sbm_ci-class {swash} | R Documentation |
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 numberR_{0A}
integrals
:Object of class
"numeric"
Model result: integralsS_A
,I_A
, andR_A
velocity
:Object of class
"numeric"
Model result: velocity measurest_{FE}
andt_{LE}
occ_regions
:Object of class
"data.frame"
Model result: Occurence at regional levelcases_by_date
:Object of class
"data.frame"
Total cases by datecases_by_region
:Object of class
"data.frame"
Cumulative cases by regioninput_data
:Object of class
"data.frame"
Input datadata_statistics
:Object of class
"numeric"
Diagnostics of input datacol_names
:Object of class
"character"
Column names in input dataintegrals_ci
:Object of class
"list"
Confidence intervals for integralsS_A
,I_A
, andR_A
velocity_ci
:Object of class
"list"
Confidence intervals for velocity measurest_{FE}
andt_{LE}
R_0A_ci
:Object of class
"numeric"
Confidence intervals for spatial reproduction numberR_{0A}
iterations
:Object of class
"data.frame"
Results of bootstrap sampling iterationsci
:Object of class
"numeric"
Lower and upper confidence intervals based on user inputconfig
: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}
, andR_{0A}
signature(x = "sbm_ci")
: Prints ansbm_ci
object; usesummary(sbm_ci)
for results- show
signature(object = "sbm_ci")
: Prints ansbm_ci
object; usesummary(sbm_ci)
for results- summary
signature(object = "sbm_ci")
: Prints a summary ofsbm_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. doi: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. doi: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. doi: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). doi:10.1016/B978-0-12-817815-7.00013-0
Examples
showClass("sbm_ci")