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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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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
hhh4addon/json (API)

# Install 'hhh4addon' in R:

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

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:

4.75 score 7 stars 54 scripts 22 exports 16 dependencies

Last updated from:bb2bb243b5. Checks:7 WARNING, 2 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	WARNING	188
source / vignettes	OK	242
linux-release-x86_64	WARNING	133
macos-release-arm64	WARNING	119
macos-oldrel-arm64	WARNING	148
windows-devel	WARNING	91
windows-release	WARNING	117
windows-oldrel	WARNING	94
wasm-release	OK	101

Exports:aggregate_moments ar2_lag decompose.hhh4 distr_lag ds_score_hhh4 fanplot_prediction fanplot_stationary fit_par_lag geometric_lag hhh4_lag linear_lag log_normal_lag oneStepAhead_hhh4lag plot_moments_by_unit plotHHH4lag_fitted plotHHH4lag_maps poisson_lag predictive_moments profile_par_lag psi2size.hhh4lag stationary_moments unrestricted_lag

Dependencies:deldir fanplot lattice MASS Matrix nlme numDeriv polyclip polyCub sp spatstat.data spatstat.geom spatstat.univar spatstat.utils surveillance xtable

hhh4addon: extending the functionality of surveillance:hhh4

Purpose of the R package hhh4addon | The endemic-epidemic model class and its extension to higher-order lags | Computing predictive and marginal moments | References

Rendered fromhhh4addon.Rmdusingknitr::rmarkdown

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

Help page	Topics
Aggregation of stationary or predictive moments	aggregate_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$funct_lag' argument.	ar2_lag
confidence intervals for one-step-ahead predictions	confint.oneStepAhead
A wrapper around 'decompose.hhh4lag' and 'surveillance::decompose.hhh4'	decompose.hhh4
A modified version of 'decompose.hhh4'	decompose.hhh4lag
Data set on dengue in San Juan, Puerto Rico	dengueSJ
Display the function and parameters used for distributed lags	distr_lag
Calculate Dawid-Sebastiani score	ds_score_hhh4
Display prediction as a fan plot	fanplot_prediction
Display stationary distribution as a fanplot	fanplot_stationary
Estimating the lag decay parameter of an 'hhh4_lag' model using profile likelihood	fit_par_lag
A modified version of 'fixef.hhh4'	fixef.hhh4lag
Function to obtain geometric weights This function generates geometric weights which are subsequently used inside of 'get_weighted_lags'. To be passed to 'hhh4_lag' or 'profile_par_lag' as the 'control$funct_lag' argument.	geometric_lag
Get diagnoal elements of all slices of an array	get_diags_of_array
Transform matrix of first-order lagged observations to matrix of weighted sums of past observation	get_weighted_lags
Fitting hhh4 models with distributed lags	hhh4_lag
Interpolate between quantiles to avoid edgy display	interpolate_qnbinom
Determine whether an hhh4 object was fitted using one of the more complex techniques for handling neighbourhoods	is_complex_neighbourhood
Check if the par_lag parameter was fitted	is_fitted_par_lag
Extracting Lambda_Tilde from an hhh4 object with complex neighbourhood structure	lambda_tilde
Extracting Lambda_Tilde from an hhh4 object with complex neighbourhood structure	lambda_tilde_complex_neighbourhood
Function to obtain linearly decaying weights	linear_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 pattern	matrix_is_cyclic
A modified version of 'neOffsetArray'	neOffsetArray.hhh4lag
Data set on norovirus gastroenteritis in Bremen and Lower Saxony	noroBL
Numerical evaluation of the covariance matrix including the additional parameter 'par_lg'	numeric_fisher_hhh4lag
Predictive Model Assessment for hhh4_lag Models	oneStepAhead_hhh4lag
Plot predictive or stationary moments by unit	plot_moments_by_unit
simple plot of one-step-ahead forecasts	plot.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' model	predictive_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 likelihood	profile_par_lag
A modified version of 'psi2size.hhh4'	psi2size.hhh4lag
quantiles of the one-step-ahead forecasts	quantile.oneStepAhead
A modified version of 'ranef.hhh4'	ranef.hhh4lag
A modified version of 'residuals.hhh4'	residuals.hhh4lag
Simulate "hhh4_lag" Count Time Series	simulate.hhh4lag
Analytic calculation of periodically stationary moments implied by a 'hhh4'-model	stationary_moments
A modified version of 'surveillance::summary.hhh4'	summary.hhh4lag
A modified version of 'terms.hhh4'	terms.hhh4lag
Function to obtain unrestricted lags	unrestricted_lag
A modified version of 'update.hhh4'	update.hhh4lag

Package: hhh4addon 0.0.0.0.9014

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

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