netdiffuseR: Analysis of Diffusion and Contagion Processes on Networks

Empirical statistical analysis, visualization and simulation of diffusion and contagion processes on networks. The package implements algorithms for calculating network diffusion statistics such as transmission rate, hazard rates, exposure models, network threshold levels, infectiousness (contagion), and susceptibility. The package is inspired by work published in Valente, et al., (2015) <DOI:10.1016/j.socscimed.2015.10.001>; Valente (1995) <ISBN:9781881303213>, Myers (2000) <DOI:10.1086/303110>, Iyengar and others (2011) <DOI:10.1287/mksc.1100.0566>, Burt (1987) <DOI:10.1086/228667>; among others.

Install the latest version of this package by entering the following in R:
install.packages("netdiffuseR")
AuthorGeorge Vega Yon [aut, cre] (Rewrite functions with Rcpp, plus new features), Stephanie Dyal [aut] (Package's first version), Timothy Hayes [aut] (Package's first version), Thomas Valente [aut, cph] (R original code)
Date of publication2016-11-11 00:07:16
MaintainerGeorge Vega Yon <g.vegayon@gmail.com>
LicenseMIT + file LICENSE
Version1.17.0
https://github.com/USCCANA/netdiffuseR

View on CRAN

Man pages

as.array.diffnet: Coerce a diffnet graph into an array

as_diffnet: Creates a 'diffnet' class object

brfarmers: Brazilian Farmers

brfarmersDiffNet: 'diffnet' version of the Brazilian Farmers data

c.diffnet: Combine diffnet objects

classify_adopters: Classify adopters accordingly to Time of Adoption and...

classify_graph: Analyze an R object to identify the class of graph (if any)

cumulative_adopt_count: Cummulative count of adopters

dgr: Indegree, outdegree and degree of the vertices

diag_expand: Creates a square matrix suitable for spatial statistics...

diffnet-arithmetic: 'diffnet' Arithmetic and Logical Operators

diffnet_check_attr_class: Infer whether 'value' is dynamic or static.

diffnet_index: Indexing diffnet objects (on development)

diffnetmatmult: Matrix multiplication

diffnet_to_igraph: Convertion between graph classes

diffusion-data: Diffusion Network Datasets

diffusionMap: Creates a heatmap based on a graph layout and a vertex...

drawColorKey: Draw a color key in the current device

edgelist_to_adjmat: Conversion between adjacency matrix and edgelist

edges_coords: Compute ego/alter edge coordinates considering alter's size...

egonet_attrs: Retrieve alter's attributes (network effects)

ego_variance: Computes variance of Y at ego level

exposure: Ego exposure

fakeDynEdgelist: Fake dynamic edgelist

fakeEdgelist: Fake static edgelist

fakesurvey: Fake survey data

fakesurveyDyn: Fake longitudinal survey data

grid_distribution: Distribution over a grid

hazard_rate: Network Hazard Rate

infection: Susceptibility and Infection

isolated: Find and remove isolated vertices

kfamily: Korean Family Planning

kfamilyDiffNet: 'diffnet' version of the Korean Family Planning data

medInnovations: Medical Innovation

medInnovationsDiffNet: 'diffnet' version of the Medical Innovation data

moran: Computes Moran's I correlation index

netdiffuseR: netdiffuseR

netdiffuseR-graphs: Network data formats

netdiffuseR-options: 'netdiffuseR' default options

nvertices: Count the number of vertices/edges/slices in a graph

permute_graph: Permute the values of a matrix

plot_adopters: Visualize adopters and cumulative adopters

plot_diffnet: Plot the diffusion process

plot_diffnet2: Another way of visualizing diffusion

plot_infectsuscep: Plot distribution of infect/suscep

plot_threshold: Threshold levels through time

pretty_within: Pretty numbers within a range.

rdiffnet: Random diffnet network

read_pajek: Read foreign graph formats

read_ucinet_head: Reads UCINET files

recode: Recodes an edgelist such that ids go from 1 to n

rescale_vertex_igraph: Rescale vertex size to be used in 'plot.igraph'.

rewire_graph: Graph rewiring algorithms

rgraph_ba: Scale-free and Homophilic Random Networks

rgraph_er: Erdos-Renyi model

rgraph_ws: Watts-Strogatz model

ring_lattice: Ring lattice graph

round_to_seq: Takes a numeric vector and maps it into a finite length...

select_egoalter: Calculate the number of adoption changes between ego and...

struct_equiv: Structural Equivalence

struct_test: Structure dependence test

survey_to_diffnet: Convert survey-like data and edgelists to a 'diffnet' object

threshold: Retrive threshold levels from the exposure matrix

toa_diff: Difference in Time of Adoption (TOA) between individuals

toa_mat: Time of adoption matrix

transformGraphBy: Apply a function to a graph considering non-diagonal...

vertex_covariate_compare: Comparisons at dyadic level

vertex_covariate_dist: Computes covariate distance between connected vertices

weighted_var: Computes weighted variance

Functions

\%*\% Man page
adjmat_to_edgelist Man page
adopt_changes Man page
as.array.diffnet Man page
as.data.frame.diffnet_adopters Man page
as_diffnet Man page
bernoulli Man page
brfarmers Man page
brfarmersDiffNet Man page
c.diffnet Man page
c.diffnet_struct_test Man page
classify Man page
classify_adopters Man page
classify_adopters.default Man page
classify_adopters.diffnet Man page
classify_graph Man page
CUG Man page
cumulative_adopt_count Man page
\%*\%.default Man page
degree Man page
dgr Man page
diag_expand Man page
diag_expand.array Man page
diag_expand.dgCMatrix Man page
diag_expand.diffnet Man page
diag_expand.list Man page
diag_expand.matrix Man page
diffmap Man page
diffnet Man page
^.diffnet Man page
|.diffnet Man page
-.diffnet Man page
/.diffnet Man page
[<-.diffnet Man page
[.diffnet Man page
[[<-.diffnet Man page
[[.diffnet Man page
*.diffnet Man page
\%*\%.diffnet Man page
&.diffnet Man page
diffnet-arithmetic Man page
diffnet.attrs Man page
diffnet.attrs<- Man page
diffnet_check_attr_class Man page
diffnet-class Man page
diffnet_index Man page
diffnetLapply Man page
diffnet.toa Man page
diffnet.toa<- Man page
diffnet_to_igraph Man page
diffusion-data Man page
diffusionMap Man page
diffusionMap.default Man page
diffusionMap.diffnet Man page
dim.diffnet Man page
dimnames.diffnet Man page
drawColorKey Man page
drop_isolated Man page
edgelist_to_adjmat Man page
edgelist_to_diffnet Man page
edges_coords Man page
egonet_attrs Man page
ego_variance Man page
exposure Man page
fakeDynEdgelist Man page
fakeEdgelist Man page
fakesurvey Man page
fakesurveyDyn Man page
ftable.diffnet_adopters Man page
graph_power Man page
grid_distribution Man page
hazard_rate Man page
hist.diffnet_struct_test Man page
igraph_to_diffnet Man page
image.diffnet_diffmap Man page
indegree Man page
infection Man page
isolated Man page
kfamily Man page
kfamilyDiffNet Man page
mahalanobis Man page
medInnovations Man page
medInnovationsDiffNet Man page
moran Man page
nedges Man page
netdiffuseR Man page
netdiffuseR-graphs Man page
netdiffuseR-options Man page
netdiffuseR-package Man page
nlinks Man page
nnodes Man page
nodes Man page
n_rewires Man page
nslices Man page
nvertices Man page
outdegree Man page
permute_graph Man page
plot_adopters Man page
plot_diffnet Man page
plot.diffnet Man page
plot_diffnet2 Man page
plot_diffnet2.default Man page
plot_diffnet2.diffnet Man page
plot.diffnet_adopters Man page
plot.diffnet_degSeq Man page
plot.diffnet_diffmap Man page
plot.diffnet_hr Man page
plot_hazard Man page
plot_hazarrate Man page
plot_infectsuscep Man page
plot_threshold Man page
p-norm Man page
pretty_within Man page
print.diffnet Man page
print.diffnet_diffmap Man page
print.diffnet_se Man page
print.diffnet_struct_test Man page
QAP Man page
rdiffnet Man page
read_dl Man page
read_ml Man page
read_net Man page
read_pajek Man page
read_ucinet Man page
read_ucinet_head Man page
recode Man page
recode.data.frame Man page
recode.matrix Man page
rescale_vertex_igraph Man page
rewire_graph Man page
rewire_permute Man page
rewire_qap Man page
rgraph_ba Man page
rgraph_er Man page
rgraph_ws Man page
ring_lattice Man page
round_to_seq Man page
scale-free Man page
select_egoalter Man page
small-world Man page
str.diffnet Man page
struct_equiv Man page
struct_test Man page
struct_test_asymp Man page
summary.diffnet Man page
summary.diffnet_adoptChanges Man page
survey_to_diffnet Man page
susceptibility Man page
t.diffnet Man page
threshold Man page
toa_diff Man page
toa_mat Man page
transformGraphBy Man page
transformGraphBy.dgCMatrix Man page
transformGraphBy.diffnet Man page
ucinet Man page
UCINET Man page
vertex_covariate_compare Man page
vertex_covariate_dist Man page
vertex_mahalanobis_dist Man page
weighted_var Man page
wvar Man page

Files

inst
inst/CITATION
inst/NEWS
inst/extdata
inst/extdata/sampson.##h
inst/extdata/SAMPSON.DAT
inst/extdata/SAMPSONL.NET
inst/extdata/SAMPSON_W_DEGREE.vec
inst/extdata/sampson.##d
inst/extdata/SAMPSON.NET
inst/doc
inst/doc/analyzing-medical-innovation-data.html
inst/doc/introduction-to-netdiffuser.Rmd
inst/doc/analyzing-medical-innovation-data.Rmd
inst/doc/analyzing-medical-innovation-data.R
inst/doc/time_discount_suscep_infect.Rmd
inst/doc/not-lost-in-translation-importing-and-exporting-graphs.html
inst/doc/introduction-to-netdiffuser.R
inst/doc/not-lost-in-translation-importing-and-exporting-graphs.Rmd
inst/doc/time_discount_suscep_infect.html
inst/doc/introduction-to-netdiffuser.html
inst/doc/not-lost-in-translation-importing-and-exporting-graphs.R
tests
tests/testthat.R
tests/testthat
tests/testthat/test-sparse_indexes.R tests/testthat/test-stats.R tests/testthat/test-plot_diffnet2.R tests/testthat/test-diffnet-methods.R tests/testthat/test-rewire.R tests/testthat/test-foreign.R tests/testthat/test-spatial.R tests/testthat/test-struct_equiv.R tests/testthat/test-examples.R tests/testthat/test-rdiffnet.R tests/testthat/test-diffnet-class.R tests/testthat/test-cumulative_adopt_count.R tests/testthat/test-struct_test.R tests/testthat/test-read_write_foreign.R tests/testthat/test-netdiffuser_extra.R tests/testthat/test-options.R tests/testthat/test-diffnet-indexing.R tests/testthat/test-select_egoalter.R tests/testthat/test-survey_to_diffnet.R tests/testthat/test-adjmat.R tests/testthat/test-infect_suscept.R tests/testthat/test-egonets.R tests/testthat/test-random_graph.R tests/testthat/test-graph_data.R tests/testthat/test-dgr.R tests/testthat/test-imports.R tests/testthat/test-misc.R
src
src/adjmat.h
src/infection.h
src/Makevars
src/stats.cpp
src/infection.cpp
src/stats.h
src/adjmat.cpp
src/struct_test.h
src/netdiffuser_extra.h
src/struct_test.cpp
src/plot.h
src/rgraph.cpp
src/plot.cpp
src/Makevars.win
src/netdiffuser_extra.cpp
src/RcppExports.cpp
src/rgraph.h
NAMESPACE
data
data/fakesurvey.rdata
data/brfarmers.rdata
data/brfarmersDiffNet.rdata
data/medInnovationsDiffNet.rdata
data/fakeDynEdgelist.rdata
data/fakeEdgelist.rdata
data/fakesurveyDyn.rdata
data/kfamily.rdata
data/medInnovations.rdata
data/kfamilyDiffNet.rdata
R
R/spatial.R R/struct_equiv.R R/graph_data.R R/diffnet-indexing.R R/diffnet-c.R R/random_graph.R R/egonets.R R/moran.R R/rewire.R R/adjmat.R R/data.R R/plot_diffnet2.R R/struct_test.R R/rdiffnet.R R/options.R R/diffnet-methods.R R/RcppExports.R R/stats.R R/infect_suscept.R R/package-doc.R R/misc.R R/select_egoalter.R R/read_write_foreign.R R/imports.R R/igraph.R R/diffnet-class.R R/survey_to_diffnet.R
vignettes
vignettes/introduction-to-netdiffuser.Rmd
vignettes/analyzing-medical-innovation-data.Rmd
vignettes/time_discount_suscep_infect.Rmd
vignettes/not-lost-in-translation-importing-and-exporting-graphs.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
ChangeLog
man
man/threshold.Rd man/diffnet_check_attr_class.Rd man/diffnet_to_igraph.Rd man/rewire_graph.Rd man/as.array.diffnet.Rd man/struct_test.Rd man/diffnetmatmult.Rd man/dgr.Rd man/moran.Rd man/infection.Rd man/vertex_covariate_compare.Rd man/plot_diffnet.Rd man/exposure.Rd man/fakeDynEdgelist.Rd man/grid_distribution.Rd man/pretty_within.Rd man/diffnet-arithmetic.Rd man/ego_variance.Rd man/rgraph_ba.Rd man/toa_mat.Rd man/medInnovationsDiffNet.Rd man/netdiffuseR-options.Rd man/netdiffuseR-graphs.Rd man/c.diffnet.Rd man/as_diffnet.Rd man/ring_lattice.Rd man/kfamily.Rd man/classify_adopters.Rd man/netdiffuseR.Rd man/struct_equiv.Rd man/plot_adopters.Rd man/cumulative_adopt_count.Rd man/edgelist_to_adjmat.Rd man/brfarmers.Rd man/diffusion-data.Rd man/weighted_var.Rd man/rgraph_er.Rd man/vertex_covariate_dist.Rd man/read_pajek.Rd man/transformGraphBy.Rd man/rdiffnet.Rd man/fakesurveyDyn.Rd man/classify_graph.Rd man/hazard_rate.Rd man/select_egoalter.Rd man/read_ucinet_head.Rd man/round_to_seq.Rd man/fakeEdgelist.Rd man/toa_diff.Rd man/kfamilyDiffNet.Rd man/medInnovations.Rd man/fakesurvey.Rd man/isolated.Rd
man/macros
man/macros/struct_test.Rd man/rgraph_ws.Rd man/nvertices.Rd man/diag_expand.Rd man/plot_infectsuscep.Rd man/diffusionMap.Rd man/brfarmersDiffNet.Rd man/plot_threshold.Rd man/permute_graph.Rd man/rescale_vertex_igraph.Rd man/egonet_attrs.Rd man/recode.Rd man/edges_coords.Rd man/drawColorKey.Rd man/survey_to_diffnet.Rd man/diffnet_index.Rd man/plot_diffnet2.Rd
LICENSE

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