roxygen2
issue #1491Solved 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.)
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).
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.