# Analysis of Diffusion and Contagion Processes on Networks

## Documentation for package ‘netdiffuseR’ version 1.19.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I K L M N O P Q R S T U V W misc

netdiffuseR-package | netdiffuseR

## -- A --

adjmat_to_edgelist | Conversion between adjacency matrix and edgelist
adopt_changes | Calculate the number of adoption changes between ego and alter.
approx_geodesic | Approximate Geodesic Distances
approx_geodist | Approximate Geodesic Distances
as.array.diffnet | Coerce a diffnet graph into an array
as.data.frame.diffnet | Creates a 'diffnet' class object
as.data.frame.diffnet_adopters | Classify adopters accordingly to Time of Adoption and Threshold levels.
as.dgCMatrix | Coerce a matrix-like objects to 'dgCMatrix' (sparse matrix)
as_dgCMatrix | Coerce a matrix-like objects to 'dgCMatrix' (sparse matrix)
as_dgCMatrix.array | Coerce a matrix-like objects to 'dgCMatrix' (sparse matrix)
as_dgCMatrix.default | Coerce a matrix-like objects to 'dgCMatrix' (sparse matrix)
as_dgCMatrix.diffnet | Coerce a matrix-like objects to 'dgCMatrix' (sparse matrix)
as_dgCMatrix.igraph | Coerce a matrix-like objects to 'dgCMatrix' (sparse matrix)
as_dgCMatrix.list | Coerce a matrix-like objects to 'dgCMatrix' (sparse matrix)
as_dgCMatrix.network | Coerce a matrix-like objects to 'dgCMatrix' (sparse matrix)
as_diffnet | Creates a 'diffnet' class object
as_diffnet.default | Creates a 'diffnet' class object
as_diffnet.networkDynamic | Creates a 'diffnet' class object
as_spmat | Coerce a matrix-like objects to 'dgCMatrix' (sparse matrix)

## -- B --

bass | Bass Model
bass_dF | Bass Model
bass_F | Bass Model
bass_f | Bass Model
bernoulli | Erdos-Renyi model
binary-functions | Non-zero element-wise comparison between two sparse matrices
bootnet | Network Bootstrapping
brfarmers | Brazilian Farmers
brfarmersDiffNet | 'diffnet' version of the Brazilian Farmers data

## -- C --

c.diffnet | Combine diffnet objects
c.diffnet_bootnet | Network Bootstrapping
c.diffnet_struct_test | Structure dependence test
classify | Classify adopters accordingly to Time of Adoption and Threshold levels.
classify_adopters | Classify adopters accordingly to Time of Adoption and Threshold levels.
classify_adopters.default | Classify adopters accordingly to Time of Adoption and Threshold levels.
classify_adopters.diffnet | Classify adopters accordingly to Time of Adoption and Threshold levels.
classify_graph | Analyze an R object to identify the class of graph (if any)
compare_matrix | Non-zero element-wise comparison between two sparse matrices
CUG | Permute the values of a matrix
cumulative_adopt_count | Cummulative count of adopters

## -- D --

degree | Indegree, outdegree and degree of the vertices
dgr | Indegree, outdegree and degree of the vertices
diag_expand | Creates a square matrix suitable for spatial statistics models.
diag_expand.array | Creates a square matrix suitable for spatial statistics models.
diag_expand.dgCMatrix | Creates a square matrix suitable for spatial statistics models.
diag_expand.diffnet | Creates a square matrix suitable for spatial statistics models.
diag_expand.list | Creates a square matrix suitable for spatial statistics models.
diag_expand.matrix | Creates a square matrix suitable for spatial statistics models.
diffmap | Creates a heatmap based on a graph layout and a vertex attribute
diffnet | Creates a 'diffnet' class object
diffnet-arithmetic | 'diffnet' Arithmetic and Logical Operators
diffnet-class | Creates a 'diffnet' class object
diffnet.attrs | Creates a 'diffnet' class object
diffnet.attrs<- | Creates a 'diffnet' class object
diffnet.toa | Creates a 'diffnet' class object
diffnet.toa<- | Creates a 'diffnet' class object
diffnetLapply | Creates a 'diffnet' class object
diffnet_check_attr_class | Infer whether 'value' is dynamic or static.
diffnet_index | Indexing diffnet objects (on development)
diffnet_to_igraph | Coercion between graph classes
diffnet_to_network | Coercion between 'diffnet', 'network' and 'networkDynamic'
diffnet_to_networkDynamic | Coercion between 'diffnet', 'network' and 'networkDynamic'
diffusion-data | Diffusion Network Datasets
diffusionMap | Creates a heatmap based on a graph layout and a vertex attribute
diffusionMap.default | Creates a heatmap based on a graph layout and a vertex attribute
diffusionMap.diffnet | Creates a heatmap based on a graph layout and a vertex attribute
dim.diffnet | Creates a 'diffnet' class object
dimnames.diffnet | Creates a 'diffnet' class object
drawColorKey | Draw a color key in the current device
drop_isolated | Find and remove isolated vertices

## -- E --

edgelist_to_adjmat | Conversion between adjacency matrix and edgelist
edgelist_to_diffnet | Convert survey-like data and edgelists to a 'diffnet' object
edges_coords | Compute ego/alter edge coordinates considering alter's size and aspect ratio
egonet_attrs | Retrieve alter's attributes (network effects)
ego_variance | Computes variance of Y at ego level
exposure | Ego exposure

## -- F --

fakeDynEdgelist | Fake dynamic edgelist
fakeEdgelist | Fake static edgelist
fakesurvey | Fake survey data
fakesurveyDyn | Fake longitudinal survey data
fitbass | Bass Model
fitbass.default | Bass Model
fitbass.diffnet | Bass Model
ftable.diffnet_adopters | Classify adopters accordingly to Time of Adoption and Threshold levels.

## -- G --

Geodesic | Approximate Geodesic Distances
graph_power | 'diffnet' Arithmetic and Logical Operators
grid_distribution | Distribution over a grid

## -- H --

hazard_rate | Network Hazard Rate
hist.diffnet_bootnet | Network Bootstrapping
hist.diffnet_struct_test | Structure dependence test

## -- I --

igraph | Coercion between graph classes
igraph_to_diffnet | Coercion between graph classes
igraph_vertex_rescale | Rescale vertex size to be used in 'plot.igraph'.
image.diffnet_diffmap | Creates a heatmap based on a graph layout and a vertex attribute
indegree | Indegree, outdegree and degree of the vertices
infection | Susceptibility and Infection
isolated | Find and remove isolated vertices

## -- K --

kfamily | Korean Family Planning
kfamilyDiffNet | 'diffnet' version of the Korean Family Planning data

## -- L --

leader_matching | Optimal Leader/Mentor Matching

## -- M --

mahalanobis | Computes covariate distance between connected vertices
matrix_compare | Non-zero element-wise comparison between two sparse matrices
medInnovations | Medical Innovation
medInnovationsDiffNet | 'diffnet' version of the Medical Innovation data
mentor_matching | Optimal Leader/Mentor Matching
minkowski | Computes covariate distance between connected vertices
moran | Computes Moran's I correlation index

## -- N --

nedges | Count the number of vertices/edges/slices in a graph
netdiffuseR | netdiffuseR
netdiffuseR-graphs | Network data formats
netdiffuseR-options | 'netdiffuseR' default options
netmatch | Matching Estimators with Network Data
netmatch_prepare | Matching Estimators with Network Data
network | Coercion between 'diffnet', 'network' and 'networkDynamic'
networkDynamic | Coercion between 'diffnet', 'network' and 'networkDynamic'
networkDynamic_to_diffnet | Coercion between 'diffnet', 'network' and 'networkDynamic'
network_to_diffnet | Coercion between 'diffnet', 'network' and 'networkDynamic'
new_diffnet | Creates a 'diffnet' class object
nlinks | Count the number of vertices/edges/slices in a graph
nnodes | Count the number of vertices/edges/slices in a graph
nodes | Creates a 'diffnet' class object
nslices | Count the number of vertices/edges/slices in a graph
nvertices | Count the number of vertices/edges/slices in a graph
n_rewires | Structure dependence test

## -- O --

outdegree | Indegree, outdegree and degree of the vertices

## -- P --

p-norm | Computes covariate distance between connected vertices
permute_graph | Permute the values of a matrix
plot.diffnet | S3 plotting method for diffnet objects.
plot.diffnet_adopters | Classify adopters accordingly to Time of Adoption and Threshold levels.
plot.diffnet_bass | Bass Model
plot.diffnet_degSeq | Indegree, outdegree and degree of the vertices
plot.diffnet_diffmap | Creates a heatmap based on a graph layout and a vertex attribute
plot.diffnet_hr | Network Hazard Rate
plot.diffnet_mentor | Optimal Leader/Mentor Matching
plot_adopters | Visualize adopters and cumulative adopters
plot_diffnet | Plot the diffusion process
plot_diffnet.default | Plot the diffusion process
plot_diffnet.diffnet | Plot the diffusion process
plot_diffnet2 | Another way of visualizing diffusion
plot_diffnet2.default | Another way of visualizing diffusion
plot_diffnet2.diffnet | Another way of visualizing diffusion
plot_hazard | Network Hazard Rate
plot_hazarrate | Network Hazard Rate
plot_infectsuscep | Plot distribution of infect/suscep
plot_threshold | Threshold levels through time
plot_threshold.array | Threshold levels through time
plot_threshold.default | Threshold levels through time
plot_threshold.diffnet | Threshold levels through time
pretty_within | Pretty numbers within a range.
print.diffnet | Creates a 'diffnet' class object
print.diffnet_bootnet | Network Bootstrapping
print.diffnet_diffmap | Creates a heatmap based on a graph layout and a vertex attribute
print.diffnet_se | Structural Equivalence
print.diffnet_struct_test | Structure dependence test

## -- Q --

QAP | Permute the values of a matrix

## -- R --

rdiffnet | Random diffnet network
rdiffnet_multiple | Random diffnet network
read_dl | Read foreign graph formats
read_ml | Read foreign graph formats
read_net | Read foreign graph formats
read_pajek | Read foreign graph formats
read_ucinet | Reads UCINET files
read_ucinet_head | Reads UCINET files
recode | Recodes an edgelist such that ids go from 1 to n
recode.data.frame | Recodes an edgelist such that ids go from 1 to n
recode.matrix | Recodes an edgelist such that ids go from 1 to n
resample_graph | Network Bootstrapping
rescale_vertex_igraph | Rescale vertex size to be used in 'plot.igraph'.
rewire_graph | Graph rewiring algorithms
rewire_permute | Permute the values of a matrix
rewire_qap | Permute the values of a matrix
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 sequence

## -- S --

scale-free | Scale-free and Homophilic Random Networks
select_egoalter | Calculate the number of adoption changes between ego and alter.
Shortest-Path | Approximate Geodesic Distances
small-world | Watts-Strogatz model
str.diffnet | Creates a 'diffnet' class object
struct_equiv | Structural Equivalence
struct_test | Structure dependence test
struct_test_asymp | Structure dependence test
summary.diffnet | Summary of diffnet objects
summary.diffnet_adoptChanges | Calculate the number of adoption changes between ego and alter.
survey_to_diffnet | Convert survey-like data and edgelists to a 'diffnet' object
susceptibility | Susceptibility and Infection

## -- T --

t.diffnet | Creates a 'diffnet' class 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 structural zeros
transformGraphBy.dgCMatrix | Apply a function to a graph considering non-diagonal structural zeros
transformGraphBy.diffnet | Apply a function to a graph considering non-diagonal structural zeros

## -- U --

UCINET | Reads UCINET files
ucinet | Reads UCINET files

## -- V --

vertex_covariate_compare | Comparisons at dyadic level
vertex_covariate_dist | Computes covariate distance between connected vertices
vertex_mahalanobis_dist | Computes covariate distance between connected vertices
vertex_rescale_igraph | Rescale vertex size to be used in 'plot.igraph'.

## -- W --

weighted_var | Computes weighted variance
wvar | Computes weighted variance

## -- misc --

%*% | Matrix multiplication
%*%.default | Matrix multiplication
%*%.diffnet | Matrix multiplication
&.diffnet | 'diffnet' Arithmetic and Logical Operators
*.diffnet | 'diffnet' Arithmetic and Logical Operators
-.diffnet | 'diffnet' Arithmetic and Logical Operators
/.diffnet | 'diffnet' Arithmetic and Logical Operators
[.diffnet | Indexing diffnet objects (on development)
[<-.diffnet | Indexing diffnet objects (on development)
[[.diffnet | Indexing diffnet objects (on development)
[[<-.diffnet | Indexing diffnet objects (on development)
^.diffnet | 'diffnet' Arithmetic and Logical Operators
|.diffnet | 'diffnet' Arithmetic and Logical Operators