-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathChangeLog
569 lines (353 loc) · 13.9 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
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
Version 4.2.6
* Fix tests on CRAN for timezone
Version 4.2.5
* Fix no remap issue
Version 4.2.4
* Change from sp::identicalCRS to terra::same.crs to prepare for future raster release
Version 4.2.2
* Resolve check errors on macos (skip suncalc for timezone bug)
Version 4.2.0
* getDataRepositoryData is Defunct as movebank changed setup
* Import of rgdal droped
* In preparation for rgdal being retired spTransform now uses sf this might have consequencs for the consistency of attributes of for example bbox
* Proper forwarding of arguments in coridor function when called on stack (#77)
* Remove dependency on `maptools` by adopting some functions and working with `suncalc` in vignette
Version 4.1.12
* Rebuild example data to work with new raster package
Version 4.1.10
* Fix cran errors in example
* Integrate download suggestions
* Style package
* Fix stacking timestamps in unused records
* Fix getMovebankLocationData for multiple sensors
Version 4.1.8
* Check namespace requirements in examples and tests
* Clarify examples for emd and angles
* Change class inheritance checks
Version 4.1.6
* Fix distance error
* use licence_terms in download
* Update vignette
* Improved error reporting long url
* Fixed bug in brownian.bridge.dyn where window.size was not used
Version 4.0.4
* Changes to movestack test as R changes behaviour
Version 4.0.2
* fix small issues with cran checks
Version 4.0.0
* updates to account for changes in rgdal and sp
Version 3.3.0
* Updated and completed both vignettes
* move function now accepts movement objects from the libraries ctmm, bcpa, EMbC and a data.frame object
* Added getMovebankLocationData function to download location data as a data.frame from Movebank
Version 3.2.0
* Use updated movebank api for downloading data, now depend on visible column. This might lead to small changes in the downloaded dataset if specific outlier combinations are used.
* Added getMovebankReferenceTable function to download reference data from movebank study.
* Added namesIndiv to get names of individuals in a move/moveStack object.
* Now getMovebankData includes user defined tag number information.
Version 3.1.0
* Add track thining
* Maintenance release with bug fixes to solve some issues
Version 3.0.2
* Maintenance release to solve some issues with testing
Version 3.0.0
* Remove constraint to have no unused timestamps at observed timestamps
* Add download function for movebank data repository
* Now getMovebankData gets records per individual and not deployment (make sure code is adjusted where needed)
* Now the move function does not create or remove extra columns
* moveStack can stack multiple animals directly and can force a timestamp
* getMovebankData now includes license terms, study name and citation (reported by Scott LaPoint)
* Implemented variance methods for MoveStacks
* Various small updates in error reporting
* Implemented download of acc and other extra movebank data
Version 2.1.0
* Added earth movers distance functions
* Added replacement methods for burstIds
* Added functionality to change burstStacks to Udstacks
Version 2.0.0
* Increases speed of the Brownian bridge calculation by not
calculation for the whole grid any more (no need any more to minimize
raster size)
* Use httr for downloads
2015-10-22 bart
* Test ltraj move function a bit
2015-10-20 bart
* dont require package in test
* Documentation update
2015-10-16 bart
* typo
* Switch download to httr away from rcurl
2015-10-15 bart
* Make sure ltraj is recoginized as a class
* Fix test so they are neatly implemented but need new testthat so
currently skipped
* Fix documentation
* Allow non verbose brownian bridge
2015-10-14 bart
* Make move function work for ltraj objects and fix split for ud
stacks
2015-09-16 bart
* Seg length was accidentally calculating a square matrix, further
small fixes and updates to examples and tests
* Seglength calculated a square matrix for stacks which was not
intended
* Moved all example data to data folder and adjusted examples and
tests accordingly, also update plotBurst for multispatial points
2015-09-15 bart
* adding data in the data folder
* Make idData deal with sp MultiPoints
* update checks and the spatial lines function which was broken
* Added turnAngleGc for stacks and some checks for turnAngleGc
2015-09-03 bart
* Update make procedures
* reformat and generalized test
2015-07-29 bart
* Update checking of unused records stack and subsetting function
2015-07-15 bart
* Fix reading of envdata files (related to R version 3.1.0 that had
an other type convert)
2015-07-08 bart
* Update help of download functions
* clarified removeduplicatedtimestamps option for getmovebankdata
2015-07-07 bart
* the time.lag function is removed
2015-07-06 bart
* Updated the test to present the new distance calculations which
are on an ellipsoid
2015-06-29 bart
* import inorder to meet devel checks
* lines for burst also allow to color segments
* fix test for citation and lineMidpoints, the last now returns
numberd names in the coordinates
* Removed warnings due to duplicated names in hrBootstrap sampling
due to tracking of coordinates names in spatial opject
* Added function burstId to retrieve burst Ids
2015-06-23 bart
* change hrBootstrap from print to message
2015-05-27 bart
* Some updates to corridor function when no corridor points are
found
2015-04-15 bart
* Update tests
2015-04-14 bart
* Additional tests
* fix bug on windows
* Also allow missing projection in move function
* Updated move function to accomodate character and numeric input
* Removing most warning messages from tests
* Move doesnt assume the utm column in movebank output any more
* Move all test to testthat and add some
2015-03-23 bart
* Specify ellipsoid everywhere to accomodate new proj library (4.9)
2015-03-19 bart
* Deprecated time.lag function please use timeLag now
2015-03-13 bart
* Some small updates to Description file
* Addressing some issues with notes for new R versions, to prepare
for new release. Improved error reporting for brownian bridge
function. Prepare for new movebank download. Preparing tests for
SP keeping rownames.
2015-01-22 bart
* moved seglength test
2015-01-16 bart
* Adhere to new namespace checks
* Made character string or vector of location errors worki on
stacks thanks to reporting of JW. Beeman
2015-01-07 bart
2014-11-17 bart
* Add function to find number of individuals
2014-10-06 bart
* More clear error message BGBvar fun
2014-08-18 bart
* improved error reporting for dbbmm
2014-08-04 bart
* Update documentation
* Add functions for extracting sensor data and trackId from
unUsedStack
* Updates the removeDuplicatedTimestamps to also remove records
that are in the real records from the unUsedRecords
2014-07-22 bart
* compressed move.RData
2014-07-02 bart
* Make sure locations are read as numeric even if it has many
decimals, this accomodates a change in R 3.1.0
2014-06-11 bart
2014-06-10 bart
* define a split method for a UDStack and make the number of
contour plots square
* improve error reporting when object is smaller than the window
size
2014-05-21 bart
2014-04-25 bart
* Changes for new release, the release adds the bivariate gaussian
bridges, brownian bridges per burst and many small changes
2014-04-24 bart
* fix getMotion variance
* fix to minimal margins brownian bridge dyn stack
2014-04-23 bart
* start adding getMotionVariance
* match ud calculation between dbgb and dbbmm
2014-04-16 bart
* update email adres
2014-04-15 bart
* make test more relyable
* fix documentation
* speed up dynBGB example
* Check for error with projections for bridge calculations
* move tests brownian bridge to testthat
2014-04-14 bart
2014-04-10 bart
* small cleanup
2014-04-08 bart
* Fix bug in identifying unique columns in idData when stacking
move objects, reported by Stef Sijben
2014-04-04 bart
* remove unused variables for window calculation
2014-04-03 bart
* Make it work with new sp where there is stronger checking in the
CRS function
2014-03-04 bart
* Updating test improving speed of examples
2014-02-26 bart
* introducing testthat
2014-02-25 bart
* Update to documentation and testing of dBGB
2014-02-21 bart
* Start with including BGB functions in move
* use n.locs in brownianbridgedyn
2014-01-29 bart
* bug in line mid points causing wrong plot in plotBursts
2014-01-24 bart
* Fix error to movestack introduced in last change. Make dependency
to new geosphere for right distRhumb function
2014-01-20 bart
* Switch to usage of validNames in raster (adds dependency on
recent raster version)
* added bursted dbbmm tests and speeded up some examples
* adding initial documentation for interpolation and bursted dbbmm
* Fixes to bursted dBBMM
* functions for dealing with dBMvarianceBurst objects
* Added linear time interpolation function
* added bursted brownian bridges
2013-10-21 bart
2013-10-17 bart
* shortend some examples and fixed order problem when adding
columns in moveStack
* Fixes to movestack to ensure orderd unused records, fixes to the
import of unused records in the web import
2013-10-07 bart
* some fixes for stacking unused records
2013-09-17 bart
* make equal proj return true if none is set
2013-09-03 bart
* Removed extra imports that were not needed
2013-09-02 bart
* Added function trackId for returning the id of individuals in a
stack. Made the [[ subset function return a stack for multiple
individuals and made it work for ligics and numbers. Also ensure
order of factor levels is same as order of individuals. Use rbind
spatial points in moveStack for consistency in column names
* Made examples match equal projection changes
2013-08-26 bart
* Change the equal projection function, it did not work on objects
with long projection strings it is now based on identicalCRS from
the SP package
2013-08-19 bart
* fixed various bugs noticed durring the animove course, speed
summary (Runit added), double usage of spTransform
2013-08-01 bart
* require newer version of R due to presence of paste0
2013-07-23 bart
* Decreased size corridor example
* small typo
* Limit some move checks, to occasions were only sed and zcat work
2013-07-22 bart
* Cleaning up the svn & making subset work for extracting
individuals from a stack where none used sensors are present in
the factor levels
* Resolve two notes in Rdevel about line length in manuals and
inst/doc vs vignette directory
* Make vignettes indepenent of stamen servers and prepare for
release
2013-07-09 bart
* added checks for the move function and updated the documentation
accordingly
2013-07-08 bart
* There have been updates to the import function that allow to
remove duplicated timestamps. The move function now accepts text
connections and zip files from the annotation tool. There was
also a bug fix to getMovebankData fixed by ordering the idData
dataframe
* fix to documentation of corridor
2013-07-02 bart
* update citation in coridor documentation
* made searchMovebankStudies return a character vector and
specified it in the manual. Also clarified an error message in
brownian bridge dyn
2013-06-26 bart
* Update to some documentation. Some extra tests. Fix when multiple
sensors are imported through the web interface (reported by B
Carlson)
2013-06-24 bart
2013-06-21 bart
* new optimization for unique per id given that the previous would
fail with repeated values in different individuals
* speed up in test for idData in .move
2013-06-11 bart
* Bug fixed when no variance estimate is present for segment of
interest reported by: Alexandra Bell
2013-06-04 bart
* Updated documentation \n change printing of computational size to
message \n reduced the number of installed datasets to also speed
up things
2013-06-03 bart
* added documentation for idData\n added some test for attached
data and idData\n modified split functions for code reuse\n
update documentation for download functions
2013-05-29 bart
* further simplification of web import so getMovebank does not
convert characters anymore. Also fix for making data frame with
difftime object in the idData
* More improvements to web import making things more straight
forward.
2013-05-28 bart
* make burst return the burst if no factor is supplied
2013-05-27 bart
* subset for columns with character
2013-05-24 bart
* Fixes to the web import when haveing not a 1:1 relation between
sensors, individuals & when there are indiv without data also
drop sensor levels in unUsed
2013-05-22 bart
* Make sure that subseting a movestack doesnt screw up order
* ensure order in idData is the same as order in trackId also
ensure this is represented in color usage in the plot
2013-05-21 bart
* let move function work if a movebank file only has unused records
for individuals
* restricted line ploting to individuals with 2 or more datapoints
2013-05-20 bart
* added export of id data when converting to dataframe
function do access and modify the iddata + some small tests
documents asp arugment for plot
2013-05-16 bart
* ensure aspect ratio for plots
2013-05-08 bart
2013-04-29 bart
* Improved error reporting when movebank is down for maintainance
2013-04-23 bart
* Suggest solution in error for UDs not summing to one
2013-04-22 bart
* fix to accomodate new rgdal
2013-04-19 bart
* movebank files now read with strings as factors
2013-04-12 bart
2013-04-11 bart
* add spatialLines
2013-04-10 bart
* speed up corridor example
* updated checks for R 3.1.0
2013-04-08 bart
2013-04-05 bart
* fix for web import in case of numeric indiviual names
2013-04-04 bart