1. matter
  2. NAMESPACE
Browse code

bplocal() => bpislocal(); add bptrystart() and bptrystop()

Kylie Bemis authored on 15/10/2024 03:46:22
Showing 1 changed files
NAMESPACE
History View file @ 529cd3ef6
... ... 
@@ -625,7 +625,9 @@ export("matter_defaults")
625 625
626 626 
 export(
627 627 
 	"SnowfastParam",
628 
-	"bplocal",
629 
-	"bplocalized")
628 
+	"bpislocal",
629 
+	"bplocalized",
630 
+	"bptrystart",
631 
+	"bptrystop")
630 632
631 633 
 useDynLib("matter", .registration=TRUE, .fixes="C_")
Browse code

add bplocalized() to make sure fetch() and flash() stay on 1 machine

Kylie Bemis authored on 08/10/2024 04:28:35
Showing 1 changed files
NAMESPACE
History View file @ b8414bd95
... ... 
@@ -625,6 +625,7 @@ export("matter_defaults")
625 625
626 626 
 export(
627 627 
 	"SnowfastParam",
628 
-	"bplocal")
628 
+	"bplocal",
629 
+	"bplocalized")
629 630
630 631 
 useDynLib("matter", .registration=TRUE, .fixes="C_")
Browse code

add bplocal(); minor reorganization of internal parallelization functions

Kylie Bemis authored on 08/10/2024 04:15:01
Showing 1 changed files
NAMESPACE
History View file @ 2ae1ca45d
... ... 
@@ -623,6 +623,8 @@ export(
623 623
624 624 
 export("matter_defaults")
625 625
626 
-export("SnowfastParam")
626 
+export(
627 
+	"SnowfastParam",
628 
+	"bplocal")
627 629
628 630 
 useDynLib("matter", .registration=TRUE, .fixes="C_")
Browse code

add/export matter_message()

Kylie Bemis authored on 07/09/2024 19:30:37
Showing 1 changed files
NAMESPACE
History View file @ 21da085ad
... ... 
@@ -606,6 +606,7 @@ export(
606 606
607 607 
 export(
608 608 
 	"matter_log",
609 
+	"matter_message",
609 610 
 	"matter_warn",
610 611 
 	"matter_error")
611 612
Browse code

improve RNG for non-L'Ecuyer seeds--still not parallel safe though

Kylie Bemis authored on 01/09/2024 18:15:40
Showing 1 changed files
NAMESPACE
History View file @ 0138312ce
... ... 
@@ -72,6 +72,7 @@ importFrom("stats",
72 72 
 	"resid",
73 73 
 	"rlnorm",
74 74 
 	"rnorm",
75 
+	"runif",
75 76 
 	"runmed",
76 77 
 	"smooth.spline",
77 78 
 	"spline",
Browse code

update sgmix(); deprecate sgmixn()

Kylie Bemis authored on 30/08/2024 21:24:47
Showing 1 changed files
NAMESPACE
History View file @ 245bede09
... ... 
@@ -513,9 +513,6 @@ S3method("fitted", "sgmix")
513 513 
 S3method("print", "sgmix")
514 514 
 S3method("logLik", "sgmix")
515 515
516 
-S3method("print", "sgmixn")
517 
-S3method("logLik", "sgmixn")
518 
-
519 516 
 S3method("predict", "fastmap")
520 517 
 S3method("print", "fastmap")
521 518
Browse code

v2.7.6 bump to include .rowDists() + .colDists() export

Kylie Bemis authored on 24/08/2024 21:24:53
Showing 1 changed files
NAMESPACE
History View file @ f161f3a11
... ... 
@@ -310,6 +310,21 @@ export(
310 310 
 	".rowStats",
311 311 
 	".colStats")
312 312
313 
+export(
314 
+	"inpoly",
315 
+	"rowdist",
316 
+	"coldist",
317 
+	"rowdist_at",
318 
+	"coldist_at")
319 
+
320 
+exportMethods(
321 
+	"rowDists",
322 
+	"colDists")
323 
+
324 
+export(
325 
+	".rowDists",
326 
+	".colDists")
327 
+
313 328 
 export(
314 329 
 	"chunked_vec",
315 330 
 	"chunked_mat",
... ... 
@@ -426,17 +441,6 @@ export(
426 441 
 	"estdim",
427 442 
 	"trans2d")
428 443
429 
-export(
430 
-	"inpoly",
431 
-	"rowdist",
432 
-	"coldist",
433 
-	"rowdist_at",
434 
-	"coldist_at")
435 
-
436 
-exportMethods(
437 
-	"rowDists",
438 
-	"colDists")
439 
-
440 444 
 export(
441 445 
 	"array_ind",
442 446 
 	"linear_ind")
Browse code

update fastmap() and nscentroids() to use distfun=rowDists()/colDists()

Kylie Bemis authored on 19/08/2024 22:15:04
Showing 1 changed files
NAMESPACE
History View file @ 611d003ab
... ... 
@@ -437,10 +437,6 @@ exportMethods(
437 437 
 	"rowDists",
438 438 
 	"colDists")
439 439
440 
-export(
441 
-	"rowDistFun",
442 
-	"colDistFun")
443 
-
444 440 
 export(
445 441 
 	"array_ind",
446 442 
 	"linear_ind")
Browse code

add cpals() and dpals()

Kylie Bemis authored on 14/08/2024 21:19:46
Showing 1 changed files
NAMESPACE
History View file @ 2f7183537
... ... 
@@ -463,8 +463,10 @@ export(
463 463 
 	"setRNGStream")
464 464
465 465 
 export(
466 
-	"dpal",
467 466 
 	"cpal",
467 
+	"cpals",
468 
+	"dpal",
469 
+	"dpals",
468 470 
 	"add_alpha")
469 471
470 472 
 exportMethods("prcomp")
Browse code

add memcl()

Kylie Bemis authored on 13/08/2024 17:31:06
Showing 1 changed files
NAMESPACE
History View file @ 0f33608b8
... ... 
@@ -611,6 +611,7 @@ export(
611 611
612 612 
 export(
613 613 
 	"mem",
614 
+	"memcl",
614 615 
 	"memtime",
615 616 
 	"profmem")
616 617
Browse code

minor edits

Kylie Bemis authored on 12/08/2024 05:11:45
Showing 1 changed files
NAMESPACE
History View file @ 492e0eca2
... ... 
@@ -450,11 +450,13 @@ export(
450 450 
 	"isoclos")
451 451
452 452 
 export(
453 
-	"seq_rel",
454 
-	"shingles",
455 453 
 	"pinv",
456 454 
 	"avg")
457 455
456 
+export("seq_rel")
457 
+
458 
+export("shingles")
459 
+
458 460 
 export(
459 461 
 	"RNGStreams",
460 462 
 	"getRNGStream",
Browse code

start refactoring some utility functions

Kylie Bemis authored on 12/08/2024 01:29:19
Showing 1 changed files
NAMESPACE
History View file @ 2dd88719d
... ... 
@@ -362,8 +362,9 @@ export(
362 362 
 	"warp1_dtw",
363 363 
 	"warp1_cow",
364 364 
 	"icor",
365 
-	"binvec",
365 
+	"roll",
366 366 
 	"rollvec",
367 
+	"binvec",
367 368 
 	"findbins",
368 369 
 	"downsample",
369 370 
 	"estbase_loc",
... ... 
@@ -445,13 +446,10 @@ export(
445 446 
 	"linear_ind")
446 447
447 448 
 export(
448 
-	"update_attr",
449 
-	"copy_env",
450 449 
 	"isofun",
451 450 
 	"isoclos")
452 451
453 452 
 export(
454 
-	"roll",
455 453 
 	"seq_rel",
456 454 
 	"shingles",
457 455 
 	"pinv",
... ... 
@@ -595,10 +593,10 @@ exportMethods(
595 593 
 	"plot")
596 594
597 595 
 export(
596 
+	"iQuote",
598 597 
 	"parse_formula",
599 598 
 	"eval_at",
600 
-	"eval_exprs",
601 
-	"varquote")
599 
+	"eval_exprs")
602 600
603 601 
 export(
604 602 
 	"simple_logger",
Browse code

add isofun() and isoclos()

Kylie Bemis authored on 12/08/2024 00:14:48
Showing 1 changed files
NAMESPACE
History View file @ d70b7da63
... ... 
@@ -446,7 +446,9 @@ export(
446 446
447 447 
 export(
448 448 
 	"update_attr",
449 
-	"copy_env")
449 
+	"copy_env",
450 
+	"isofun",
451 
+	"isoclos")
450 452
451 453 
 export(
452 454 
 	"roll",
... ... 
@@ -485,16 +487,16 @@ S3method("print", "kdtree")
485 487
486 488 
 export(
487 489 
 	"cv_do",
488 
-	"sgmix",
489 
-	"sgmixn",
490 
-	"fastmap",
491 490 
 	"mi_learn",
492 491 
 	"predscore",
493 492 
 	"rocscore",
493 
+	"fastmap",
494 494 
 	"nndsvd",
495 495 
 	"nnmf_als",
496 496 
 	"nnmf_mult",
497 497 
 	"nscentroids",
498 
+	"sgmix",
499 
+	"sgmixn",
498 500 
 	"prcomp_lanczos",
499 501 
 	"pls_nipals",
500 502 
 	"pls_simpls",
Browse code

add fetch() and flash()

Kylie Bemis authored on 10/08/2024 00:54:57
Showing 1 changed files
NAMESPACE
History View file @ b4dfa6458
... ... 
@@ -191,7 +191,10 @@ exportMethods(
191 191 
 	"nnzero",
192 192 
 	"rowMaj")
193 193
194 
-exportMethods("checksum")
194 
+exportMethods(
195 
+	"fetch",
196 
+	"flash",
197 
+	"checksum")
195 198
196 199 
 exportMethods(
197 200 
 	"describe_for_display",
Browse code

rename vm_realized => mem_realized()

Kylie Bemis authored on 08/08/2024 01:42:15
Showing 1 changed files
NAMESPACE
History View file @ 7e859c4ef
... ... 
@@ -339,9 +339,9 @@ S3method("format", "size_bytes")
339 339 
 export(
340 340 
 	"size_bytes",
341 341 
 	"sizeof",
342 
-	"shm_used",
343 342 
 	"vm_used",
344 
-	"vm_realized")
343 
+	"shm_used",
344 
+	"mem_realized")
345 345
346 346 
 export(
347 347 
 	"approx1",
Browse code

add as.shared() and is.shared()

Kylie Bemis authored on 07/08/2024 20:55:11
Showing 1 changed files
NAMESPACE
History View file @ 39ccdf7c5
... ... 
@@ -138,6 +138,8 @@ export(
138 138 
 	"matter",
139 139 
 	"is.matter",
140 140 
 	"as.matter",
141 
+	"is.shared",
142 
+	"as.shared",
141 143 
 	"matter_arr",
142 144 
 	"matter_mat",
143 145 
 	"matter_vec",
Browse code

added support for clusters to mem()

Kylie Bemis authored on 04/08/2024 23:06:48
Showing 1 changed files
NAMESPACE
History View file @ bd5d9cded
... ... 
@@ -98,6 +98,7 @@ importFrom("irlba",
98 98 
 importFrom("parallel",
99 99 
 	"makeCluster",
100 100 
 	"stopCluster",
101 
+	"clusterEvalQ",
101 102 
 	"nextRNGStream",
102 103 
 	"nextRNGSubStream")
103 104
Browse code

add shm_used() generic; update mem()

Kylie Bemis authored on 04/08/2024 20:30:04
Showing 1 changed files
NAMESPACE
History View file @ 4c66022cc
... ... 
@@ -336,6 +336,7 @@ S3method("format", "size_bytes")
336 336 
 export(
337 337 
 	"size_bytes",
338 338 
 	"sizeof",
339 
+	"shm_used",
339 340 
 	"vm_used",
340 341 
 	"vm_realized")
341 342
Browse code

add create_memory_resource() and remove_memory_resource()

Kylie Bemis authored on 03/08/2024 18:31:09
Showing 1 changed files
NAMESPACE
History View file @ 9bb5c2ee2
... ... 
@@ -325,6 +325,7 @@ export(
325 325
326 326 
 export(
327 327 
 	"uuid",
328 
+	"tempmem",
328 329 
 	"hex2raw",
329 330 
 	"raw2hex")
330 331
Browse code

revert mtime() => memtime()

Kylie Bemis authored on 03/08/2024 16:40:37
Showing 1 changed files
NAMESPACE
History View file @ 222c4aaa2
... ... 
@@ -601,7 +601,6 @@ export(
601 601
602 602 
 export(
603 603 
 	"mem",
604 
-	"mtime",
605 604 
 	"memtime",
606 605 
 	"profmem")
607 606
Browse code

add shared resource manager

Kylie Bemis authored on 02/08/2024 19:27:00
Showing 1 changed files
NAMESPACE
History View file @ e10e26853
... ... 
@@ -605,6 +605,11 @@ export(
605 605 
 	"memtime",
606 606 
 	"profmem")
607 607
608 
+export(
609 
+	"matter_shared_resource",
610 
+	"matter_shared_resource_list",
611 
+	"matter_shared_resource_pool")
612 
+
608 613 
 export("matter_defaults")
609 614
610 615 
 export("SnowfastParam")
Browse code

fix leaky rowDistFun()/colDistFun(); export copy_env()

Kylie Bemis authored on 01/08/2024 21:14:01
Showing 1 changed files
NAMESPACE
History View file @ 5f68a12e4
... ... 
@@ -436,14 +436,16 @@ export(
436 436 
 	"array_ind",
437 437 
 	"linear_ind")
438 438
439 
-export("update_attr")
439 
+export(
440 
+	"update_attr",
441 
+	"copy_env")
440 442
441 443 
 export(
442 444 
 	"roll",
443 445 
 	"seq_rel",
444 446 
 	"shingles",
445 
-	"avg",
446 
-	"pinv")
447 
+	"pinv",
448 
+	"avg")
447 449
448 450 
 export(
449 451 
 	"RNGStreams",
... ... 
@@ -592,6 +594,11 @@ export(
592 594 
 	"simple_logger",
593 595 
 	"matter_logger")
594 596
597 
+export(
598 
+	"matter_log",
599 
+	"matter_warn",
600 
+	"matter_error")
601 
+
595 602 
 export(
596 603 
 	"mem",
597 604 
 	"mtime",
Browse code

fix NAMESPACE; add simple_logger docs

Kylie Bemis authored on 01/08/2024 18:03:32
Showing 1 changed files
NAMESPACE
History View file @ ceeaeabd3
... ... 
@@ -4,6 +4,8 @@ import("methods")
4 4 
 importFrom("utils",
5 5 
 	"head",
6 6 
 	"tail",
7 
+	"sessionInfo",
8 
+	"capture.output",
7 9 
 	"object.size")
8 10
9 11 
 importFrom("grDevices",
... ... 
@@ -586,7 +588,9 @@ export(
586 588 
 	"eval_exprs",
587 589 
 	"varquote")
588 590
589 
-export("simple_logger")
591 
+export(
592 
+	"simple_logger",
593 
+	"matter_logger")
590 594
591 595 
 export(
592 596 
 	"mem",
Browse code

add simple_logger()

Kylie Bemis authored on 01/08/2024 17:25:16
Showing 1 changed files
NAMESPACE
History View file @ 6b6048650
... ... 
@@ -580,18 +580,20 @@ exportMethods(
580 580 
 	"preplot",
581 581 
 	"plot")
582 582
583 
-export(
584 
-	"mem",
585 
-	"mtime",
586 
-	"memtime",
587 
-	"profmem")
588 
-
589 583 
 export(
590 584 
 	"parse_formula",
591 585 
 	"eval_at",
592 586 
 	"eval_exprs",
593 587 
 	"varquote")
594 588
589 
+export("simple_logger")
590 
+
591 
+export(
592 
+	"mem",
593 
+	"mtime",
594 
+	"memtime",
595 
+	"profmem")
596 
+
595 597 
 export("matter_defaults")
596 598
597 599 
 export("SnowfastParam")
Browse code

fix bugs with serialize=FALSE

Kylie Bemis authored on 31/07/2024 03:56:20
Showing 1 changed files
NAMESPACE
History View file @ 7a6bbe4f6
... ... 
@@ -158,6 +158,8 @@ exportMethods(
158 158 
 	"as.factor",
159 159 
 	"as.data.frame")
160 160
161 
+export("as.vector")
162 
+
161 163 
 exportMethods(
162 164 
 	"adata",
163 165 
 	"atomdata",
Browse code

switch to 'chunkopts' arg for chunk options; changes to chunked class

Kylie Bemis authored on 31/07/2024 02:14:08
Showing 1 changed files
NAMESPACE
History View file @ fa6111cdf
... ... 
@@ -590,6 +590,8 @@ export(
590 590 
 	"eval_exprs",
591 591 
 	"varquote")
592 592
593 
+export("matter_defaults")
594 
+
593 595 
 export("SnowfastParam")
594 596
595 597 
 useDynLib("matter", .registration=TRUE, .fixes="C_")
Browse code

rename vquote=>varquote

Kylie Bemis authored on 29/07/2024 15:18:14
Showing 1 changed files
NAMESPACE
History View file @ ccf35bd9f
... ... 
@@ -588,7 +588,7 @@ export(
588 588 
 	"parse_formula",
589 589 
 	"eval_at",
590 590 
 	"eval_exprs",
591 
-	"vquote")
591 
+	"varquote")
592 592
593 593 
 export("SnowfastParam")
594 594
Browse code

rename btquote=>vquote

Kylie Bemis authored on 29/07/2024 15:16:50
Showing 1 changed files
NAMESPACE
History View file @ e78e1cfcf
... ... 
@@ -588,7 +588,7 @@ export(
588 588 
 	"parse_formula",
589 589 
 	"eval_at",
590 590 
 	"eval_exprs",
591 
-	"btquote")
591 
+	"vquote")
592 592
593 593 
 export("SnowfastParam")
594 594
Browse code

fix eval_exprs() bug where recursive attribute set incorrectly

Kylie Bemis authored on 29/07/2024 15:13:37
Showing 1 changed files
NAMESPACE
History View file @ beb76d11b
... ... 
@@ -587,7 +587,8 @@ export(
587 587 
 export(
588 588 
 	"parse_formula",
589 589 
 	"eval_at",
590 
-	"eval_exprs")
590 
+	"eval_exprs",
591 
+	"btquote")
591 592
592 593 
 export("SnowfastParam")
593 594
Browse code

fix leaky closures in chunk loop functions

Kylie Bemis authored on 28/07/2024 14:35:41
Showing 1 changed files
NAMESPACE
History View file @ 164d958fe
... ... 
@@ -432,6 +432,8 @@ export(
432 432 
 	"array_ind",
433 433 
 	"linear_ind")
434 434
435 
+export("update_attr")
436 
+
435 437 
 export(
436 438 
 	"roll",
437 439 
 	"seq_rel",
Browse code

add SnowfastParam()

Kylie Bemis authored on 27/07/2024 23:03:03
Showing 1 changed files
NAMESPACE
History View file @ ec469aa48
... ... 
@@ -94,6 +94,8 @@ importFrom("irlba",
94 94 
 	"irlba")
95 95
96 96 
 importFrom("parallel",
97 
+	"makeCluster",
98 
+	"stopCluster",
97 99 
 	"nextRNGStream",
98 100 
 	"nextRNGSubStream")
99 101
... ... 
@@ -585,4 +587,6 @@ export(
585 587 
 	"eval_at",
586 588 
 	"eval_exprs")
587 589
590 
+export("SnowfastParam")
591 
+
588 592 
 useDynLib("matter", .registration=TRUE, .fixes="C_")
Browse code

add option matter.default.chunksize + vm_realized()

Kylie Bemis authored on 27/07/2024 16:30:20
Showing 1 changed files
NAMESPACE
History View file @ c064f97fd
... ... 
@@ -329,7 +329,8 @@ S3method("format", "size_bytes")
329 329 
 export(
330 330 
 	"size_bytes",
331 331 
 	"sizeof",
332 
-	"vm_used")
332 
+	"vm_used",
333 
+	"vm_realized")
333 334
334 335 
 export(
335 336 
 	"approx1",
Browse code

add findpeaks_knn()

Kylie Bemis authored on 26/07/2024 19:51:35
Showing 1 changed files
NAMESPACE
History View file @ 3fb093f87
... ... 
@@ -402,6 +402,7 @@ export(
402 402 
 	"enhance_adapt",
403 403 
 	"knnmax",
404 404 
 	"knnmin",
405 
+	"findpeaks_knn",
405 406 
 	"coscore",
406 407 
 	"is_gridded",
407 408 
 	"to_raster",
Browse code

update estnoise_*() functions; add matter2-signal vignette draft

Kylie Bemis authored on 18/07/2024 04:13:33
Showing 1 changed files
NAMESPACE
History View file @ 0013285c8
... ... 
@@ -532,7 +532,8 @@ export(
532 532 
 	"set_coord",
533 533 
 	"set_par",
534 534 
 	"set_engine",
535 
-	"as_facets")
535 
+	"as_facets",
536 
+	"as_layers")
536 537
537 538 
 export(
538 539 
 	"vizi_par",
Browse code

add filtn_bi() and filtn_adapt() w/ adaptive smoothing fixes

Kylie Bemis authored on 06/07/2024 19:53:57
Showing 1 changed files
NAMESPACE
History View file @ 002cb57a8
... ... 
@@ -393,6 +393,8 @@ export(
393 393 
 	"filtn_ma",
394 394 
 	"filtn_conv",
395 395 
 	"filtn_gauss",
396 
+	"filtn_bi",
397 
+	"filtn_adapt",
396 398 
 	"warp2_trans",
397 399 
 	"mi",
398 400 
 	"enhance_adj",
Browse code

rename locmax_knn => knnmax()

kuwisdelu authored on 26/06/2024 19:26:00
Showing 1 changed files
NAMESPACE
History View file @ bce1e80ee
... ... 
@@ -351,8 +351,6 @@ export(
351 351 
 	"rollvec",
352 352 
 	"findbins",
353 353 
 	"downsample",
354 
-	"locmax",
355 
-	"locmin",
356 354 
 	"estbase_loc",
357 355 
 	"estbase_hull",
358 356 
 	"estbase_snip",
... ... 
@@ -362,6 +360,8 @@ export(
362 360 
 	"estnoise_diff",
363 361 
 	"estnoise_quant",
364 362 
 	"estnoise_filt",
363 
+	"locmax",
364 
+	"locmin",
365 365 
 	"findpeaks",
366 366 
 	"findpeaks_cwt",
367 367 
 	"findridges",
... ... 
@@ -398,8 +398,8 @@ export(
398 398 
 	"enhance_adj",
399 399 
 	"enhance_hist",
400 400 
 	"enhance_adapt",
401 
-	"locmax_knn",
402 
-	"locmin_knn",
401 
+	"knnmax",
402 
+	"knnmin",
403 403 
 	"coscore",
404 404 
 	"is_gridded",
405 405 
 	"to_raster",
Browse code

add filtn_xxx() functions

kuwisdelu authored on 26/06/2024 19:21:39
Showing 1 changed files
NAMESPACE
History View file @ d5f8880ce
... ... 
@@ -390,6 +390,9 @@ export(
390 390 
 	"filt2_adapt",
391 391 
 	"filt2_diff",
392 392 
 	"filt2_guide",
393 
+	"filtn_ma",
394 
+	"filtn_conv",
395 
+	"filtn_gauss",
393 396 
 	"warp2_trans",
394 397 
 	"mi",
395 398 
 	"enhance_adj",
Browse code

add locmax_knn() and locmin_knn(); rm ... from locmax() and locmin()

Kylie Bemis authored on 18/06/2024 16:57:12
Showing 1 changed files
NAMESPACE
History View file @ 13843ea50
... ... 
@@ -395,6 +395,8 @@ export(
395 395 
 	"enhance_adj",
396 396 
 	"enhance_hist",
397 397 
 	"enhance_adapt",
398 
+	"locmax_knn",
399 
+	"locmin_knn",
398 400 
 	"coscore",
399 401 
 	"is_gridded",
400 402 
 	"to_raster",
Browse code

rm locmax2() and locmax2()

Kylie Bemis authored on 17/06/2024 18:59:05
Showing 1 changed files
NAMESPACE
History View file @ 34d4bea65
... ... 
@@ -395,8 +395,6 @@ export(
395 395 
 	"enhance_adj",
396 396 
 	"enhance_hist",
397 397 
 	"enhance_adapt",
398 
-	"locmax2",
399 
-	"locmin2",
400 398 
 	"coscore",
401 399 
 	"is_gridded",
402 400 
 	"to_raster",
Browse code

add locmax2() and locmin2()

Kylie Bemis authored on 15/06/2024 21:12:09
Showing 1 changed files
NAMESPACE
History View file @ 1b375d4a0
... ... 
@@ -395,6 +395,8 @@ export(
395 395 
 	"enhance_adj",
396 396 
 	"enhance_hist",
397 397 
 	"enhance_adapt",
398 
+	"locmax2",
399 
+	"locmin2",
398 400 
 	"coscore",
399 401 
 	"is_gridded",
400 402 
 	"to_raster",
Browse code

update eval_exprs(); rename eval_expr() => eval_at()

Kylie Bemis authored on 13/06/2024 20:00:12
Showing 1 changed files
NAMESPACE
History View file @ 2268be42c
... ... 
@@ -572,7 +572,7 @@ export(
572 572
573 573 
 export(
574 574 
 	"parse_formula",
575 
-	"eval_expr",
575 
+	"eval_at",
576 576 
 	"eval_exprs")
577 577
578 578 
 useDynLib("matter", .registration=TRUE, .fixes="C_")
Browse code

sum bar counts for vizi_bars mark

Kylie Bemis authored on 12/06/2024 21:23:17
Showing 1 changed files
NAMESPACE
History View file @ 8850a7deb
... ... 
@@ -46,6 +46,7 @@ importFrom("graphics",
46 46 
 	"title")
47 47
48 48 
 importFrom("stats",
49 
+	"aggregate",
49 50 
 	"approx",
50 51 
 	"coef",
51 52 
 	"cor",
... ... 
@@ -547,9 +548,9 @@ S3method("plot", "vizi_points")
547 548 
 S3method("plot", "vizi_lines")
548 549 
 S3method("plot", "vizi_peaks")
549 550 
 S3method("plot", "vizi_text")
551 
+S3method("plot", "vizi_intervals")
550 552 
 S3method("plot", "vizi_rules")
551 553 
 S3method("plot", "vizi_bars")
552 
-S3method("plot", "vizi_intervals")
553 554 
 S3method("plot", "vizi_boxplot")
554 555 
 S3method("plot", "vizi_image")
555 556 
 S3method("plot", "vizi_pixels")
Browse code

rm parse_vars(); add eval_exprs(); rename memtime() => mtime()

kuwisdelu authored on 23/05/2024 21:47:30
Showing 1 changed files
NAMESPACE
History View file @ 3981089f4
... ... 
@@ -565,11 +565,13 @@ exportMethods(
565 565
566 566 
 export(
567 567 
 	"mem",
568 
+	"mtime",
568 569 
 	"memtime",
569 570 
 	"profmem")
570 571
571 572 
 export(
572 573 
 	"parse_formula",
573 
-	"parse_vars")
574 
+	"eval_expr",
575 
+	"eval_exprs")
574 576
575 577 
 useDynLib("matter", .registration=TRUE, .fixes="C_")
Browse code

add 'parse_vars()'

kuwisdelu authored on 21/05/2024 23:04:47
Showing 1 changed files
NAMESPACE
History View file @ e7bf6286f
... ... 
@@ -568,6 +568,8 @@ export(
568 568 
 	"memtime",
569 569 
 	"profmem")
570 570
571 
-export("parse_formula")
571 
+export(
572 
+	"parse_formula",
573 
+	"parse_vars")
572 574
573 575 
 useDynLib("matter", .registration=TRUE, .fixes="C_")
Browse code

updated enhance_*() to support multiple channels; added enhance_adj()

kuwisdelu authored on 17/05/2024 23:42:00
Showing 1 changed files
NAMESPACE
History View file @ 0f5aecde4
... ... 
@@ -7,23 +7,23 @@ importFrom("utils",
7 7 
 	"object.size")
8 8
9 9 
 importFrom("grDevices",
10 
+	"as.raster",
11 
+	"col2rgb",
10 12 
 	"dev.capabilities",
11 13 
 	"dev.cur",
12 14 
 	"dev.flush",
13 15 
 	"dev.hold",
14 
-	"col2rgb",
15 
-	"rgb",
16 
-	"trans3d",
17 
-	"as.raster",
18 16 
 	"hcl.colors",
19 17 
 	"hcl.pals",
20 18 
 	"palette.colors",
21 19 
 	"palette.pals",
20 
+	"rgb",
21 
+	"trans3d",
22 22 
 	"xy.coords")
23 23
24 24 
 importFrom("graphics",
25 
-	"abline",
26 25 
 	"Axis",
26 
+	"abline",
27 27 
 	"arrows",
28 28 
 	"box",
29 29 
 	"boxplot.default",
... ... 
@@ -47,36 +47,37 @@ importFrom("graphics",
47 47
48 48 
 importFrom("stats",
49 49 
 	"approx",
50 
+	"coef",
50 51 
 	"cor",
51 52 
 	"cov",
52 
-	"coef",
53 
-	"fitted",
54 
-	"resid",
55 
-	"loadings",
56 53 
 	"dnorm",
57 54 
 	"fft",
58 
-	"median",
59 
-	"nextn",
55 
+	"fitted",
56 
+	"kmeans",
57 
+	"loadings",
60 58 
 	"loess",
61 59 
 	"lowess",
60 
+	"median",
62 61 
 	"na.omit",
62 
+	"nextn",
63 63 
 	"nobs",
64 64 
 	"optim",
65 
+	"optimize",
65 66 
 	"predict",
66 67 
 	"qnorm",
68 
+	"quantile",
69 
+	"resid",
67 70 
 	"rlnorm",
68 71 
 	"rnorm",
69 72 
 	"runmed",
70 
-	"kmeans",
71 
-	"optimize",
72 73 
 	"smooth.spline",
73 74 
 	"spline",
74 75 
 	"update")
75 76
76 77 
 importFrom("stats4",
77 78 
 	"plot",
78 
-	"update",
79 
-	"summary")
79 
+	"summary",
80 
+	"update")
80 81
81 82 
 importFrom("Matrix",
82 83 
 	"nnzero",
... ... 
@@ -390,6 +391,7 @@ export(
390 391 
 	"filt2_guide",
391 392 
 	"warp2_trans",
392 393 
 	"mi",
394 
+	"enhance_adj",
393 395 
 	"enhance_hist",
394 396 
 	"enhance_adapt",
395 397 
 	"coscore",
Browse code

add s_stat()

kuwisdelu authored on 15/05/2024 23:57:37
Showing 1 changed files
NAMESPACE
History View file @ 91198af3f
... ... 
@@ -255,6 +255,7 @@ export(
255 255 
 	"s_any",
256 256 
 	"s_all",
257 257 
 	"s_nnzero",
258 
+	"s_stat",
258 259 
 	"s_colstats",
259 260 
 	"s_rowstats",
260 261 
 	"stat_c")
Browse code

add subsetting of deferred ops

kuwisdelu authored on 15/05/2024 20:26:39
Showing 1 changed files
NAMESPACE
History View file @ a71df9ffd
... ... 
@@ -221,8 +221,11 @@ S3method("rbind", "sparse_arr")
221 221
222 222 
 exportMethods(
223 223 
 	"Arith",
224 
-	"Compare",
225 
-	"Logic")
224 
+	"exp",
225 
+	"log",
226 
+	"log2",
227 
+	"log10",
228 
+	"log1p")
226 229
227 230 
 exportMethods(
228 231 
 	"range",
Browse code

add chunked docs, update chunked classes

kuwisdelu authored on 15/05/2024 00:59:09
Showing 1 changed files
NAMESPACE
History View file @ 380eca2a1
... ... 
@@ -292,17 +292,19 @@ export(
292 292 
 	".rowStats",
293 293 
 	".colStats")
294 294
295 
+export(
296 
+	"chunked_vec",
297 
+	"chunked_mat",
298 
+	"chunked_list",
299 
+	"chunkify")
300 
+
295 301 
 export(
296 302 
 	"chunk_apply",
297 303 
 	"chunk_rowapply",
298 304 
 	"chunk_colapply",
299 305 
 	"chunk_lapply",
300 306 
 	"chunk_mapply",
301 
-	"chunked_vector",
302 
-	"chunked_matrix",
303 
-	"chunked_list",
304 
-	"chunk_writer",
305 
-	"chunkify")
307 
+	"chunk_writer")
306 308
307 309 
 export(
308 310 
 	"chunkApply",
Browse code

internal replace setNames => set_names

kuwisdelu authored on 14/05/2024 00:59:02
Showing 1 changed files
NAMESPACE
History View file @ 970eac89c
... ... 
@@ -69,7 +69,6 @@ importFrom("stats",
69 69 
 	"runmed",
70 70 
 	"kmeans",
71 71 
 	"optimize",
72 
-	"setNames",
73 72 
 	"smooth.spline",
74 73 
 	"spline",
75 74 
 	"update")
Browse code

add chunked tests

kuwisdelu authored on 13/05/2024 23:15:01
Showing 1 changed files
NAMESPACE
History View file @ efd381602
... ... 
@@ -430,9 +430,7 @@ export(
430 430 
 	"cpal",
431 431 
 	"add_alpha")
432 432
433 
-exportMethods(
434 
-	"prcomp",
435 
-	"bigglm")
433 
+exportMethods("prcomp")
436 434
437 435 
 export(
438 436 
 	"qrank",
Browse code

remove biglm from imports; add chunked.R

kuwisdelu authored on 13/05/2024 23:10:26
Showing 1 changed files
NAMESPACE
History View file @ a92bd6899
... ... 
@@ -92,8 +92,6 @@ importFrom("digest",
92 92 
 importFrom("irlba",
93 93 
 	"irlba")
94 94
95 
-import("biglm")
96 
-
97 95 
 importFrom("parallel",
98 96 
 	"nextRNGStream",
99 97 
 	"nextRNGSubStream")
Browse code

update chunk_*apply functions

kuwisdelu authored on 13/05/2024 22:56:15
Showing 1 changed files
NAMESPACE
History View file @ 6313cbafd
... ... 
@@ -295,14 +295,15 @@ export(
295 295 
 	".rowStats",
296 296 
 	".colStats")
297 297
298 
-
299 
-
300 298 
 export(
301 299 
 	"chunk_apply",
302 300 
 	"chunk_rowapply",
303 301 
 	"chunk_colapply",
304 302 
 	"chunk_lapply",
305 303 
 	"chunk_mapply",
304 
+	"chunked_vector",
305 
+	"chunked_matrix",
306 
+	"chunked_list",
306 307 
 	"chunk_writer",
307 308 
 	"chunkify")
308 309
Browse code

add vizi_image; safely pass ... to plot_init()

Kylie Bemis authored on 26/04/2024 21:39:48
Showing 1 changed files
NAMESPACE
History View file @ e3f1198f2
... ... 
@@ -547,6 +547,7 @@ S3method("plot", "vizi_rules")
547 547 
 S3method("plot", "vizi_bars")
548 548 
 S3method("plot", "vizi_intervals")
549 549 
 S3method("plot", "vizi_boxplot")
550 
+S3method("plot", "vizi_image")
550 551 
 S3method("plot", "vizi_pixels")
551 552 
 S3method("plot", "vizi_voxels")
552 553
Browse code

v2.5.19

Kylie Bemis authored on 26/04/2024 03:12:01
Showing 1 changed files
NAMESPACE
History View file @ e2e24b158
... ... 
@@ -22,6 +22,7 @@ importFrom("grDevices",
22 22 
 	"xy.coords")
23 23
24 24 
 importFrom("graphics",
25 
+	"abline",
25 26 
 	"Axis",
26 27 
 	"arrows",
27 28 
 	"box",
... ... 
@@ -542,6 +543,7 @@ S3method("plot", "vizi_points")
542 543 
 S3method("plot", "vizi_lines")
543 544 
 S3method("plot", "vizi_peaks")
544 545 
 S3method("plot", "vizi_text")
546 
+S3method("plot", "vizi_rules")
545 547 
 S3method("plot", "vizi_bars")
546 548 
 S3method("plot", "vizi_intervals")
547 549 
 S3method("plot", "vizi_boxplot")
Browse code

export parse_formula()

Kylie Bemis authored on 24/04/2024 22:22:45
Showing 1 changed files
NAMESPACE
History View file @ 55dcb6a99
... ... 
@@ -561,4 +561,6 @@ export(
561 561 
 	"memtime",
562 562 
 	"profmem")
563 563
564 
+export("parse_formula")
565 
+
564 566 
 useDynLib("matter", .registration=TRUE, .fixes="C_")
Browse code

add vizi_engine()

Kylie Bemis authored on 24/04/2024 16:51:41
Showing 1 changed files
NAMESPACE
History View file @ aaf2cb7d7
... ... 
@@ -523,7 +523,8 @@ export(
523 523
524 524 
 export(
525 525 
 	"vizi_par",
526 
-	"vizi_style")
526 
+	"vizi_style",
527 
+	"vizi_engine")
527 528
528 529 
 S3method("preplot", "vizi_plot")
529 530 
 S3method("preplot", "vizi_facets")
Browse code

cleanup NAMESPACE

Kylie Bemis authored on 24/04/2024 00:37:39
Showing 1 changed files
NAMESPACE
History View file @ 321095970
... ... 
@@ -35,7 +35,7 @@ importFrom("graphics",
35 35 
 	"plot.window",
36 36 
 	"plot.xy",
37 37 
 	"persp",
38 
-	"points"
38 
+	"points",
39 39 
 	"polygon",
40 40 
 	"rasterImage",
41 41 
 	"rect",
Browse code

finish up 1st draft plotly support

Kylie Bemis authored on 24/04/2024 00:34:39
Showing 1 changed files
NAMESPACE
History View file @ ac8343d7c
... ... 
@@ -35,8 +35,10 @@ importFrom("graphics",
35 35 
 	"plot.window",
36 36 
 	"plot.xy",
37 37 
 	"persp",
38 
+	"points"
38 39 
 	"polygon",
39 40 
 	"rasterImage",
41 
+	"rect",
40 42 
 	"strheight",
41 43 
 	"strwidth",
42 44 
 	"text.default",
... ... 
@@ -516,6 +518,7 @@ export(
516 518 
 	"set_channel",
517 519 
 	"set_coord",
518 520 
 	"set_par",
521 
+	"set_engine",
519 522 
 	"as_facets")
520 523
521 524 
 export(
Browse code

added mark vizi_bars

Kylie Bemis authored on 22/04/2024 21:43:15
Showing 1 changed files
NAMESPACE
History View file @ bdca4767e
... ... 
@@ -538,6 +538,7 @@ S3method("plot", "vizi_points")
538 538 
 S3method("plot", "vizi_lines")
539 539 
 S3method("plot", "vizi_peaks")
540 540 
 S3method("plot", "vizi_text")
541 
+S3method("plot", "vizi_bars")
541 542 
 S3method("plot", "vizi_intervals")
542 543 
 S3method("plot", "vizi_boxplot")
543 544 
 S3method("plot", "vizi_pixels")
Browse code

updated cv_do() and mi_learn()

kuwisdelu authored on 19/04/2024 04:53:13
Showing 1 changed files
NAMESPACE
History View file @ 5d68a4efa
... ... 
@@ -494,6 +494,9 @@ S3method("fitted", "pls")
494 494 
 S3method("predict", "pls")
495 495 
 S3method("print", "pls")
496 496
497 
+S3method("coef", "opls")
498 
+S3method("residuals", "opls")
499 
+S3method("fitted", "opls")
497 500 
 S3method("predict", "opls")
498 501 
 S3method("print", "opls")
499 502
Browse code

add rocscore()

Kylie Bemis authored on 10/04/2024 03:20:43
Showing 1 changed files
NAMESPACE
History View file @ 8d5a893a5
... ... 
@@ -455,6 +455,7 @@ export(
455 455 
 	"fastmap",
456 456 
 	"mi_learn",
457 457 
 	"predscore",
458 
+	"rocscore",
458 459 
 	"nndsvd",
459 460 
 	"nnmf_als",
460 461 
 	"nnmf_mult",
Browse code

export size_bytes(), chunk_writer(), and chunkify()

Kylie Bemis authored on 07/04/2024 18:57:05
Showing 1 changed files
NAMESPACE
History View file @ d6ff8644d
... ... 
@@ -299,7 +299,9 @@ export(
299 299 
 	"chunk_rowapply",
300 300 
 	"chunk_colapply",
301 301 
 	"chunk_lapply",
302 
-	"chunk_mapply")
302 
+	"chunk_mapply",
303 
+	"chunk_writer",
304 
+	"chunkify")
303 305
304 306 
 export(
305 307 
 	"chunkApply",
... ... 
@@ -316,6 +318,7 @@ S3method("print", "size_bytes")
316 318 
 S3method("format", "size_bytes")
317 319
318 320 
 export(
321 
+	"size_bytes",
319 322 
 	"sizeof",
320 323 
 	"vm_used")
321 324
Browse code

return fitted.values in cv_do()

Kylie Bemis authored on 05/04/2024 01:26:39
Showing 1 changed files
NAMESPACE
History View file @ b25f1996b
... ... 
@@ -463,6 +463,7 @@ export(
463 463 
 	"opls_nipals",
464 464 
 	"vip")
465 465
466 
+S3method("fitted", "cv")
466 467 
 S3method("print", "cv")
467 468
468 469 
 S3method("fitted", "sgmix")
Browse code

plotting/vizi improvements

Kylie Bemis authored on 04/04/2024 21:06:12
Showing 1 changed files
NAMESPACE
History View file @ 7eb7bcdb0
... ... 
@@ -16,7 +16,9 @@ importFrom("grDevices",
16 16 
 	"trans3d",
17 17 
 	"as.raster",
18 18 
 	"hcl.colors",
19 
+	"hcl.pals",
19 20 
 	"palette.colors",
21 
+	"palette.pals",
20 22 
 	"xy.coords")
21 23
22 24 
 importFrom("graphics",
Browse code

cv_do()

Kylie Bemis authored on 02/04/2024 20:22:34
Showing 1 changed files
NAMESPACE
History View file @ f055039f1
... ... 
@@ -444,6 +444,7 @@ export(
444 444 
 S3method("print", "kdtree")
445 445
446 446 
 export(
447 
+	"cv_do",
447 448 
 	"sgmix",
448 449 
 	"sgmixn",
449 450 
 	"fastmap",
... ... 
@@ -460,6 +461,8 @@ export(
460 461 
 	"opls_nipals",
461 462 
 	"vip")
462 463
464 
+S3method("print", "cv")
465 
+
463 466 
 S3method("fitted", "sgmix")
464 467 
 S3method("print", "sgmix")
465 468 
 S3method("logLik", "sgmix")
Browse code

export avg()

kuwisdelu authored on 01/04/2024 21:32:02
Showing 1 changed files
NAMESPACE
History View file @ 043f8da0a
... ... 
@@ -404,11 +404,14 @@ export(
404 404
405 405 
 export(
406 406 
 	"array_ind",
407 
-	"linear_ind",
408 
-	"pinv",
407 
+	"linear_ind")
408 
+
409 
+export(
409 410 
 	"roll",
410 411 
 	"seq_rel",
411 
-	"shingles")
412 
+	"shingles",
413 
+	"avg",
414 
+	"pinv")
412 415
413 416 
 export(
414 417 
 	"RNGStreams",
Browse code

updates to mscore() => coscore()

Kylie Bemis authored on 01/04/2024 15:54:06
Showing 1 changed files
NAMESPACE
History View file @ 8c3d8bf37
... ... 
@@ -380,7 +380,7 @@ export(
380 380 
 	"mi",
381 381 
 	"enhance_hist",
382 382 
 	"enhance_adapt",
383 
-	"mscore",
383 
+	"coscore",
384 384 
 	"is_gridded",
385 385 
 	"to_raster",
386 386 
 	"to_raster3",
Browse code

add predscore()

Kylie Bemis authored on 01/04/2024 04:28:07
Showing 1 changed files
NAMESPACE
History View file @ f225cbac6
... ... 
@@ -445,6 +445,7 @@ export(
445 445 
 	"sgmixn",
446 446 
 	"fastmap",
447 447 
 	"mi_learn",
448 
+	"predscore",
448 449 
 	"nndsvd",
449 450 
 	"nnmf_als",
450 451 
 	"nnmf_mult",
Browse code

add vizi marks 'intervals' and 'boxplot'

Kylie Bemis authored on 01/04/2024 03:49:52
Showing 1 changed files
NAMESPACE
History View file @ a192ec27a
... ... 
@@ -21,7 +21,9 @@ importFrom("grDevices",
21 21
22 22 
 importFrom("graphics",
23 23 
 	"Axis",
24 
+	"arrows",
24 25 
 	"box",
26 
+	"boxplot.default",
25 27 
 	"co.intervals",
26 28 
 	"grid",
27 29 
 	"legend",
... ... 
@@ -518,6 +520,9 @@ S3method("plot", "vizi_colorkey")
518 520 
 S3method("plot", "vizi_points")
519 521 
 S3method("plot", "vizi_lines")
520 522 
 S3method("plot", "vizi_peaks")
523 
+S3method("plot", "vizi_text")
524 
+S3method("plot", "vizi_intervals")
525 
+S3method("plot", "vizi_boxplot")
521 526 
 S3method("plot", "vizi_pixels")
522 527 
 S3method("plot", "vizi_voxels")
523 528
Browse code

big updates to sgmix(), sgmixn(), and drle()

Kylie Bemis authored on 30/03/2024 20:00:43
Showing 1 changed files
NAMESPACE
History View file @ 50dffb39c
... ... 
@@ -203,6 +203,7 @@ exportMethods(
203 203 
 	"dimnames<-",
204 204 
 	"levels",
205 205 
 	"levels<-",
206 
+	"droplevels",
206 207 
 	"Encoding",
207 208 
 	"Encoding<-",
208 209 
 	"t",
... ... 
@@ -457,6 +458,9 @@ S3method("fitted", "sgmix")
457 458 
 S3method("print", "sgmix")
458 459 
 S3method("logLik", "sgmix")
459 460
461 
+S3method("print", "sgmixn")
462 
+S3method("logLik", "sgmixn")
463 
+
460 464 
 S3method("predict", "fastmap")
461 465 
 S3method("print", "fastmap")
462 466
Browse code

add RNG utils and 'seeds' arg to chunk apply functions

kuwisdelu authored on 29/03/2024 18:14:55
Showing 1 changed files
NAMESPACE
History View file @ 93fc9d673
... ... 
@@ -87,6 +87,10 @@ importFrom("irlba",
87 87
88 88 
 import("biglm")
89 89
90 
+importFrom("parallel",
91 
+	"nextRNGStream",
92 
+	"nextRNGSubStream")
93 
+
90 94 
 import("BiocParallel")
91 95
92 96 
 import("BiocGenerics")
... ... 
@@ -403,6 +407,11 @@ export(
403 407 
 	"seq_rel",
404 408 
 	"shingles")
405 409
410 
+export(
411 
+	"RNGStreams",
412 
+	"getRNGStream",
413 
+	"setRNGStream")
414 
+
406 415 
 export(
407 416 
 	"dpal",
408 417 
 	"cpal",
Browse code

update print() methods

Kylie Bemis authored on 27/03/2024 16:55:09
Showing 1 changed files
NAMESPACE
History View file @ a57fcd887
... ... 
@@ -454,6 +454,8 @@ S3method("print", "fastmap")
454 454 
 S3method("predict", "nnmf")
455 455 
 S3method("print", "nnmf")
456 456
457 
+S3method("print", "prcomp_lanczos")
458 
+
457 459 
 S3method("fitted", "nscentroids")
458 460 
 S3method("predict", "nscentroids")
459 461 
 S3method("print", "nscentroids")
Browse code

in fitted() change 'probability'=>'response'

kuwisdelu authored on 26/03/2024 18:31:35
Showing 1 changed files
NAMESPACE
History View file @ ece9d7445
... ... 
@@ -459,6 +459,7 @@ S3method("predict", "nscentroids")
459 459 
 S3method("print", "nscentroids")
460 460 
 S3method("logLik", "nscentroids")
461 461
462 
+S3method("fitted", "pls")
462 463 
 S3method("predict", "pls")
463 464 
 S3method("print", "pls")
464 465
Browse code

mi_learn()

Kylie Bemis authored on 26/03/2024 02:10:10
Showing 1 changed files
NAMESPACE
History View file @ 1b7c35a94
... ... 
@@ -432,6 +432,7 @@ export(
432 432 
 	"sgmix",
433 433 
 	"sgmixn",
434 434 
 	"fastmap",
435 
+	"mi_learn",
435 436 
 	"nndsvd",
436 437 
 	"nnmf_als",
437 438 
 	"nnmf_mult",
Browse code

mscore()

Kylie Bemis authored on 25/03/2024 23:26:47
Showing 1 changed files
NAMESPACE
History View file @ f6626a516
... ... 
@@ -40,6 +40,7 @@ importFrom("graphics",
40 40
41 41 
 importFrom("stats",
42 42 
 	"approx",
43 
+	"cor",
43 44 
 	"cov",
44 45 
 	"coef",
45 46 
 	"fitted",
... ... 
@@ -372,6 +373,7 @@ export(
372 373 
 	"mi",
373 374 
 	"enhance_hist",
374 375 
 	"enhance_adapt",
376 
+	"mscore",
375 377 
 	"is_gridded",
376 378 
 	"to_raster",
377 379 
 	"to_raster3",
Browse code

sgmix()

Kylie Bemis authored on 25/03/2024 21:20:39
Showing 1 changed files
NAMESPACE
History View file @ 29df2313a
... ... 
@@ -59,6 +59,8 @@ importFrom("stats",
59 59 
 	"rlnorm",
60 60 
 	"rnorm",
61 61 
 	"runmed",
62 
+	"kmeans",
63 
+	"optimize",
62 64 
 	"setNames",
63 65 
 	"smooth.spline",
64 66 
 	"spline",
... ... 
@@ -425,6 +427,8 @@ export(
425 427 
 S3method("print", "kdtree")
426 428
427 429 
 export(
430 
+	"sgmix",
431 
+	"sgmixn",
428 432 
 	"fastmap",
429 433 
 	"nndsvd",
430 434 
 	"nnmf_als",
... ... 
@@ -437,17 +441,21 @@ export(
437 441 
 	"opls_nipals",
438 442 
 	"vip")
439 443
444 
+S3method("fitted", "sgmix")
445 
+S3method("print", "sgmix")
446 
+S3method("logLik", "sgmix")
447 
+
440 448 
 S3method("predict", "fastmap")
441 449 
 S3method("print", "fastmap")
442 450
451 
+S3method("predict", "nnmf")
452 
+S3method("print", "nnmf")
453 
+
443 454 
 S3method("fitted", "nscentroids")
444 455 
 S3method("predict", "nscentroids")
445 456 
 S3method("print", "nscentroids")
446 457 
 S3method("logLik", "nscentroids")
447 458
448 
-S3method("predict", "nnmf")
449 
-S3method("print", "nnmf")
450 
-
451 459 
 S3method("predict", "pls")
452 460 
 S3method("print", "pls")
453 461
Browse code

nscentroids()

kuwisdelu authored on 25/03/2024 01:27:11
Showing 1 changed files
NAMESPACE
History View file @ a365b2bf9
... ... 
@@ -429,6 +429,7 @@ export(
429 429 
 	"nndsvd",
430 430 
 	"nnmf_als",
431 431 
 	"nnmf_mult",
432 
+	"nscentroids",
432 433 
 	"prcomp_lanczos",
433 434 
 	"pls_nipals",
434 435 
 	"pls_simpls",
... ... 
@@ -439,6 +440,11 @@ export(
439 440 
 S3method("predict", "fastmap")
440 441 
 S3method("print", "fastmap")
441 442
443 
+S3method("fitted", "nscentroids")
444 
+S3method("predict", "nscentroids")
445 
+S3method("print", "nscentroids")
446 
+S3method("logLik", "nscentroids")
447 
+
442 448 
 S3method("predict", "nnmf")
443 449 
 S3method("print", "nnmf")
444 450
Browse code

export linear_ind() and array_ind()

kuwisdelu authored on 18/03/2024 17:04:44
Showing 1 changed files
NAMESPACE
History View file @ b7d76ceec
... ... 
@@ -392,10 +392,12 @@ export(
392 392 
 	"colDistFun")
393 393
394 394 
 export(
395 
+	"array_ind",
396 
+	"linear_ind",
397 
+	"pinv",
395 398 
 	"roll",
396 399 
 	"seq_rel",
397 
-	"shingles",
398 
-	"pinv")
400 
+	"shingles")
399 401
400 402 
 export(
401 403 
 	"dpal",
Browse code

add peakheights()

kuwisdelu authored on 16/03/2024 16:39:35
Showing 1 changed files
NAMESPACE
History View file @ eeea9a5b1
... ... 
@@ -350,6 +350,7 @@ export(
350 350 
 	"cwt",
351 351 
 	"peakwidths",
352 352 
 	"peakareas",
353 
+	"peakheights",
353 354 
 	"binpeaks",
354 355 
 	"mergepeaks",
355 356 
 	"estres",
Browse code

v2.5.8 rescale functions

Kylie Bemis authored on 12/03/2024 21:21:09
Showing 1 changed files
NAMESPACE
History View file @ 8b3cad593
... ... 
@@ -341,6 +341,11 @@ export(
341 341 
 	"findpeaks",
342 342 
 	"findpeaks_cwt",
343 343 
 	"findridges",
344 
+	"rescale_rms",
345 
+	"rescale_sum",
346 
+	"rescale_ref",
347 
+	"rescale_range",
348 
+	"rescale_iqr",
344 349 
 	"ricker",
345 350 
 	"cwt",
346 351 
 	"peakwidths",
... ... 
@@ -389,7 +394,6 @@ export(
389 394 
 	"roll",
390 395 
 	"seq_rel",
391 396 
 	"shingles",
392 
-	"rescale",
393 397 
 	"pinv")
394 398
395 399 
 export(
Browse code

v2.5.7 fix inpoly() and add_alpha

Kylie Bemis authored on 11/03/2024 18:16:35
Showing 1 changed files
NAMESPACE
History View file @ 56003e76c
... ... 
@@ -169,12 +169,6 @@ exportMethods(
169 169 
 	"nnzero",
170 170 
 	"rowMaj")
171 171
172 
-exportMethods(
173 
-	"keys",
174 
-	"keys<-",
175 
-	"chunksize",
176 
-	"chunksize<-")
177 
-
178 172 
 exportMethods("checksum")
179 173
180 174 
 exportMethods(
Browse code

v2.5.5 switch default vizi style to 'classic'

Kylie Bemis authored on 07/03/2024 00:57:34
Showing 1 changed files
NAMESPACE
History View file @ 47300dad9
... ... 
@@ -447,6 +447,14 @@ S3method("print", "pls")
447 447 
 S3method("predict", "opls")
448 448 
 S3method("print", "opls")
449 449
450 
+export(
451 
+	"panel_grid",
452 
+	"panel_dim",
453 
+	"panel_get",
454 
+	"panel_set",
455 
+	"panel_next",
456 
+	"panel_prev")
457 
+
450 458 
 export(
451 459 
 	"vizi",
452 460 
 	"add_mark",
Browse code

v2.5.5 bug fixes, added plot_signal() and plot_image()

Kylie Bemis authored on 06/03/2024 23:18:10
Showing 1 changed files
NAMESPACE
History View file @ 4b3bb6c83
... ... 
@@ -35,6 +35,7 @@ importFrom("graphics",
35 35 
 	"rasterImage",
36 36 
 	"strheight",
37 37 
 	"strwidth",
38 
+	"text.default",
38 39 
 	"title")
39 40
40 41 
 importFrom("stats",
... ... 
@@ -417,7 +418,8 @@ export(
417 418 
 	"bsearch",
418 419 
 	"kdtree",
419 420 
 	"kdsearch",
420 
-	"knnsearch")
421 
+	"knnsearch",
422 
+	"nnpairs")
421 423
422 424 
 S3method("print", "kdtree")
423 425
... ... 
@@ -453,7 +455,7 @@ export(
453 455 
 	"set_channel",
454 456 
 	"set_coord",
455 457 
 	"set_par",
456 
-	"plot_facets")
458 
+	"as_facets")
457 459
458 460 
 export(
459 461 
 	"vizi_par",
... ... 
@@ -477,6 +479,10 @@ S3method("plot", "vizi_peaks")
477 479 
 S3method("plot", "vizi_pixels")
478 480 
 S3method("plot", "vizi_voxels")
479 481
482 
+export(
483 
+	"plot_signal",
484 
+	"plot_image")
485 
+
480 486 
 exportMethods(
481 487 
 	"preplot",
482 488 
 	"plot")
Browse code

add rowMaj() generic and method

kuwisdelu authored on 02/08/2023 15:12:30
Showing 1 changed files
NAMESPACE
History View file @ 887d2994d
... ... 
@@ -37,19 +37,6 @@ importFrom("graphics",
37 37 
 	"strwidth",
38 38 
 	"title")
39 39
40 
-importFrom("digest",
41 
-	"digest")
42 
-
43 
-importFrom("irlba",
44 
-	"irlba")
45 
-
46 
-importFrom("Matrix",
47 
-	"nnzero",
48 
-	"rowSums",
49 
-	"rowMeans",
50 
-	"colSums",
51 
-	"colMeans")
52 
-
53 40 
 importFrom("stats",
54 41 
 	"approx",
55 42 
 	"cov",
... ... 
@@ -81,6 +68,19 @@ importFrom("stats4",
81 68 
 	"update",
82 69 
 	"summary")
83 70
71 
+importFrom("Matrix",
72 
+	"nnzero",
73 
+	"rowSums",
74 
+	"rowMeans",
75 
+	"colSums",
76 
+	"colMeans")
77 
+
78 
+importFrom("digest",
79 
+	"digest")
80 
+
81 
+importFrom("irlba",
82 
+	"irlba")
83 
+
84 84 
 import("biglm")
85 85
86 86 
 import("BiocParallel")
... ... 
@@ -165,7 +165,8 @@ exportMethods(
165 165 
 	"tolerance<-",
166 166 
 	"sampler",
167 167 
 	"sampler<-",
168 
-	"nnzero")
168 
+	"nnzero",
169 
+	"rowMaj")
169 170
170 171 
 exportMethods(
171 172 
 	"keys",
Browse code

removed remaining defunct functions/methods

kuwisdelu authored on 02/08/2023 14:03:35
Showing 1 changed files
NAMESPACE
History View file @ 5dc7d7a56
... ... 
@@ -151,9 +151,7 @@ exportMethods(
151 151 
 	"path",
152 152 
 	"path<-",
153 153 
 	"readonly",
154 
-	"readonly<-",
155 
-	"chunksize",
156 
-	"chunksize<-")
154 
+	"readonly<-")
157 155
158 156 
 exportMethods(
159 157 
 	"aindex",
... ... 
@@ -172,14 +170,8 @@ exportMethods(
172 170 
 exportMethods(
173 171 
 	"keys",
174 172 
 	"keys<-",
175 
-	"paths",
176 
-	"paths<-",
177 
-	"datamode",
178 
-	"datamode<-",
179 
-	"filemode",
180 
-	"filemode<-",
181 
-	"combiner",
182 
-	"combiner<-")
173 
+	"chunksize",
174 
+	"chunksize<-")
183 175
184 176 
 exportMethods("checksum")
185 177
... ... 
@@ -240,12 +232,6 @@ exportMethods(
240 232 
 	"colSums",
241 233 
 	"colMeans")
242 234
243 
-exportMethods(
244 
-	"rowVars",
245 
-	"rowSds",
246 
-	"colVars",
247 
-	"colSds")
248 
-
249 235 
 export(
250 236 
 	"s_range",
251 237 
 	"s_min",
... ... 
@@ -262,10 +248,6 @@ export(
262 248 
 	"s_rowstats",
263 249 
 	"stat_c")
264 250
265 
-export(
266 
-	"colstreamStats",
267 
-	"rowstreamStats")
268 
-
269 251 
 S3method("c", "stream_stat")
270 252 
 S3method("cbind", "stream_stat")
271 253 
 S3method("rbind", "stream_stat")
Browse code

remove scale() and apply() generics

kuwisdelu authored on 02/08/2023 13:49:25
Showing 1 changed files
NAMESPACE
History View file @ f6679751e
... ... 
@@ -419,13 +419,6 @@ export(
419 419 
 	"cpal",
420 420 
 	"add_alpha")
421 421
422 
-exportMethods(
423 
-	"apply",
424 
-	"lapply",
425 
-	"sapply")
426 
-
427 
-exportMethods("scale")
428 
-
429 422 
 exportMethods(
430 423 
 	"prcomp",
431 424 
 	"bigglm")
Browse code

added vizi_voxels mark

kuwisdelu authored on 01/08/2023 23:47:37
Showing 1 changed files
NAMESPACE
History View file @ 92aa4eddc
... ... 
@@ -485,8 +485,10 @@ export(
485 485
486 486 
 S3method("preplot", "vizi_plot")
487 487 
 S3method("preplot", "vizi_facets")
488 
+
488 489 
 S3method("plot", "vizi_plot")
489 490 
 S3method("plot", "vizi_facets")
491 
+
490 492 
 S3method("print", "vizi_plot")
491 493 
 S3method("print", "vizi_facets")
492 494
... ... 
@@ -496,6 +498,8 @@ S3method("plot", "vizi_colorkey")
496 498 
 S3method("plot", "vizi_points")
497 499 
 S3method("plot", "vizi_lines")
498 500 
 S3method("plot", "vizi_peaks")
501 
+S3method("plot", "vizi_pixels")
502 
+S3method("plot", "vizi_voxels")
499 503
500 504 
 exportMethods(
501 505 
 	"preplot",
Browse code

added 3d support to vizi xy plots

kuwisdelu authored on 01/08/2023 05:39:45
Showing 1 changed files
NAMESPACE
History View file @ f25694ee5
... ... 
@@ -13,6 +13,7 @@ importFrom("grDevices",
13 13 
 	"dev.hold",
14 14 
 	"col2rgb",
15 15 
 	"rgb",
16 
+	"trans3d",
16 17 
 	"as.raster",
17 18 
 	"hcl.colors",
18 19 
 	"palette.colors",
... ... 
@@ -29,6 +30,7 @@ importFrom("graphics",
29 30 
 	"plot.new",
30 31 
 	"plot.window",
31 32 
 	"plot.xy",
33 
+	"persp",
32 34 
 	"polygon",
33 35 
 	"rasterImage",
34 36 
 	"strheight",
... ... 
@@ -300,7 +302,7 @@ export(
300 302 
 	".rowStats",
301 303 
 	".colStats")
302 304
303 
-export("pinv")
305 
+
304 306
305 307 
 export(
306 308 
 	"chunk_apply",
... ... 
@@ -409,6 +411,10 @@ export(
409 411 
 	"roll",
410 412 
 	"seq_rel",
411 413 
 	"shingles",
414 
+	"rescale",
415 
+	"pinv")
416 
+
417 
+export(
412 418 
 	"dpal",
413 419 
 	"cpal",
414 420 
 	"add_alpha")
Browse code

added useRaster=TRUE and polygon fallback for vizi_pixels

kuwisdelu authored on 31/07/2023 18:00:46
Showing 1 changed files
NAMESPACE
History View file @ 24d6d237f
... ... 
@@ -7,6 +7,7 @@ importFrom("utils",
7 7 
 	"object.size")
8 8
9 9 
 importFrom("grDevices",
10 
+	"dev.capabilities",
10 11 
 	"dev.cur",
11 12 
 	"dev.flush",
12 13 
 	"dev.hold",
... ... 
@@ -28,6 +29,7 @@ importFrom("graphics",
28 29 
 	"plot.new",
29 30 
 	"plot.window",
30 31 
 	"plot.xy",
32 
+	"polygon",
31 33 
 	"rasterImage",
32 34 
 	"strheight",
33 35 
 	"strwidth",
Browse code

revised add_mark() to pass encodings via dots

kuwisdelu authored on 31/07/2023 07:25:41
Showing 1 changed files
NAMESPACE
History View file @ eba372c4d
... ... 
@@ -463,12 +463,12 @@ S3method("print", "opls")
463 463
464 464 
 export(
465 465 
 	"vizi",
466 
+	"add_mark",
467 
+	"add_facets",
466 468 
 	"set_title",
467 469 
 	"set_channel",
468 470 
 	"set_coord",
469 471 
 	"set_par",
470 
-	"add_mark",
471 
-	"add_facets",
472 472 
 	"plot_facets")
473 473
474 474 
 export(
Browse code

added vizi_pixels for image plotting

kuwisdelu authored on 31/07/2023 04:15:30
Showing 1 changed files
NAMESPACE
History View file @ 482990e69
... ... 
@@ -12,6 +12,7 @@ importFrom("grDevices",
12 12 
 	"dev.hold",
13 13 
 	"col2rgb",
14 14 
 	"rgb",
15 
+	"as.raster",
15 16 
 	"hcl.colors",
16 17 
 	"palette.colors",
17 18 
 	"xy.coords")
... ... 
@@ -27,6 +28,7 @@ importFrom("graphics",
27 28 
 	"plot.new",
28 29 
 	"plot.window",
29 30 
 	"plot.xy",
31 
+	"rasterImage",
30 32 
 	"strheight",
31 33 
 	"strwidth",
32 34 
 	"title")
... ... 
@@ -464,6 +466,7 @@ export(
464 466 
 	"set_title",
465 467 
 	"set_channel",
466 468 
 	"set_coord",
469 
+	"set_par",
467 470 
 	"add_mark",
468 471 
 	"add_facets",
469 472 
 	"plot_facets")
Browse code

add alpha support to vizi plotting; fixed more bugs

kuwisdelu authored on 30/07/2023 23:16:34
Showing 1 changed files
NAMESPACE
History View file @ 3e2a70528
... ... 
@@ -10,6 +10,8 @@ importFrom("grDevices",
10 10 
 	"dev.cur",
11 11 
 	"dev.flush",
12 12 
 	"dev.hold",
13 
+	"col2rgb",
14 
+	"rgb",
13 15 
 	"hcl.colors",
14 16 
 	"palette.colors",
15 17 
 	"xy.coords")
... ... 
@@ -404,7 +406,8 @@ export(
404 406 
 	"seq_rel",
405 407 
 	"shingles",
406 408 
 	"dpal",
407 
-	"cpal")
409 
+	"cpal",
410 
+	"add_alpha")
408 411
409 412 
 exportMethods(
410 413 
 	"apply",
Browse code

added internal filt1_fun(), estnoise_fun(), etc. functions

kuwisdelu authored on 30/07/2023 20:43:06
Showing 1 changed files
NAMESPACE
History View file @ c9cabb485
... ... 
@@ -1,7 +1,33 @@
1 1
2 2 
 import("methods")
3 3
4 
-import("biglm")
4 
+importFrom("utils",
5 
+	"head",
6 
+	"tail",
7 
+	"object.size")
8 
+
9 
+importFrom("grDevices",
10 
+	"dev.cur",
11 
+	"dev.flush",
12 
+	"dev.hold",
13 
+	"hcl.colors",
14 
+	"palette.colors",
15 
+	"xy.coords")
16 
+
17 
+importFrom("graphics",
18 
+	"Axis",
19 
+	"box",
20 
+	"co.intervals",
21 
+	"grid",
22 
+	"legend",
23 
+	"mtext",
24 
+	"par",
25 
+	"plot.new",
26 
+	"plot.window",
27 
+	"plot.xy",
28 
+	"strheight",
29 
+	"strwidth",
30 
+	"title")
5 31
6 32 
 importFrom("digest",
7 33 
 	"digest")
... ... 
@@ -47,40 +73,14 @@ importFrom("stats4",
47 73 
 	"update",
48 74 
 	"summary")
49 75
76 
+import("biglm")
77 
+
50 78 
 import("BiocParallel")
51 79
52 80 
 import("BiocGenerics")
53 81
54 82 
 import("ProtGenerics")
55 83
56 
-importFrom("utils",
57 
-	"head",
58 
-	"tail",
59 
-	"object.size")
60 
-
61 
-importFrom("grDevices",
62 
-	"dev.cur",
63 
-	"dev.flush",
64 
-	"dev.hold",
65 
-	"hcl.colors",
66 
-	"palette.colors",
67 
-	"xy.coords")
68 
-
69 
-importFrom("graphics",
70 
-	"Axis",
71 
-	"box",
72 
-	"co.intervals",
73 
-	"grid",
74 
-	"legend",
75 
-	"mtext",
76 
-	"par",
77 
-	"plot.new",
78 
-	"plot.window",
79 
-	"plot.xy",
80 
-	"strheight",
81 
-	"strwidth",
82 
-	"title")
83 
-
84 84 
 exportClasses(
85 85 
 	"drle",
86 86 
 	"drle_fct",
Browse code

added vizi tests, fixed bugs, and added print methods

kuwisdelu authored on 30/07/2023 18:28:17
Showing 1 changed files
NAMESPACE
History View file @ 9415b94a4
... ... 
@@ -458,6 +458,7 @@ S3method("print", "opls")
458 458
459 459 
 export(
460 460 
 	"vizi",
461 
+	"set_title",
461 462 
 	"set_channel",
462 463 
 	"set_coord",
463 464 
 	"add_mark",
... ... 
@@ -472,6 +473,9 @@ S3method("preplot", "vizi_plot")
472 473 
 S3method("preplot", "vizi_facets")
473 474 
 S3method("plot", "vizi_plot")
474 475 
 S3method("plot", "vizi_facets")
476 
+S3method("print", "vizi_plot")
477 
+S3method("print", "vizi_facets")
478 
+
475 479 
 S3method("plot", "vizi_key")
476 480 
 S3method("plot", "vizi_colorkey")
477 481
Browse code

rename profmem() => memtime()

kuwisdelu authored on 30/07/2023 07:08:49
Showing 1 changed files
NAMESPACE
History View file @ e03c06962
... ... 
@@ -485,6 +485,7 @@ exportMethods(
485 485
486 486 
 export(
487 487 
 	"mem",
488 
+	"memtime",
488 489 
 	"profmem")
489 490
490 491 
 useDynLib("matter", .registration=TRUE, .fixes="C_")
Browse code

added to_raster() and to_raster3()

kuwisdelu authored on 30/07/2023 06:35:00
Showing 1 changed files
NAMESPACE
History View file @ 843af8969
... ... 
@@ -378,6 +378,10 @@ export(
378 378 
 	"mi",
379 379 
 	"enhance_hist",
380 380 
 	"enhance_adapt",
381 
+	"is_gridded",
382 
+	"to_raster",
383 
+	"to_raster3",
384 
+	"estdim",
381 385 
 	"trans2d")
382 386
383 387 
 export(
Browse code

added convolve_at() + docs and tests

kuwisdelu authored on 29/07/2023 20:51:38
Showing 1 changed files
NAMESPACE
History View file @ bd96007ee
... ... 
@@ -332,6 +332,7 @@ export(
332 332 
 	"filt1_guide",
333 333 
 	"filt1_pag",
334 334 
 	"filt1_sg",
335 
+	"convolve_at",
335 336 
 	"warp1_loc",
336 337 
 	"warp1_dtw",
337 338 
 	"warp1_cow",
Browse code

added fastmap() docs

kuwisdelu authored on 28/07/2023 23:14:18
Showing 1 changed files
NAMESPACE
History View file @ 23e319028
... ... 
@@ -296,30 +296,6 @@ export(
296 296
297 297 
 export("pinv")
298 298
299 
-export(
300 
-	"nndsvd",
301 
-	"nnmf_als",
302 
-	"nnmf_mult",
303 
-	"fastmap_func",
304 
-	"prcomp_lanczos",
305 
-	"pls_nipals",
306 
-	"pls_simpls",
307 
-	"pls_kernel",
308 
-	"opls_nipals",
309 
-	"vip")
310 
-
311 
-S3method("predict", "nnmf")
312 
-S3method("print", "nnmf")
313 
-
314 
-S3method("predict", "fastmap")
315 
-S3method("print", "fastmap")
316 
-
317 
-S3method("predict", "pls")
318 
-S3method("print", "pls")
319 
-
320 
-S3method("predict", "opls")
321 
-S3method("print", "opls")
322 
-
323 299 
 export(
324 300 
 	"chunk_apply",
325 301 
 	"chunk_rowapply",
... ... 
@@ -415,8 +391,8 @@ exportMethods(
415 391 
 	"colDists")
416 392
417 393 
 export(
418 
-	".rowDists",
419 
-	".colDists")
394 
+	"rowDistFun",
395 
+	"colDistFun")
420 396
421 397 
 export(
422 398 
 	"roll",
... ... 
@@ -430,9 +406,9 @@ exportMethods(
430 406 
 	"lapply",
431 407 
 	"sapply")
432 408
409 
+exportMethods("scale")
410 
+
433 411 
 exportMethods(
434 
-	"scale",
435 
-	"fastmap",
436 412 
 	"prcomp",
437 413 
 	"bigglm")
438 414
... ... 
@@ -451,6 +427,30 @@ export(
451 427
452 428 
 S3method("print", "kdtree")
453 429
430 
+export(
431 
+	"fastmap",
432 
+	"nndsvd",
433 
+	"nnmf_als",
434 
+	"nnmf_mult",
435 
+	"prcomp_lanczos",
436 
+	"pls_nipals",
437 
+	"pls_simpls",
438 
+	"pls_kernel",
439 
+	"opls_nipals",
440 
+	"vip")
441 
+
442 
+S3method("predict", "fastmap")
443 
+S3method("print", "fastmap")
444 
+
445 
+S3method("predict", "nnmf")
446 
+S3method("print", "nnmf")
447 
+
448 
+S3method("predict", "pls")
449 
+S3method("print", "pls")
450 
+
451 
+S3method("predict", "opls")
452 
+S3method("print", "opls")
453 
+
454 454 
 export(
455 455 
 	"vizi",
456 456 
 	"set_channel",
Browse code

updated fastmap()

kuwisdelu authored on 28/07/2023 21:18:22
Showing 1 changed files
NAMESPACE
History View file @ 4a9c2cd53
... ... 
@@ -300,7 +300,7 @@ export(
300 300 
 	"nndsvd",
301 301 
 	"nnmf_als",
302 302 
 	"nnmf_mult",
303 
-	"fastmap_fun",
303 
+	"fastmap_func",
304 304 
 	"prcomp_lanczos",
305 305 
 	"pls_nipals",
306 306 
 	"pls_simpls",
... ... 
@@ -311,6 +311,9 @@ export(
311 311 
 S3method("predict", "nnmf")
312 312 
 S3method("print", "nnmf")
313 313
314 
+S3method("predict", "fastmap")
315 
+S3method("print", "fastmap")
316 
+
314 317 
 S3method("predict", "pls")
315 318 
 S3method("print", "pls")
316 319
Browse code

added rowDists() and colDists()

kuwisdelu authored on 28/07/2023 06:53:36
Showing 1 changed files
NAMESPACE
History View file @ 3fad69ffd
... ... 
@@ -407,6 +407,14 @@ export(
407 407 
 	"rowdist_at",
408 408 
 	"coldist_at")
409 409
410 
+exportMethods(
411 
+	"rowDists",
412 
+	"colDists")
413 
+
414 
+export(
415 
+	".rowDists",
416 
+	".colDists")
417 
+
410 418 
 export(
411 419 
 	"roll",
412 420 
 	"seq_rel",
Browse code

added fastmap() projection

kuwisdelu authored on 27/07/2023 19:08:51
Showing 1 changed files
NAMESPACE
History View file @ 532f4f63e
... ... 
@@ -300,12 +300,13 @@ export(
300 300 
 	"nndsvd",
301 301 
 	"nnmf_als",
302 302 
 	"nnmf_mult",
303 
+	"fastmap_fun",
303 304 
 	"prcomp_lanczos",
304 305 
 	"pls_nipals",
305 306 
 	"pls_simpls",
306 307 
 	"pls_kernel",
307 
-	"vip",
308 
-	"opls_nipals")
308 
+	"opls_nipals",
309 
+	"vip")
309 310
310 311 
 S3method("predict", "nnmf")
311 312 
 S3method("print", "nnmf")
... ... 
@@ -418,11 +419,11 @@ exportMethods(
418 419 
 	"lapply",
419 420 
 	"sapply")
420 421
421 
-exportMethods("scale")
422 
-
423 
-exportMethods("prcomp")
424 
-
425 
-exportMethods("bigglm")
422 
+exportMethods(
423 
+	"scale",
424 
+	"fastmap",
425 
+	"prcomp",
426 
+	"bigglm")
426 427
427 428 
 export(
428 429 
 	"qrank",
Browse code

added variable importance in projection vip() scores

kuwisdelu authored on 26/07/2023 04:32:13
Showing 1 changed files
NAMESPACE
History View file @ 1422ca0fd
... ... 
@@ -304,6 +304,7 @@ export(
304 304 
 	"pls_nipals",
305 305 
 	"pls_simpls",
306 306 
 	"pls_kernel",
307 
+	"vip",
307 308 
 	"opls_nipals")
308 309
309 310 
 S3method("predict", "nnmf")
Browse code

added pls_simpls()

kuwisdelu authored on 25/07/2023 23:17:33
Showing 1 changed files
NAMESPACE
History View file @ 592fd6e11
... ... 
@@ -302,6 +302,7 @@ export(
302 302 
 	"nnmf_mult",
303 303 
 	"prcomp_lanczos",
304 304 
 	"pls_nipals",
305 
+	"pls_simpls",
305 306 
 	"pls_kernel",
306 307 
 	"opls_nipals")
307 308
Browse code

added pls + opls docs; fixed bug in predict.nnmf

kuwisdelu authored on 25/07/2023 21:07:09
Showing 1 changed files
NAMESPACE
History View file @ 410b47af5
... ... 
@@ -19,6 +19,10 @@ importFrom("Matrix",
19 19 
 importFrom("stats",
20 20 
 	"approx",
21 21 
 	"cov",
22 
+	"coef",
23 
+	"fitted",
24 
+	"resid",
25 
+	"loadings",
22 26 
 	"dnorm",
23 27 
 	"fft",
24 28 
 	"median",
Browse code

added pls_kernel()

kuwisdelu authored on 25/07/2023 18:48:24
Showing 1 changed files
NAMESPACE
History View file @ 52feb27d2
... ... 
@@ -298,6 +298,7 @@ export(
298 298 
 	"nnmf_mult",
299 299 
 	"prcomp_lanczos",
300 300 
 	"pls_nipals",
301 
+	"pls_kernel",
301 302 
 	"opls_nipals")
302 303
303 304 
 S3method("predict", "nnmf")
Browse code

fixed bug for multi-y opls; added predict.opls()

kuwisdelu authored on 24/07/2023 22:59:39
Showing 1 changed files
NAMESPACE
History View file @ d245cc3fa
... ... 
@@ -306,6 +306,9 @@ S3method("print", "nnmf")
306 306 
 S3method("predict", "pls")
307 307 
 S3method("print", "pls")
308 308
309 
+S3method("predict", "opls")
310 
+S3method("print", "opls")
311 
+
309 312 
 export(
310 313 
 	"chunk_apply",
311 314 
 	"chunk_rowapply",
Browse code

added print() and predict() for pls

kuwisdelu authored on 24/07/2023 19:25:29
Showing 1 changed files
NAMESPACE
History View file @ c131147b0
... ... 
@@ -296,13 +296,16 @@ export(
296 296 
 	"nndsvd",
297 297 
 	"nnmf_als",
298 298 
 	"nnmf_mult",
299 
-	"prcomp_lanczos"
299 
+	"prcomp_lanczos",
300 300 
 	"pls_nipals",
301 301 
 	"opls_nipals")
302 302
303 303 
 S3method("predict", "nnmf")
304 304 
 S3method("print", "nnmf")
305 305
306 
+S3method("predict", "pls")
307 
+S3method("print", "pls")
308 
+
306 309 
 export(
307 310 
 	"chunk_apply",
308 311 
 	"chunk_rowapply",
Browse code

added opls_nipals()

kuwisdelu authored on 24/07/2023 18:54:45
Showing 1 changed files
NAMESPACE
History View file @ 8067bf177
... ... 
@@ -297,7 +297,8 @@ export(
297 297 
 	"nnmf_als",
298 298 
 	"nnmf_mult",
299 299 
 	"prcomp_lanczos"
300 
-	"pls_nipals")
300 
+	"pls_nipals",
301 
+	"opls_nipals")
301 302
302 303 
 S3method("predict", "nnmf")
303 304 
 S3method("print", "nnmf")
Browse code

added pls_nipals()

kuwisdelu authored on 24/07/2023 16:19:32
Showing 1 changed files
NAMESPACE
History View file @ 1797f3cd0
... ... 
@@ -296,7 +296,8 @@ export(
296 296 
 	"nndsvd",
297 297 
 	"nnmf_als",
298 298 
 	"nnmf_mult",
299 
-	"prcomp_lanczos")
299 
+	"prcomp_lanczos"
300 
+	"pls_nipals")
300 301
301 302 
 S3method("predict", "nnmf")
302 303 
 S3method("print", "nnmf")
Browse code

added estres()

kuwisdelu authored on 24/07/2023 02:02:16
Showing 1 changed files
NAMESPACE
History View file @ 4bd796586
... ... 
@@ -365,6 +365,7 @@ export(
365 365 
 	"peakareas",
366 366 
 	"binpeaks",
367 367 
 	"mergepeaks",
368 
+	"estres",
368 369 
 	"simspec",
369 370 
 	"simspec1")
370 371
Browse code

split up vizi marks plotting; update docs

kuwisdelu authored on 21/07/2023 16:07:49
Showing 1 changed files
NAMESPACE
History View file @ 192ed833a
... ... 
@@ -437,14 +437,14 @@ export(
437 437
438 438 
 S3method("preplot", "vizi_plot")
439 439 
 S3method("preplot", "vizi_facets")
440 
-
441 440 
 S3method("plot", "vizi_plot")
442 441 
 S3method("plot", "vizi_facets")
442 
+S3method("plot", "vizi_key")
443 
+S3method("plot", "vizi_colorkey")
444 
+
443 445 
 S3method("plot", "vizi_points")
444 446 
 S3method("plot", "vizi_lines")
445 447 
 S3method("plot", "vizi_peaks")
446 
-S3method("plot", "vizi_key")
447 
-S3method("plot", "vizi_colorkey")
448 448
449 449 
 exportMethods(
450 450 
 	"preplot",
Browse code

added nmf_als() using alternating least squares

kuwisdelu authored on 21/07/2023 05:11:52
Showing 1 changed files
NAMESPACE
History View file @ 16dbd92a5
... ... 
@@ -294,6 +294,7 @@ export("pinv")
294 294
295 295 
 export(
296 296 
 	"nndsvd",
297 
+	"nnmf_als",
297 298 
 	"nnmf_mult",
298 299 
 	"prcomp_lanczos")
299 300
Browse code

rename nmf() => nnmf()

kuwisdelu authored on 21/07/2023 04:25:14
Showing 1 changed files
NAMESPACE
History View file @ eafd4c44c
... ... 
@@ -294,11 +294,11 @@ export("pinv")
294 294
295 295 
 export(
296 296 
 	"nndsvd",
297 
-	"nmf_mu",
297 
+	"nnmf_mult",
298 298 
 	"prcomp_lanczos")
299 299
300 
-S3method("predict", "nmf")
301 
-S3method("print", "nmf")
300 
+S3method("predict", "nnmf")
301 
+S3method("print", "nnmf")
302 302
303 303 
 export(
304 304 
 	"chunk_apply",
Browse code

added predict.nmf and docs

kuwisdelu authored on 21/07/2023 02:46:24
Showing 1 changed files
NAMESPACE
History View file @ f2dbcaefc
... ... 
@@ -290,11 +290,14 @@ export(
290 290 
 	".rowStats",
291 291 
 	".colStats")
292 292
293 
+export("pinv")
294 
+
293 295 
 export(
294 296 
 	"nndsvd",
295 297 
 	"nmf_mu",
296 298 
 	"prcomp_lanczos")
297 299
300 
+S3method("predict", "nmf")
298 301 
 S3method("print", "nmf")
299 302
300 303 
 export(
Browse code

updated nmf_mu() and added NMF docs + tests

kuwisdelu authored on 20/07/2023 22:04:04
Showing 1 changed files
NAMESPACE
History View file @ 4e2215e10
... ... 
@@ -291,8 +291,12 @@ export(
291 291 
 	".colStats")
292 292
293 293 
 export(
294 
+	"nndsvd",
295 
+	"nmf_mu",
294 296 
 	"prcomp_lanczos")
295 297
298 
+S3method("print", "nmf")
299 
+
296 300 
 export(
297 301 
 	"chunk_apply",
298 302 
 	"chunk_rowapply",
Browse code

fixed bugs in prcomp; added prcomp_lanczos(); added nmf_mu()

kuwisdelu authored on 20/07/2023 19:25:33
Showing 1 changed files
NAMESPACE
History View file @ c1a6e4a5f
... ... 
@@ -290,6 +290,9 @@ export(
290 290 
 	".rowStats",
291 291 
 	".colStats")
292 292
293 
+export(
294 
+	"prcomp_lanczos")
295 
+
293 296 
 export(
294 297 
 	"chunk_apply",
295 298 
 	"chunk_rowapply",
Browse code

updated bigglm() args; rearranged some utility functions

kuwisdelu authored on 19/07/2023 22:18:47
Showing 1 changed files
NAMESPACE
History View file @ 5be3b9993
... ... 
@@ -418,7 +418,7 @@ export(
418 418 
 	"set_coord",
419 419 
 	"add_mark",
420 420 
 	"add_facets",
421 
-	"as_facets")
421 
+	"plot_facets")
422 422
423 423 
 export(
424 424 
 	"vizi_par",
Browse code

added rowdist_at() and coldist_at()

kuwisdelu authored on 15/07/2023 05:16:46
Showing 1 changed files
NAMESPACE
History View file @ 364dc685a
... ... 
@@ -375,7 +375,9 @@ export(
375 375 
 export(
376 376 
 	"inpoly",
377 377 
 	"rowdist",
378 
-	"coldist")
378 
+	"coldist",
379 
+	"rowdist_at",
380 
+	"coldist_at")
379 381
380 382 
 export(
381 383 
 	"roll",
Browse code

added knnsearch(), rowdist() and coldist()

kuwisdelu authored on 13/07/2023 18:02:10
Showing 1 changed files
NAMESPACE
History View file @ dfb0c3322
... ... 
@@ -372,7 +372,10 @@ export(
372 372 
 	"enhance_adapt",
373 373 
 	"trans2d")
374 374
375 
-export("inpoly")
375 
+export(
376 
+	"inpoly",
377 
+	"rowdist",
378 
+	"coldist")
376 379
377 380 
 export(
378 381 
 	"roll",
... ... 
@@ -401,8 +404,9 @@ export(
401 404 
 	"reldiff",
402 405 
 	"asearch",
403 406 
 	"bsearch",
407 
+	"kdtree",
404 408 
 	"kdsearch",
405 
-	"kdtree")
409 
+	"knnsearch")
406 410
407 411 
 S3method("print", "kdtree")
408 412
Browse code

added in_poly()

kuwisdelu authored on 11/07/2023 02:45:01
Showing 1 changed files
NAMESPACE
History View file @ fc9f95522
... ... 
@@ -372,6 +372,8 @@ export(
372 372 
 	"enhance_adapt",
373 373 
 	"trans2d")
374 374
375 
+export("inpoly")
376 
+
375 377 
 export(
376 378 
 	"roll",
377 379 
 	"seq_rel",
Browse code

added CLAHE; enhance_heq => enhance_hist(), enhance_aheq => enhance_adapt()

kuwisdelu authored on 10/07/2023 21:26:38
Showing 1 changed files
NAMESPACE
History View file @ 97a8319fb
... ... 
@@ -368,8 +368,8 @@ export(
368 368 
 	"filt2_guide",
369 369 
 	"warp2_trans",
370 370 
 	"mi",
371 
-	"enhance_heq",
372 
-	"enhance_aheq",
371 
+	"enhance_hist",
372 
+	"enhance_adapt",
373 373 
 	"trans2d")
374 374
375 375 
 export(
Browse code

added enhance_aheq()

kuwisdelu authored on 09/07/2023 19:55:54
Showing 1 changed files
NAMESPACE
History View file @ 584b04625
... ... 
@@ -369,6 +369,7 @@ export(
369 369 
 	"warp2_trans",
370 370 
 	"mi",
371 371 
 	"enhance_heq",
372 
+	"enhance_aheq",
372 373 
 	"trans2d")
373 374
374 375 
 export(
Browse code

added qrank() and enhance_heq()

kuwisdelu authored on 09/07/2023 15:30:19
Showing 1 changed files
NAMESPACE
History View file @ 627d5a01e
... ... 
@@ -368,6 +368,7 @@ export(
368 368 
 	"filt2_guide",
369 369 
 	"warp2_trans",
370 370 
 	"mi",
371 
+	"enhance_heq",
371 372 
 	"trans2d")
372 373
373 374 
 export(
... ... 
@@ -389,6 +390,7 @@ exportMethods("prcomp")
389 390 
 exportMethods("bigglm")
390 391
391 392 
 export(
393 
+	"qrank",
392 394 
 	"qorder",
393 395 
 	"qselect",
394 396 
 	"qmedian",
Browse code

added snr to findpeaks(); fixed some more bugs; updated docs

kuwisdelu authored on 08/07/2023 05:43:21
Showing 1 changed files
NAMESPACE
History View file @ cae75c446
... ... 
@@ -344,7 +344,6 @@ export(
344 344 
 	"estnoise_mad",
345 345 
 	"estnoise_diff",
346 346 
 	"estnoise_quant",
347 
-	"estnoise_smooth",
348 347 
 	"estnoise_filt",
349 348 
 	"findpeaks",
350 349 
 	"findpeaks_cwt",
... ... 
@@ -361,6 +360,7 @@ export(
361 360 
 export(
362 361 
 	"approx2",
363 362 
 	"filt2_ma",
363 
+	"filt2_conv",
364 364 
 	"filt2_gauss",
365 365 
 	"filt2_bi",
366 366 
 	"filt2_adapt",
Browse code

improved estnoise_xxx() functions

kuwisdelu authored on 08/07/2023 00:18:45
Showing 1 changed files
NAMESPACE
History View file @ c040dd880
... ... 
@@ -318,6 +318,7 @@ export(
318 318 
 export(
319 319 
 	"approx1",
320 320 
 	"filt1_ma",
321 
+	"filt1_conv",
321 322 
 	"filt1_gauss",
322 323 
 	"filt1_bi",
323 324 
 	"filt1_adapt",
... ... 
@@ -342,7 +343,8 @@ export(
342 343 
 	"estnoise_sd",
343 344 
 	"estnoise_mad",
344 345 
 	"estnoise_diff",
345 
-	"estnoise_loess",
346 
+	"estnoise_quant",
347 
+	"estnoise_smooth",
346 348 
 	"estnoise_filt",
347 349 
 	"findpeaks",
348 350 
 	"findpeaks_cwt",
Browse code

fixed bugs in findpeaks_cwt()

kuwisdelu authored on 07/07/2023 08:47:23
Showing 1 changed files
NAMESPACE
History View file @ 8fb68e001
... ... 
@@ -302,10 +302,6 @@ export(
302 302 
 	"chunkLapply",
303 303 
 	"chunkMapply")
304 304
305 
-export(
306 
-	"roll",
307 
-	"rollapply")
308 
-
309 305 
 export(
310 306 
 	"uuid",
311 307 
 	"hex2raw",
... ... 
@@ -334,6 +330,7 @@ export(
334 330 
 	"warp1_cow",
335 331 
 	"icor",
336 332 
 	"binvec",
333 
+	"rollvec",
337 334 
 	"findbins",
338 335 
 	"downsample",
339 336 
 	"locmax",
... ... 
@@ -372,6 +369,7 @@ export(
372 369 
 	"trans2d")
373 370
374 371 
 export(
372 
+	"roll",
375 373 
 	"seq_rel",
376 374 
 	"shingles",
377 375 
 	"dpal",
Browse code

added findpeaks_cwt(); removed Rprof output

kuwisdelu authored on 07/07/2023 03:18:36
Showing 1 changed files
NAMESPACE
History View file @ b08c7023b
... ... 
@@ -302,6 +302,10 @@ export(
302 302 
 	"chunkLapply",
303 303 
 	"chunkMapply")
304 304
305 
+export(
306 
+	"roll",
307 
+	"rollapply")
308 
+
305 309 
 export(
306 310 
 	"uuid",
307 311 
 	"hex2raw",
... ... 
@@ -344,6 +348,10 @@ export(
344 348 
 	"estnoise_loess",
345 349 
 	"estnoise_filt",
346 350 
 	"findpeaks",
351 
+	"findpeaks_cwt",
352 
+	"findridges",
353 
+	"ricker",
354 
+	"cwt",
347 355 
 	"peakwidths",
348 356 
 	"peakareas",
349 357 
 	"binpeaks",
... ... 
@@ -364,7 +372,6 @@ export(
364 372 
 	"trans2d")
365 373
366 374 
 export(
367 
-	"roll",
368 375 
 	"seq_rel",
369 376 
 	"shingles",
370 377 
 	"dpal",
Browse code

added cwt() and findridges(); reverted binsum() => binvec()

kuwisdelu authored on 06/07/2023 23:27:40
Showing 1 changed files
NAMESPACE
History View file @ e05022737
... ... 
@@ -20,7 +20,9 @@ importFrom("stats",
20 20 
 	"approx",
21 21 
 	"cov",
22 22 
 	"dnorm",
23 
+	"fft",
23 24 
 	"median",
25 
+	"nextn",
24 26 
 	"loess",
25 27 
 	"lowess",
26 28 
 	"na.omit",
... ... 
@@ -327,7 +329,6 @@ export(
327 329 
 	"warp1_dtw",
328 330 
 	"warp1_cow",
329 331 
 	"icor",
330 
-	"binsum",
331 332 
 	"binvec",
332 333 
 	"findbins",
333 334 
 	"downsample",
Browse code

added warp2_trans() unit test

kuwisdelu authored on 05/07/2023 08:01:02
Showing 1 changed files
NAMESPACE
History View file @ c9dcfb4e1
... ... 
@@ -352,7 +352,6 @@ export(
352 352
353 353 
 export(
354 354 
 	"approx2",
355 
-	"trans2d"
356 355 
 	"filt2_ma",
357 356 
 	"filt2_gauss",
358 357 
 	"filt2_bi",
... ... 
@@ -360,7 +359,8 @@ export(
360 359 
 	"filt2_diff",
361 360 
 	"filt2_guide",
362 361 
 	"warp2_trans",
363 
-	"mi")
362 
+	"mi",
363 
+	"trans2d")
364 364
365 365 
 export(
366 366 
 	"roll",
Browse code

added warp2_trans() and mi(); binvec() -> binsum()

kuwisdelu authored on 05/07/2023 07:34:08
Showing 1 changed files
NAMESPACE
History View file @ 196f551c0
... ... 
@@ -25,6 +25,7 @@ importFrom("stats",
25 25 
 	"lowess",
26 26 
 	"na.omit",
27 27 
 	"nobs",
28 
+	"optim",
28 29 
 	"predict",
29 30 
 	"qnorm",
30 31 
 	"rlnorm",
... ... 
@@ -326,6 +327,7 @@ export(
326 327 
 	"warp1_dtw",
327 328 
 	"warp1_cow",
328 329 
 	"icor",
330 
+	"binsum",
329 331 
 	"binvec",
330 332 
 	"findbins",
331 333 
 	"downsample",
... ... 
@@ -350,12 +352,15 @@ export(
350 352
351 353 
 export(
352 354 
 	"approx2",
355 
+	"trans2d"
353 356 
 	"filt2_ma",
354 357 
 	"filt2_gauss",
355 358 
 	"filt2_bi",
356 359 
 	"filt2_adapt",
357 360 
 	"filt2_diff",
358 
-	"filt2_guide")
361 
+	"filt2_guide",
362 
+	"warp2_trans",
363 
+	"mi")
359 364
360 365 
 export(
361 366 
 	"roll",
Browse code

added diffusion filters + savitsky-golay 1d filter

kuwisdelu authored on 04/07/2023 07:54:33
Showing 1 changed files
NAMESPACE
History View file @ b50099fc7
... ... 
@@ -318,8 +318,10 @@ export(
318 318 
 	"filt1_gauss",
319 319 
 	"filt1_bi",
320 320 
 	"filt1_adapt",
321 
+	"filt1_diff",
321 322 
 	"filt1_guide",
322 323 
 	"filt1_pag",
324 
+	"filt1_sg",
323 325 
 	"warp1_loc",
324 326 
 	"warp1_dtw",
325 327 
 	"warp1_cow",
... ... 
@@ -352,6 +354,7 @@ export(
352 354 
 	"filt2_gauss",
353 355 
 	"filt2_bi",
354 356 
 	"filt2_adapt",
357 
+	"filt2_diff",
355 358 
 	"filt2_guide")
356 359
357 360 
 export(
Browse code

added filt2_guide() + fixed bug in filt2_bi()

kuwisdelu authored on 03/07/2023 22:44:17
Showing 1 changed files
NAMESPACE
History View file @ 64b7bcf48
... ... 
@@ -351,7 +351,8 @@ export(
351 351 
 	"filt2_ma",
352 352 
 	"filt2_gauss",
353 353 
 	"filt2_bi",
354 
-	"filt2_adapt")
354 
+	"filt2_adapt",
355 
+	"filt2_guide")
355 356
356 357 
 export(
357 358 
 	"roll",
Browse code

added filt2_ma(), filt2_gauss(), filt2_bi(), and filt2_adapt()

kuwisdelu authored on 03/07/2023 05:15:52
Showing 1 changed files
NAMESPACE
History View file @ 0cb9e1011
... ... 
@@ -314,7 +314,6 @@ export(
314 314
315 315 
 export(
316 316 
 	"approx1",
317 
-	"approx2",
318 317 
 	"filt1_ma",
319 318 
 	"filt1_gauss",
320 319 
 	"filt1_bi",
... ... 
@@ -347,6 +346,13 @@ export(
347 346 
 	"simspec",
348 347 
 	"simspec1")
349 348
349 
+export(
350 
+	"approx2",
351 
+	"filt2_ma",
352 
+	"filt2_gauss",
353 
+	"filt2_bi",
354 
+	"filt2_adapt")
355 
+
350 356 
 export(
351 357 
 	"roll",
352 358 
 	"seq_rel",
Browse code

added approx2() for 2D nonuniform interpolation

kuwisdelu authored on 02/07/2023 05:00:13
Showing 1 changed files
NAMESPACE
History View file @ 2583eb45e
... ... 
@@ -314,6 +314,7 @@ export(
314 314
315 315 
 export(
316 316 
 	"approx1",
317 
+	"approx2",
317 318 
 	"filt1_ma",
318 319 
 	"filt1_gauss",
319 320 
 	"filt1_bi",
Browse code

added kdtree() and kdsearch()

kuwisdelu authored on 29/06/2023 05:52:51
Showing 1 changed files
NAMESPACE
History View file @ 12062285e
... ... 
@@ -371,7 +371,11 @@ export(
371 371 
 	"qmad",
372 372 
 	"reldiff",
373 373 
 	"asearch",
374 
-	"bsearch")
374 
+	"bsearch",
375 
+	"kdsearch",
376 
+	"kdtree")
377 
+
378 
+S3method("print", "kdtree")
375 379
376 380 
 export(
377 381 
 	"vizi",
Browse code

missing comma in NAMESPACE

kuwisdelu authored on 28/06/2023 15:49:02
Showing 1 changed files
NAMESPACE
History View file @ 1ef683f02
... ... 
@@ -313,7 +313,7 @@ export(
313 313 
 	"vm_used")
314 314
315 315 
 export(
316 
-	"approx1"
316 
+	"approx1",
317 317 
 	"filt1_ma",
318 318 
 	"filt1_gauss",
319 319 
 	"filt1_bi",
Browse code

small NAMESPACE reorder

Kylie Bemis authored on 28/06/2023 05:05:21
Showing 1 changed files
NAMESPACE
History View file @ 5d3815e2e
... ... 
@@ -313,8 +313,7 @@ export(
313 313 
 	"vm_used")
314 314
315 315 
 export(
316 
-	"simspec",
317 
-	"simspec1",
316 
+	"approx1"
318 317 
 	"filt1_ma",
319 318 
 	"filt1_gauss",
320 319 
 	"filt1_bi",
... ... 
@@ -344,7 +343,8 @@ export(
344 343 
 	"peakareas",
345 344 
 	"binpeaks",
346 345 
 	"mergepeaks",
347 
-	"approx1")
346 
+	"simspec",
347 
+	"simspec1")
348 348
349 349 
 export(
350 350 
 	"roll",
Browse code

updated simspec() and simspec1()

kuwisdelu authored on 27/06/2023 05:42:52
Showing 1 changed files
NAMESPACE
History View file @ 1364642f0
... ... 
@@ -340,10 +340,10 @@ export(
340 340 
 	"estnoise_loess",
341 341 
 	"estnoise_filt",
342 342 
 	"findpeaks",
343 
-	"binpeaks",
344 
-	"mergepeaks",
345 343 
 	"peakwidths",
346 344 
 	"peakareas",
345 
+	"binpeaks",
346 
+	"mergepeaks",
347 347 
 	"approx1")
348 348
349 349 
 export(
Browse code

documented most signal processing stuff

kuwisdelu authored on 27/06/2023 04:18:59
Showing 1 changed files
NAMESPACE
History View file @ 79d185ccf
... ... 
@@ -313,6 +313,8 @@ export(
313 313 
 	"vm_used")
314 314
315 315 
 export(
316 
+	"simspec",
317 
+	"simspec1",
316 318 
 	"filt1_ma",
317 319 
 	"filt1_gauss",
318 320 
 	"filt1_bi",
... ... 
@@ -332,18 +334,17 @@ export(
332 334 
 	"estbase_hull",
333 335 
 	"estbase_snip",
334 336 
 	"estbase_med",
335 
-	"estnoise_filt",
336 337 
 	"estnoise_sd",
337 338 
 	"estnoise_mad",
338 339 
 	"estnoise_diff",
339 
-	"estnoise_smooth",
340 
+	"estnoise_loess",
341 
+	"estnoise_filt",
340 342 
 	"findpeaks",
341 343 
 	"binpeaks",
342 344 
 	"mergepeaks",
343 345 
 	"peakwidths",
344 346 
 	"peakareas",
345 
-	"approx1",
346 
-	"simspectra")
347 
+	"approx1")
347 348
348 349 
 export(
349 350 
 	"roll",
Browse code

added quick_order()/qorder()

kuwisdelu authored on 26/06/2023 04:06:11
Showing 1 changed files
NAMESPACE
History View file @ 5325c7b2c
... ... 
@@ -364,6 +364,7 @@ exportMethods("prcomp")
364 364 
 exportMethods("bigglm")
365 365
366 366 
 export(
367 
+	"qorder",
367 368 
 	"qselect",
368 369 
 	"qmedian",
369 370 
 	"qmad",
Browse code

minor changes

kuwisdelu authored on 25/06/2023 20:05:03
Showing 1 changed files
NAMESPACE
History View file @ 60a6a1333
... ... 
@@ -373,13 +373,15 @@ export(
373 373
374 374 
 export(
375 375 
 	"vizi",
376 
-	"vizi_par",
377 
-	"vizi_style",
376 
+	"set_channel",
377 
+	"set_coord",
378 378 
 	"add_mark",
379 379 
 	"add_facets",
380 
-	"as_facets",
381 
-	"set_channel",
382 
-	"set_coord")
380 
+	"as_facets")
381 
+
382 
+export(
383 
+	"vizi_par",
384 
+	"vizi_style")
383 385
384 386 
 S3method("preplot", "vizi_plot")
385 387 
 S3method("preplot", "vizi_facets")
Browse code

cleaned up NAMESPACE

kuwisdelu authored on 25/06/2023 18:01:05
Showing 1 changed files
NAMESPACE
History View file @ 13648044c
... ... 
@@ -17,11 +17,23 @@ importFrom("Matrix",
17 17 
 	"colMeans")
18 18
19 19 
 importFrom("stats",
20 
-	"runmed",
20 
+	"approx",
21 
+	"cov",
22 
+	"dnorm",
21 23 
 	"median",
22 
-	"update",
24 
+	"loess",
25 
+	"lowess",
26 
+	"na.omit",
23 27 
 	"nobs",
24 
-	"na.omit")
28 
+	"predict",
29 
+	"qnorm",
30 
+	"rlnorm",
31 
+	"rnorm",
32 
+	"runmed",
33 
+	"setNames",
34 
+	"smooth.spline",
35 
+	"spline",
36 
+	"update")
25 37
26 38 
 importFrom("stats4",
27 39 
 	"plot",
... ... 
@@ -39,6 +51,29 @@ importFrom("utils",
39 51 
 	"tail",
40 52 
 	"object.size")
41 53
54 
+importFrom("grDevices",
55 
+	"dev.cur",
56 
+	"dev.flush",
57 
+	"dev.hold",
58 
+	"hcl.colors",
59 
+	"palette.colors",
60 
+	"xy.coords")
61 
+
62 
+importFrom("graphics",
63 
+	"Axis",
64 
+	"box",
65 
+	"co.intervals",
66 
+	"grid",
67 
+	"legend",
68 
+	"mtext",
69 
+	"par",
70 
+	"plot.new",
71 
+	"plot.window",
72 
+	"plot.xy",
73 
+	"strheight",
74 
+	"strwidth",
75 
+	"title")
76 
+
42 77 
 exportClasses(
43 78 
 	"drle",
44 79 
 	"drle_fct",
... ... 
@@ -253,7 +288,6 @@ export(
253 288 
 	".colStats")
254 289
255 290 
 export(
256 
-	"chunkify",
257 291 
 	"chunk_apply",
258 292 
 	"chunk_rowapply",
259 293 
 	"chunk_colapply",
Browse code

rename resample1() => approx1()

kuwisdelu authored on 25/06/2023 17:33:34
Showing 1 changed files
NAMESPACE
History View file @ 79dd3af91
... ... 
@@ -308,7 +308,7 @@ export(
308 308 
 	"mergepeaks",
309 309 
 	"peakwidths",
310 310 
 	"peakareas",
311 
-	"resample1",
311 
+	"approx1",
312 312 
 	"simspectra")
313 313
314 314 
 export(
Browse code

fixed bugs in bsearch() + some other things

kuwisdelu authored on 25/06/2023 17:01:13
Showing 1 changed files
NAMESPACE
History View file @ 922892e16
... ... 
@@ -20,6 +20,7 @@ importFrom("stats",
20 20 
 	"runmed",
21 21 
 	"median",
22 22 
 	"update",
23 
+	"nobs",
23 24 
 	"na.omit")
24 25
25 26 
 importFrom("stats4",
Browse code

added more faceting support (add marks to faceted plot, free x/y)

kuwisdelu authored on 25/06/2023 04:11:56
Showing 1 changed files
NAMESPACE
History View file @ c44d658a6
... ... 
@@ -357,6 +357,10 @@ S3method("plot", "vizi_peaks")
357 357 
 S3method("plot", "vizi_key")
358 358 
 S3method("plot", "vizi_colorkey")
359 359
360 
+exportMethods(
361 
+	"preplot",
362 
+	"plot")
363 
+
360 364 
 export(
361 365 
 	"mem",
362 366 
 	"profmem")
Browse code

added set_channel() and set_coord()

kuwisdelu authored on 24/06/2023 23:10:56
Showing 1 changed files
NAMESPACE
History View file @ a257d446d
... ... 
@@ -312,7 +312,10 @@ export(
312 312
313 313 
 export(
314 314 
 	"roll",
315 
-	"seq_rel")
315 
+	"seq_rel",
316 
+	"shingles",
317 
+	"dpal",
318 
+	"cpal")
316 319
317 320 
 exportMethods(
318 321 
 	"apply",
... ... 
@@ -339,7 +342,9 @@ export(
339 342 
 	"vizi_style",
340 343 
 	"add_mark",
341 344 
 	"add_facets",
342 
-	"as_facets")
345 
+	"as_facets",
346 
+	"set_channel",
347 
+	"set_coord")
343 348
344 349 
 S3method("preplot", "vizi_plot")
345 350 
 S3method("preplot", "vizi_facets")
Browse code

split facet() => add_facets() + as_facets()

kuwisdelu authored on 24/06/2023 21:35:08
Showing 1 changed files
NAMESPACE
History View file @ fc2fce168
... ... 
@@ -338,7 +338,8 @@ export(
338 338 
 	"vizi_par",
339 339 
 	"vizi_style",
340 340 
 	"add_mark",
341 
-	"facet")
341 
+	"add_facets",
342 
+	"as_facets")
342 343
343 344 
 S3method("preplot", "vizi_plot")
344 345 
 S3method("preplot", "vizi_facets")
Browse code

added vizi_style() convenience function

kuwisdelu authored on 23/06/2023 21:06:39
Showing 1 changed files
NAMESPACE
History View file @ 02697e95a
... ... 
@@ -336,6 +336,7 @@ export(
336 336 
 export(
337 337 
 	"vizi",
338 338 
 	"vizi_par",
339 
+	"vizi_style",
339 340 
 	"add_mark",
340 341 
 	"facet")
341 342
Browse code

added vizi faceting support

kuwisdelu authored on 23/06/2023 18:44:01
Showing 1 changed files
NAMESPACE
History View file @ 3db50f5b4
... ... 
@@ -336,10 +336,14 @@ export(
336 336 
 export(
337 337 
 	"vizi",
338 338 
 	"vizi_par",
339 
-	"add_mark")
339 
+	"add_mark",
340 
+	"facet")
340 341
341 342 
 S3method("preplot", "vizi_plot")
343 
+S3method("preplot", "vizi_facets")
344 
+
342 345 
 S3method("plot", "vizi_plot")
346 
+S3method("plot", "vizi_facets")
343 347 
 S3method("plot", "vizi_points")
344 348 
 S3method("plot", "vizi_lines")
345 349 
 S3method("plot", "vizi_peaks")
Browse code

added vizi legend support

kuwisdelu authored on 23/06/2023 12:36:24
Showing 1 changed files
NAMESPACE
History View file @ 945728b6d
... ... 
@@ -340,10 +340,11 @@ export(
340 340
341 341 
 S3method("preplot", "vizi_plot")
342 342 
 S3method("plot", "vizi_plot")
343 
-
344 343 
 S3method("plot", "vizi_points")
345 344 
 S3method("plot", "vizi_lines")
346 345 
 S3method("plot", "vizi_peaks")
346 
+S3method("plot", "vizi_key")
347 
+S3method("plot", "vizi_colorkey")
347 348
348 349 
 export(
349 350 
 	"mem",
Browse code

rewrote vizi plotting to use simpler S3 design

Kylie Bemis authored on 21/06/2023 23:29:46
Showing 1 changed files
NAMESPACE
History View file @ 686995d03
... ... 
@@ -333,6 +333,18 @@ export(
333 333 
 	"asearch",
334 334 
 	"bsearch")
335 335
336 
+export(
337 
+	"vizi",
338 
+	"vizi_par",
339 
+	"add_mark")
340 
+
341 
+S3method("preplot", "vizi_plot")
342 
+S3method("plot", "vizi_plot")
343 
+
344 
+S3method("plot", "vizi_points")
345 
+S3method("plot", "vizi_lines")
346 
+S3method("plot", "vizi_peaks")
347 
+
336 348 
 export(
337 349 
 	"mem",
338 350 
 	"profmem")
Browse code

Merge branch 'signal' into vizi

kuwisdelu authored on 16/06/2023 20:54:40
Showing 0 changed files
Browse code

added correlation optimized warping w/ warp1_cow()

kuwisdelu authored on 12/06/2023 00:04:17
Showing 1 changed files
NAMESPACE
History View file @ 71a31ee37
... ... 
@@ -281,6 +281,7 @@ export(
281 281 
 	"filt1_pag",
282 282 
 	"warp1_loc",
283 283 
 	"warp1_dtw",
284 
+	"warp1_cow",
284 285 
 	"icor",
285 286 
 	"binvec",
286 287 
 	"findbins",
Browse code

added icor() for correlation w/ interpolation

kuwisdelu authored on 11/06/2023 00:14:38
Showing 1 changed files
NAMESPACE
History View file @ 5dfd742d7
... ... 
@@ -281,6 +281,7 @@ export(
281 281 
 	"filt1_pag",
282 282 
 	"warp1_loc",
283 283 
 	"warp1_dtw",
284 
+	"icor",
284 285 
 	"binvec",
285 286 
 	"findbins",
286 287 
 	"downsample",
Browse code

reverted warp1_shift() => warp1_loc() again

kuwisdelu authored on 08/06/2023 20:17:52
Showing 1 changed files
NAMESPACE
History View file @ 49c082b64
... ... 
@@ -279,7 +279,7 @@ export(
279 279 
 	"filt1_adapt",
280 280 
 	"filt1_guide",
281 281 
 	"filt1_pag",
282 
-	"warp1_shift",
282 
+	"warp1_loc",
283 283 
 	"warp1_dtw",
284 284 
 	"binvec",
285 285 
 	"findbins",
Browse code

separated unit tests for resample1() and asearch()

kuwisdelu authored on 07/06/2023 04:39:17
Showing 1 changed files
NAMESPACE
History View file @ 0804712a3
... ... 
@@ -281,7 +281,6 @@ export(
281 281 
 	"filt1_pag",
282 282 
 	"warp1_shift",
283 283 
 	"warp1_dtw",
284 
-	"resample1",
285 284 
 	"binvec",
286 285 
 	"findbins",
287 286 
 	"downsample",
... ... 
@@ -301,6 +300,7 @@ export(
301 300 
 	"mergepeaks",
302 301 
 	"peakwidths",
303 302 
 	"peakareas",
303 
+	"resample1",
304 304 
 	"simspectra")
305 305
306 306 
 export(
Browse code

changed name of warp1_loc() => warp1_shift()

kuwisdelu authored on 06/06/2023 07:41:03
Showing 1 changed files
NAMESPACE
History View file @ 2d8d59740
... ... 
@@ -279,7 +279,7 @@ export(
279 279 
 	"filt1_adapt",
280 280 
 	"filt1_guide",
281 281 
 	"filt1_pag",
282 
-	"warp1_loc",
282 
+	"warp1_shift",
283 283 
 	"warp1_dtw",
284 284 
 	"resample1",
285 285 
 	"binvec",
Browse code

added dynamic time warping w/ warp1_dtw(); minor changes to warp1_loc()

kuwisdelu authored on 06/06/2023 07:21:44
Showing 1 changed files
NAMESPACE
History View file @ aaa7e80a8
... ... 
@@ -280,6 +280,7 @@ export(
280 280 
 	"filt1_guide",
281 281 
 	"filt1_pag",
282 282 
 	"warp1_loc",
283 
+	"warp1_dtw",
283 284 
 	"resample1",
284 285 
 	"binvec",
285 286 
 	"findbins",
Browse code

warp_loc() => warp1_loc()

kuwisdelu authored on 05/06/2023 20:51:30
Showing 1 changed files
NAMESPACE
History View file @ 214eecf5f
... ... 
@@ -279,13 +279,13 @@ export(
279 279 
 	"filt1_adapt",
280 280 
 	"filt1_guide",
281 281 
 	"filt1_pag",
282 
+	"warp1_loc",
283 
+	"resample1",
282 284 
 	"binvec",
283 285 
 	"findbins",
284 286 
 	"downsample",
285 
-	"resample1",
286 287 
 	"locmax",
287 288 
 	"locmin",
288 
-	"warp_loc",
289 289 
 	"estbase_loc",
290 290 
 	"estbase_hull",
291 291 
 	"estbase_snip",
Browse code

added peak-aware guided filtering w/ filt1_pag(); some changes to filt1_adapt()

kuwisdelu authored on 04/06/2023 22:39:02
Showing 1 changed files
NAMESPACE
History View file @ 714b4a86d
... ... 
@@ -278,6 +278,7 @@ export(
278 278 
 	"filt1_bi",
279 279 
 	"filt1_adapt",
280 280 
 	"filt1_guide",
281 
+	"filt1_pag",
281 282 
 	"binvec",
282 283 
 	"findbins",
283 284 
 	"downsample",
Browse code

added guided filtering w/ filt1_guide(); improved speed of filt1_ma(); added qmad()

kuwisdelu authored on 04/06/2023 04:37:50
Showing 1 changed files
NAMESPACE
History View file @ 9616d940a
... ... 
@@ -277,6 +277,7 @@ export(
277 277 
 	"filt1_gauss",
278 278 
 	"filt1_bi",
279 279 
 	"filt1_adapt",
280 
+	"filt1_guide",
280 281 
 	"binvec",
281 282 
 	"findbins",
282 283 
 	"downsample",
... ... 
@@ -318,6 +319,7 @@ exportMethods("bigglm")
318 319 
 export(
319 320 
 	"qselect",
320 321 
 	"qmedian",
322 
+	"qmad",
321 323 
 	"reldiff",
322 324 
 	"asearch",
323 325 
 	"bsearch")
Browse code

minor change to bilateral_filter() args order

kuwisdelu authored on 02/06/2023 19:46:30
Showing 1 changed files
NAMESPACE
History View file @ 6ce94127d
... ... 
@@ -276,6 +276,7 @@ export(
276 276 
 	"filt1_ma",
277 277 
 	"filt1_gauss",
278 278 
 	"filt1_bi",
279 
+	"filt1_adapt",
279 280 
 	"binvec",
280 281 
 	"findbins",
281 282 
 	"downsample",
Browse code

added warp_loc() + unit test

kuwisdelu authored on 02/06/2023 08:14:29
Showing 1 changed files
NAMESPACE
History View file @ 4c6fb620e
... ... 
@@ -282,6 +282,7 @@ export(
282 282 
 	"resample1",
283 283 
 	"locmax",
284 284 
 	"locmin",
285 
+	"warp_loc",
285 286 
 	"estbase_loc",
286 287 
 	"estbase_hull",
287 288 
 	"estbase_snip",
Browse code

added binpeaks() and mergepeaks(); fixed some tolerance comparisons

kuwisdelu authored on 01/06/2023 22:19:27
Showing 1 changed files
NAMESPACE
History View file @ cbbffecf4
... ... 
@@ -292,11 +292,15 @@ export(
292 292 
 	"estnoise_diff",
293 293 
 	"estnoise_smooth",
294 294 
 	"findpeaks",
295 
+	"binpeaks",
296 
+	"mergepeaks",
295 297 
 	"peakwidths",
296 298 
 	"peakareas",
297 299 
 	"simspectra")
298 300
299 
-export("roll")
301 
+export(
302 
+	"roll",
303 
+	"seq_rel")
300 304
301 305 
 exportMethods(
302 306 
 	"apply",
Browse code

added noise estimation functions

kuwisdelu authored on 25/05/2023 05:56:41
Showing 1 changed files
NAMESPACE
History View file @ 92c28d364
... ... 
@@ -273,7 +273,7 @@ export(
273 273 
 	"vm_used")
274 274
275 275 
 export(
276 
-	"filt1",
276 
+	"filt1_ma",
277 277 
 	"filt1_gauss",
278 278 
 	"filt1_bi",
279 279 
 	"binvec",
... ... 
@@ -282,10 +282,15 @@ export(
282 282 
 	"resample1",
283 283 
 	"locmax",
284 284 
 	"locmin",
285 
-	"estbase",
285 
+	"estbase_loc",
286 286 
 	"estbase_hull",
287 287 
 	"estbase_snip",
288 288 
 	"estbase_med",
289 
+	"estnoise_filt",
290 
+	"estnoise_sd",
291 
+	"estnoise_mad",
292 
+	"estnoise_diff",
293 
+	"estnoise_smooth",
289 294 
 	"findpeaks",
290 295 
 	"peakwidths",
291 296 
 	"peakareas",
Browse code

updated findbins() to return limits only or list of x bins

kuwisdelu authored on 24/05/2023 18:40:16
Showing 1 changed files
NAMESPACE
History View file @ 8ee7cd97c
... ... 
@@ -247,6 +247,7 @@ export(
247 247 
 	".colStats")
248 248
249 249 
 export(
250 
+	"chunkify",
250 251 
 	"chunk_apply",
251 252 
 	"chunk_rowapply",
252 253 
 	"chunk_colapply",
Browse code

added quick_select() to C files

kuwisdelu authored on 22/05/2023 21:43:01
Showing 1 changed files
NAMESPACE
History View file @ 0d430de70
... ... 
@@ -304,6 +304,8 @@ exportMethods("prcomp")
304 304 
 exportMethods("bigglm")
305 305
306 306 
 export(
307 
+	"qselect",
308 
+	"qmedian",
307 309 
 	"reldiff",
308 310 
 	"asearch",
309 311 
 	"bsearch")
Browse code

added filt1_gauss() and filt1_bi()

kuwisdelu authored on 21/05/2023 04:10:53
Showing 1 changed files
NAMESPACE
History View file @ 815e43fd0
... ... 
@@ -272,9 +272,13 @@ export(
272 272 
 	"vm_used")
273 273
274 274 
 export(
275 
+	"filt1",
276 
+	"filt1_gauss",
277 
+	"filt1_bi",
275 278 
 	"binvec",
276 279 
 	"findbins",
277 280 
 	"downsample",
281 
+	"resample1",
278 282 
 	"locmax",
279 283 
 	"locmin",
280 284 
 	"estbase",
Browse code

updated baseline estimation functions

kuwisdelu authored on 15/05/2023 19:19:05
Showing 1 changed files
NAMESPACE
History View file @ 6760279dc
... ... 
@@ -17,6 +17,7 @@ importFrom("Matrix",
17 17 
 	"colMeans")
18 18
19 19 
 importFrom("stats",
20 
+	"runmed",
20 21 
 	"median",
21 22 
 	"update",
22 23 
 	"na.omit")
... ... 
@@ -279,6 +280,7 @@ export(
279 280 
 	"estbase",
280 281 
 	"estbase_hull",
281 282 
 	"estbase_snip",
283 
+	"estbase_med",
282 284 
 	"findpeaks",
283 285 
 	"peakwidths",
284 286 
 	"peakareas",
Browse code

remove resample() functions -- not needed

Kylie Bemis authored on 14/05/2023 21:13:38
Showing 1 changed files
NAMESPACE
History View file @ e9ea8d0e7
... ... 
@@ -274,7 +274,6 @@ export(
274 274 
 	"binvec",
275 275 
 	"findbins",
276 276 
 	"downsample",
277 
-	"resample",
278 277 
 	"locmax",
279 278 
 	"locmin",
280 279 
 	"estbase",
Browse code

added SNIP baseline estimation

Kylie Bemis authored on 14/05/2023 21:11:22
Showing 1 changed files
NAMESPACE
History View file @ bd879cbbe
... ... 
@@ -279,6 +279,7 @@ export(
279 279 
 	"locmin",
280 280 
 	"estbase",
281 281 
 	"estbase_hull",
282 
+	"estbase_snip",
282 283 
 	"findpeaks",
283 284 
 	"peakwidths",
284 285 
 	"peakareas",
Browse code

added convex hull continuum estimation

Kylie Bemis authored on 14/05/2023 20:13:52
Showing 1 changed files
NAMESPACE
History View file @ 07094a6ae
... ... 
@@ -278,6 +278,7 @@ export(
278 278 
 	"locmax",
279 279 
 	"locmin",
280 280 
 	"estbase",
281 
+	"estbase_hull",
281 282 
 	"findpeaks",
282 283 
 	"peakwidths",
283 284 
 	"peakareas",
Browse code

add locmin baseline estimation + code comments

Kylie Bemis authored on 14/05/2023 18:08:39
Showing 1 changed files
NAMESPACE
History View file @ 7a6fe928c
... ... 
@@ -276,6 +276,8 @@ export(
276 276 
 	"downsample",
277 277 
 	"resample",
278 278 
 	"locmax",
279 
+	"locmin",
280 
+	"estbase",
279 281 
 	"findpeaks",
280 282 
 	"peakwidths",
281 283 
 	"peakareas",
Browse code

minor change to downsample(); added resample()

Kylie Bemis authored on 14/05/2023 05:34:26
Showing 1 changed files
NAMESPACE
History View file @ 7c40f460f
... ... 
@@ -274,6 +274,7 @@ export(
274 274 
 	"binvec",
275 275 
 	"findbins",
276 276 
 	"downsample",
277 
+	"resample",
277 278 
 	"locmax",
278 279 
 	"findpeaks",
279 280 
 	"peakwidths",
Browse code

added LTOB downsampling + unit tests

kuwisdelu authored on 13/05/2023 18:03:32
Showing 1 changed files
NAMESPACE
History View file @ 6c1e48478
... ... 
@@ -272,8 +272,9 @@ export(
272 272
273 273 
 export(
274 274 
 	"binvec",
275 
-	"locmax",
276 275 
 	"findbins",
276 
+	"downsample",
277 
+	"locmax",
277 278 
 	"findpeaks",
278 279 
 	"peakwidths",
279 280 
 	"peakareas",
Browse code

add peakareas(); clean up peak C function arg order

kuwisdelu authored on 13/05/2023 00:11:19
Showing 1 changed files
NAMESPACE
History View file @ 136d8c880
... ... 
@@ -276,6 +276,7 @@ export(
276 276 
 	"findbins",
277 277 
 	"findpeaks",
278 278 
 	"peakwidths",
279 
+	"peakareas",
279 280 
 	"simspectra")
280 281
281 282 
 export("roll")
Browse code

added peakwidths() and unit tests

Kylie Bemis authored on 12/05/2023 22:00:54
Showing 1 changed files
NAMESPACE
History View file @ bc10d0415
... ... 
@@ -273,7 +273,10 @@ export(
273 273 
 export(
274 274 
 	"binvec",
275 275 
 	"locmax",
276 
-	"findpeaks")
276 
+	"findbins",
277 
+	"findpeaks",
278 
+	"peakwidths",
279 
+	"simspectra")
277 280
278 281 
 export("roll")
279 282
Browse code

added draft/skeleton of vizi code

kuwisdelu authored on 10/05/2023 19:40:00
Showing 1 changed files
NAMESPACE
History View file @ d3e92a733
... ... 
@@ -21,6 +21,11 @@ importFrom("stats",
21 21 
 	"update",
22 22 
 	"na.omit")
23 23
24 
+importFrom("stats4",
25 
+	"plot",
26 
+	"update",
27 
+	"summary")
28 
+
24 29 
 import("BiocParallel")
25 30
26 31 
 import("BiocGenerics")
Browse code

v2.1.1 fixed NAMESPACE issue with rowSums() etc

Kylie Bemis authored on 13/04/2023 16:18:12
Showing 1 changed files
NAMESPACE
History View file @ 07601a28e
... ... 
@@ -10,7 +10,11 @@ importFrom("irlba",
10 10 
 	"irlba")
11 11
12 12 
 importFrom("Matrix",
13 
-	"nnzero")
13 
+	"nnzero",
14 
+	"rowSums",
15 
+	"rowMeans",
16 
+	"colSums",
17 
+	"colMeans")
14 18
15 19 
 importFrom("stats",
16 20 
 	"median",
Browse code

fixed 'size_bytes' class bug

Kylie Bemis authored on 31/10/2022 20:18:53
Showing 1 changed files
NAMESPACE
History View file @ 072267100
... ... 
@@ -258,6 +258,7 @@ export(
258 258 
 	"hex2raw",
259 259 
 	"raw2hex")
260 260
261 
+S3method("[", "size_bytes")
261 262 
 S3method("print", "size_bytes")
262 263 
 S3method("format", "size_bytes")
263 264
Browse code

added cbind2 and cbind2 for arrays

kuwisdelu authored on 25/10/2022 02:51:26
Showing 1 changed files
NAMESPACE
History View file @ 1ed147c6e
... ... 
@@ -153,6 +153,11 @@ exportMethods(
153 153 
 	"crossprod",
154 154 
 	"tcrossprod")
155 155
156 
+S3method("cbind", "matter_arr")
157 
+S3method("rbind", "matter_arr")
158 
+S3method("cbind", "sparse_arr")
159 
+S3method("rbind", "sparse_arr")
160 
+
156 161 
 exportMethods(
157 162 
 	"Arith",
158 163 
 	"Compare",
Browse code

added findpeaks()

kuwisdelu authored on 24/10/2022 03:59:01
Showing 1 changed files
NAMESPACE
History View file @ 31a014fc2
... ... 
@@ -262,7 +262,8 @@ export(
262 262
263 263 
 export(
264 264 
 	"binvec",
265 
-	"locmax")
265 
+	"locmax",
266 
+	"findpeaks")
266 267
267 268 
 export("roll")
268 269
Browse code

working on docs

Kylie Bemis authored on 15/10/2022 22:17:49
Showing 1 changed files
NAMESPACE
History View file @ aa06e8e81
... ... 
@@ -232,6 +232,10 @@ exportMethods(
232 232 
 	"rowStats",
233 233 
 	"colStats")
234 234
235 
+export(
236 
+	".rowStats",
237 
+	".colStats")
238 
+
235 239 
 export(
236 240 
 	"chunk_apply",
237 241 
 	"chunk_rowapply",
Browse code

re-add some old code and start cleaning up docs

kuwisdelu authored on 13/10/2022 03:41:48
Showing 1 changed files
NAMESPACE
History View file @ c9247cc08
... ... 
@@ -55,17 +55,22 @@ export(
55 55 
 	"write_atoms")
56 56
57 57 
 export(
58 
+	"matter",
58 59 
 	"is.matter",
60 
+	"as.matter",
59 61 
 	"matter_arr",
60 62 
 	"matter_mat",
61 63 
 	"matter_vec",
62 64 
 	"matter_fct",
63 65 
 	"matter_list",
64 66 
 	"matter_str",
65 
-	"sparse_mat",
66 
-	"sparse_vec",
67 
+	"struct")
68 
+
69 
+export(
67 70 
 	"is.sparse",
68 
-	"as.sparse")
71 
+	"as.sparse",
72 
+	"sparse_mat",
73 
+	"sparse_vec")
69 74
70 75 
 exportMethods(
71 76 
 	"as.altrep",
... ... 
@@ -101,11 +106,11 @@ exportMethods(
101 106 
 	"tolerance<-",
102 107 
 	"sampler",
103 108 
 	"sampler<-",
104 
-	"keys",
105 
-	"keys<-",
106 109 
 	"nnzero")
107 110
108 111 
 exportMethods(
112 
+	"keys",
113 
+	"keys<-",
109 114 
 	"paths",
110 115 
 	"paths<-",
111 116 
 	"datamode",
Browse code

added prcomp, biglm, and summary stats

kuwisdelu authored on 13/10/2022 01:45:46
Showing 1 changed files
NAMESPACE
History View file @ 9c6db9e36
... ... 
@@ -251,7 +251,9 @@ export(
251 251 
 	"sizeof",
252 252 
 	"vm_used")
253 253
254 
-export("locmax")
254 
+export(
255 
+	"binvec",
256 
+	"locmax")
255 257
256 258 
 export("roll")
257 259
... ... 
@@ -262,12 +264,10 @@ exportMethods(
262 264
263 265 
 exportMethods("scale")
264 266
265 
-exportMethods(
266 
-	"biglm",
267 
-	"bigglm")
268 
-
269 267 
 exportMethods("prcomp")
270 268
269 
+exportMethods("bigglm")
270 
+
271 271 
 export(
272 272 
 	"reldiff",
273 273 
 	"asearch",
Browse code

updated s_rowstats() and s_colstats() to support group arg

Kylie Bemis authored on 22/09/2022 18:11:55
Showing 1 changed files
NAMESPACE
History View file @ ae1c5667e
... ... 
@@ -196,6 +196,8 @@ export(
196 196 
 	"rowstreamStats")
197 197
198 198 
 S3method("c", "stream_stat")
199 
+S3method("cbind", "stream_stat")
200 
+S3method("rbind", "stream_stat")
199 201 
 S3method("print", "stream_stat")
200 202 
 S3method("nobs", "stream_stat")
201 203 
 S3method("[", "stream_stat")
Browse code

updated stream stats to support dims

kuwisdelu authored on 22/09/2022 03:53:27
Showing 1 changed files
NAMESPACE
History View file @ 2d03e9ef7
... ... 
@@ -213,6 +213,8 @@ S3method("stat_c", "stream_any")
213 213 
 S3method("stat_c", "stream_all")
214 214 
 S3method("stat_c", "stream_nnzero")
215 215
216 
+S3method("as.data.frame", "stream_stat")
217 
+
216 218 
 exportMethods(
217 219 
 	"rowsweep",
218 220 
 	"colsweep",
... ... 
@@ -224,6 +226,7 @@ exportMethods(
224 226 
 	"colStats")
225 227
226 228 
 export(
229 
+	"chunk_apply",
227 230 
 	"chunk_rowapply",
228 231 
 	"chunk_colapply",
229 232 
 	"chunk_lapply",
Browse code

added chunkApply, chunkLapply, and chunkMapply

kuwisdelu authored on 20/09/2022 04:09:08
Showing 1 changed files
NAMESPACE
History View file @ 1c306e2a1
... ... 
@@ -31,6 +31,7 @@ importFrom("utils",
31 31 
 exportClasses(
32 32 
 	"drle",
33 33 
 	"drle_fct",
34 
+	"atoms",
34 35 
 	"matter",
35 36 
 	"matter_arr",
36 37 
 	"matter_mat",
... ... 
@@ -47,6 +48,7 @@ export(
47 48 
 	"is.drle")
48 49
49 50 
 export(
51 
+	"atoms",
50 52 
 	"read_atom",
51 53 
 	"write_atom",
52 54 
 	"read_atoms",
... ... 
@@ -60,8 +62,8 @@ export(
60 62 
 	"matter_fct",
61 63 
 	"matter_list",
62 64 
 	"matter_str",
63 
-	"sparse_vec",
64 65 
 	"sparse_mat",
66 
+	"sparse_vec",
65 67 
 	"is.sparse",
66 68 
 	"as.sparse")
67 69
... ... 
@@ -185,6 +187,8 @@ export(
185 187 
 	"s_any",
186 188 
 	"s_all",
187 189 
 	"s_nnzero",
190 
+	"s_colstats",
191 
+	"s_rowstats",
188 192 
 	"stat_c")
189 193
190 194 
 export(
... ... 
@@ -213,17 +217,22 @@ exportMethods(
213 217 
 	"rowsweep",
214 218 
 	"colsweep",
215 219 
 	"rowscale",
216 
-	"colscale",
220 
+	"colscale")
221 
+
222 
+exportMethods(
217 223 
 	"rowStats",
218 224 
 	"colStats")
219 225
220 226 
 export(
221 
-	"chunk_apply",
227 
+	"chunk_rowapply",
228 
+	"chunk_colapply",
229 
+	"chunk_lapply",
222 230 
 	"chunk_mapply")
223 231
224 232 
 export(
225 
-	"atoms",
226 
-	"atoms")
233 
+	"chunkApply",
234 
+	"chunkLapply",
235 
+	"chunkMapply")
227 236
228 237 
 export(
229 238 
 	"uuid",
... ... 
@@ -239,6 +248,8 @@ export(
239 248
240 249 
 export("locmax")
241 250
251 
+export("roll")
252 
+
242 253 
 exportMethods(
243 254 
 	"apply",
244 255 
 	"lapply",
Browse code

overhauled sparse array cpp implementation

Kylie Bemis authored on 19/09/2022 16:04:12
Showing 1 changed files
NAMESPACE
History View file @ 124ac8a21
... ... 
@@ -38,10 +38,9 @@ exportClasses(
38 38 
 	"matter_list",
39 39 
 	"matter_str",
40 40 
 	"matter_fct",
41 
-	"sparse_vec",
41 
+	"sparse_arr",
42 42 
 	"sparse_mat",
43 
-	"sparse_matc",
44 
-	"sparse_matr")
43 
+	"sparse_vec")
45 44
46 45 
 export(
47 46 
 	"drle",
... ... 
@@ -92,10 +91,10 @@ exportMethods(
92 91 
 	"aindex",
93 92 
 	"atomindex",
94 93 
 	"atomindex<-",
95 
-	"domain",
96 
-	"domain<-",
97 94 
 	"pointers",
98 95 
 	"pointers<-",
96 
+	"domain",
97 
+	"domain<-",
99 98 
 	"tolerance",
100 99 
 	"tolerance<-",
101 100 
 	"sampler",
Browse code

added ungroup_atoms() utility function

kuwisdelu authored on 16/09/2022 02:49:44
Showing 1 changed files
NAMESPACE
History View file @ 098ef9fa3
... ... 
@@ -101,7 +101,7 @@ exportMethods(
101 101 
 	"sampler",
102 102 
 	"sampler<-",
103 103 
 	"keys",
104 
-	"keys<-"
104 
+	"keys<-",
105 105 
 	"nnzero")
106 106
107 107 
 exportMethods(
Browse code

update generics and namespace

kuwisdelu authored on 15/09/2022 20:18:30
Showing 1 changed files
NAMESPACE
History View file @ 595dc67d1
... ... 
@@ -19,30 +19,9 @@ importFrom("stats",
19 19
20 20 
 import("BiocParallel")
21 21
22 
-importFrom("BiocGenerics",
23 
-	"as.data.frame",
24 
-	"as.list",
25 
-	"as.vector",
26 
-	"mean",
27 
-	"sd",
28 
-	"var",
29 
-	"colMeans",
30 
-	"colSums",
31 
-	"rowMeans",
32 
-	"rowSums",
33 
-	"t",
34 
-	"dims",
35 
-	"type",
36 
-	"type<-",
37 
-	"path",
38 
-	"path<-",
39 
-	"combine",
40 
-	"which",
41 
-	"lapply",
42 
-	"sapply")
22 
+import("BiocGenerics")
43 23
44 
-importFrom("ProtGenerics",
45 
-	"tolerance")
24 
+import("ProtGenerics")
46 25
47 26 
 importFrom("utils",
48 27 
 	"head",
... ... 
@@ -115,10 +94,14 @@ exportMethods(
115 94 
 	"atomindex<-",
116 95 
 	"domain",
117 96 
 	"domain<-",
97 
+	"pointers",
98 
+	"pointers<-",
118 99 
 	"tolerance",
119 100 
 	"tolerance<-",
120 101 
 	"sampler",
121 102 
 	"sampler<-",
103 
+	"keys",
104 
+	"keys<-"
122 105 
 	"nnzero")
123 106
124 107 
 exportMethods(
... ... 
@@ -129,9 +112,7 @@ exportMethods(
129 112 
 	"filemode",
130 113 
 	"filemode<-",
131 114 
 	"combiner",
132 
-	"combiner<-",
133 
-	"keys",
134 
-	"keys<-")
115 
+	"combiner<-")
135 116
136 117 
 exportMethods("checksum")
137 118
Browse code

added rowsweep and colsweep

kuwisdelu authored on 15/09/2022 04:08:01
Showing 1 changed files
NAMESPACE
History View file @ 4052ab5d9
... ... 
@@ -102,14 +102,8 @@ exportMethods(
102 102 
 	"atomdata<-",
103 103 
 	"type",
104 104 
 	"type<-",
105 
-	"datamode",
106 
-	"datamode<-",
107 
-	"paths",
108 
-	"paths<-",
109 105 
 	"path",
110 106 
 	"path<-",
111 
-	"filemode",
112 
-	"filemode<-",
113 107 
 	"readonly",
114 108 
 	"readonly<-",
115 109 
 	"chunksize",
... ... 
@@ -121,15 +115,23 @@ exportMethods(
121 115 
 	"atomindex<-",
122 116 
 	"domain",
123 117 
 	"domain<-",
124 
-	"keys",
125 
-	"keys<-",
126 118 
 	"tolerance",
127 119 
 	"tolerance<-",
128 120 
 	"sampler",
129 121 
 	"sampler<-",
122 
+	"nnzero")
123 
+
124 
+exportMethods(
125 
+	"paths",
126 
+	"paths<-",
127 
+	"datamode",
128 
+	"datamode<-",
129 
+	"filemode",
130 
+	"filemode<-",
130 131 
 	"combiner",
131 132 
 	"combiner<-",
132 
-	"nnzero")
133 
+	"keys",
134 
+	"keys<-")
133 135
134 136 
 exportMethods("checksum")
135 137
... ... 
@@ -180,14 +182,16 @@ exportMethods(
180 182 
 	"sd",
181 183 
 	"any",
182 184 
 	"all",
183 
-	"colSums",
184 
-	"colMeans",
185 
-	"colVars",
186 
-	"colSds",
187 185 
 	"rowSums",
188 186 
 	"rowMeans",
187 
+	"colSums",
188 
+	"colMeans")
189 
+
190 
+exportMethods(
189 191 
 	"rowVars",
190 
-	"rowSds")
192 
+	"rowSds",
193 
+	"colVars",
194 
+	"colSds")
191 195
192 196 
 export(
193 197 
 	"s_range",
... ... 
@@ -226,8 +230,12 @@ S3method("stat_c", "stream_all")
226 230 
 S3method("stat_c", "stream_nnzero")
227 231
228 232 
 exportMethods(
229 
-	"colStats",
230 
-	"rowStats")
233 
+	"rowsweep",
234 
+	"colsweep",
235 
+	"rowscale",
236 
+	"colscale",
237 
+	"rowStats",
238 
+	"colStats")
231 239
232 240 
 export(
233 241 
 	"chunk_apply",
Browse code

cleaned up utils

kuwisdelu authored on 11/09/2022 17:11:41
Showing 1 changed files
NAMESPACE
History View file @ cf4d4e37d
... ... 
@@ -242,23 +242,14 @@ export(
242 242 
 	"hex2raw",
243 243 
 	"raw2hex")
244 244
245 
-S3method("print", "num_bytes")
246 
-S3method("format", "num_bytes")
247 
-
248 
-export(
249 
-	"make_filemode",
250 
-	"common_filemode")
245 
+S3method("print", "size_bytes")
246 
+S3method("format", "size_bytes")
251 247
252 248 
 export(
253 249 
 	"sizeof",
254 
-	"make_datamode",
255 
-	"convert_datamode",
256 
-	"widest_datamode",
257 250 
 	"vm_used")
258 251
259 
-export(
260 
-	"binvec",
261 
-	"locmax")
252 
+export("locmax")
262 253
263 254 
 exportMethods(
264 255 
 	"apply",
Browse code

fixed matter array logical type bugs

kuwisdelu authored on 11/09/2022 15:02:14
Showing 1 changed files
NAMESPACE
History View file @ 47efde6d2
... ... 
@@ -75,6 +75,7 @@ export(
75 75 
 	"write_atoms")
76 76
77 77 
 export(
78 
+	"is.matter",
78 79 
 	"matter_arr",
79 80 
 	"matter_mat",
80 81 
 	"matter_vec",
Browse code

updated native routine registration calls

kuwisdelu authored on 11/09/2022 14:16:38
Showing 1 changed files
NAMESPACE
History View file @ 3c5bd683b
... ... 
@@ -281,4 +281,4 @@ export(
281 281 
 	"mem",
282 282 
 	"profmem")
283 283
284 
-useDynLib("matter", .registration=TRUE)
284 
+useDynLib("matter", .registration=TRUE, .fixes="C_")
Browse code

cleaned up build errors

kuwisdelu authored on 10/09/2022 18:27:49
Showing 1 changed files
NAMESPACE
History View file @ 993170883
... ... 
@@ -37,8 +37,6 @@ importFrom("BiocGenerics",
37 37 
 	"path",
38 38 
 	"path<-",
39 39 
 	"combine",
40 
-	"cbind",
41 
-	"rbind",
42 40 
 	"which",
43 41 
 	"lapply",
44 42 
 	"sapply")
... ... 
@@ -55,25 +53,16 @@ exportClasses(
55 53 
 	"drle",
56 54 
 	"drle_fct",
57 55 
 	"matter",
58 
-	"matter_vec",
59 
-	"matter_mat",
60 
-	"matter_matc",
61 
-	"matter_matr",
62 56 
 	"matter_arr",
57 
+	"matter_mat",
58 
+	"matter_vec",
63 59 
 	"matter_list",
64 60 
 	"matter_str",
65 
-	"matter_fc",
66 
-	"matter_df",
67 
-	"rep_vt",
61 
+	"matter_fct",
68 62 
 	"sparse_vec",
69 63 
 	"sparse_mat",
70 64 
 	"sparse_matc",
71 
-	"sparse_matr",
72 
-	"virtual_mat",
73 
-	"virtual_matc",
74 
-	"virtual_matr",
75 
-	"virtual_tbl",
76 
-	"virtual_df")
65 
+	"sparse_matr")
77 66
78 67 
 export(
79 68 
 	"drle",
... ... 
@@ -86,32 +75,16 @@ export(
86 75 
 	"write_atoms")
87 76
88 77 
 export(
89 
-	"matter",
90 
-	"matter_vec",
91 
-	"matter_mat",
92 
-	"matter_arr",
93 78 
 	"matter_arr",
94 79 
 	"matter_mat",
95 80 
 	"matter_vec",
96 81 
 	"matter_fct",
97 82 
 	"matter_list",
98 83 
 	"matter_str",
99 
-	"matter_list",
100 
-	"matter_str",
101 
-	"matter_fc",
102 
-	"matter_df",
103 
-	"rep_vt",
104 84 
 	"sparse_vec",
105 85 
 	"sparse_mat",
106 
-	"is.matter",
107 
-	"as.matter",
108 86 
 	"is.sparse",
109 
-	"as.sparse",
110 
-	"is.virtual",
111 
-	"as.virtual",
112 
-	"virtual_mat",
113 
-	"virtual_df",
114 
-	"struct")
87 
+	"as.sparse")
115 88
116 89 
 exportMethods(
117 90 
 	"as.altrep",
... ... 
@@ -171,13 +144,10 @@ exportMethods(
171 144 
 	"$<-",
172 145 
 	"c",
173 146 
 	"combine",
174 
-	"cbind",
175 
-	"rbind",
176 147 
 	"cbind2",
177 148 
 	"rbind2",
178 149 
 	"lengths",
179 150 
 	"length",
180 
-	"length<-",
181 151 
 	"dims",
182 152 
 	"dim",
183 153 
 	"dim<-",
... ... 
@@ -196,15 +166,9 @@ exportMethods(
196 166 
 exportMethods(
197 167 
 	"Arith",
198 168 
 	"Compare",
199 
-	"Logic",
200 
-	"exp",
201 
-	"log",
202 
-	"log2",
203 
-	"log10")
169 
+	"Logic")
204 170
205 171 
 exportMethods(
206 
-	"head",
207 
-	"tail",
208 172 
 	"range",
209 173 
 	"min",
210 174 
 	"max",
... ... 
@@ -222,8 +186,7 @@ exportMethods(
222 186 
 	"rowSums",
223 187 
 	"rowMeans",
224 188 
 	"rowVars",
225 
-	"rowSds",
226 
-	"which")
189 
+	"rowSds")
227 190
228 191 
 export(
229 192 
 	"s_range",
Browse code

removed legacy R codebase

kuwisdelu authored on 09/09/2022 21:43:10
Showing 1 changed files
NAMESPACE
History View file @ c77be9f8b
... ... 
@@ -90,12 +90,12 @@ export(
90 90 
 	"matter_vec",
91 91 
 	"matter_mat",
92 92 
 	"matter_arr",
93 
-	"matter2_arr",
94 
-	"matter2_mat",
95 
-	"matter2_vec",
96 
-	"matter2_fct",
97 
-	"matter2_list",
98 
-	"matter2_str",
93 
+	"matter_arr",
94 
+	"matter_mat",
95 
+	"matter_vec",
96 
+	"matter_fct",
97 
+	"matter_list",
98 
+	"matter_str",
99 99 
 	"matter_list",
100 100 
 	"matter_str",
101 101 
 	"matter_fc",
... ... 
@@ -271,7 +271,7 @@ export(
271 271
272 272 
 export(
273 273 
 	"atoms",
274 
-	"atoms2")
274 
+	"atoms")
275 275
276 276 
 export(
277 277 
 	"uuid",
Browse code

fixed matter factor bugs--require atoms have double offset+extent

kuwisdelu authored on 09/09/2022 15:39:03
Showing 1 changed files
NAMESPACE
History View file @ d64b868dc
... ... 
@@ -93,6 +93,7 @@ export(
93 93 
 	"matter2_arr",
94 94 
 	"matter2_mat",
95 95 
 	"matter2_vec",
96 
+	"matter2_fct",
96 97 
 	"matter2_list",
97 98 
 	"matter2_str",
98 99 
 	"matter_list",
... ... 
@@ -184,7 +185,6 @@ exportMethods(
184 185 
 	"names<-",
185 186 
 	"dimnames",
186 187 
 	"dimnames<-",
187 
-	"labels",
188 188 
 	"levels",
189 189 
 	"levels<-",
190 190 
 	"Encoding",
Browse code

added new matter factor

kuwisdelu authored on 08/09/2022 22:17:22
Showing 1 changed files
NAMESPACE
History View file @ c137cf8ec
... ... 
@@ -184,6 +184,7 @@ exportMethods(
184 184 
 	"names<-",
185 185 
 	"dimnames",
186 186 
 	"dimnames<-",
187 
+	"labels",
187 188 
 	"levels",
188 189 
 	"levels<-",
189 190 
 	"Encoding",
Browse code

changed drle_fc -> drle_fct & matter_chr -> matter_str

kuwisdelu authored on 08/09/2022 20:45:09
Showing 1 changed files
NAMESPACE
History View file @ 0209dacde
... ... 
@@ -53,7 +53,7 @@ importFrom("utils",
53 53
54 54 
 exportClasses(
55 55 
 	"drle",
56 
-	"drle_fc",
56 
+	"drle_fct",
57 57 
 	"matter",
58 58 
 	"matter_vec",
59 59 
 	"matter_mat",
... ... 
@@ -93,8 +93,8 @@ export(
93 93 
 	"matter2_arr",
94 94 
 	"matter2_mat",
95 95 
 	"matter2_vec",
96 
-	"matter2_chr",
97 96 
 	"matter2_list",
97 
+	"matter2_str",
98 98 
 	"matter_list",
99 99 
 	"matter_str",
100 100 
 	"matter_fc",
Browse code

fixed new matter string subsetting bugs

Kylie Bemis authored on 06/09/2022 17:48:14
Showing 1 changed files
NAMESPACE
History View file @ d9b089556
... ... 
@@ -186,6 +186,8 @@ exportMethods(
186 186 
 	"dimnames<-",
187 187 
 	"levels",
188 188 
 	"levels<-",
189 
+	"Encoding",
190 
+	"Encoding<-",
189 191 
 	"t",
190 192 
 	"crossprod",
191 193 
 	"tcrossprod")
Browse code

updated matter character vector cpp implementation

Kylie Bemis authored on 06/09/2022 15:56:28
Showing 1 changed files
NAMESPACE
History View file @ b9eac8493
... ... 
@@ -93,6 +93,7 @@ export(
93 93 
 	"matter2_arr",
94 94 
 	"matter2_mat",
95 95 
 	"matter2_vec",
96 
+	"matter2_chr",
96 97 
 	"matter2_list",
97 98 
 	"matter_list",
98 99 
 	"matter_str",
Browse code

fixed new matter_list indexing bugs

Kylie Bemis authored on 06/09/2022 03:55:56
Showing 1 changed files
NAMESPACE
History View file @ e531684be
... ... 
@@ -93,6 +93,7 @@ export(
93 93 
 	"matter2_arr",
94 94 
 	"matter2_mat",
95 95 
 	"matter2_vec",
96 
+	"matter2_list",
96 97 
 	"matter_list",
97 98 
 	"matter_str",
98 99 
 	"matter_fc",
Browse code

added new matter_vec and new matter_mat

kuwisdelu authored on 04/09/2022 04:51:13
Showing 1 changed files
NAMESPACE
History View file @ c6375be1c
... ... 
@@ -91,6 +91,8 @@ export(
91 91 
 	"matter_mat",
92 92 
 	"matter_arr",
93 93 
 	"matter2_arr",
94 
+	"matter2_mat",
95 
+	"matter2_vec",
94 96 
 	"matter_list",
95 97 
 	"matter_str",
96 98 
 	"matter_fc",
Browse code

started new matter_arr implementation

kuwisdelu authored on 02/09/2022 04:34:57
Showing 1 changed files
NAMESPACE
History View file @ 4cae74a27
... ... 
@@ -90,6 +90,7 @@ export(
90 90 
 	"matter_vec",
91 91 
 	"matter_mat",
92 92 
 	"matter_arr",
93 
+	"matter2_arr",
93 94 
 	"matter_list",
94 95 
 	"matter_str",
95 96 
 	"matter_fc",
Browse code

start implementing new matter classes

kuwisdelu authored on 01/09/2022 21:34:13
Showing 1 changed files
NAMESPACE
History View file @ c129095de
... ... 
@@ -15,7 +15,6 @@ importFrom("Matrix",
15 15 
 importFrom("stats",
16 16 
 	"median",
17 17 
 	"update",
18 
-	"setNames",
19 18 
 	"na.omit")
20 19
21 20 
 import("BiocParallel")
... ... 
@@ -33,6 +32,8 @@ importFrom("BiocGenerics",
33 32 
 	"rowSums",
34 33 
 	"t",
35 34 
 	"dims",
35 
+	"type",
36 
+	"type<-",
36 37 
 	"path",
37 38 
 	"path<-",
38 39 
 	"combine",
... ... 
@@ -119,6 +120,8 @@ exportMethods(
119 120 
 	"adata",
120 121 
 	"atomdata",
121 122 
 	"atomdata<-",
123 
+	"type",
124 
+	"type<-",
122 125 
 	"datamode",
123 126 
 	"datamode<-",
124 127 
 	"paths",
Browse code

implemented atoms combining/subsetting

kuwisdelu authored on 31/08/2022 03:02:53
Showing 1 changed files
NAMESPACE
History View file @ 80143b3ea
... ... 
@@ -169,6 +169,7 @@ exportMethods(
169 169 
 	"lengths",
170 170 
 	"length",
171 171 
 	"length<-",
172 
+	"dims",
172 173 
 	"dim",
173 174 
 	"dim<-",
174 175 
 	"names",
Browse code

work on new atoms R-level class

Kylie Bemis authored on 30/08/2022 22:37:55
Showing 1 changed files
NAMESPACE
History View file @ 43b74906d
... ... 
@@ -32,6 +32,7 @@ importFrom("BiocGenerics",
32 32 
 	"rowMeans",
33 33 
 	"rowSums",
34 34 
 	"t",
35 
+	"dims",
35 36 
 	"path",
36 37 
 	"path<-",
37 38 
 	"combine",
... ... 
@@ -77,6 +78,12 @@ export(
77 78 
 	"drle",
78 79 
 	"is.drle")
79 80
81 
+export(
82 
+	"read_atom",
83 
+	"write_atom",
84 
+	"read_atoms",
85 
+	"write_atoms")
86 
+
80 87 
 export(
81 88 
 	"matter",
82 89 
 	"matter_vec",
... ... 
@@ -125,12 +132,6 @@ exportMethods(
125 132 
 	"chunksize",
126 133 
 	"chunksize<-")
127 134
128 
-exportMethods("checksum")
129 
-
130 
-exportMethods(
131 
-	"describe_for_display",
132 
-	"preview_for_display")
133 
-
134 135 
 exportMethods(
135 136 
 	"aindex",
136 137 
 	"atomindex",
... ... 
@@ -147,6 +148,12 @@ exportMethods(
147 148 
 	"combiner<-",
148 149 
 	"nnzero")
149 150
151 
+exportMethods("checksum")
152 
+
153 
+exportMethods(
154 
+	"describe_for_display",
155 
+	"preview_for_display")
156 
+
150 157 
 exportMethods(
151 158 
 	"%*%",
152 159 
 	"[",
... ... 
@@ -157,6 +164,8 @@ exportMethods(
157 164 
 	"combine",
158 165 
 	"cbind",
159 166 
 	"rbind",
167 
+	"cbind2",
168 
+	"rbind2",
160 169 
 	"lengths",
161 170 
 	"length",
162 171 
 	"length<-",
... ... 
@@ -288,7 +297,8 @@ exportMethods(
288 297
289 298 
 exportMethods("prcomp")
290 299
291 
-export("reldiff",
300 
+export(
301 
+	"reldiff",
292 302 
 	"asearch",
293 303 
 	"bsearch")
294 304
Browse code

started new Atoms cpp re-implementation

Kylie Bemis authored on 30/08/2022 02:28:42
Showing 1 changed files
NAMESPACE
History View file @ 4e7684953
... ... 
@@ -248,7 +248,9 @@ export(
248 248 
 	"chunk_apply",
249 249 
 	"chunk_mapply")
250 250
251 
-export("atoms")
251 
+export(
252 
+	"atoms",
253 
+	"atoms2")
252 254
253 255 
 export(
254 256 
 	"uuid",
Browse code

added drle_fc class for factors

kuwisdelu authored on 28/08/2022 19:06:54
Showing 1 changed files
NAMESPACE
History View file @ 7991d3549
... ... 
@@ -51,6 +51,7 @@ importFrom("utils",
51 51
52 52 
 exportClasses(
53 53 
 	"drle",
54 
+	"drle_fc",
54 55 
 	"matter",
55 56 
 	"matter_vec",
56 57 
 	"matter_mat",
Browse code

reimplemented DRLE class

kuwisdelu authored on 27/08/2022 01:57:13
Showing 1 changed files
NAMESPACE
History View file @ 77dec03b6
... ... 
@@ -107,10 +107,6 @@ exportMethods(
107 107 
 	"as.factor",
108 108 
 	"as.data.frame")
109 109
110 
-export(
111 
-	"push",
112 
-	"pull")
113 
-
114 110 
 exportMethods(
115 111 
 	"adata",
116 112 
 	"atomdata",
Browse code

cleaned up docs for new sparse data--more later

kuwisdelu authored on 24/08/2022 02:06:40
Showing 1 changed files
NAMESPACE
History View file @ 4cda2829f
... ... 
@@ -148,7 +148,7 @@ exportMethods(
148 148 
 	"sampler<-",
149 149 
 	"combiner",
150 150 
 	"combiner<-",
151 
-	"nnz")
151 
+	"nnzero")
152 152
153 153 
 exportMethods(
154 154 
 	"%*%",
... ... 
@@ -207,8 +207,6 @@ exportMethods(
207 207 
 	"rowSds",
208 208 
 	"which")
209 209
210 
-export("nnzero")
211 
-
212 210 
 export(
213 211 
 	"s_range",
214 212 
 	"s_min",
Browse code

removed old sparse matrix code

kuwisdelu authored on 24/08/2022 01:11:06
Showing 1 changed files
NAMESPACE
History View file @ f7f0b1d6f
... ... 
@@ -66,9 +66,6 @@ exportClasses(
66 66 
 	"sparse_mat",
67 67 
 	"sparse_matc",
68 68 
 	"sparse_matr",
69 
-	"sparse_old_mat",
70 
-	"sparse_old_matc",
71 
-	"sparse_old_matr",
72 69 
 	"virtual_mat",
73 70 
 	"virtual_matc",
74 71 
 	"virtual_matr",
... ... 
@@ -91,8 +88,6 @@ export(
91 88 
 	"rep_vt",
92 89 
 	"sparse_vec",
93 90 
 	"sparse_mat",
94 
-	"sparse_mat2",
95 
-	"sparse_old_mat",
96 91 
 	"is.matter",
97 92 
 	"as.matter",
98 93 
 	"is.sparse",
Browse code

implemented new sparse_mat classes

kuwisdelu authored on 18/08/2022 22:48:27
Showing 1 changed files
NAMESPACE
History View file @ d7e9a86bd
... ... 
@@ -64,6 +64,8 @@ exportClasses(
64 64 
 	"rep_vt",
65 65 
 	"sparse_vec",
66 66 
 	"sparse_mat",
67 
+	"sparse_matc",
68 
+	"sparse_matr",
67 69 
 	"sparse_old_mat",
68 70 
 	"sparse_old_matc",
69 71 
 	"sparse_old_matr",
... ... 
@@ -89,6 +91,7 @@ export(
89 91 
 	"rep_vt",
90 92 
 	"sparse_vec",
91 93 
 	"sparse_mat",
94 
+	"sparse_mat2",
92 95 
 	"sparse_old_mat",
93 96 
 	"is.matter",
94 97 
 	"as.matter",
... ... 
@@ -146,6 +149,8 @@ exportMethods(
146 149 
 	"keys<-",
147 150 
 	"tolerance",
148 151 
 	"tolerance<-",
152 
+	"sampler",
153 
+	"sampler<-",
149 154 
 	"combiner",
150 155 
 	"combiner<-",
151 156 
 	"nnz")
Browse code

kvsearch -> asearch (for approximate search w/ interp

kuwisdelu authored on 11/08/2022 21:39:50
Showing 1 changed files
NAMESPACE
History View file @ 02227b72f
... ... 
@@ -292,8 +292,8 @@ exportMethods(
292 292 
 exportMethods("prcomp")
293 293
294 294 
 export("reldiff",
295 
-	"bsearch",
296 
-	"kvsearch")
295 
+	"asearch",
296 
+	"bsearch")
297 297
298 298 
 export(
299 299 
 	"mem",
Browse code

bsearch signals unsorted table; kvsearch falls back to linear search

Kylie Bemis authored on 10/08/2022 04:50:42
Showing 1 changed files
NAMESPACE
History View file @ d46584eca
... ... 
@@ -140,6 +140,8 @@ exportMethods(
140 140 
 	"aindex",
141 141 
 	"atomindex",
142 142 
 	"atomindex<-",
143 
+	"domain",
144 
+	"domain<-",
143 145 
 	"keys",
144 146 
 	"keys<-",
145 147 
 	"tolerance",
Browse code

added mean summarization to kvsearch

Kylie Bemis authored on 08/08/2022 21:45:57
Showing 1 changed files
NAMESPACE
History View file @ 69e481c37
... ... 
@@ -63,6 +63,7 @@ exportClasses(
63 63 
 	"matter_df",
64 64 
 	"rep_vt",
65 65 
 	"sparse_vec",
66 
+	"sparse_mat",
66 67 
 	"sparse_old_mat",
67 68 
 	"sparse_old_matc",
68 69 
 	"sparse_old_matr",
... ... 
@@ -87,6 +88,7 @@ export(
87 88 
 	"matter_df",
88 89 
 	"rep_vt",
89 90 
 	"sparse_vec",
91 
+	"sparse_mat",
90 92 
 	"sparse_old_mat",
91 93 
 	"is.matter",
92 94 
 	"as.matter",
Browse code

started sparse_mat implementation

kuwisdelu authored on 04/08/2022 17:55:15
Showing 1 changed files
NAMESPACE
History View file @ 21b146ff3
... ... 
@@ -63,9 +63,9 @@ exportClasses(
63 63 
 	"matter_df",
64 64 
 	"rep_vt",
65 65 
 	"sparse_vec",
66 
-	"sparse_mat",
67 
-	"sparse_matc",
68 
-	"sparse_matr",
66 
+	"sparse_old_mat",
67 
+	"sparse_old_matc",
68 
+	"sparse_old_matr",
69 69 
 	"virtual_mat",
70 70 
 	"virtual_matc",
71 71 
 	"virtual_matr",
... ... 
@@ -87,7 +87,7 @@ export(
87 87 
 	"matter_df",
88 88 
 	"rep_vt",
89 89 
 	"sparse_vec",
90 
-	"sparse_mat",
90 
+	"sparse_old_mat",
91 91 
 	"is.matter",
92 92 
 	"as.matter",
93 93 
 	"is.sparse",
... ... 
@@ -135,12 +135,16 @@ exportMethods(
135 135 
 	"preview_for_display")
136 136
137 137 
 exportMethods(
138 
+	"aindex",
139 
+	"atomindex",
140 
+	"atomindex<-",
138 141 
 	"keys",
139 142 
 	"keys<-",
140 143 
 	"tolerance",
141 144 
 	"tolerance<-",
142 145 
 	"combiner",
143 
-	"combiner<-")
146 
+	"combiner<-",
147 
+	"nnz")
144 148
145 149 
 exportMethods(
146 150 
 	"%*%",
Browse code

revise bsearch.cpp => search.cpp

kuwisdelu authored on 02/01/2022 07:09:40
Showing 1 changed files
NAMESPACE
History View file @ 15f3fa7c3
... ... 
@@ -62,6 +62,7 @@ exportClasses(
62 62 
 	"matter_fc",
63 63 
 	"matter_df",
64 64 
 	"rep_vt",
65 
+	"sparse_vec",
65 66 
 	"sparse_mat",
66 67 
 	"sparse_matc",
67 68 
 	"sparse_matr",
... ... 
@@ -85,6 +86,7 @@ export(
85 86 
 	"matter_fc",
86 87 
 	"matter_df",
87 88 
 	"rep_vt",
89 
+	"sparse_vec",
88 90 
 	"sparse_mat",
89 91 
 	"is.matter",
90 92 
 	"as.matter",
Browse code

added kvsearch() for key-value search

kuwisdelu authored on 31/12/2021 20:50:31
Showing 1 changed files
NAMESPACE
History View file @ 00ea5f248
... ... 
@@ -282,8 +282,8 @@ exportMethods(
282 282 
 exportMethods("prcomp")
283 283
284 284 
 export("reldiff",
285 
-	"lsearch",
286 
-	"bsearch")
285 
+	"bsearch",
286 
+	"kvsearch")
287 287
288 288 
 export(
289 289 
 	"mem",
Browse code

refactor bsearch(); add lsearch()

Kylie Bemis authored on 28/10/2021 05:37:27
Showing 1 changed files
NAMESPACE
History View file @ 814ec8727
... ... 
@@ -281,7 +281,9 @@ exportMethods(
281 281
282 282 
 exportMethods("prcomp")
283 283
284 
-export("bsearch")
284 
+export("reldiff",
285 
+	"lsearch",
286 
+	"bsearch")
285 287
286 288 
 export(
287 289 
 	"mem",
Browse code

v1.13.10 added s_nnzero() stream stat; added push/pull generics

kuwisdelu authored on 20/04/2020 23:48:20
Showing 1 changed files
NAMESPACE
History View file @ 688245734
... ... 
@@ -105,6 +105,10 @@ exportMethods(
105 105 
 	"as.factor",
106 106 
 	"as.data.frame")
107 107
108 
+export(
109 
+	"push",
110 
+	"pull")
111 
+
108 112 
 exportMethods(
109 113 
 	"adata",
110 114 
 	"atomdata",
Browse code

added nnzero stream stat

kuwisdelu authored on 20/04/2020 23:24:56
Showing 1 changed files
NAMESPACE
History View file @ 1ef94a99f
... ... 
@@ -9,6 +9,9 @@ importFrom("digest",
9 9 
 importFrom("irlba",
10 10 
 	"irlba")
11 11
12 
+importFrom("Matrix",
13 
+	"nnzero")
14 
+
12 15 
 importFrom("stats",
13 16 
 	"median",
14 17 
 	"update",
... ... 
@@ -190,6 +193,8 @@ exportMethods(
190 193 
 	"rowSds",
191 194 
 	"which")
192 195
196 
+export("nnzero")
197 
+
193 198 
 export(
194 199 
 	"s_range",
195 200 
 	"s_min",
... ... 
@@ -201,6 +206,7 @@ export(
201 206 
 	"s_sd",
202 207 
 	"s_any",
203 208 
 	"s_all",
209 
+	"s_nnzero",
204 210 
 	"stat_c")
205 211
206 212 
 export(
... ... 
@@ -223,6 +229,7 @@ S3method("stat_c", "stream_var")
223 229 
 S3method("stat_c", "stream_sd")
224 230 
 S3method("stat_c", "stream_any")
225 231 
 S3method("stat_c", "stream_all")
232 
+S3method("stat_c", "stream_nnzero")
226 233
227 234 
 exportMethods(
228 235 
 	"colStats",
Browse code

v.1.13.1 added chunk_mapply()

kuwisdelu authored on 30/10/2019 18:11:32
Showing 1 changed files
NAMESPACE
History View file @ c9f2579d6
... ... 
@@ -228,7 +228,9 @@ exportMethods(
228 228 
 	"colStats",
229 229 
 	"rowStats")
230 230
231 
-export("chunk_apply")
231 
+export(
232 
+	"chunk_apply",
233 
+	"chunk_mapply")
232 234
233 235 
 export("atoms")
234 236
Browse code

v1.11.6 added locmax() and binvec()

kuwisdelu authored on 24/10/2019 07:34:32
Showing 1 changed files
NAMESPACE
History View file @ d269e79ed
... ... 
@@ -251,6 +251,10 @@ export(
251 251 
 	"widest_datamode",
252 252 
 	"vm_used")
253 253
254 
+export(
255 
+	"binvec",
256 
+	"locmax")
257 
+
254 258 
 exportMethods(
255 259 
 	"apply",
256 260 
 	"lapply",
Browse code

v1.11.5 chunk_apply()

kuwisdelu authored on 13/10/2019 18:13:18
Showing 1 changed files
NAMESPACE
History View file @ d1203215c
... ... 
@@ -228,6 +228,8 @@ exportMethods(
228 228 
 	"colStats",
229 229 
 	"rowStats")
230 230
231 
+export("chunk_apply")
232 
+
231 233 
 export("atoms")
232 234
233 235 
 export(
Browse code

updated docs and bugs for rowStats() + colStats()

kuwisdelu authored on 13/10/2019 09:23:23
Showing 1 changed files
NAMESPACE
History View file @ 084f4c8e0
... ... 
@@ -10,6 +10,7 @@ importFrom("irlba",
10 10 
 	"irlba")
11 11
12 12 
 importFrom("stats",
13 
+	"median",
13 14 
 	"update",
14 15 
 	"setNames",
15 16 
 	"na.omit")
... ... 
@@ -202,6 +203,10 @@ export(
202 203 
 	"s_all",
203 204 
 	"stat_c")
204 205
206 
+export(
207 
+	"colstreamStats",
208 
+	"rowstreamStats")
209 
+
205 210 
 S3method("c", "stream_stat")
206 211 
 S3method("print", "stream_stat")
207 212 
 S3method("nobs", "stream_stat")
... ... 
@@ -219,8 +224,6 @@ S3method("stat_c", "stream_sd")
219 224 
 S3method("stat_c", "stream_any")
220 225 
 S3method("stat_c", "stream_all")
221 226
222 
-export("chunkapply")
223 
-
224 227 
 exportMethods(
225 228 
 	"colStats",
226 229 
 	"rowStats")
Browse code

added chunkapply(); big rowStats() + colStats() update

kuwisdelu authored on 13/10/2019 07:43:25
Showing 1 changed files
NAMESPACE
History View file @ c7396200b
... ... 
@@ -219,7 +219,9 @@ S3method("stat_c", "stream_sd")
219 219 
 S3method("stat_c", "stream_any")
220 220 
 S3method("stat_c", "stream_all")
221 221
222 
-export(
222 
+export("chunkapply")
223 
+
224 
+exportMethods(
223 225 
 	"colStats",
224 226 
 	"rowStats")
225 227
Browse code

bsearch() now finds closest match when tol > 0

kuwisdelu authored on 09/10/2019 18:54:14
Showing 1 changed files
NAMESPACE
History View file @ 3400b091e
... ... 
@@ -37,6 +37,9 @@ importFrom("BiocGenerics",
37 37 
 	"lapply",
38 38 
 	"sapply")
39 39
40 
+importFrom("ProtGenerics",
41 
+	"tolerance")
42 
+
40 43 
 importFrom("utils",
41 44 
 	"head",
42 45 
 	"tail",
... ... 
@@ -220,6 +223,8 @@ export(
220 223 
 	"colStats",
221 224 
 	"rowStats")
222 225
226 
+export("atoms")
227 
+
223 228 
 export(
224 229 
 	"uuid",
225 230 
 	"hex2raw",
Browse code

updated some things for DelayedArray compatibility

kuwisdelu authored on 26/07/2019 14:06:30
Showing 1 changed files
NAMESPACE
History View file @ d1ebea213
... ... 
@@ -28,6 +28,8 @@ importFrom("BiocGenerics",
28 28 
 	"rowMeans",
29 29 
 	"rowSums",
30 30 
 	"t",
31 
+	"path",
32 
+	"path<-",
31 33 
 	"combine",
32 34 
 	"cbind",
33 35 
 	"rbind",
... ... 
@@ -104,6 +106,8 @@ exportMethods(
104 106 
 	"datamode<-",
105 107 
 	"paths",
106 108 
 	"paths<-",
109 
+	"path",
110 
+	"path<-",
107 111 
 	"filemode",
108 112 
 	"filemode<-",
109 113 
 	"readonly",
Browse code

vectorized stream_stat class; added rowStats()/colStats()

kuwisdelu authored on 25/07/2019 14:45:03
Showing 1 changed files
NAMESPACE
History View file @ 340852bae
... ... 
@@ -195,6 +195,12 @@ export(
195 195 
 	"s_all",
196 196 
 	"stat_c")
197 197
198 
+S3method("c", "stream_stat")
199 
+S3method("print", "stream_stat")
200 
+S3method("nobs", "stream_stat")
201 
+S3method("[", "stream_stat")
202 
+S3method("[[", "stream_stat")
203 
+
198 204 
 S3method("stat_c", "stream_range")
199 205 
 S3method("stat_c", "stream_min")
200 206 
 S3method("stat_c", "stream_max")
... ... 
@@ -206,8 +212,9 @@ S3method("stat_c", "stream_sd")
206 212 
 S3method("stat_c", "stream_any")
207 213 
 S3method("stat_c", "stream_all")
208 214
209 
-S3method("print", "stream_stat")
210 
-S3method("nobs", "stream_stat")
215 
+export(
216 
+	"colStats",
217 
+	"rowStats")
211 218
212 219 
 export(
213 220 
 	"uuid",
Browse code

updated show methods + virtual_df

kuwisdelu authored on 23/07/2019 09:18:36
Showing 1 changed files
NAMESPACE
History View file @ 51c56751f
... ... 
@@ -58,7 +58,9 @@ exportClasses(
58 58 
 	"sparse_matr",
59 59 
 	"virtual_mat",
60 60 
 	"virtual_matc",
61 
-	"virtual_matr")
61 
+	"virtual_matr",
62 
+	"virtual_tbl",
63 
+	"virtual_df")
62 64
63 65 
 export(
64 66 
 	"drle",
... ... 
@@ -75,13 +77,14 @@ export(
75 77 
 	"matter_df",
76 78 
 	"rep_vt",
77 79 
 	"sparse_mat",
78 
-	"virtual_mat",
79 80 
 	"is.matter",
80 81 
 	"as.matter",
81 82 
 	"is.sparse",
82 83 
 	"as.sparse",
83 84 
 	"is.virtual",
84 85 
 	"as.virtual",
86 
+	"virtual_mat",
87 
+	"virtual_df",
85 88 
 	"struct")
86 89
87 90 
 exportMethods(
Browse code

updated show methods

kuwisdelu authored on 22/07/2019 12:54:38
Showing 1 changed files
NAMESPACE
History View file @ cab92b492
... ... 
@@ -110,6 +110,10 @@ exportMethods(
110 110
111 111 
 exportMethods("checksum")
112 112
113 
+exportMethods(
114 
+	"describe_for_display",
115 
+	"preview_for_display")
116 
+
113 117 
 exportMethods(
114 118 
 	"keys",
115 119 
 	"keys<-",
Browse code

use R_tryWrap to add attributes; add coercion methods and altrep options

kuwisdelu authored on 19/07/2019 09:39:20
Showing 1 changed files
NAMESPACE
History View file @ 20e876e15
... ... 
@@ -90,6 +90,7 @@ exportMethods(
90 90 
 	"as.matrix",
91 91 
 	"as.array",
92 92 
 	"as.list",
93 
+	"as.factor",
93 94 
 	"as.data.frame")
94 95
95 96 
 exportMethods(
Browse code

add altrep serialize/unserialize; add altrep raw/logical

kuwisdelu authored on 17/07/2019 09:42:29
Showing 1 changed files
NAMESPACE
History View file @ ddb04ef6b
... ... 
@@ -85,6 +85,7 @@ export(
85 85 
 	"struct")
86 86
87 87 
 exportMethods(
88 
+	"as.altrep",
88 89 
 	"as.vector",
89 90 
 	"as.matrix",
90 91 
 	"as.array",
Browse code

added stream_stat docs

kuwisdelu authored on 06/05/2019 20:01:19
Showing 1 changed files
NAMESPACE
History View file @ 06f7f5101
... ... 
@@ -123,6 +123,7 @@ exportMethods(
123 123 
 	"$",
124 124 
 	"$<-",
125 125 
 	"c",
126 
+	"combine",
126 127 
 	"cbind",
127 128 
 	"rbind",
128 129 
 	"lengths",
... ... 
@@ -172,6 +173,33 @@ exportMethods(
172 173 
 	"rowSds",
173 174 
 	"which")
174 175
176 
+export(
177 
+	"s_range",
178 
+	"s_min",
179 
+	"s_max",
180 
+	"s_prod",
181 
+	"s_sum",
182 
+	"s_mean",
183 
+	"s_var",
184 
+	"s_sd",
185 
+	"s_any",
186 
+	"s_all",
187 
+	"stat_c")
188 
+
189 
+S3method("stat_c", "stream_range")
190 
+S3method("stat_c", "stream_min")
191 
+S3method("stat_c", "stream_max")
192 
+S3method("stat_c", "stream_prod")
193 
+S3method("stat_c", "stream_sum")
194 
+S3method("stat_c", "stream_mean")
195 
+S3method("stat_c", "stream_var")
196 
+S3method("stat_c", "stream_sd")
197 
+S3method("stat_c", "stream_any")
198 
+S3method("stat_c", "stream_all")
199 
+
200 
+S3method("print", "stream_stat")
201 
+S3method("nobs", "stream_stat")
202 
+
175 203 
 export(
176 204 
 	"uuid",
177 205 
 	"hex2raw",
Browse code

changed filemode to factor: r, w, rw

kuwisdelu authored on 14/12/2018 01:58:49
Showing 1 changed files
NAMESPACE
History View file @ fb0b92188
... ... 
@@ -180,6 +180,10 @@ export(
180 180 
 S3method("print", "num_bytes")
181 181 
 S3method("format", "num_bytes")
182 182
183 
+export(
184 
+	"make_filemode",
185 
+	"common_filemode")
186 
+
183 187 
 export(
184 188 
 	"sizeof",
185 189 
 	"make_datamode",
Browse code

added lapply, sapply, and BiocParallel support

kuwisdelu authored on 09/12/2018 01:54:35
Showing 1 changed files
NAMESPACE
History View file @ 51831dcdc
... ... 
@@ -14,6 +14,8 @@ importFrom("stats",
14 14 
 	"setNames",
15 15 
 	"na.omit")
16 16
17 
+import("BiocParallel")
18 
+
17 19 
 importFrom("BiocGenerics",
18 20 
 	"as.data.frame",
19 21 
 	"as.list",
... ... 
@@ -29,7 +31,9 @@ importFrom("BiocGenerics",
29 31 
 	"combine",
30 32 
 	"cbind",
31 33 
 	"rbind",
32 
-	"which")
34 
+	"which",
35 
+	"lapply",
36 
+	"sapply")
33 37
34 38 
 importFrom("utils",
35 39 
 	"head",
... ... 
@@ -139,6 +143,7 @@ exportMethods(
139 143 
 exportMethods(
140 144 
 	"Arith",
141 145 
 	"Compare",
146 
+	"Logic",
142 147 
 	"exp",
143 148 
 	"log",
144 149 
 	"log2",
... ... 
@@ -182,7 +187,10 @@ export(
182 187 
 	"widest_datamode",
183 188 
 	"vm_used")
184 189
185 
-exportMethods("apply")
190 
+exportMethods(
191 
+	"apply",
192 
+	"lapply",
193 
+	"sapply")
186 194
187 195 
 exportMethods("scale")
188 196
Browse code

v1.9.3 matrix multiplication for sparse_mat+virtual_mat

kuwisdelu authored on 08/12/2018 22:00:11
Showing 1 changed files
NAMESPACE
History View file @ 3f21256d7
... ... 
@@ -172,8 +172,8 @@ export(
172 172 
 	"hex2raw",
173 173 
 	"raw2hex")
174 174
175 
-S3method("print", "nbytes")
176 
-S3method("format", "nbytes")
175 
+S3method("print", "num_bytes")
176 
+S3method("format", "num_bytes")
177 177
178 178 
 export(
179 179 
 	"sizeof",
Browse code

renamed internal bytes class to nbytes due to Rcpp

kuwisdelu authored on 12/11/2018 19:38:02
Showing 1 changed files
NAMESPACE
History View file @ a60b3f3ac
... ... 
@@ -172,8 +172,8 @@ export(
172 172 
 	"hex2raw",
173 173 
 	"raw2hex")
174 174
175 
-S3method("print", "bytes")
176 
-S3method("format", "bytes")
175 
+S3method("print", "nbytes")
176 
+S3method("format", "nbytes")
177 177
178 178 
 export(
179 179 
 	"sizeof",
Browse code

fixed lengths() bug in namespace

kuwisdelu authored on 12/11/2018 19:04:51
Showing 1 changed files
NAMESPACE
History View file @ 5f98c6d1f
... ... 
@@ -29,7 +29,6 @@ importFrom("BiocGenerics",
29 29 
 	"combine",
30 30 
 	"cbind",
31 31 
 	"rbind",
32 
-	"lengths",
33 32 
 	"which")
34 33
35 34 
 importFrom("utils",
Browse code

v1.7.6 added some features for Cardinal

kuwisdelu authored on 26/07/2018 00:47:33
Showing 1 changed files
NAMESPACE
History View file @ 4228bb1c1
... ... 
@@ -173,11 +173,15 @@ export(
173 173 
 	"hex2raw",
174 174 
 	"raw2hex")
175 175
176 
+S3method("print", "bytes")
177 
+S3method("format", "bytes")
178 
+
176 179 
 export(
177 180 
 	"sizeof",
178 181 
 	"make_datamode",
179 182 
 	"convert_datamode",
180 
-	"widest_datamode")
183 
+	"widest_datamode",
184 
+	"vm_used")
181 185
182 186 
 exportMethods("apply")
183 187
Browse code

v1.7.3 added rep_vt

kuwisdelu authored on 23/07/2018 21:31:51
Showing 1 changed files
NAMESPACE
History View file @ 4b0320208
... ... 
@@ -49,6 +49,7 @@ exportClasses(
49 49 
 	"matter_str",
50 50 
 	"matter_fc",
51 51 
 	"matter_df",
52 
+	"rep_vt",
52 53 
 	"sparse_mat",
53 54 
 	"sparse_matc",
54 55 
 	"sparse_matr",
... ... 
@@ -69,6 +70,7 @@ export(
69 70 
 	"matter_str",
70 71 
 	"matter_fc",
71 72 
 	"matter_df",
73 
+	"rep_vt",
72 74 
 	"sparse_mat",
73 75 
 	"virtual_mat",
74 76 
 	"is.matter",
Browse code

added struct function for C-style structs on disk

kuwisdelu authored on 02/12/2017 19:28:30
Showing 1 changed files
NAMESPACE
History View file @ 0c3535f49
... ... 
@@ -76,7 +76,8 @@ export(
76 76 
 	"is.sparse",
77 77 
 	"as.sparse",
78 78 
 	"is.virtual",
79 
-	"as.virtual")
79 
+	"as.virtual",
80 
+	"struct")
80 81
81 82 
 exportMethods(
82 83 
 	"as.vector",
Browse code

added combiner generic and min/max combiner methods

kuwisdelu authored on 02/12/2017 01:32:09
Showing 1 changed files
NAMESPACE
History View file @ 289b689b8
... ... 
@@ -106,7 +106,9 @@ exportMethods(
106 106 
 	"keys",
107 107 
 	"keys<-",
108 108 
 	"tolerance",
109 
-	"tolerance<-")
109 
+	"tolerance<-",
110 
+	"combiner",
111 
+	"combiner<-")
110 112
111 113 
 exportMethods(
112 114 
 	"%*%",
Browse code

added options for cast warning, biglm method, and exported low-level utils

kuwisdelu authored on 02/12/2017 00:27:52
Showing 1 changed files
NAMESPACE
History View file @ 3928355a4
... ... 
@@ -10,6 +10,7 @@ importFrom("irlba",
10 10 
 	"irlba")
11 11
12 12 
 importFrom("stats",
13 
+	"update",
13 14 
 	"setNames",
14 15 
 	"na.omit")
15 16
... ... 
@@ -167,11 +168,19 @@ export(
167 168 
 	"hex2raw",
168 169 
 	"raw2hex")
169 170
171 
+export(
172 
+	"sizeof",
173 
+	"make_datamode",
174 
+	"convert_datamode",
175 
+	"widest_datamode")
176 
+
170 177 
 exportMethods("apply")
171 178
172 179 
 exportMethods("scale")
173 180
174 
-exportMethods("bigglm")
181 
+exportMethods(
182 
+	"biglm",
183 
+	"bigglm")
175 184
176 185 
 exportMethods("prcomp")
177 186
Browse code

v1.5.3 added rest of Summary group

kuwisdelu authored on 01/12/2017 21:38:18
Showing 1 changed files
NAMESPACE
History View file @ 0b8f43e38
... ... 
@@ -142,10 +142,16 @@ exportMethods(
142 142 
 exportMethods(
143 143 
 	"head",
144 144 
 	"tail",
145 
+	"range",
146 
+	"min",
147 
+	"max",
148 
+	"prod",
145 149 
 	"sum",
146 150 
 	"mean",
147 151 
 	"var",
148 152 
 	"sd",
153 
+	"any",
154 
+	"all",
149 155 
 	"colSums",
150 156 
 	"colMeans",
151 157 
 	"colVars",
Browse code

transpose virtual_mat matrices

kuwisdelu authored on 12/11/2017 04:53:14
Showing 1 changed files
NAMESPACE
History View file @ 9b762a053
... ... 
@@ -131,11 +131,6 @@ exportMethods(
131 131 
 	"crossprod",
132 132 
 	"tcrossprod")
133 133
134 
-export(
135 
-	"t.matter",
136 
-	"mean.matter",
137 
-	"scale.matter")
138 
-
139 134 
 exportMethods(
140 135 
 	"Arith",
141 136 
 	"Compare",
Browse code

combine virtual_mat matrices

kuwisdelu authored on 12/11/2017 01:55:23
Showing 1 changed files
NAMESPACE
History View file @ 51a51628b
... ... 
@@ -177,7 +177,6 @@ exportMethods("prcomp")
177 177 
 export("bsearch")
178 178
179 179 
 export(
180 
-	"disk_used",
181 180 
 	"mem",
182 181 
 	"profmem")
183 182
Browse code

more virtual_mat

kuwisdelu authored on 11/11/2017 22:14:27
Showing 1 changed files
NAMESPACE
History View file @ a3bdcb6c0
... ... 
@@ -71,7 +71,11 @@ export(
71 71 
 	"sparse_mat",
72 72 
 	"virtual_mat",
73 73 
 	"is.matter",
74 
-	"as.matter")
74 
+	"as.matter",
75 
+	"is.sparse",
76 
+	"as.sparse",
77 
+	"is.virtual",
78 
+	"as.virtual")
75 79
76 80 
 exportMethods(
77 81 
 	"as.vector",
... ... 
@@ -172,7 +176,9 @@ exportMethods("prcomp")
172 176
173 177 
 export("bsearch")
174 178
175 
-export("mem",
179 
+export(
180 
+	"disk_used",
181 
+	"mem",
176 182 
 	"profmem")
177 183
178 184 
 useDynLib("matter", .registration=TRUE)
Browse code

virtual_mat class

kuwisdelu authored on 11/11/2017 18:51:23
Showing 1 changed files
NAMESPACE
History View file @ 7a4396fbb
... ... 
@@ -50,7 +50,10 @@ exportClasses(
50 50 
 	"matter_df",
51 51 
 	"sparse_mat",
52 52 
 	"sparse_matc",
53 
-	"sparse_matr")
53 
+	"sparse_matr",
54 
+	"virtual_mat",
55 
+	"virtual_matc",
56 
+	"virtual_matr")
54 57
55 58 
 export(
56 59 
 	"drle",
... ... 
@@ -66,6 +69,7 @@ export(
66 69 
 	"matter_fc",
67 70 
 	"matter_df",
68 71 
 	"sparse_mat",
72 
+	"virtual_mat",
69 73 
 	"is.matter",
70 74 
 	"as.matter")
71 75
Browse code

created matter_vt and matter_tbl classes

kuwisdelu authored on 11/11/2017 04:31:54
Showing 1 changed files
NAMESPACE
History View file @ 7b2e6a109
... ... 
@@ -86,6 +86,8 @@ exportMethods(
86 86 
 	"paths<-",
87 87 
 	"filemode",
88 88 
 	"filemode<-",
89 
+	"readonly",
90 
+	"readonly<-",
89 91 
 	"chunksize",
90 92 
 	"chunksize<-")
91 93
Browse code

better support for endomorphic subsetting via drop=NULL

kuwisdelu authored on 10/11/2017 04:14:34
Showing 1 changed files
NAMESPACE
History View file @ 7cc8fdf76
... ... 
@@ -14,15 +14,20 @@ importFrom("stats",
14 14 
 	"na.omit")
15 15
16 16 
 importFrom("BiocGenerics",
17 
+	"as.data.frame",
18 
+	"as.list",
19 
+	"as.vector",
20 
+	"mean",
17 21 
 	"sd",
18 22 
 	"var",
19 
-	"combine",
20 
-	"cbind",
21 
-	"rbind",
22 23 
 	"colMeans",
23 24 
 	"colSums",
24 25 
 	"rowMeans",
25 26 
 	"rowSums",
27 
+	"t",
28 
+	"combine",
29 
+	"cbind",
30 
+	"rbind",
26 31 
 	"lengths",
27 32 
 	"which")
28 33
... ... 
@@ -64,6 +69,13 @@ export(
64 69 
 	"is.matter",
65 70 
 	"as.matter")
66 71
72 
+exportMethods(
73 
+	"as.vector",
74 
+	"as.matrix",
75 
+	"as.array",
76 
+	"as.list",
77 
+	"as.data.frame")
78 
+
67 79 
 exportMethods(
68 80 
 	"adata",
69 81 
 	"atomdata",
Browse code

cleaned up docs and stuff

kuwisdelu authored on 30/10/2017 21:54:42
Showing 1 changed files
NAMESPACE
History View file @ 2167a3b0b
... ... 
@@ -10,7 +10,8 @@ importFrom("irlba",
10 10 
 	"irlba")
11 11
12 12 
 importFrom("stats",
13 
-	"setNames")
13 
+	"setNames",
14 
+	"na.omit")
14 15
15 16 
 importFrom("BiocGenerics",
16 17 
 	"sd",
Browse code

faster sparse_mat subsetting

kuwisdelu authored on 30/10/2017 19:48:17
Showing 1 changed files
NAMESPACE
History View file @ 435eeff4a
... ... 
@@ -10,8 +10,7 @@ importFrom("irlba",
10 10 
 	"irlba")
11 11
12 12 
 importFrom("stats",
13 
-	"setNames",
14 
-	"na.omit")
13 
+	"setNames")
15 14
16 15 
 importFrom("BiocGenerics",
17 16 
 	"sd",
Browse code

added sparse_mat class

kuwisdelu authored on 30/10/2017 03:29:23
Showing 1 changed files
NAMESPACE
History View file @ 74f98ee93
... ... 
@@ -9,6 +9,10 @@ importFrom("digest",
9 9 
 importFrom("irlba",
10 10 
 	"irlba")
11 11
12 
+importFrom("stats",
13 
+	"setNames",
14 
+	"na.omit")
15 
+
12 16 
 importFrom("BiocGenerics",
13 17 
 	"sd",
14 18 
 	"var",
... ... 
@@ -22,9 +26,6 @@ importFrom("BiocGenerics",
22 26 
 	"lengths",
23 27 
 	"which")
24 28
25 
-importFrom("stats",
26 
-	"setNames")
27 
-
28 29 
 importFrom("utils",
29 30 
 	"head",
30 31 
 	"tail",
... ... 
@@ -41,7 +42,10 @@ exportClasses(
41 42 
 	"matter_list",
42 43 
 	"matter_str",
43 44 
 	"matter_fc",
44 
-	"matter_df")
45 
+	"matter_df",
46 
+	"sparse_mat",
47 
+	"sparse_matc",
48 
+	"sparse_matr")
45 49
46 50 
 export(
47 51 
 	"drle",
... ... 
@@ -56,6 +60,7 @@ export(
56 60 
 	"matter_str",
57 61 
 	"matter_fc",
58 62 
 	"matter_df",
63 
+	"sparse_mat",
59 64 
 	"is.matter",
60 65 
 	"as.matter")
61 66
... ... 
@@ -70,8 +75,15 @@ exportMethods(
70 75 
 	"filemode",
71 76 
 	"filemode<-",
72 77 
 	"chunksize",
73 
-	"chunksize<-",
74 
-	"checksum")
78 
+	"chunksize<-")
79 
+
80 
+exportMethods("checksum")
81 
+
82 
+exportMethods(
83 
+	"keys",
84 
+	"keys<-",
85 
+	"tolerance",
86 
+	"tolerance<-")
75 87
76 88 
 exportMethods(
77 89 
 	"%*%",
Browse code

added uuid and checksums

kuwisdelu authored on 27/10/2017 03:04:08
Showing 1 changed files
NAMESPACE
History View file @ 57ebaf6d3
... ... 
@@ -3,6 +3,9 @@ import("methods")
3 3
4 4 
 import("biglm")
5 5
6 
+importFrom("digest",
7 
+	"digest")
8 
+
6 9 
 importFrom("irlba",
7 10 
 	"irlba")
8 11
... ... 
@@ -67,7 +70,8 @@ exportMethods(
67 70 
 	"filemode",
68 71 
 	"filemode<-",
69 72 
 	"chunksize",
70 
-	"chunksize<-")
73 
+	"chunksize<-",
74 
+	"checksum")
71 75
72 76 
 exportMethods(
73 77 
 	"%*%",
... ... 
@@ -123,6 +127,11 @@ exportMethods(
123 127 
 	"rowSds",
124 128 
 	"which")
125 129
130 
+export(
131 
+	"uuid",
132 
+	"hex2raw",
133 
+	"raw2hex")
134 
+
126 135 
 exportMethods("apply")
127 136
128 137 
 exportMethods("scale")
Browse code

moved bsearch to utils

kuwisdelu authored on 26/10/2017 22:38:20
Showing 0 changed files
Browse code

added factors, fixed data frame bugs

kuwisdelu authored on 26/10/2017 22:11:36
Showing 1 changed files
NAMESPACE
History View file @ 745e35699
... ... 
@@ -37,6 +37,7 @@ exportClasses(
37 37 
 	"matter_arr",
38 38 
 	"matter_list",
39 39 
 	"matter_str",
40 
+	"matter_fc",
40 41 
 	"matter_df")
41 42
42 43 
 export(
... ... 
@@ -49,8 +50,9 @@ export(
49 50 
 	"matter_mat",
50 51 
 	"matter_arr",
51 52 
 	"matter_list",
52 
-	"matter_df",
53 53 
 	"matter_str",
54 
+	"matter_fc",
55 
+	"matter_df",
54 56 
 	"is.matter",
55 57 
 	"as.matter")
56 58
... ... 
@@ -85,6 +87,8 @@ exportMethods(
85 87 
 	"names<-",
86 88 
 	"dimnames",
87 89 
 	"dimnames<-",
90 
+	"levels",
91 
+	"levels<-",
88 92 
 	"t",
89 93 
 	"crossprod",
90 94 
 	"tcrossprod")
Browse code

binary search

kuwisdelu authored on 25/10/2017 22:39:59
Showing 1 changed files
NAMESPACE
History View file @ e45aadf7f
... ... 
@@ -127,6 +127,8 @@ exportMethods("bigglm")
127 127
128 128 
 exportMethods("prcomp")
129 129
130 
+export("bsearch")
131 
+
130 132 
 export("mem",
131 133 
 	"profmem")
132 134
Browse code

changed back to matter_str

kuwisdelu authored on 20/10/2017 07:13:06
Showing 1 changed files
NAMESPACE
History View file @ 48e714253
... ... 
@@ -36,7 +36,7 @@ exportClasses(
36 36 
 	"matter_matr",
37 37 
 	"matter_arr",
38 38 
 	"matter_list",
39 
-	"matter_char",
39 
+	"matter_str",
40 40 
 	"matter_df")
41 41
42 42 
 export(
... ... 
@@ -50,7 +50,7 @@ export(
50 50 
 	"matter_arr",
51 51 
 	"matter_list",
52 52 
 	"matter_df",
53 
-	"matter_char",
53 
+	"matter_str",
54 54 
 	"is.matter",
55 55 
 	"as.matter")
56 56
Browse code

changed matter_str to matter_char and updated docs

kuwisdelu authored on 20/10/2017 06:44:03
Showing 1 changed files
NAMESPACE
History View file @ 542733a06
... ... 
@@ -36,7 +36,7 @@ exportClasses(
36 36 
 	"matter_matr",
37 37 
 	"matter_arr",
38 38 
 	"matter_list",
39 
-	"matter_str",
39 
+	"matter_char",
40 40 
 	"matter_df")
41 41
42 42 
 export(
... ... 
@@ -50,7 +50,7 @@ export(
50 50 
 	"matter_arr",
51 51 
 	"matter_list",
52 52 
 	"matter_df",
53 
-	"matter_str",
53 
+	"matter_char",
54 54 
 	"is.matter",
55 55 
 	"as.matter")
56 56
Browse code

file created by default

kuwisdelu authored on 20/10/2017 05:57:04
Showing 1 changed files
NAMESPACE
History View file @ 8bca0d827
... ... 
@@ -16,6 +16,7 @@ importFrom("BiocGenerics",
16 16 
 	"colSums",
17 17 
 	"rowMeans",
18 18 
 	"rowSums",
19 
+	"lengths",
19 20 
 	"which")
20 21
21 22 
 importFrom("stats",
... ... 
@@ -75,6 +76,7 @@ exportMethods(
75 76 
 	"c",
76 77 
 	"cbind",
77 78 
 	"rbind",
79 
+	"lengths",
78 80 
 	"length",
79 81 
 	"length<-",
80 82 
 	"dim",
Browse code

updated vignettes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/matter@129783 bc3139a8-67e5-0310-9ffc-ced21a209358

Kyle D. Bemis authored on 21/05/2017 01:13:57
Showing 1 changed files
NAMESPACE
History View file @ ee0e1b083
... ... 
@@ -125,4 +125,7 @@ exportMethods("bigglm")
125 125
126 126 
 exportMethods("prcomp")
127 127
128 
+export("mem",
129 
+	"profmem")
130 
+
128 131 
 useDynLib("matter", .registration=TRUE)
Browse code

fixed bug in matrix mult

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/matter@129782 bc3139a8-67e5-0310-9ffc-ced21a209358

Kyle D. Bemis authored on 21/05/2017 01:13:33
Showing 1 changed files
NAMESPACE
History View file @ 6c7d819e6
... ... 
@@ -18,6 +18,9 @@ importFrom("BiocGenerics",
18 18 
 	"rowSums",
19 19 
 	"which")
20 20
21 
+importFrom("stats",
22 
+	"setNames")
23 
+
21 24 
 importFrom("utils",
22 25 
 	"head",
23 26 
 	"tail",
Browse code

bug fixes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/matter@129781 bc3139a8-67e5-0310-9ffc-ced21a209358

Kyle D. Bemis authored on 21/05/2017 01:13:25
Showing 1 changed files
NAMESPACE
History View file @ 07b631cdc
... ... 
@@ -19,6 +19,8 @@ importFrom("BiocGenerics",
19 19 
 	"which")
20 20
21 21 
 importFrom("utils",
22 
+	"head",
23 
+	"tail",
22 24 
 	"object.size")
23 25
24 26 
 exportClasses(
... ... 
@@ -45,7 +47,8 @@ export(
45 47 
 	"matter_list",
46 48 
 	"matter_df",
47 49 
 	"matter_str",
48 
-	"is.matter")
50 
+	"is.matter",
51 
+	"as.matter")
49 52
50 53 
 exportMethods(
51 54 
 	"adata",
... ... 
@@ -95,6 +98,8 @@ exportMethods(
95 98 
 	"log10")
96 99
97 100 
 exportMethods(
101 
+	"head",
102 
+	"tail",
98 103 
 	"sum",
99 104 
 	"mean",
100 105 
 	"var",
Browse code

v1.3.2 added df and list classes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/matter@129780 bc3139a8-67e5-0310-9ffc-ced21a209358

Kyle D. Bemis authored on 21/05/2017 01:13:15
Showing 1 changed files
NAMESPACE
History View file @ f040af9de
... ... 
@@ -27,11 +27,30 @@ exportClasses(
27 27 
 	"matter_vec",
28 28 
 	"matter_mat",
29 29 
 	"matter_matc",
30 
-	"matter_matr")
30 
+	"matter_matr",
31 
+	"matter_arr",
32 
+	"matter_list",
33 
+	"matter_str",
34 
+	"matter_df")
35 
+
36 
+export(
37 
+	"drle",
38 
+	"is.drle")
39 
+
40 
+export(
41 
+	"matter",
42 
+	"matter_vec",
43 
+	"matter_mat",
44 
+	"matter_arr",
45 
+	"matter_list",
46 
+	"matter_df",
47 
+	"matter_str",
48 
+	"is.matter")
31 49
32 50 
 exportMethods(
33 51 
 	"adata",
34 52 
 	"atomdata",
53 
+	"atomdata<-",
35 54 
 	"datamode",
36 55 
 	"datamode<-",
37 56 
 	"paths",
... ... 
@@ -45,6 +64,8 @@ exportMethods(
45 64 
 	"%*%",
46 65 
 	"[",
47 66 
 	"[<-",
67 
+	"$",
68 
+	"$<-",
48 69 
 	"c",
49 70 
 	"cbind",
50 71 
 	"rbind",
... ... 
@@ -60,10 +81,6 @@ exportMethods(
60 81 
 	"crossprod",
61 82 
 	"tcrossprod")
62 83
63 
-export(
64 
-	"drle",
65 
-	"is.drle")
66 
-
67 84 
 export(
68 85 
 	"t.matter",
69 86 
 	"mean.matter",
... ... 
@@ -100,9 +117,4 @@ exportMethods("bigglm")
100 117
101 118 
 exportMethods("prcomp")
102 119
103 
-export(
104 
-	"matter",
105 
-	"matter_vec",
106 
-	"matter_mat")
107 
-
108 120 
 useDynLib("matter", .registration=TRUE)
Browse code

added logical delayed ops

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/matter@129779 bc3139a8-67e5-0310-9ffc-ced21a209358

Kyle D. Bemis authored on 21/05/2017 01:13:06
Showing 1 changed files
NAMESPACE
History View file @ 259d83ae5
... ... 
@@ -15,7 +15,8 @@ importFrom("BiocGenerics",
15 15 
 	"colMeans",
16 16 
 	"colSums",
17 17 
 	"rowMeans",
18 
-	"rowSums")
18 
+	"rowSums",
19 
+	"which")
19 20
20 21 
 importFrom("utils",
21 22 
 	"object.size")
... ... 
@@ -69,11 +70,8 @@ export(
69 70 
 	"scale.matter")
70 71
71 72 
 exportMethods(
72 
-	"+",
73 
-	"-",
74 
-	"*",
75 
-	"/",
76 
-	"^",
73 
+	"Arith",
74 
+	"Compare",
77 75 
 	"exp",
78 76 
 	"log",
79 77 
 	"log2",
... ... 
@@ -91,7 +89,8 @@ exportMethods(
91 89 
 	"rowSums",
92 90 
 	"rowMeans",
93 91 
 	"rowVars",
94 
-	"rowSds")
92 
+	"rowSds",
93 
+	"which")
95 94
96 95 
 exportMethods("apply")
97 96
Browse code

removed S4Vectors import

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/matter@128179 bc3139a8-67e5-0310-9ffc-ced21a209358

Kyle D. Bemis authored on 06/04/2017 20:39:25
Showing 1 changed files
NAMESPACE
History View file @ 26fbb8856
... ... 
@@ -17,8 +17,6 @@ importFrom("BiocGenerics",
17 17 
 	"rowMeans",
18 18 
 	"rowSums")
19 19
20 
-importClassFrom("S4Vectors", "character_OR_NULL")
21 
-
22 20 
 importFrom("utils",
23 21 
 	"object.size")
24 22
Browse code

cherry-pick 4

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/matter@128171 bc3139a8-67e5-0310-9ffc-ced21a209358

Kyle D. Bemis authored on 06/04/2017 19:48:46
Showing 1 changed files
NAMESPACE
History View file @ f8fcfd6ea
... ... 
@@ -1,19 +1,17 @@
1 1
2 2 
 import("methods")
3 3
4 
-import("stats")
5 
-
6 4 
 import("biglm")
7 5
8 
-importFrom("BiocGenerics",
9 
-	"combine",
10 
-	"cbind",
11 
-	"rbind")
12 
-
13 6 
 importFrom("irlba",
14 7 
 	"irlba")
15 8
16 
-importFrom("S4Vectors",
9 
+importFrom("BiocGenerics",
10 
+	"sd",
11 
+	"var",
12 
+	"combine",
13 
+	"cbind",
14 
+	"rbind",
17 15 
 	"colMeans",
18 16 
 	"colSums",
19 17 
 	"rowMeans",
Browse code

optimizations on delayed ops

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/matter@128170 bc3139a8-67e5-0310-9ffc-ced21a209358

Kyle D. Bemis authored on 06/04/2017 19:48:38
Showing 1 changed files
NAMESPACE
History View file @ e36c8621d
... ... 
@@ -65,7 +65,6 @@ exportMethods(
65 65
66 66 
 export(
67 67 
 	"drle",
68 
-	"drleCompress",
69 68 
 	"is.drle")
70 69
71 70 
 export(
Browse code

cherry-pick 3

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/matter@128168 bc3139a8-67e5-0310-9ffc-ced21a209358

Kyle D. Bemis authored on 06/04/2017 19:48:22
Showing 1 changed files
NAMESPACE
History View file @ 605926c9f
... ... 
@@ -73,6 +73,17 @@ export(
73 73 
 	"mean.matter",
74 74 
 	"scale.matter")
75 75
76 
+exportMethods(
77 
+	"+",
78 
+	"-",
79 
+	"*",
80 
+	"/",
81 
+	"^",
82 
+	"exp",
83 
+	"log",
84 
+	"log2",
85 
+	"log10")
86 
+
76 87 
 exportMethods(
77 88 
 	"sum",
78 89 
 	"mean",
Browse code

cherry-pick 2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/matter@128167 bc3139a8-67e5-0310-9ffc-ced21a209358

Kyle D. Bemis authored on 06/04/2017 19:48:13
Showing 1 changed files
NAMESPACE
History View file @ 8f0972b46
... ... 
@@ -25,6 +25,7 @@ importFrom("utils",
25 25 
 	"object.size")
26 26
27 27 
 exportClasses(
28 
+	"drle",
28 29 
 	"matter",
29 30 
 	"matter_vec",
30 31 
 	"matter_mat",
... ... 
@@ -62,6 +63,11 @@ exportMethods(
62 63 
 	"crossprod",
63 64 
 	"tcrossprod")
64 65
66 
+export(
67 
+	"drle",
68 
+	"drleCompress",
69 
+	"is.drle")
70 
+
65 71 
 export(
66 72 
 	"t.matter",
67 73 
 	"mean.matter",
Browse code

v1.1.1 changes for paper submission

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/matter@128164 bc3139a8-67e5-0310-9ffc-ced21a209358

Kyle D. Bemis authored on 06/04/2017 19:47:47
Showing 1 changed files
NAMESPACE
History View file @ 294c92343
... ... 
@@ -33,6 +33,7 @@ exportClasses(
33 33
34 34 
 exportMethods(
35 35 
 	"adata",
36 
+	"atomdata",
36 37 
 	"datamode",
37 38 
 	"datamode<-",
38 39 
 	"paths",
... ... 
@@ -57,7 +58,14 @@ exportMethods(
57 58 
 	"names<-",
58 59 
 	"dimnames",
59 60 
 	"dimnames<-",
60 
-	"t")
61 
+	"t",
62 
+	"crossprod",
63 
+	"tcrossprod")
64 
+
65 
+export(
66 
+	"t.matter",
67 
+	"mean.matter",
68 
+	"scale.matter")
61 69
62 70 
 exportMethods(
63 71 
 	"sum",
Browse code

follow renaming of union classes in S4Vectors

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/matter@126392 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 01/02/2017 13:13:42
Showing 1 changed files
NAMESPACE
History View file @ ab766a553
... ... 
@@ -19,6 +19,8 @@ importFrom("S4Vectors",
19 19 
 	"rowMeans",
20 20 
 	"rowSums")
21 21
22 
+importClassFrom("S4Vectors", "character_OR_NULL")
23 
+
22 24 
 importFrom("utils",
23 25 
 	"object.size")
24 26
Browse code

Adding KEGGlincs, flowPloidy, MAST, PathoStat, matter, MoonlightR, psichomics, anamiR, MutationalPatterns, HelloRanges, crisprseekplus, annotatr, meshes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/matter@122278 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 12/10/2016 17:44:52
Showing 1 changed files
NAMESPACE
History View file @ b2af78d14
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,87 @@
1 
+
2 
+import("methods")
3 
+
4 
+import("stats")
5 
+
6 
+import("biglm")
7 
+
8 
+importFrom("BiocGenerics",
9 
+	"combine",
10 
+	"cbind",
11 
+	"rbind")
12 
+
13 
+importFrom("irlba",
14 
+	"irlba")
15 
+
16 
+importFrom("S4Vectors",
17 
+	"colMeans",
18 
+	"colSums",
19 
+	"rowMeans",
20 
+	"rowSums")
21 
+
22 
+importFrom("utils",
23 
+	"object.size")
24 
+
25 
+exportClasses(
26 
+	"matter",
27 
+	"matter_vec",
28 
+	"matter_mat",
29 
+	"matter_matc",
30 
+	"matter_matr")
31 
+
32 
+exportMethods(
33 
+	"adata",
34 
+	"datamode",
35 
+	"datamode<-",
36 
+	"paths",
37 
+	"paths<-",
38 
+	"filemode",
39 
+	"filemode<-",
40 
+	"chunksize",
41 
+	"chunksize<-")
42 
+
43 
+exportMethods(
44 
+	"%*%",
45 
+	"[",
46 
+	"[<-",
47 
+	"c",
48 
+	"cbind",
49 
+	"rbind",
50 
+	"length",
51 
+	"length<-",
52 
+	"dim",
53 
+	"dim<-",
54 
+	"names",
55 
+	"names<-",
56 
+	"dimnames",
57 
+	"dimnames<-",
58 
+	"t")
59 
+
60 
+exportMethods(
61 
+	"sum",
62 
+	"mean",
63 
+	"var",
64 
+	"sd",
65 
+	"colSums",
66 
+	"colMeans",
67 
+	"colVars",
68 
+	"colSds",
69 
+	"rowSums",
70 
+	"rowMeans",
71 
+	"rowVars",
72 
+	"rowSds")
73 
+
74 
+exportMethods("apply")
75 
+
76 
+exportMethods("scale")
77 
+
78 
+exportMethods("bigglm")
79 
+
80 
+exportMethods("prcomp")
81 
+
82 
+export(
83 
+	"matter",
84 
+	"matter_vec",
85 
+	"matter_mat")
86 
+
87 
+useDynLib("matter", .registration=TRUE)