2018-04-04 George G. Vega Yon <g.vegayon@gmail.com> * src/plot.cpp: Separating edge from arrow. * R/diffnet-methods.r: Idem 2018-04-02 George G. Vega Yon <g.vegayon@gmail.com> * R/plot_diffnet2.r: Fixing bug in diffMap on plot_diffnet2. * R/rdiffnet.r: Loading netdiffuseR when using ncpus. 2018-03-26 George G. Vega Yon <g.vegayon@gmail.com> * R/formulas.r: Adding diffreg (including tests). * vignettes/*: idem * tests/*: idem 2017-10-23 George G. Vega Yon <g.vegayon@gmail.com> * R/igraph.r: Uncesary permutation + adding undirected. * R/mentor.r: Fixing bug in plotting method. Sorting was wrong. * R/*.r: Idem. 2017-10-16 George G. Vega Yon <g.vegayon@gmail.com> * R/stats.R: New argument for exposure. * : Adding new examples in vignettes. * : Getting ready for cran. 2017-10-09 George G. Vega Yon <g.vegayon@gmail.com> * R/misc.r: add_dimnames is now based on environments and more general. * R/stats.r: Cleanning code * *: Trying to pin down problem with Armadillo 0.8+. Solved. 2017-10-02 George G. Vega Yon <g.vegayon@gmail.com> * R/igraph.r: Working on function to set default plot params. * R/rdiffnet-methods.r: Cleaner code. * R/rdiffnet.r: New function rdiffnet_multiple. 2017-09-22 George G. Vega Yon <g.vegayon@gmail.com> * R/diffnet_methods.r: Keep working on consistency * R/igraph.r: New function to set defaults for any plot function. 2017-09-22 George G. Vega Yon <g.vegayon@gmail.com> * R/diffnet-methods.r: Working on plotting methods. Adding arguments consistency across the package, and fixing some bugs in plot_diffnet regarding the colors of vertices. 2017-09-20 George G. Vega Yon <g.vegayon@gmail.com> * R/misc.r: Fixed bug in compute_size. * R/diffnet-methods.r: Added title to plot_diffnet. 2017-09-18 George G. Vega Yon <g.vegayon@gmail.com> * R/diffnet-methods.r: Rewritten plot functions. * R/misc.r: New function to set size according to degree. * R/igraph.r: New set of functions and default (aesthetics). 2017-09-15 George G. Vega Yon <g.vegayon@gmail.com> * R/diffnet-methods.r: Making the coding more neat. * R/plot_diffnet2.r: Changing defaults * R/rdiffnet.r: Working on way the function is written. Also now threshold.dist can be a scalar and no diffusion can be ok as well. 2017-09-11 George G. Vega Yon <g.vegayon@gmail.com> * R/plot_diffnet2.r: Change name of the file and fixed bug in setting the color of the colorKey. * R/diffnet-methods.r: Simplifying functions. * R/misc.r: Idem. 2017-09-01 George G. Vega Yon <g.vegayon@gmail.com> * src/netdiffuser_extra.cpp: Since atan2 checks the quadrant, the angle() function is no longer needed. 2017-08-24 George G. Vega Yon <g.vegayon@gmail.com> * : Creating the configure.ac, src/Makevars.in, and cleanup files so that autoconf sets OpenMP. 2017-08-23 George G. Vega Yon <g.vegayon@gmail.com> * R/egonets.R: Working on possible bug reported by CRAN. * R/stats.R: Documentation. * src/Makevars*: Adding OpenMP support via RcppArmadillo update * src/stats.cpp: Fixing bug in vertex_covariate_distance plus making some speed fixes. * src/rgraph.cpp: More efficient rgraph_ba_cpp. 2017-07-23 George G. Vega Yon <g.vegayon@gmail.com> * : Working on making the package more light weight. * : Checking included datasets duplicated columns. * : Working on documentation 2017-07-23 George G. Vega Yon <g.vegayon@gmail.com> * src/adjmat.cpp: rewriting egonet_attrs_cpp. Now more efficient should correct errors produced on windows. * R/*: Fixing various bugs and spelling. 2017-07-17 George G. Vega Yon <g.vegayon@gmail.com> * src/adjmat.cpp: Function for computing geodesics is now more efficient by using batch constructors when updating matrices. * R/bootnet.r, R/struct_test.r: Fixing hist methods. 2017-07-16 George G. Vega Yon <g.vegayon@gmail.com> * R/rewire.r: The function rewire_graph now also allows the method QAP. 2017-07-14 George G. Vega Yon <g.vegayon@gmail.com> * src/stats.cpp: Moran's I now computing sd. * R/moran.r: Idem. * tests/testthat/test-moran.r: Idem. 2017-04-28 George G. Vega Yon <g.vegayon@gmail.com> * src/rgraph.cpp: New version of the -rgraph_er_cpp- and -rgraph_ba_cpp- function, way faster using batch insertion of arma::sp_mat. 2017-04-07 George G. Vega Yon <g.vegayon@gmail.com> * R/bass.r: Adding the bass function w/ corresponding tests and examples. 2017-03-13 George G. Vega Yon <g.vegayon@gmail.com> * R/adjmat.R: Working on doc. * R/bootnet.r: Working on hist method. * R/egonets.R: Fixing bug in matrix methods. * R/mentor.R: Fixing bug in fetching nodes labels. * R/misc.R: New function to coerce to dgCMatrix. * R/struct_test.R: Working on print and hist methods. * tests/testthat/*.r: Adding a bunch of new tests. 2017-03-01 George G. Vega Yon <g.vegayon@gmail.com> * R/struct_equiv.R: Replaced approx_geodesic * R/adjmat.R: Fixing man. * R/diffnet-methods.R: 'Bug' when calling igraph::graph_from... didn't preserved sorting of vertices. * R/igraph.R: idem. * R/mentor.r: Migrating the algorithm to its own file. * R/random_graph.R: WS now returns an adjmat with dimnames. * R/stats.R: Working on doc. * R/struct_equiv.R: Adding examples for transformGraphBy 2017-02-27 George G. Vega Yon <g.vegayon@gmail.com> * R/adjmat.R: Adding approx_geodesic. * R/diffnet-class.R: Doc approx_geodesic in summary * R/diffnet-methods.R: idem + add * R/egonet.R: Adding example with static net * R/stats.R: Adding matrix_compare and mentor_matching * src/adjmat.cpp: approx_geodesic * src/stats.cpp: matrix_compare 2016-12-14 George G. Vega Yon <g.vegayon@gmail.com> * R/misc.R: Adding new option to the drawColorKey 2016-12-08 George G. Vega Yon <g.vegayon@gmail.com> * R/netmatch.r: New set of functions for matching with networks. * R/bootnet.r: Documenting and fixing some bugs. 2016-12-07 George G. Vega Yon <g.vegayon@gmail.com> * src/netdiffuser_extra.cpp: Removed unused function. * R/bootnet.r: Adding methods for other types of graphs. * R/rewire.R: Recycling code in list vs array. * R/diffnet-methods.R: Adding new methods for -nodes-. 2016-12-06 George G. Vega Yon <g.vegayon@gmail.com> * R/bootnet.r: Still working on the BS. * src/netdiffuser_extra.*: Adding bootnet_fillself to deal with i sampled more than once. * R/struct_test.R: Fixing bug in variance calculation. 2016-12-05 George G. Vega Yon <g.vegayon@gmail.com> * bootnet.r: Implementing Snijders and Borgatti's bootstrapping on networks. 2016-11-03 George G. Vega Yon <g.vegayon@gmail.com> * README.Rmd: In mosaicplot (workhorse of plot.diffnet_adopters), the color= option wasn't coloring cell by cell. So removed example. 2016-11-02 George G. Vega Yon <g.vegayon@gmail.com> * R/stats.R: Fixed bug with NA in classify_adopters.default. * tests/testthat/test-stats.R: Adjusted expectation according to change in classify. * .travis.ci: r-devel not working. * .appveyor: r-patch not working. 2016-11-01 George G. Vega Yon <g.vegayon@gmail.com> * src/*: Re-organized functions + headers, reducing lib space. * R/*: Tweaked a couple of examples for reducing running time. * tests/testtat/*: idem. 2016-10-28 George G. Vega Yon <g.vegayon@gmail.com> * src/rewire_swap.cpp: 'Commented' alt.hexagons since the implementation is flawed. * R/rewire.R: Idem. * test/testthat/*.R: More tests. 2016-10-27 George G. Vega Yon <g.vegayon@gmail.com> * src/rgraph_ba.*: Renamed files (and header def) to fix build error. * R/diffnet-methods.R: Fixing small bugs in -.diffnet and data-checks in plot_threshold. * test/testthat/*.R: More tests. * R/stats.R: Small changes. 2016-10-26 George G. Vega Yon <g.vegayon@gmail.com> * R/*: Working with @template of roxygen2. * R/diffnet-class.R: Removing unsued code. * R/diffnet-methods: Fixing bugs in %*% and * for diffnet objs. * R/random_graph.R: Implementing Scale-free homophilic nets. * R/stats.R: Adding titles to plot.diffnet_degSeq. * R/survey_to_diffnet.R: More data pre-processing. * src/rgraph_scale_free.*: Added scale-free homophilic to rgraph_ba, and changed the name. * R/rewire.R: New functions permute_graph and rewire_qap. * man-roxygen/: Where templates live (roxygen2). * src/rgraph.cpp: permute_graph. 2016-10-18 George G. Vega Yon <g.vegayon@gmail.com> * R/diffnet-indexing.R: Fixing bug on [[<-.diffnet. * R/rewire.R: althex is currently on dev (so change when TRUE). * src/netdiffuser_extra.h: Removing unsued function. * src/rgraph_er.cpp: Removing redundant function. * R/random_graph.R: rgraph_ws uses a single cpp fun. (idem) * test/testthat/*: More tests. 2016-10-17 George G. Vega Yon <g.vegayon@gmail.com> * R/graph_data.R: Bug in ordering (now its preserved) * test/testthat/*: New select_egoalter and graph_data tests. 2016-10-13 George G. Vega Yon <g.vegayon@gmail.com> * R/diffnet-class.R: Function -diffnet.attrs<-- Defunct-ed. * R/select_egoalter.R: New summary method+fix bug with arrays. * R/struct_test.R: Working on doc. * src/struct_test.cpp: Removing unused function -hatf-. * tests/testthat/*.R: Several new tests. 2016-10-12 George G. Vega Yon <g.vegayon@gmail.com> * R/diffnet-class.R: Small bug when reading dynamic attributes. and printing bug+removing dimnames. * R/adjmat.R: no dimnames. * R/diffnet-c.R: idem. * R/diffnet-indexing.R: idem. * R/igraph.R: idem. * R/read_write_foreign.R: Working on bug with read_net (still on dev). * R/diffnet-methods.R: Bug in ^ operator. And plot_adopters returned NULL. * R/spatial.R: Fixing bugs + adding it as a function in the namespace. * tests/testthat/*.R: Adding several new tests to cover code. * R/stats.R: Rewriting functions in R. * R/stats.cpp: idem + new function mahalanobis distance. * R/rdiffnet.R: Adding default name and behavior. * src/netdiffuser_extra.cpp: Fixing bug. * src/rgraph_ba.cpp: Removing unused version of ba model. 2016-10-07 George G. Vega Yon <g.vegayon@gmail.com> * R/adjmat.R: Changing syntax. * R/graph_data.R: Working on new function to convert igraph,network, etc. to 'generic graphs' so methods in netdiffuseR work. * R/stats.R: New plot method for the output of degree seq (which is now a diffnet_degSeq, matrix class object. rm -degree_cpp- and add -.dgr-. Same with -exposure_cpp- and -.exposure-. * src/stats.cpp: See above. * src/adjmat.cpp: Fixing bug on undirected graphs. * R/diffnet-class.R: New desc meta for the class (and methods). * R/diffnet-methods.R: Idem. * R/igraph.R: Idem. 2016-10-05 George G. Vega Yon <g.vegayon@gmail.com> * R/plot_diffnet2.R: Added new options, adding sharp criter for diffmap. * R/random_graph.R: New argument for -rgraph_ba-. Now allows for !self. * R/read_write_foreign.R: New function for reading binary files from UCINET. * R/struct_test.R: Fixing bug in c. method. * src/rgraph_ba.cpp: New argument for !self. 2016-09-02 George G. Vega Yon <g.vegayon@gmail.com> * R/struct_equiv.R: New function to apply transformation to a matrix considering structural zeros -transformGraphBy-. * .travis.yml: Removing dev version from tests. 2016-08-31 George G. Vega Yon <g.vegayon@gmail.com> * src/struct_test.cpp: New function to compare vertices at dyadic level. -ego_variance-. * src/stats.cpp: Changing name of function sqdistance to quaddistance. * src/rewire_swap.cpp: Adding alternating hexagons algorithm (on dev). 2016-08-25 George G. Vega Yon <g.vegayon@gmail.com> * src/stats.cpp: New function to compare vertices at dyadic level. 2016-08-23 George G. Vega Yon <g.vegayon@gmail.com> * src/rewire_swap.cpp: New argument for assuring aperiodicity on MCMC. * R/rewire.R: Documenting new argument. 2016-08-19 George G. Vega Yon <g.vegayon@gmail.com> * src/netdiffuser_extra.cpp: Functions for dyadic comparison. * src/stats.cpp: Changing definition of vertex_compare. * R/struct_test.R: Working on doc + adding some debugs. 2016-08-12 George G. Vega Yon <g.vegayon@gmail.com> * R/diffnet-methods.R: Fixing bug in plot_diffnet on the range of the plot. * R/struct_test.R: New function for exact test (experimental). 2016-08-02 George G. Vega Yon <g.vegayon@gmail.com> * src/struct_test.cpp: Adding new functions for computing exact text. * R/struct_test.R: Adding new functions for computing exact text. 2016-08-02 George G. Vega Yon <g.vegayon@gmail.com> * src/netdiffuser_extra.cpp: Adding internal function to compute distances. This is used in the new version of rgraph_ba. * src/rgraph_ba.cpp: Working on new algorithm for scale-free + covariates. 2016-08-01 George G. Vega Yon <g.vegayon@gmail.com> * R/rewire.R: Changing default number in `n_rewires` from 100 to 20 + adding explaination. 2016-07-23 George G. Vega Yon <g.vegayon@gmail.com> * R/moran.R: Adding variance of Moran's I (not user visible yet) * R/diffnet-methods.R: idem. 2016-07-07 George G. Vega Yon <g.vegayon@gmail.com> * R/diffnet-indexing.R: Adding method for [[.diffnet <- NULL * tests/testthat/*: Adding more tests + small changes to reduce time. 2016-07-06 George G. Vega Yon <g.vegayon@gmail.com> * R/struc_test.R: Changing defaults in n_rewires. 2016-06-26 George G. Vega Yon <g.vegayon@gmail.com> * R/egonets.R: Fixing small bug on the matrix methods * R/diffnet-methods.R: No actual significant changes * R/plot_diffnet2.R: Fixing small bug and improving doc. 2016-06-21 George G. Vega Yon <g.vegayon@gmail.com> * R/misc.R: Changing defaults and adding examples * R/struct_test.R: Adding example with c.diffnet_struct_test * DESCRIPTION: Getting ready for CRAN 2016-06-20 George G. Vega Yon <g.vegayon@gmail.com> * R/struct_test.R: Changes in hist.diffnet_struc_test method. * R/diffnet-methods.R: Extending the %*% method. * R/stats.R: New argument for threshold. 2016-06-17 George G. Vega Yon <g.vegayon@gmail.com> * R/plot_diffnet2.R: Adding new arguments to deal with new function to rescale the size of vertices. * R/misc.R: Adding new function to rescale vertex size. * R/diffnet-methods.R: Update to plot_diffnet. 2016-06-13 George G. Vega Yon <g.vegayon@gmail.com> * R/diffnet-methods.R: Fixing warnings from R CMD check. * R/imports.R: idem. * R/misc.R: idem. * R/plot_diffnet2.R: idem * R/stats.R: idem. * R/struct_test.R: idem. 2016-06-10 George G. Vega Yon <g.vegayon@gmail.com> * ChangeLog: Sarting ChangeLog * R/adjmat.R: Adding new function `simmelian_mat` * R/diffnet-methods.R: New methods str, dimnames, t, &, |, dim, %*%. * R/egonets.R: Adding new arg. * R/misc.R: New function to create a color key. * R/plot_diffnet2.R: Fixing small bugs and improving doc. * R/rewire.R: Fixing bug. * R/stats.R: New function to classify adopters. * R/struct_test.R: New method c and helper function. * man/*: Adding documentation.