology_MHmcmc_p
Generates set of parameters to be used with phenology_MHmcmc()
summary.mcmcComposite
Summarize the result of a MCMC search
barplot_errbar
Plot a barplot graph with error bar on y
as.par.mcmcComposite
Extract parameters at maximum likelihood from the result of MHmcmc
remove_site
Removes site information from a set of parameters.
result_Gratiot_mcmc
Result of the mcmc for Leatherback nest counts
phenology_MHmcmc
Run the Metropolis-Hastings algorithm for data
likelihood_phenology
Estimate the likelihood of timeseries based on a set of parameters.
summary.phenology
Print the result information from a result object.
summary.phenologymap
Print information on a phenologymap object.
plot_errbar
Plot a xy graph with error bar on x and/or y
print.phenologyout
Print the information from a ouput object.
asc
Return the codes (in UTF-8) of a string
compare_AIC
Compares the AIC of several outputs
plot.phenology
Plot the phenology from a result.
Gratiot
Leatherback nest counts from Gratiot et al. (2006) Figure 1
chr
Return the characters defined by the codes
plot_phi
Plot the best likelihood for fixed Phi value.
map_Gratiot
Likelihood map of Leatherback nest counts
ScalePreviousPlot
Return the scale of the previous plot
LBLE_to_BE
Transform a set of parameters from LengthB LengthE to Begin End.
plot_add
Add a plot to a previous one
summary.phenologyout
Print the summary information from a ouput object.
plot.phenologymap
Plot a likelihood map with Delta and Phi varying.
print.phenologymap
Print information on a phenologymap object.
map_phenology
Generate a likelihood map varying Phi and Delta.
result_Gratiot_Flat
Result of the fit of Leatherback nest counts
ChangeCoordinate
Return a value in a changed coordinate
as.mcmc.mcmcComposite
Extract mcmc object from the result of MHmcmc to be used with coda package
growlnotify
Send growl notification for MacOs X system.
adapt_parameters
Extract the parameters from a set of parameters to be used with another dataset.
print.phenology
Print the result information from a result object.
phenology-package
The package phenology
phenology_swot
Fit a nesting season of marine turtles
LBLE_to_L
Transform a set of parameters from LengthB LengthE format to Length
read_folder
Reads all files present in a folder and creates a list with the the content of these files
result_Gratiot1
Result of the fit of Leatherback nest counts
phenology
Run a shiny application for basic functions of phenology
ind_long_lat
Return or the index in ncdf object from lat/longitude or inverse
getTide
Annual tide calendar for one particular location
result_Gratiot2
Result of the fit of Leatherback nest counts
par_init
Calculate initial set of parameters.
toggle_Min_PMin
Transform a set of parameters from Min, MinB or MinE to PMin, PminB or PminE, or reverse
MinBMinE_to_Min
Transform a set of parameters from MinB and MinE to Min
plot.mcmcComposite
Plot the result of a MCMC search
result_Gratiot
Result of the fit of Leatherback nest counts