sbm_ci-class: Class '"sbm_ci"'

In swash: Swash-Backwash Model for the Single Epidemic Wave

Class "sbm_ci"

Description

The class "sbm_ci" contains the results of the Swash-Backwash Model, confidence intervals for the model estimates, and the related input data as well as additional information. Use summary(sbm_ci) and plot(sbm_ci) for results summary and plotting, respectively.

Objects from the Class

Objects can be created by the function confint(sbm).

Slots

R_0A:

Object of class "numeric" Model result: spatial reproduction number R_{0A}

integrals:

Object of class "numeric" Model result: integrals S_A, I_A, and R_A

velocity:

Object of class "numeric" Model result: velocity measures t_{FE} and t_{LE}

occ_regions:

Object of class "data.frame" Model result: Occurence at regional level

cases_by_date:

Object of class "data.frame" Total cases by date

cases_by_region:

Object of class "data.frame" Cumulative cases by region

input_data:

Object of class "data.frame" Input data

data_statistics:

Object of class "numeric" Diagnostics of input data

col_names:

Object of class "character" Column names in input data

integrals_ci:

Object of class "list" Confidence intervals for integrals S_A, I_A, and R_A

velocity_ci:

Object of class "list" Confidence intervals for velocity measures t_{FE} and t_{LE}

R_0A_ci:

Object of class "numeric" Confidence intervals for spatial reproduction number R_{0A}

iterations:

Object of class "data.frame" Results of bootstrap sampling iterations

ci:

Object of class "numeric" Lower and upper confidence intervals based on user input

config:

Object of class "list" Configuration details for bootstrap sampling

Methods

plot

signature(x = "sbm_ci"): Plots the results of bootstrap confidence intervals for the Swash-Backwash Model; one figure with six plots: S_A, I_A, R_A, t_{FE}, t_{LE}, and R_{0A}

print

signature(x = "sbm_ci"): Prints an sbm_ci object; use summary(sbm_ci) for results

show

signature(object = "sbm_ci"): Prints an sbm_ci object; use summary(sbm_ci) for results

summary

signature(object = "sbm_ci"): Prints a summary of sbm_ci objects (bootstrap confidence intervals for Swash-Backwash Model estimates)

Author(s)

Thomas Wieland

References

Swash-Backwash Model:

Cliff AD, Haggett P (2006) A swash-backwash model of the single epidemic wave. Journal of Geographical Systems 8(3), 227-252. \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.1007/s10109-006-0027-8")}

Smallman-Raynor MR, Cliff AD, Stickler PJ (2022) Meningococcal Meningitis and Coal Mining in Provincial England: Geographical Perspectives on a Major Epidemic, 1929–33. Geographical Analysis 54, 197–216. \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.1111/gean.12272")}

Smallman-Raynor MR, Cliff AD, The COVID-19 Genomics UK (COG-UK) Consortium (2022) Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020–December 2021. Epidemiology and Infection 150, e145. \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.1017/S0950268822001285")}.

Bootstrapping und bootstrap confidence intervals:

Efron B, Tibshirani RJ (1993) An Introduction to the Bootstrap.

Ramachandran KM, Tsokos CP (2021) Mathematical Statistics with Applications in R (Third Edition). Ch. 13.3.1 (Bootstrap confidence intervals). \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.1016/B978-0-12-817815-7.00013-0")}

Examples

showClass("sbm_ci")

swash documentation built on April 12, 2025, 2:23 a.m.