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phenology (version 7.3)
Tools to Manage a Parametric Function that Describes Phenology
Description
Functions used to fit and test the phenology of species based on counts.
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Install
install.packages('phenology')
Monthly Downloads
295
Version
7.3
License
GPL-2
Maintainer
Marc Girondot
Last Published
January 4th, 2019
Functions in phenology (7.3)
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ECFOCF_f
Calculate a table of probabilities of ECF and OCF.
Tagloss_LengthObs
Return a list with the number of days for different kinds of individuals are seen.
Tagloss_cumul
Return the cumulative rate of tag loss.
IPPredict
Predict the possible clutch number based on observed Internesting Period.
fitRMU_MHmcmc
Run the Metropolis-Hastings algorithm for RMU.data
AutoFitPhenology
Automatic fit for phenology and tests
fitRMU_MHmcmc_p
Generates set of parameters to be used with fitRMU_MHmcmc()
BE_to_LBLE
Transform a set of parameters from Begin End to LengthB LengthE.
Tagloss_format
Format a CMR dataset into a file that Tagloss_L can use.
logLik.phenology
Return Log Likelihood of a fit generated by fit_phenology
LBLE_to_BE
Transform a set of parameters from LengthB LengthE to Begin End.
Tagloss_model
Return the daily rate of tag loss.
Tagloss_simulate
Return a list with the number of days different kinds of individuals are seen.
Gratiot
Leatherback nest counts from Gratiot et al. (2006) Figure 1
TableECFOCF
Format a CMR dataset into a file that fitCF can use.
plot.phenologymap
Plot a likelihood map with Delta and Phi varying.
map_Gratiot
Likelihood map of Leatherback nest counts
adapt_parameters
Extract the parameters from a set of parameters to be used with another dataset.
fitCF
Fit a model of Clutch Frequency for marine turtles.
phenology
Run a shiny application for basic functions of phenology package
plot_delta
Plot a likelihood lineplot obtained after map_phenology.
Tagloss_L
Return the -log likelihood of a set of individuals under a model of tagloss.
.read_phenology
The function .read_phenology
toggle_Min_PMin
Transform a set of parameters from Min, MinB or MinE to PMin, PminB or PminE, or reverse
summary.phenologyout
Print the summary information from a ouput object.
fitRMU
Adjust incomplete timeseries with various constraints.
logLik.Tagloss
Return Log Likelihood of a fit generated by Tagloss_fit
phenology_MHmcmc
Run the Metropolis-Hastings algorithm for data
LBLE_to_L
Transform a set of parameters from LengthB LengthE format to Length
remove_site
Removes site information from a set of parameters.
L_to_LBLE
Transform a set of parameters from Length format to LengthB LengthE
logLik.fitRMU
Return Log Likelihood of a fit generated by fitRMU
phenology_MHmcmc_p
Generates set of parameters to be used with phenology_MHmcmc()
plot.ECFOCF
Plot a result of clutch frequency fit.
IPModel
Estimates the pattern of internesting intervals for a set of parameters.
IPFit
Fit a model of Internesting Period for marine turtles.
result_Gratiot_Flat
Result of the fit of Leatherback nest counts
extract_result
Extract the set of parameters from a result object.
fit_phenology
Fit the phenology parameters to timeseries of counts.
Tagloss_daymax
Return the maximum number of days an individual has been observed in a dataset.
MarineTurtles_2002
Database of tagged marine turtles in 2002
likelihood_phenology
Estimate the likelihood of timeseries based on a set of parameters.
result_Gratiot
Result of the fit of Leatherback nest counts
result_Gratiot1
Result of the fit of Leatherback nest counts
MinBMinE_to_Min
Transform a set of parameters from MinB and MinE to Min
plot.TaglossData
Plot data used for tagloss analysis.
plot.Tagloss
Plot the daily rate of tag loss.
result_Gratiot_mcmc
Result of the mcmc for Leatherback nest counts
plot.fitRMU
Plot the synthesis of RMU fit.
Tagloss_fit
fit a model of tag loss using a CMR database.
plot.phenology
Plot the phenology from a result.
result_Gratiot2
Result of the fit of Leatherback nest counts
summary.phenology
Print the result information from a result object.
map_phenology
Generate a likelihood map varying Phi and Delta.
add_phenology
Create a new dataset or add a timeserie to a previous dataset.
add_SE
Add standard error for a fixed parameter.
outLR
Database of leatherback CMR in French Guiana
summary.phenologymap
Print information on a phenologymap object.
par_init
Calculate initial set of parameters.
lnLCF
Calculate the -log likelihood of data within a model.
phenology-package
Tools to Manage a Parametric Function that Describes Phenology
logLik.ECFOCF
Return Log Likelihood of a fit done using fitCF
plot_phi
Plot the best likelihood for fixed Phi value.
print.phenology
Print the result information from a result x.
plot.IP
Plot a result of Internesting Period fit or data.
plot.TableECFOCF
Plot a TableECFOCF dataset.
print.phenologymap
Print information on a phenologymap object.
print.phenologyout
Print the information from a ouput x.
shift_sinusoid
Shift sinusoid information.
summary.IP
Print the result information from a IP object.