-
Notifications
You must be signed in to change notification settings - Fork 21
/
ChangeLog
393 lines (295 loc) · 14.5 KB
/
ChangeLog
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
2018-04-04 George G. Vega Yon <[email protected]>
* src/plot.cpp: Separating edge from arrow.
* R/diffnet-methods.r: Idem
2018-04-02 George G. Vega Yon <[email protected]>
* 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 <[email protected]>
* R/formulas.r: Adding diffreg (including tests).
* vignettes/*: idem
* tests/*: idem
2017-10-23 George G. Vega Yon <[email protected]>
* 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 <[email protected]>
* R/stats.R: New argument for exposure.
* : Adding new examples in vignettes.
* : Getting ready for cran.
2017-10-09 George G. Vega Yon <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* R/misc.r: Fixed bug in compute_size.
* R/diffnet-methods.r: Added title to plot_diffnet.
2017-09-18 George G. Vega Yon <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* src/netdiffuser_extra.cpp: Since atan2 checks the quadrant,
the angle() function is no longer needed.
2017-08-24 George G. Vega Yon <[email protected]>
* : Creating the configure.ac, src/Makevars.in, and cleanup
files so that autoconf sets OpenMP.
2017-08-23 George G. Vega Yon <[email protected]>
* 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 <[email protected]>
* : Working on making the package more light weight.
* : Checking included datasets duplicated columns.
* : Working on documentation
2017-07-23 George G. Vega Yon <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* R/rewire.r: The function rewire_graph now also allows the method
QAP.
2017-07-14 George G. Vega Yon <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* R/bass.r: Adding the bass function w/ corresponding
tests and examples.
2017-03-13 George G. Vega Yon <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* R/misc.R: Adding new option to the drawColorKey
2016-12-08 George G. Vega Yon <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* bootnet.r: Implementing Snijders and Borgatti's bootstrapping
on networks.
2016-11-03 George G. Vega Yon <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* src/stats.cpp: New function to compare vertices at dyadic level.
2016-08-23 George G. Vega Yon <[email protected]>
* src/rewire_swap.cpp: New argument for assuring aperiodicity on MCMC.
* R/rewire.R: Documenting new argument.
2016-08-19 George G. Vega Yon <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* R/rewire.R: Changing default number in `n_rewires` from 100 to 20 + adding
explaination.
2016-07-23 George G. Vega Yon <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* R/struc_test.R: Changing defaults in n_rewires.
2016-06-26 George G. Vega Yon <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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.