NetOrigin package
Performs network-based source estimation. Different approaches are available: effective distance median, recursive backtracking, and centrality-based source estimation. Additionally, we provide public transportation network data as well as methods for data preparation, source estimation performance analysis and visualization.
Installation
You can install the latest production version from CRAN
install.packages("NetOrigin", dependencies = TRUE)or the current development version from GitHub
library("devtools")
install_github("jmanitz/NetOrigin")Then, load the package
library("NetOrigin")Example: Effective Distance
data(delayGoe)
# compute effective distance
data(ptnGoe)
goenet <- igraph::as_adjacency_matrix(ptnGoe, sparse=FALSE)
p <- goenet/rowSums(goenet)
eff <- eff_dist(p)## Computing the effective distance between 257 nodes:
## 1...................................................................................................
## 100...................................................................................................
## 200.........................................................done# apply effective distance median source estimation
om <- origin(events=delayGoe[10,-c(1:2)], type='edm', distance=eff)
summary(om)## Effective distance median origin estimation:
##
## estimated node of origin 91: X.Gotthelf.Leimbach.Strasse
##
## auxiliary variables:
## id events wmean wvar
## Min. : 1 Min. : 0.0000 Min. : 5.482 Min. :0.3987
## 1st Qu.: 65 1st Qu.: 0.0000 1st Qu.:21.572 1st Qu.:2.2761
## Median :129 Median : 0.0000 Median :27.345 Median :2.4050
## Mean :129 Mean : 0.6459 Mean :26.948 Mean :2.4989
## 3rd Qu.:193 3rd Qu.: 0.0000 3rd Qu.:33.359 3rd Qu.:2.9986
## Max. :257 Max. :46.0000 Max. :47.762 Max. :6.2052
## mdist
## Min. :14.34
## 1st Qu.:20.75
## Median :24.23
## Mean :24.92
## 3rd Qu.:28.88
## Max. :39.16plot(om, 'mdist', start=1)plot(om, 'wvar', start=1)performance(om, start=1, graph=ptnGoe)## start est hitt rank spj dist
## 1 X.Adolf.Hoyer.Strasse X.Gotthelf.Leimbach.Strasse FALSE 2 2 1332Example: Backtracking
# backtracking origin estimation (Manitz et al., 2016)
ob <- origin(events=delayGoe[10,-c(1:2)], type='backtracking', graph=ptnGoe)
summary(ob)## Backtracking origin estimation:
##
## estimated node of origin 87: X.Gesundbrunnen
##
## auxiliary variables:
## id events bcount
## Min. : 1 Min. : 0.0000 Min. :0.00000
## 1st Qu.: 65 1st Qu.: 0.0000 1st Qu.:0.00000
## Median :129 Median : 0.0000 Median :0.00000
## Mean :129 Mean : 0.6459 Mean :0.03891
## 3rd Qu.:193 3rd Qu.: 0.0000 3rd Qu.:0.00000
## Max. :257 Max. :46.0000 Max. :3.00000plot(ob, start=1)performance(ob, start=1, graph=ptnGoe)## start est hitt rank spj dist
## 1 X.Adolf.Hoyer.Strasse X.Gesundbrunnen FALSE 4 8 5328Example: Multiple Origins
data(ptnAth)
origin_multiple(events=delayAth[10,-c(1:2)], type='backtracking', graph=ptnAth, no=2)## [[1]]
## Backtracking origin estimation:
##
## estimated node of origin 6: 6
##
## [[2]]
## Backtracking origin estimation:
##
## estimated node of origin 1: 1# edm
athnet <- igraph::as_adjacency_matrix(ptnAth, sparse=FALSE)
p <- athnet/rowSums(athnet)
eff <- eff_dist(p)## Computing the effective distance between 51 nodes:
## 1...................................................doneorigin_multiple(events=delayAth[10,-c(1:2)], type='edm', graph=ptnAth, no=2, distance=eff)## [[1]]
## Effective distance median origin estimation:
##
## estimated node of origin 3: 3
##
## [[2]]
## Effective distance median origin estimation:
##
## estimated node of origin 2: 2References
Li, J., J. Manitz, E. Bertuzzo, and E.D. Kolaczyk (2021): Sensor-based localization of epidemic sources on human mobility networks. PLoS Comput Biol 17(1): e1008545. <DOI: 10.1371/journal.pcbi.1008545>
Manitz, J., J. Harbering, M. Schmidt, T. Kneib, and A. Schoebel (2017): Source Estimation for Propagation Processes on Complex Networks with an Application to Delays in Public Transportation Systems. Journal of Royal Statistical Society C (Applied Statistics), 66: 521–536. <DOI: 10.1111/rssc.12176>
Manitz, J., T. Kneib, M. Schlather, J. Helbing, and D. Brockmann (2014): Origin detection during food-borne disease outbreaks - a case study of the 2011 EHEC/HUS outbreak in Germany. PLoS Currents Outbreaks, 1. <DOI: 10.1371/currents.outbreaks.f3fdeb08c5b9de7c09ed9cbcef5f01f2>
Comin, C. H. and da Fontoura Costa, L. (2011) Identifying the starting point of a spreading process in complex networks. Physical Review E, 84. <DOI: 10.1103/PhysRevE.84.056105>
To cite package ‘NetOrigin’ in publications use:
Juliane Manitz (2018). NetOrigin: Origin Estimation for Propagation Processes on Complex Networks. R package version 1.0-3. https://CRAN.R-project.org/package=NetOrigin
Use toBibtex(citation("NetOrigin")) in R to extract BibTeX references.