In jmanitz/NetOrigin: Origin Estimation for Propagation Processes on Complex Networks

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)

# apply effective distance median source estimation
om <- origin(events=delayGoe[10,-c(1:2)], type='edm', distance=eff)
summary(om)
plot(om, 'mdist', start=1)
plot(om, 'wvar', start=1)
performance(om, start=1, graph=ptnGoe)

Example: Backtracking

# backtracking origin estimation (Manitz et al., 2016)
ob <- origin(events=delayGoe[10,-c(1:2)], type='backtracking', graph=ptnGoe)
summary(ob)
plot(ob, start=1)
performance(ob, start=1, graph=ptnGoe)

Example: Multiple Origins

data(ptnAth)
origin_multiple(events=delayAth[10,-c(1:2)], type='backtracking', graph=ptnAth, no=2)
# edm
athnet <- igraph::as_adjacency_matrix(ptnAth, sparse=FALSE)
p <- athnet/rowSums(athnet)
eff <- eff_dist(p)
origin_multiple(events=delayAth[10,-c(1:2)], type='edm', graph=ptnAth, no=2, distance=eff)

References

• 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.

• 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.

• 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.

• Comin, C. H. and da Fontoura Costa, L. (2011) Identifying the starting point of a spreading process in complex networks. Physical Review E, 84.

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.

jmanitz/NetOrigin documentation built on Sept. 5, 2023, 6:10 a.m.