Man pages for phenology
Tools to Manage a Parametric Function that Describes Phenology and More

adapt_parametersExtract the parameters from a set of parameters to be used...
add_phenologyCreate a new dataset or add a timeserie to a previous...
add_SEAdd standard error for a fixed parameter.
AutoFitPhenologyAutomatic fit for phenology and tests
Bayesian.remigrationReturn a posterior remigration interval.
BE_to_LBLETransform a set of parameters from Begin End to LengthB...
CI.RMUCalculate the confidence interval of the results of fitRMU()
ECFOCF_fCalculate a table of probabilities of ECF and OCF.
ECFOCF_fullCalculate a table of probabilities of ECF and OCF.
ExponentialRegressionNon-biased exponential regression
extract_resultExtract the set of parameters from a result object.
fitCFFit a model of Clutch Frequency for marine turtles.
fitCF_MHmcmcRun the Metropolis-Hastings algorithm for ECFOCF data
fitCF_MHmcmc_pGenerate set of parameters to be used with fitCF_MHmcmc()
fit_phenologyFit the phenology parameters to timeseries of counts.
fitRMUAdjust incomplete timeseries with various constraints.
fitRMU_MHmcmcRun the Metropolis-Hastings algorithm for RMU.data
fitRMU_MHmcmc_pGenerates set of parameters to be used with fitRMU_MHmcmc()
fixed.parameters0Generate a set of fixed parameters for series with only 0...
generateCFGenerate a set of data to test Clutch Frequency for marine...
GratiotLeatherback nest counts from Gratiot et al. (2006) Figure 1
IPFitFit a model of Internesting Period for marine turtles.
IPModelEstimates the pattern of internesting intervals for a set of...
IPPredictPredict the possible clutch number based on observed...
LBLE_to_BETransform a set of parameters from LengthB LengthE to Begin...
LBLE_to_LTransform a set of parameters from LengthB LengthE format to...
likelihood_phenologyEstimate the likelihood of timeseries based on a set of...
lnLCFCalculate the -log likelihood of data within a model.
LnRI_normReturn a remigration interval.
logLik.ECFOCFReturn Log Likelihood of a fit done using fitCF
logLik.fitRMUReturn Log Likelihood of a fit generated by fitRMU
logLik.phenologyReturn Log Likelihood of a fit generated by fit_phenology
logLik.TaglossReturn Log Likelihood of a fit generated by Tagloss_fit
L_to_LBLETransform a set of parameters from Length format to LengthB...
map_GratiotLikelihood map of Leatherback nest counts
map_phenologyGenerate a likelihood map varying Phi and Delta.
MarineTurtles_2002Database of tagged marine turtles in 2002
MinBMinE_to_MinTransform a set of parameters from MinB and MinE to Min
o_4p_p1p2Model of tagloss based on Rivalan data
outLRDatabase of leatherback CMR in French Guiana
Parameter_Global_YearTransform a set of parameters from Year to global effect, or...
par_initCalculate initial set of parameters.
phenologyRun a shiny application for basic functions of phenology...
phenology2fitRMUCreate the data to be used with fitRMU() for a...
phenology_MHmcmcRun the Metropolis-Hastings algorithm for data
phenology_MHmcmc_pGenerates set of parameters to be used with...
phenology-packageTools to Manage a Parametric Function that Describes...
plot_deltaPlot a likelihood lineplot obtained after map_phenology.
plot.ECFOCFPlot a result of clutch frequency fit.
plot.fitRMUPlot the synthesis of RMU fit.
plot.IPPlot a result of Internesting Period fit or data.
plot.phenologyPlot the phenology from a result.
plot.phenologymapPlot a likelihood map with Delta and Phi varying.
plot_phiPlot the best likelihood for fixed Phi value.
plot.RemigrationPlot the remigration intervals.
plot.TableECFOCFPlot a TableECFOCF dataset.
plot.TaglossPlot the daily rate of tag loss.
plot.TaglossDataPlot data used for tagloss analysis.
print.phenologyPrint the result information from a result x.
print.phenologymapPrint information on a phenologymap object.
print.phenologyoutPrint the information from a ouput x.
remove_siteRemoves site information from a set of parameters.
result_GratiotResult of the fit of Leatherback nest counts
result_Gratiot1Result of the fit of Leatherback nest counts
result_Gratiot2Result of the fit of Leatherback nest counts
result_Gratiot_FlatResult of the fit of Leatherback nest counts
result_Gratiot_mcmcResult of the mcmc for Leatherback nest counts
RIReturn an expected remigration interval.
shift_sinusoidShift sinusoid information.
summary.IPPrint the result information from a IP object.
summary.phenologyPrint the result information from a result object.
summary.phenologymapPrint information on a phenologymap object.
summary.phenologyoutPrint the summary information from a ouput object.
TableECFOCFFormat a CMR dataset into a file that fitCF can use.
Tagloss_cumulReturn the cumulative rate of tag loss.
Tagloss_daymaxReturn the maximum number of days an individual has been...
Tagloss_fitfit a model of tag loss using a CMR database.
Tagloss_formatFormat a CMR dataset into a file that Tagloss_L can use.
Tagloss_LReturn the -log likelihood of a set of individuals under a...
Tagloss_LengthObsReturn a list with the number of days for different kinds of...
Tagloss_mcmcBayesian model of tag loss using a CMR database.
Tagloss_mcmc_pGenerates set of parameters to be used with Tagloss_mcmc()
Tagloss_modelReturn the daily rate of tag loss.
Tagloss_simulateReturn a list with the number of days different kinds of...
toggle_Min_PMinTransform a set of parameters from Min, MinB or MinE to PMin,...
phenology documentation built on Sept. 11, 2024, 6:07 p.m.