Package: hhh4addon 0.0.0.0.9014

Johannes Bracher

hhh4addon: Extensions to endemic-epidemic timeseries modeling from package surveillance

Extending surveillance::hhh4 to allow for distributed lags, solutions for longterm prediction and (periodically) stationary moments.

Authors:Johannes Bracher [aut, cre], Maria Bekker-Nielsen Dunbar [ctb], the authors and contributors of the surveillance package, https://cran.r-project.org/package=surveillance [ctb], R Core Team [ctb]

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hhh4addon.pdf |hhh4addon.html✨
hhh4addon/json (API)

# Install 'hhh4addon' in R:
install.packages('hhh4addon', repos = c('https://ee-lib.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jbracher/hhh4addon/issues

Datasets:
  • dengueSJ - Data set on dengue in San Juan, Puerto Rico
  • noroBL - Data set on norovirus gastroenteritis in Bremen and Lower Saxony

On CRAN:

4.91 score 6 stars 45 scripts 22 exports 16 dependencies

Last updated 4 months agofrom:bb2bb243b5. Checks:OK: 1 WARNING: 6. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 07 2024
R-4.5-winWARNINGDec 07 2024
R-4.5-linuxWARNINGDec 07 2024
R-4.4-winWARNINGDec 07 2024
R-4.4-macWARNINGDec 07 2024
R-4.3-winWARNINGDec 07 2024
R-4.3-macWARNINGDec 07 2024

Exports:aggregate_momentsar2_lagdecompose.hhh4distr_lagds_score_hhh4fanplot_predictionfanplot_stationaryfit_par_laggeometric_laghhh4_laglinear_laglog_normal_lagoneStepAhead_hhh4lagplot_moments_by_unitplotHHH4lag_fittedplotHHH4lag_mapspoisson_lagpredictive_momentsprofile_par_lagpsi2size.hhh4lagstationary_momentsunrestricted_lag

Dependencies:deldirfanplotlatticeMASSMatrixnlmenumDerivpolyclippolyCubspspatstat.dataspatstat.geomspatstat.univarspatstat.utilssurveillancextable

hhh4addon: extending the functionality of surveillance:hhh4

Johannes Bracher ([email protected]), University of Zurich

Rendered fromhhh4addon.Rmdusingknitr::rmarkdownon Dec 07 2024.

Last update: 2020-04-19
Started: 2017-09-13

Readme and manuals

Help Manual

Help pageTopics
Aggregation of stationary or predictive momentsaggregate_moments
Function to obtain AR2 weights This function generates AR2 weights which are subsequently used inside of 'get_weighted_lags'. To be passed to 'hhh4_lag' or 'profile_par_lag' as the 'control$funct_lag' argument.ar2_lag
confidence intervals for one-step-ahead predictionsconfint.oneStepAhead
A wrapper around 'decompose.hhh4lag' and 'surveillance::decompose.hhh4'decompose.hhh4
A modified version of 'decompose.hhh4'decompose.hhh4lag
Data set on dengue in San Juan, Puerto RicodengueSJ
Display the function and parameters used for distributed lagsdistr_lag
Calculate Dawid-Sebastiani scoreds_score_hhh4
Display prediction as a fan plotfanplot_prediction
Display stationary distribution as a fanplotfanplot_stationary
Estimating the lag decay parameter of an 'hhh4_lag' model using profile likelihoodfit_par_lag
A modified version of 'fixef.hhh4'fixef.hhh4lag
Function to obtain geometric weights This function generates geometric weights which are subsequently used inside of 'get_weighted_lags'. To be passed to 'hhh4_lag' or 'profile_par_lag' as the 'control$funct_lag' argument.geometric_lag
Get diagnoal elements of all slices of an arrayget_diags_of_array
Transform matrix of first-order lagged observations to matrix of weighted sums of past observationget_weighted_lags
Fitting hhh4 models with distributed lagshhh4_lag
Interpolate between quantiles to avoid edgy displayinterpolate_qnbinom
Determine whether an hhh4 object was fitted using one of the more complex techniques for handling neighbourhoodsis_complex_neighbourhood
Check if the par_lag parameter was fittedis_fitted_par_lag
Extracting Lambda_Tilde from an hhh4 object with complex neighbourhood structurelambda_tilde
Extracting Lambda_Tilde from an hhh4 object with complex neighbourhood structurelambda_tilde_complex_neighbourhood
Function to obtain linearly decaying weightslinear_lag
#' This function generates (shifted) discrete gamma weights which are subsequently used inside of 'get_weighted_lags'. To be passed #' to 'hhh4_lag' or 'profile_par_lag' as the 'control$funct_lag' argument. #' @param par_lag a parameter vector of length 2 to steer the lag structure, here log(shape) and log(rate), #' where shape and rate are the parameters of the discrete gamma distribution as implemented in the 'extraDistr' package. #' @param min_lag smallest lag to include; the support of the Poisson form starts only at 'min_lag'. Defaults to 1. #' @param max_lag highest lag to include; higher lags are cut off and he remaining weights standardized. Defaults to 5. #' @author Maria Dunbar, Johannes Bracher #' @export This function generates discretized log-normal weights which are subsequently used inside of 'get_weighted_lags'. To be passed to 'hhh4_lag' or 'profile_par_lag' as the 'control$funct_lag' argument.log_normal_lag
A modified version of 'logLik.hhh4'logLik.hhh4lag
Check whether the rows of a matrix show a cyclic patternmatrix_is_cyclic
A modified version of 'neOffsetArray'neOffsetArray.hhh4lag
Data set on norovirus gastroenteritis in Bremen and Lower SaxonynoroBL
Numerical evaluation of the covariance matrix including the additional parameter 'par_lg'numeric_fisher_hhh4lag
Predictive Model Assessment for hhh4_lag ModelsoneStepAhead_hhh4lag
Plot predictive or stationary moments by unitplot_moments_by_unit
simple plot of one-step-ahead forecastsplot.oneStepAhead
Function to obtain Poisson weights This function generates Poisson weights which are subsequently used inside of 'get_weighted_lags'. To be passed to 'hhh4_lag' or 'profile_par_lag' as the 'control$funct_lag' argument.poisson_lag
Analytical computation of predictive moments for an 'hhh4' modelpredictive_moments
A modified version of 'surveillance::print.hhh4'print.hhh4lag
A modified version of 'print.summary.hhh4'print.summary.hhh4lag
Estimating the lag decay parameter of an 'hhh4_lag' model using profile likelihoodprofile_par_lag
A modified version of 'psi2size.hhh4'psi2size.hhh4lag
quantiles of the one-step-ahead forecastsquantile.oneStepAhead
A modified version of 'ranef.hhh4'ranef.hhh4lag
A modified version of 'residuals.hhh4'residuals.hhh4lag
Simulate "hhh4_lag" Count Time Seriessimulate.hhh4lag
Analytic calculation of periodically stationary moments implied by a 'hhh4'-modelstationary_moments
A modified version of 'surveillance::summary.hhh4'summary.hhh4lag
A modified version of 'terms.hhh4'terms.hhh4lag
Function to obtain unrestricted lagsunrestricted_lag
A modified version of 'update.hhh4'update.hhh4lag