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phenology (version 7.2)
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
7.2
License
GPL-2
Maintainer
Marc Girondot
Last Published
September 27th, 2018
Functions in phenology (7.2)
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Tagloss_simulate
Return a list with the number of days different kinds of individuals are seen.
fitRMU_MHmcmc_p
Generates set of parameters to be used with fitRMU_MHmcmc()
fit_phenology
Fit the phenology parameters to timeseries of counts.
par_init
Calculate initial set of parameters.
plot.phenologymap
Plot a likelihood map with Delta and Phi varying.
plot_delta
Plot a likelihood lineplot obtained after map_phenology.
outLR
Database of leatherback CMR in French Guiana
result_Gratiot_mcmc
Result of the mcmc for Leatherback nest counts
result_Gratiot_Flat
Result of the fit of Leatherback nest counts
Gratiot
Leatherback nest counts from Gratiot et al. (2006) Figure 1
MarineTurtles_2002
Database of tagged marine turtles in 2002
TableECFOCF
Format a CMR dataset into a file that fitCF can use.
add_phenology
Create a new dataset or add a timeserie to a previous dataset.
MinBMinE_to_Min
Transform a set of parameters from MinB and MinE to Min
Tagloss_L
Return the -log likelihood of a set of individuals under a model of tagloss.
Tagloss_LengthObs
Return a list with the number of days different kinds of individuals are seen.
Tagloss_daymax
Return the maximum number of days an individual has been observed in a dataset.
Tagloss_fit
fit a model of tag loss using a CMR database.
adapt_parameters
Extract the parameters from a set of parameters to be used with another dataset.
IPModel
Estimates the pattern of internesting intervals for a set of parameters.
add_SD
Add SD for a fixed parameter.
fitRMU
Adjust incomplete timeseries with various constraints.
fitRMU_MHmcmc
Run the Metropolis-Hastings algorithm for RMU.data
Tagloss_format
Format a CMR dataset into a file that Tagloss_L can use.
extract_result
Extract the set of parameters from a result object.
likelihood_phenology
Estimate the likelihood of timeseries based on a set of parameters.
lnLCF
Calculate the -log likelihood of data within a model.
phenology_MHmcmc
Run the Metropolis-Hastings algorithm for data
phenology_MHmcmc_p
Generates set of parameters to be used with phenology_MHmcmc()
fitCF
Fit a model of Clutch Frequency for marine turtles.
plot.fitRMU
Plot the synthesis of RMU fit.
logLik.fitRMU
Return Log Likelihood of a fit generated by fitRMU
logLik.ECFOCF
Return Log Likelihood of a fit done using fitCF
plot.TableECFOCF
Plot a TableECFOCF dataset.
plot.phenology
Plot the phenology from a result.
logLik.Tagloss
Return Log Likelihood of a fit generated by Tagloss_fit
shift_sinusoid
Shift sinusoid information.
print.phenologymap
Print information on a phenologymap object.
logLik.phenology
Return Log Likelihood of a fit generated by fit_phenology
print.phenologyout
Print the information from a ouput x.
.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
plot.Tagloss
Plot the daily rate of tag loss.
map_Gratiot
Likelihood map of Leatherback nest counts
summary.phenologyout
Print the summary information from a ouput object.
result_Gratiot2
Result of the fit of Leatherback nest counts
result_Gratiot1
Result of the fit of Leatherback nest counts
map_phenology
Generate a likelihood map varying Phi and Delta.
summary.IP
Print the result information from a IP object.
phenology-package
Tools to Manage a Parametric Function that Describes Phenology
phenology
Run a shiny application for basic functions of phenology package
plot.ECFOCF
Plot a result of clutch frequency fit.
plot_phi
Plot the best likelihood for fixed Phi value.
plot.IP
Plot a result of Internesting Period fit or data.
remove_site
Removes site information from a set of parameters.
summary.phenologymap
Print information on a phenologymap object.
summary.phenology
Print the result information from a result object.
print.phenology
Print the result information from a result x.
result_Gratiot
Result of the fit of Leatherback nest counts
IPPredict
Predict the possible clutch number based on observed Internesting Period.
BE_to_LBLE
Transform a set of parameters from Begin End to LengthB LengthE.
AutoFitPhenology
Automatic fit for phenology and tests
LBLE_to_L
Transform a set of parameters from LengthB LengthE format to Length
IPFit
Fit a model of Internesting Period for marine turtles.
L_to_LBLE
Transform a set of parameters from Length format to LengthB LengthE
ECFOCF_f
Calculate a table of probabilities of ECF and OCF.
LBLE_to_BE
Transform a set of parameters from LengthB LengthE to Begin End.
Tagloss_model
Return the daily rate of tag loss.