netdiffuseR - v1.23.0 Multiadoption (CRAN)

What's Changed

• New fix by @KristinaMiljkovic in https://github.com/USCCANA/netdiffuseR/pull/38
• Refactoring exposure function by @gvegayon in https://github.com/USCCANA/netdiffuseR/pull/42
• Refactor rdiffnet by @gvegayon in https://github.com/USCCANA/netdiffuseR/pull/46
• split_behaviors - function by @aoliveram in https://github.com/USCCANA/netdiffuseR/pull/51
• Preparing for CRAN release by @gvegayon in https://github.com/USCCANA/netdiffuseR/pull/54

New Contributors

• @KristinaMiljkovic made their first contribution in https://github.com/USCCANA/netdiffuseR/pull/38
• @aoliveram made their first contribution in https://github.com/USCCANA/netdiffuseR/pull/51

Full Changelog: https://github.com/USCCANA/netdiffuseR/compare/v1.22.6...v1.23.0

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Published by gvegayon about 1 year ago

netdiffuseR - CRAN v1.22.6

Full Changelog: https://github.com/USCCANA/netdiffuseR/compare/v1.21.0...v1.22.6

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Published by gvegayon over 1 year ago

netdiffuseR - CRAN Release 1.19.0

Changes in netdiffuseR version 1.19.0 (2017-10-16)

New functions and features

• 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.

Bug fixes

• 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.

Other changes

• 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".

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Published by gvegayon over 8 years ago

netdiffuseR - CRAN Release 1.18.0

Changes in netdiffuseR version 1.18.0 (2017-07-16)

New functions

• 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.

Bugs Fixes

• 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, ...

New Features

• 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.

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Published by gvegayon almost 9 years ago

netdiffuseR - CRAN release version 1.17.0

Changes in netdiffuseR version 1.17.0 (2016-11-10)

New features and changes

• 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 Bollabas, 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.

New functions

• 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".

Bug fixes

• ^.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).

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Published by gvegayon over 9 years ago

netdiffuseR - CRAN release version 1.16.7

Bug fixes

• 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.

New features and changes

• 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 functions

• 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.

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Published by gvegayon almost 10 years ago

netdiffuseR - CRAN release v1.16.5

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Published by gvegayon about 10 years ago

netdiffuseR -

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Published by gvegayon about 10 years ago

netdiffuseR - Pre-workshop

Pre-release. Changes from CRAN to this point can be reviewed here: https://github.com/USCCANA/netdiffuseR/blob/c7c25c143a05b209bbb9b8b4c10b242179c7c79d/NEWS.md

Binary versions can be installed either within R:

``` r

install.packages("netdiffuseR_1.16.3.29.zip", repos=NULL) ```

if windows, or, if OS X:

``` r

install.packages("netdiffuseR_1.16.3.29.tgz", repos=NULL) ```

or using the command line, for the case of windows:

sh $ R CMD INSTALL netdiffuseR_1.16.3.29.zip

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Published by gvegayon about 10 years ago