- Adressing
`roxygen2`

issue #1491

Solved warning and errors reported by CRAN before the package was archived.

New S3 generic functions

`is_self`

,`is_multiple`

,`is_valued`

, and`is_undirected`

allow querying graph information for some methods.Fixed bug in

`diag_expand`

. Graphs with self ties were not transformed correctly (diagonals were excluded.)

- Replaced
`getMethod("t"...)`

by`t`

responding to changes in the`Matrix`

package.

netdiffuseR has now a logo!

Making updates after changes in knitr and Matrix.

Fixing a new issue regarding structural equivalence calculation. In the new version, the function has been fully ported to R, which should avoid problems related to the C++ code.

As documented,

`struct_equiv`

now returns he euclidean distance matrix (it was not doing that).

- Getting netdiffuseR back to CRAN. We have fixed issues that arise from the next big CRAN release, in particular, matrices are now arrays. That was creating issues throughout the package (now fixed).

- Repaired broken link in bootnet.

- This version has no user level visible changes.

Changing

`PI`

macros in C++ code as requested by RcppCore.Setting 3.5 seed version for tests so that test won’t break following message from CRAN.

`diffreg`

provides a wrapper of`glm`

to run lagged regression models.Default colors for

`plot_diffnet2`

,`plot_infectsucept`

, and others are now selected from the`viridis`

R package, which provides perceptually uniform and colorblind proof colors.

`plot_diffnet2`

now has the correct scaling in nodes positions.`rdiffnet_multiple`

calls`library(netdiffuseR)`

when using multicore.

`arrow.width`

in`plot_threshold.default`

now set to be equal to`nslices(graph)/80`

.`curved`

option passed to`plot_._threshold.default`

.The c++ function

`edges_arrow`

now returns two different elements (the edge, and the arrow).

`rdiffnet`

now allows passing scalars for`threshold.dist`

, more over, the user can also ask the function to just warn when there is no diffusion instead of returning with error.`plot.diffnet`

,`plot_diffnet`

,`plot.diffnet_mentor`

, and`plot_diffnet2`

use igraph for plotting. Also, users can now pass “degree” for -vertex.size- (vertex.cex not used anymore), allowing to “automatically” scale vertices by (in/out/.)degree. Also, plotting arguments like vertex.* or edge.* are standarized so these match igraph.`plot_diffnet`

has a new parameter:`background`

.`rdiffnet_multiple`

, a wrapper of`rdiffnet`

, allows performing simulations studies by running simulating multiple diffusion networks using`rdiffnet`

.`exposure`

has a new parameter:`lags`

. By default lags = 0, returns a lagged exposure matrix.

`igraph_to_diffnet`

was failing with the graph had no weights.`drop_isolated`

was not behaving well for diffnet objects.`vertex_covariate_dist`

was incorrectly specified. Only the default p=2 were OK. Now fixed and the tests/ folder includes a tests on this.`plot_diffnet2`

was not passing`color.ramp`

to`drawColorKey`

. Now fixed.`plot.diffnet_mentor`

had a bug. Uncesary permutation of vertices was done, but it actually had no visible effect. Similar problem was corrected in`diffnet_to_igraph`

, and other plot methods using igraph for plotting.

Replacing some C++ functions by R functions in cases in which there was no decrease in performance.

`plot_diffnet`

function now has smaller margins, so looks more appealing.New examples in vignettes “netdiffuseR showcase: Medical Innovations”, and “Simulating diffusion networks: Using the

`rdiffnet`

function”.

`network_to_diffnet`

,`diffnet_to_network`

coercion between diffnet and network objects.`networkDynamic_to_diffnet`

,`diffnet_to_networkDynamc`

coercion between diffnet and networkDynamic objects.

`new_diffnet`

and`as_diffnet`

now receive static networks as well.

`diffnet_to_igraph`

was copying over a single adjacency matrix, which did a difference in dynamic networks.`diffnet_to_igraph`

was not considering loops correctly.In unexpected situations

`egonet_attrs`

was crashing.

`bootnet`

implements network bootstrapping based on Snijders and Borgatti (1999)`mentor_matching`

implements Valente and Davis (1999) Mentor matching algorithm. including a plot method.`approx_geodesic`

an alternative to`igraph::distances`

and`sna::geodist`

. computes geodesics up to a certain number of steps and returns a sparse matrix.`matrix_compare`

Efficiently compares two sparse matrices looking only at the valued cells.`as_dgCMatrix`

Coerce matrix-like objects into dgCMatrix objects (sparse matrices from the`Matrix`

package).`fitbass`

Fits the Bass Diffusion Model to an observed vector of cumulative adopters. The estimation is done via`stats::nls`

.`netmatch`

and`netmatch_prepare`

(on development) implement matching estimators with network data.

`dgr`

returned with error when`self == TRUE`

In some calls to

`igraph::graph_from_adj...`

sorting of vertices was not preserved.The

`matrix`

method in`egonet_attrs`

was passing a list of vertices instead of the attributes. Fixed.`transformGraphBy`

was returning with error when the time periods ranged other than 1, 2, …

`rgraph_er`

is now significantly faster (orders of magnitude compare to previous versions).`rgraph_ba`

is faster too.`moran`

now returns the sd, expected and p-value.`exposure`

now receives static graphs in`alt.graph`

with a warning.`rewire_graph`

now also uses QAP. This affects directly to`structu_test`

.

The title of the package is now

*Analysis of Diffusion and Contagion Processes on Networks*.The function

`struct_test`

now allows other types of graphs. Before it only supported`diffnet`

objects.The function

`rewire_graph`

gains a new argument for the algorithm “swap”. Now to ensure aperiodicity in MCMC a chance of skiping a rewire has been included.The function

`n_rewires`

now has a default of 20 (before it was 100). This is based on Ray et al (2012) (more details in the manual).The function

`rgraph_ba`

gains a new argument,`self=TRUE`

. By default behaves as before following Bollobas, but now can deviate to generate graphs with no autolinks.In

`rgraph_ba`

, the argument`eta`

allows implementing De Almeida et al. (2013) Scale-free homophilic networks.The functions

`exposure`

and`dgr`

are now pure R code (C++ functions were replace since there were no significant speed gains).`diffnet`

class objects now have two new meta-values: name and behavior.Elements -graph-, -toa-, -adopt- and -cumadopt- in

`diffnet`

class objects have lost their dimnames (more efficient storage).`classify_adopters`

now always includes Non-Adopters.

`vertex_covariate_dist`

computes distances between vertices using both the graph and a matrix of length nxK.`vertex_mahalanobis_dist`

computes mahalanobis distance between vertices (as above).`struct_test_asymp`

an asymptotic approximation of`struct_test`

(not recomended).`ego_variance`

computes a pseudo variance at the ego level (aux function for`struct_test`

).`transformGraphBy`

applies a function that transforms a graph considering structural zeros given by groups. Similar to the idea of the -by- option in`struct_equiv`

.`read_ucinet`

read UCINET binary files (both header and graph file). Still work in progress.`plot.diffnet_degSeq`

method allows visualizing degree sequence as log-log plots (default).`diag_expand`

creates a single adjacency matrix from a dynamic graph.`summary.diffnet_adoptChange`

method generates a summary table of the df generated by`select_egoalter`

.`permute_graph`

permutes the values of an adjacency matrix (Conditional Uniform Graph).`rewire_qap`

generates isomorphic graphs by “changing the labels”.

`^.diffnet`

method was rasing to +1 power, e.g.`diffnet^2`

was actually`diffnet^3`

.`/.diffnet`

was not working.`plot_diffnet`

was computing the coordinates of the cells wrongly. Most of the time causing adding figures outside of the plotting area.The

`c.diffnet_struct_test`

method was not updating the`p.value`

.The function

`edgelist_to_adjmat`

was not processing correctly undirected graphs when the edgelist represented a lower triangular matrix.The function

`survey_to_diffnet`

had an issue processin dyn graph attrs returning errors. Now fixed.The function

`select_egoalter`

returned error when`graph`

was an array.The method

`[[<-.diffnet`

failed when replacing a dynamic attribute with a`NULL`

value (e.g.`dn[["my_dyn_att"]] <- NULL`

).

Fixed bug in

`struct_equiv`

: When`groupvar`

was a list (dynamic attr), the function returned error.Fixed bug in

`rewire_graph.array`

: Returned error when`algorithm="swap"`

Fixed bug in

`rewire_graph`

: The option`copy.first`

was not been applied correctly.In

`hist.diffnet_struct_test`

:`...`

now passed to`hist.default`

.Fixed bug on

`egonet_attrs`

: The matrix method was returning with error.

`plot_infectsuscept`

includes 2D kernel smoother via`MASS::kde2d`

.`infection`

,`susceptibility`

and`threshold`

now report`NA`

for non-adopters or excluded variables.`egonets_attrs`

now has new argument:`self.attrs`

allows including ego’s attributes as part of the outcome so it can be used by the user.`plot_diffnet`

now uses`igraph::plot.igraph`

for plotting instead`threshold`

gains a new argument:`lags`

now users can define threshold as exposure`lags`

time periods prior to the time of adoption. By default is 0 so its exposure at the time of adoption.

New method

`c.diffnet_struct_test`

: A wrapper of`boot:::c.boot`

.`diffusionMap`

computes the required matrix to be used with`image`

-like functions mapping a vertex covariate given a graph structure.`n_rewires`

: computes a suggested number of rewires per step in order to attain unbiased graph samples.`diffnetLapply`

: Apply throught periods on diffnet objects.Several new methods for the class

`diffnet`

. Now users can apply`str`

,`dimnames`

(so`colnames`

and`rownames`

),`t`

,`&`

,`|`

,`dim`

and`%*%`

.`drawColorKey`

: Handy function to draw a color key in the current plot.`classify_adopters`

: As in Valente (1995), depending on time of adoption, adopters are classified as early adopters, early majority, late majority, and laggards. The function introduces a new class and has methods for`ftable`

and`plot`

.`rescale_vertex_igraph`

: Helper function to fix the size of vertex when calling`plot.igraph`

so that the size is proportional to the x-axis.

Bug fixed on

`edgelist_to_adjmat`

: Counting number of vertices is now done right after`recode`

. (Reported by Tom)Fixed bug in

`diffnet.attrs(..., as.df=TRUE)`

. ids were wrongly retrieved.Fixed bugs for

`rgraph_ba_cpp`

: Degree of new vertices was not changing apropiately. This only was an issue when`m>1`

.Fixed bugs for the

`as_diffnet`

method for arrays.Fixed bugs in

`rewire_graph`

. Indexing of the jth component (when rewiring) was not been made correctly (now it does). Also, when rewiring, the new endpoints were truncated to n-1 (now fixed).Fixed bugs for

`as_diffnet`

: When a dynamic graph was passed with slices names different from the time periods, the slices names were kept. Now these are replaced by`meta$pers`

.

Support for

`int64_t`

in`RcppArmadillo`

now allows for creating/reading adjacency matrices with more than 4 billion elements (big graphs).In

`edgelist_to_adjmat`

`use.incomplete`

has been replaced by`keep.isolated`

which makes more sense for naming. Incomplete cases on`times`

or`weights`

are still ignored (as these cannot be processed by the c++ ‘engine’). (Reported by Tom)In

`edgelist_to_adjmat`

`times`

has been replaced by`t0`

and`t1`

. So now the user can import graphs with spells.Added new elements to the

`diffnet_struct_test`

class:`p.value`

,`t0`

,`mean_t`

, and`R`

. All these were available before either to be computed or retrieved from the`boot`

list at the class.New argument for

`threshold`

. Now, by default, threshold levels are not computed for adopters in the first time period as this can be a biased estimate. If the user wants to compute such, he/she can set`include_censored=TRUE`

.Attributes in diffnet objects are now stored as data frames (instead of matrices). This affects the function

`diffnet.attrs`

, and`egonet_attrs`

as these use attributes directly. (Requested by Tom)New features for the

`rewire_graph`

function. In particular,`p`

can now be a vector of length`T`

, so each slice can have different rewiring prob., and the new option`copy.first`

which allows to recycle the first rewired slice (see details).New features for the

`exposure`

function. When`graph`

is of class diffnet, the function accepts`attrs`

equal to the name of some the graph’s attributes. Also,`alt.graph`

can be specified as`se`

, which will be replaced by the inverse of the structural equivalence. When`valued=FALSE`

the function will switch it to`TRUE`

and warn the user.New argument for

`struct_equiv`

and`exposure`

,`groupvar`

. This new option provides a convenient way of calculating structural equivalence and exposure clusterized by group. Specially useful when there are different communities in a graph. See examples in the manual.`as_diffnet`

now has an internal function,`check_as_diffnet_attrs`

, to check input attributes dimensions and coerce them into proper class/structure. Valid attributes are now documented in the function’s manual.New arguments for

`edges_coords`

:`dev`

and`ran`

allow including device + margins aspec ratio and plotting area y/x limits for improved aspect ratio computation.New internal function

`edges_arrow`

: Computes the coordinates of a 4 points polygon allowing to draw pretty arrows considering aspec ratio of device, margins and y/x.Geodesic distances are now computed using

`igraph::distances`

instead of`sna::geodist`

as it is more flexible and faster.New arguments for

`plot_threshold`

:`vertex.sides`

,`vertex.lab.cex`

,`vertex.lab.adj`

,`vertex.lab.col`

,`vertex.rot`

,`jitter.factor`

, and`jitter.amount`

to give more control.New internal function

`vertex_coords`

: Creates polygons of any given number of sides considering aspec ratio of both x/y and device.New features for

`rdiffnet`

.`seed.graph`

can be either a function that generates a random graph, a character string (as before) indicating the class of graph to generate, or any other class of graph (either static or dynamic) as specified in`netdiffuseR-graphs`

.`seed.nodes`

can now be a vector with indices pointing to the initial adopters.The rewiring algorithm for

`rgraph_ws`

has been replaced with a`rewire_ws`

which has been implemented as it was presented in Watts and Strogatz (1998).

New function:

`survey_to_diffnet`

. This function allows importing network nomination data (in survey fashion) of both types, cross-section and panel formats (static network only varying adoption, or dynamic network varying attributes and network structure simultaneously).New function:

`edgelist_to_diffnet`

. Similar to`survey_to_diffnet`

, this function reads diffusion networks from an adjacency matrix and a vertex attributes data frame. Both the attributes and the edgelist can be static or dynamic.New method:

`as.array.diffnet`

.New functions:

`read_pajek`

and`read_ucinet`

. Still on development.New functions:

`nvertices`

and`nedges`

return the number of vertices and edges that a graph has. This can be applied to any class of graph accepted by the package.New indexing methods via

`[[.diffnet`

,`[[<-.diffnet`

, for network attributes and`[.diffnet`

and`[<-.diffnet`

for adjacency matrix. The function`diffnet.attrs<-`

will be deprecated for the next CRAN release. The function`diffnet.subset.slices`

is now not exported (internal use), so the user needs to use the`[.diffnet`

method instead.New concatenating method

`c.diffnet`

for diffnet objects. This method allows ‘adding up’ diffnet objects.New print method for

`diffnet_se`

, objects returned by`struct_equiv`

.New function

`diffnet_to_igraph`

.New rewiring algorithm,

`rewire_swap`

implements the edge-switch algorithm in an efficient way. This preserves degree sequences.

- First CRAN version.