-
Notifications
You must be signed in to change notification settings - Fork 5
/
NEWS
2321 lines (1648 loc) · 64.7 KB
/
NEWS
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
NEWS
================
<Erik.Leppo@tetratech.com>
<!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
#> Last Update: 2024-10-07 07:05:36.903175
# Version History
## Changes in version 1.0.2.9053
- refactor: Update MetricScoring.xlsx
- MN, pi_TrichNoHydro scoring formula text
## Changes in version 1.0.2.9052
- fix: Update MetricScoring.xlsx
- MN, narratives
## Changes in version 1.0.2.9051
- fix: Update MetricScoring.xlsx (MN)
## Changes in version 1.0.2.9050
- refactor: Update MetricScoring.xlsx
- MN_IBI_Fish and MN_IBI_Bugs, index numeric and narrative
## Changes in version 1.0.2.9049
- style: Clean up new additions to metric_values.R
- Move new metrics for GP to alongside previous GP metrics
- Move munging for new metrics to alongside previous munging for TYPE
## Changes in version 1.0.2.9048
- refactor: Added Great Plains fish metrics (pi_NPL and pi_SALT)
## Changes in version 1.0.2.9047
- refactor: MetricScoring.xlsx change MN IBI classes
- Flip Bugs and Fish for 8/9 and 10/11
## Changes in version 1.0.2.9046
- refactor: Update MN IBI (bugs and fish), Issue \#92
- Drop “modified” narrative
- MetricScoring.xlsx
## Changes in version 1.0.2.9045
- refactor: Update MN Fish and Bug IBI index scoring, Issue \#92
## Changes in version 1.0.2.9044
- refactor: Update MN fish metric ni_m2_notoler to ni_m_notoler, Issue
\#92
- Length (m) not area (m2)
- metric.values.R
- MetricScoring.xlsx
- MetricNames.xlsx
## Changes in version 1.0.2.9043
- refactor: Change MN Bugs Index_Class from 8 and 9 to 10 and 11, Issue
\#92
- MetricScoring.xlsx
## Changes in version 1.0.2.9042
- fix: Update fish metrics brook trout code, Issue \#92
- Change for MN to replace space invalidated code
- Added TYPE_BROOKTROUT to make metric simpler
## Changes in version 1.0.2.9041
- docs: Add “demo only” language to ORWA example data
## Changes in version 1.0.2.9040
- BREAKING: Deprecate sum_n_taxa in `taxa_translate`
- Leave in code so if fix can re-enable
- Doesn’t work all the time with match_caps and non-ascii character
code
## Changes in version 1.0.2.9039
- refactor: Update zeroind scoring for MN Bugs and Fish IBI, Issue \#111
- MetricScoring.xlsx
## Changes in version 1.0.2.9038
- refactor: Update `taxa_translate` columns for unique taxa output
## Changes in version 1.0.2.9037
- refactor: Update match_caps code in `taxa_translate`
## Changes in version 1.0.2.9036
- refactor: Add default value for match_caps in `taxa_translate`
## Changes in version 1.0.2.9035
- refactor: Update MN_Fish_IBI metrics, Issue \#111
- pi_wetland_notoler_ExclSchool to nt_wetland_notoler
- MetricScoring.xlsx
- MetricNames.xlsx
- `metric.values`
## Changes in version 1.0.2.9034
- refactor: Add pi_OligoHiru to `metric.values`
## Changes in version 1.0.2.9033
- refactor: Update MetricScoring.xlsx for MN_Fish_IBI, Issue \#111
## Changes in version 1.0.2.9032
- refactor: Update taxa_translate taxatrax_unique ouput
- Add match with CAPS
## Changes in version 1.0.2.9031
- fix: Add TolVal2 as required field for fish metrics in `metric.values`
## Changes in version 1.0.2.9030
- test: Add taxa.translate triws test
- Add white space (leading, trailing, both) and internal nbsp to test
data
## Changes in version 1.0.2.9029
- feature: Update taxa.translate trimws feature to replace internal
## Changes in version 1.0.2.9028
- feature: Update metric.scores() to account for MN_IBI_Fish, Issue
\#111
- If another metric is below a threshold then score as zero
- refactor: Add hooks in metric.scores() for score zero modifications,
Issue \#111
- refactor: Update help example for metric.scores()
## Changes in version 1.0.2.9027
- refactor: Update MetricNames.xlsx to mark bug metrics to use for Large
Rare metric calculations
- refactor: Add remove spaces to columns for metric calculation
- Bugs
- HABIT, FFG, LIFE_CYCLE, FFG2, THERMAL_INDICATOR, HABSTRUCT ,
ELEVATION_ATTR, GRADIENT_ATTR, WSAREA_ATTR
- Fish
- TROPHIC, THERMAL_INDICATOR, REPRODUCTION, HABITAT, ELEVATION_ATTR
, GRADIENT_ATTR, WSAREA_ATTR
- refactor: Add new fish metrics for MN_Fish_IBI, Issue \#111
- metric.values
- MetricNames.xlsx
- MetricScoring.xlsx
- style: Reorder some metrics in fish section of metric.values
- Organize Munge section by column name
- tests: metric.values() move time inside verbose to avoid warning
message
## Changes in version 1.0.2.9026
- refactor: Remove match_caps parameter from taxa_translate function,
Issue \#111
- tests: Remove taxa_translate match_caps test, Issue \#111
## Changes in version 1.0.2.9025
- tests: Add tests for removing white space, Issue \#111
- feature: Update taxa_translate with clean parameters, Issue \#111
## Changes in version 1.0.2.9024
- refactor: Update for MN_Fish_IBI, Issue \#92
- MetricNames.xlsx
- metric_values.R
- Updates to data munging prior to metric calculation
## Changes in version 1.0.2.9023
- refactor: Update MetricScoring.xlsx for MN_Bug_IBI, Issue \#92
## Changes in version 1.0.2.9022
- refactor: Update MetricScoring.xlsx for MN_Fish_IBI, Issue \#92
- refactor: Update MetricNames.xlsx for MN_Fish_IBI, Issue \#92
## Changes in version 1.0.2.9021
- refactor: Update MetricScoring.xlsx for MN_Fish_IBI, Issue \#92
- refactor: Update MetricNames.xlsx for MN_Fish_IBI, Issue \#92
- docs: Edit README for timeout issue
## Changes in version 1.0.2.9020
- refactor: Update pi_Cheu text in MetricNames.xlsx
## Changes in version 1.0.2.9019
- refactor: Update MetricNames.xlsx for Great Plains BCG
## Changes in version 1.0.2.9018
- refactor: Merge pull request 114
- Add metrics (bugs and fish) for Great Plains BCG
## Changes in version 1.0.2.9017
- feature: Options added to taxa_translate, Issue \#111
- Match on ALL CAPS
- Clean input names
- Not fully implemented
## Changes in version 1.0.2.9016
- refactor: Post merge updates
- Reconcile names for same calculation but different programs and
columns
- benthicInvertivore in merge to habitat_beninvert
- MetricNames.xlsx
- metric_values.R
- tests: Update fish metric names for new metrics
- refactor: Add MN_IBI_Fish metrics to MetricNames.xlsx, Issue \#92
## Changes in version 1.0.2.9015
- refactor: Merge pull request 110
- New metrics for NM BCG Fish
- MetricNames.xlsx
- metric_values.R
## Changes in version 1.0.2.9014
- refactor: New index scoring regimes, Issue \#92
- MetricScoring.xlsx
- AVERAGE_100_M10_R2 for MN_IBI_Bugs
- AVERAGE_100_M10_R3 for MN_IBI_Fish
## Changes in version 1.0.2.9013
- refactor: Modify scoring regime (AVERAGE_100_M10), Issue \#92
- Round scaling to 2 decimals
- Modify MetricScoring.xlsx
- `metric.scores`
- refactor: Add new scoring regime (CAT_0510) to `metric.scores`, Issue
\#92
- fix: Update MN_IBI_Fish thresholds, MetricScoring.xlsx, Issue \#92
## Changes in version 1.0.2.9012
- refactor: Update MetricScoring.xlsx, Issue \#92
- New scoring regime, AVERAGE_100_M10
- Change MN_Bug_IBI scoring regime
- refactor: Add new scoring regime calculation to `metric.scores` ,
Issue \#92
## Changes in version 1.0.2.9011
- fix: Update MN IBI Fish thresholds in MetricScoring.xlsx, Issue \#92
- test: Update thresholds for extra digits in MetricScoring.xlsx, Issue
\#101
- Adjust from 11 to 13 digits for one index (WY)
## Changes in version 1.0.2.9010
- fix: Update MN IBI Bugs thresholds in MetricScoring.xlsx, Issue \#92
## Changes in version 1.0.2.9009
- refactor: Update MN IBI Fish metrics in MetricScoring.xlsx, Issue \#92
## Changes in version 1.0.2.9008
- refactor: Update MN IBI Fish metrics in MetricScoring.xlsx, Issue \#92
## Changes in version 1.0.2.9007
- refactor: Update MN IBI Fish metrics in MetricScoring.xlsx, Issue \#92
## Changes in version 1.0.2.9006
- fix: Update `metric.values` pi_dom01_BCG\* metrics
- Add zero to max function to avoid max returning -Inf
- refactor: Update `metric.values` debug steps for fish
- Was 10 and changed to 12
## Changes in version 1.0.2.9005
- refactor: Update MetricScoring.xlsx for WY, Issue \#101
- fix: After testing add 4 metrics for WY from scoring, Issue \#101
- Add to MetricNames.xlsx
- Add to metric.values.R
## Changes in version 1.0.2.9004
- fix: Update MetricNames.xlsx for missing coral metric per tests
## Changes in version 1.0.2.9003
- refactor: Update Excel files for MN IBI
- MetricFlags.xlsx
- MetricNames.xlsx
- MetricScoring.xlsx
## Changes in version 1.0.2.9002
- refactor: Update GitHub Actions with usethis::use_github_action()
- check-standard
- test-coverage
- pkgdown
- docs: Update check badge in ReadMe
## Changes in version 1.0.2.9001
- fix: Remove uneeded concatenate in tests per CodeFactor
- test_metric_names
## Changes in version 1.0.2
- fix: Update to minor version number 1.0.2
- Incorrect version numbers from pull request
## Changes in pull request \#107
- refactor: Coral metrics from Blocktt
## Changes in version 1.0.1.9550 (2024-03-18)
- fix: made changes to coral metrics
- added test for Florida BCG
## Changes in version 1.0.1.9501 (2024-03-07)
- update: Added coral metrics, specifically for FL BCG
- metric_values.R
- MetricNames.xlsx
## Changes in version 1.0.0.9066 (2024-03-05)
- refactor: Additional metrics for Great Plains BCG, Issue \#106
- metric_values.R
- MetricNames.xlsx
## Changes in version 1.0.0.9065 (2024-02-22)
- fix: Update MetricScoring.xlsx
- Change MN_IBI_Bugs INDEX_CLASS from 5 IBI classes to 9 site classes,
Issue \#92
- Update all ScoreRegime from Cont_010 to Cont_0010
- Added Modify_Value and Modify_Code to adjust values before scoring
- not implemented
- style: Update spacing in metric.values
## Changes in version 1.0.0.9064 (2024-02-21)
- fix: Update MetricScoring.xlsx, ScoreRegime for MN_IBI_bugs, Issue
\#92
- Cont_010 to Cont_0010 to match code
## Changes in version 1.0.0.9063 (2024-02-15)
- fix: Update metric.values metric, nt_COETNoBraBaeHydTri, Issue \#101
- Replace Hydropsyche with Hydropsychidae
- Metric not calculating properly
- Update MetricNames.xlsx
- tests: Wrote test for nt_COETNoBraBaeHydTri, Issue \#101
## Changes in version 1.0.0.9062 (2024-01-26)
- fix: Modify metric.values() benthic metric nt_tv_toler8, Issue \#104
- Was using 6 instead of 8 as minimum
## Changes in version 1.0.0.9061 (2024-01-26)
- refactor: Add metrics for WY bug MMI, Issue \#101
- MetricNames.xlsx
- MetricScoring.xlsx
- `metric.values()`
- fix: Correct metric.values nt_PolyNoSpion, Issue \#102
- Was not calculating number of taxa
- fix: Update metric.values fun.cols2keep to ignore required cols, Issue
\#100
- fix: Change input parameter in metric.scores function, Issue \#103
- Replace col_IndexRegion with col_IndexClass
- Add col_IndexRegion at end of parameters to avoid breaking existing
code
## Changes in version 1.0.0.9060 (2024-01-10)
- refactor: Add ni_total flags (small and large) for MN_IBI_Bugs, Issue
\#92
- MetricFlags.xlsx
## Changes in version 1.0.0.9059 (2024-01-09)
- feat: Add new issue template for metric and index requests, Issue \#99
- refactor: Add metrics and index for MN IBI (bugs and fish), Issue \#92
- MetricNames.xlsx
- MetricScoring.xlsx
- `metric.values()`
- tests: Run tests for new metrics
- Tweak data and tests as needed
## Changes in version 1.0.0.9058 (2023-12-14)
- refactor: Add metrics for NM BCG, Issue \#97
- Pull request not able to easily merge, make changes by hand
## Changes in version 1.0.0.9057 (2023-12-12)
- refactor: Add testing (QC) to `metric.values` fish calc section
## Changes in version 1.0.0.9056 (2023-12-11)
- refactor: Add EXCLUDE taxa to fish metrics
- nt\_\*
- Error checking to ensure column is included
- refactor: Added QC check to fish calc in `metric.values`
- fix: Change QC sub function name for fish in `metric.values`
- refactor: Add “EXCLUDE” column to example fish data
- docs: Update description of data_fish_MBSS
## Changes in version 1.0.0.9055 (2023-12-08)
- refactor: Remove interactive TRUE from algae in `metric.values`
- Same issue with the fish but being proactive
- Not included on bugs
## Changes in version 1.0.0.9054 (2023-12-08)
- refactor: Edits to `metric.values` fish calc for error in Red Lakes
Shiny app
- N_ANOMALIES NA to 0
- Change “interactive” part of require column check
## Changes in version 1.0.0.9053 (2023-12-08)
- refactor: More edits to `metric.values` fish calc for error in Red
Lakes Shiny app
## Changes in version 1.0.0.9052 (2023-12-08)
- refactor: Edit `metric.values` fish calc for error in Red Lakes Shiny
app
## Changes in version 1.0.0.9051 (2023-12-08)
- refactor: Modify verbose statements in `metric.values`
- Change terminology in code so more generic
- Add verbose statements to fish sub function
## Changes in version 1.0.0.9050 (2023-12-06)
- refactor: Update MetricNames.xlsx with recent name changes
## Changes in version 1.0.0.9049 (2023-12-06)
- refactor: Change names of trout metrics in `metric.values`
- Better reflects contents of metrics
## Changes in version 1.0.0.9048 (2023-12-06)
- refactor: Add pi_trout to `metric.values`
## Changes in version 1.0.0.9047 (2023-12-06)
- refactor: Update MetricNames.xlsx to match function, fish metrics
- refactor: Update `metric.values` to match MetricNames.xlsx, fish
metrics
- Added “nt_BCG_att12346”
- Left “nt_BCG_att1236sp” to be added later as unsure of definition
- tests: Update taxa_translate test for file name change
## Changes in version 1.0.0.9046 (2023-12-05)
- fix: metric.values boo.shiny code updated to match bugs and algae
## Changes in version 1.0.0.9045 (2023-12-05)
- refactor: metric.values specify parameters for subfunctions
## Changes in version 1.0.0.9044 (2023-12-05)
- fix: Update metric, nt_BCG_att55a6, Issue \#92
- add ‘na.rm = TRUE’
## Changes in version 1.0.0.9043 (2023-11-21)
- fix: Add missing metric, nt_BCG_att55a6, Issue \#92
## Changes in version 1.0.0.9042 (2023-11-20)
- refactor: Fix BCG_att1236sp fish metrics, pi and pt
- Remove nt
## Changes in version 1.0.0.9041 (2023-11-20)
- feature: Add MN BCG fish metrics, Issue \#92
- BCG_att1236sp fish metrics (n=3) as NA until better defined
- refactor: Update MetricNames.xlsx with new metrics, Issue \#92
## Changes in version 1.0.0.9040 (2023-11-20)
- fix: Cheumatopsyche metrics, Issue \#93
- Search term updated; Cheumatopsyche to CHEUMATOPSYCHE
- Add missing equal sign
- Move so alphabetical in output
## Changes in version 1.0.0.9039 (2023-10-24)
- feature: Add taxaid_dni parameter to metric.values, Issue \#96
## Changes in version 1.0.0.9038 (2023-10-20)
- refactor: Modify output of `taxa_translate` function, Issue \#94
- taxatrans\$taxatrans_unique
## Changes in version 1.0.0.9037 (2023-10-20)
- feat: Add new metric, ni_totalNoDeca, Issue \#94
- style: Add spaces to code for readability
## Changes in version 1.0.0.9036 (2023-09-25)
- fix: Update Cheumatopsyche metrics in MetricNames.xlsx, Issue \#93
- pi_Cheu
- pi_EPTNoCheu
## Changes in version 1.0.0.9035 (2023-09-25)
- fix: Update code for Cheumatopsyche metrics, metric_values.R, Issue
\#93
- pi_Cheu
- pi_EPTNoCheu
## Changes in version 1.0.0.9034 (2023-08-11)
- fix: BioMonTools vignette change reference to metric names
- corecold changed to stenocold
## Changes in version 1.0.0.9033 (2023-08-11)
- fix: Fill in missing Vignette Builder for vignette_NewIndex
## Changes in version 1.0.0.9032 (2023-08-10)
- fix: Add line for “changed” taxa in `taxa_translate`
## Changes in version 1.0.0.9031 (2023-07-28)
- fix: Update domX calculations to combine taxa before calculate in
metric_values
- bugs and fish
## Changes in version 1.0.0.9030 (2023-07-28)
- refactor: Update metrics for MN BCG, Issue \#92
- In myDF remove NA for specialized dom01 calculations
## Changes in version 1.0.0.9029 (2023-07-28)
- refactor: Update metrics for MN BCG, Issue \#92
## Changes in version 1.0.0.9028 (2023-07-26)
- refactor: Add percent Cheumatopsyche metric
## Changes in version 1.0.0.9027 (2023-07-12)
- refactor: Additional metrics for MN BCG, Issue \#92
## Changes in version 1.0.0.9026 (2023-07-12)
- refactor: Add bug metrics for MN BCG, Issue \#92
- style: Update spacing in test file metric_names
## Changes in version 1.0.0.9025 (2023-05-26)
- refactor: Update MetricFlags.xlsx for MTTI index
## Changes in version 1.0.0.9024 (2023-05-26)
- refactor: Update metric.values MTTI subset metrics, Issue \#90
## Changes in version 1.0.0.9023 (2023-05-26)
- refactor: Update MetricFlags.xlsx for MTTI index
## Changes in version 1.0.0.9022 (2023-05-25)
- feature: New parameter in `metric.values` to run only subset, Issue
\#90
- style: Style changes in metric_values.R
## Changes in version 1.0.0.9021 (2023-02-02)
- docs: Add vignette for adding a new index, Issue \#87
- incomplete
- refactor: Add CO MMI (bugs)
- Draft 2006, verify with report and EDAS database
## Changes in version 1.0.0.9020 (2023-02-02)
- fix: Update `metric.values` thermal NA metrics
- Add blank (““) to NA as a condition
- test: Additional `assign_indexclass` tests
## Changes in version 1.0.0.9019 (2023-01-23)
- refactor: Update `assign_indexclass` to account or NA and ““, Issue
\#85
- fix: Update `assign_indexclass` to account non standard column names,
Isue \#85
- tests: Add tests for `assign_indexclass`, Issue \#85
- refactor: Update `assign_indexclass` to not fail if index_class in
input data, Issue \#85
## Changes in version 1.0.0.9018 (2023-01-20)
- refactor: Update MetricNames.xlsx groupings
- Added “Experimental”
## Changes in version 1.0.0.9017 (2023-01-20)
- feature: Add unique taxa crosswalk to output of `taxa_translate`
## Changes in version 1.0.0.9016 (2023-01-16)
- test: Add test for multiple stages for `taxa_translate`
## Changes in version 1.0.0.9015 (2023-01-09)
- fix: Turn off QC testing in function `assign_indexclass`
- Was using test data instead of user input
## Changes in version 1.0.0.9014 (2022-12-23)
- docs: Update `taxa_translate` example files
## Changes in version 1.0.0.9013 (2022-12-20)
- refactor: Update `taxa_translate` to drop a particular ID after
translation , Issue \#81
- Added input paramter
- Updated example
- Updated test
## Changes in version 1.0.0.9012 (2022-12-20)
- data: Update extdata for `taxa_translate` example, Issue \#81
- Revised PacNW_ORWA data file (2022-12-19)
- tests: Revise `taxa_translate` test for revised data
## Changes in version 1.0.0.9011 (2022-12-19)
- tests: Create tests for `taxa_translate`, Issue \#81
## Changes in version 1.0.0.9010 (2022-12-16)
- fix: Update `taxa_translaste`
- Update nonmatch to data frame with count and sum of occurrence,
Issue \#81
- Refine matching
- Include summed taxa properly
- Drop non-matching taxa (NA and DNI)
- Update example
## Changes in version 1.0.0.9009 (2022-12-13)
- fix: Update `taxa_translate` for when sum taxa, Issue \#81
- update: Revise taxa_translate files in extdata
## Changes in version 1.0.0.9008 (2022-12-13)
- refactor: Tweak debug code in `taxa_translate`, Issue \#81
- fix: Update `taxa_translate` for col_drop_project
- Should be debug only
## Changes in version 1.0.0.9007 (2022-12-13)
- refactor: Change internal workings of `taxa_translate`, Issue \#81
- If summarize retain the official taxa columns
- Reorder columns in the merged output
## Changes in version 1.0.0.9006 (2022-12-12)
- refactor: Change internal parameter boo_DEBUG to boo_DEBUG_tt in
`taxa_translate`, Issue \#81
## Changes in version 1.0.0.9005 (2022-12-12)
- refactor: Make `taxa_translate` as an export object, Issue \#81
## Changes in version 1.0.0.9004 (2022-12-02)
- fix: Updated `taxa_translate` function to include metadata as
parameter, Issue \#81
## Changes in version 1.0.0.9003 (2022-12-01)
- feature: Add `taxa_translate` function, Issue \#81
- More general than qc_taxa
## Changes in version 1.0.0.9002 (2022-11-17)
- fix: Update `markExclude` to avoid dplyr deprecation warnings, Issue
\#51
## Changes in version 1.0.0.9001 (2022-11-16)
- breaking change: Site_Type and Index_Region to Index_Class
- refactor: Update rarify function to save example to tempdir
## Changes in version 0.5.0.9127 (2022-11-15)
- feat: New function `assign_IndexClass`, Issue \#82
- Add IndexClass.xlsx to ext folder
## Changes in version 0.5.0.9126 (2022-11-11)
- refactor: Additional benthic metrics
- metric_values.R
- MetricNames.xlsx
- refactor: Additional column for benthic metrics; AirBreather
- modify metric_values for required column
- Add to data_benthos_PacNW
## Changes in version 0.5.0.9125 (2022-11-10)
- fix: Update and add some metrics
- metric_values.R
- MetricNames.xlsx
## Changes in version 0.5.0.9124 (2022-11-08)
- fix: Tweak secondary metric name in MetricScoring.xlsx
- GA_DNR_Fish_2020
## Changes in version 0.5.0.9123 (2022-11-03)
- refactor: Modify default term for markExcl from Excluded to Exclude
- Ensure is consistent in function, example, vignette
- refactor: markExcl warning don’t trigger for 0 levels missing, Issue
\#80
- refcator: markExcl add default of NA to Exceptions parameter, Issue
\#80
## Changes in version 0.5.0.9122 (2022-09-29)
- docs: Typo in MetricNames.xlsx (Isoptera instead of Isopoda)
- fix: Change logic in metric.values for insertion of missing column
names
- Was not working in server environment (interacive == FALSE)
- docs: Update error message in metric.values for complex columns, Issue
\#71
- Add code needed to error message (base R and tidyverse)
- refactor: Change logic for Shiny on server when encounter complex,
Issue \#71
- BCG_ATTR column only, interactive FALSE or boo.Shiny TRUE
## Changes in version 0.5.0.9121 (2022-09-27)
- feat: Additional BCG metrics, Issue \#79
- style: Surround operators with space
- metric_values
- test: Add sum of parts tests for new BCG metrics
## Changes in version 0.5.0.9120 (2022-09-22)
- fix: Update bug thermal metrics, Issue \#78
## Changes in version 0.5.0.9119 (2022-06-09)
- feature: Additional algae metrics, Issue \#75
- style: Add outlining to algae metrics
- style: Add spaces before and after operators in algae calculations
- refactor: Add missing values in MetricNames.xlsx based on tests
- refactor: Add missing algae metric pt_BC_12_adj as NA
## Changes in Version 0.5.0.9118 (2022-06-03)
- fix: Hemiptera metrics (nt and pt) not working, Issue \#74
- Fix spelling
## Changes in Version 0.5.0.9117 (2022-05-31)
- refactor: Additional metrics, Issue \#74
- fix: Change metric HabitatStruct from RW to RM, Issue \#73
## Changes in Version 0.5.0.9116 (2022-05-18)
- refactor: Additional bug and fish metrics, Issue \#73
- refactor: Add BCG_ATTR as upper case for fish metrics
- Update fish BCG metrics to use upper case letters for BCG metrics
- style: Add spacing and outlining to metric_values.R
- refactor: Updates to MetricNames.xlsx to pass tests
## Changes in Version 0.5.0.9115 (2022-04-08)
- refactor: Change variable classes in metric.scores()
- Avoid errors in import via read_excel
## Changes in Version 0.5.0.9114 (2022-03-30)
- refactor: Rename one misspelled bug thermal metrics, Issue \#72
- ‘pt_ti_cool_warm_stenowarm’ should be ‘pt_ti_warm_stenowarm’
## Changes in Version 0.5.0.9113 (2022-03-28)
- refactor: Add and modify bug thermal metrics, Issue \#72
- metric_values()
- extdata.xlsx
- style: Add extra spaces to some lines in metric_values()
## Changes in Version 0.5.0.9112 (2022-03-22)
- refactor: Add metrics and scoring for So Cal Marine Bays
- extdata.xlsx
- extdata.xlsx
- tests: Add tests for So Cal Marine Bays
- Incomplete
## Changes in Version 0.5.0.9111 (2022-03-04)
- fix: Restore extdata.xlsx
- Deleted in v0.5.0.9109, last mod was v0.5.0.9100
## Changes in Version 0.5.0.9110 (2022-03-02)
- docs: Update required fields text in metric.values()
- refactor: Copy (as comments) required fields code from bugs to other
communities in metric.values()
## Changes in Version 0.5.0.9109 (2022-02-22)
- refactor: Additional output messages to screen in metric.values()
## Changes in Version 0.5.0.9108 (2022-02-22)
- tests: Update metric_stats test for new metrics
- fix: Update metric.values() for 1i and 1m metrics, use upper case
- Recent change to have all columns to upper case make 1i into 1I
## Changes in Version 0.5.0.9107 (2022-02-21)
- fix: metric.values() remove some fields from conversion to upper case,
Issue \#69
- SAMPLEID, INDEX_NAME, INDEX_REGION
- fixes issue with vignettes flag example, Issue \#70
- fix: Update metvalgrpxl() NOTES, Issue \#69
- Input File Name to Input Data Frame
- Convert text to formula for Description of Work
- Moved from column 1 (text) to column 2 (formulas) in v0.5.0.9101
- fix: Shiny, BCG_Attr importing as complex, Issue \#71
- Specify colClasses as character
## Changes in Version 0.5.0.9106 (2022-02-21)
- refactor: Tweak error checking for bugs in metric.values()
- fix: metric.values() columns to upper case for calculation
- Error introduced in v0.5.0.9093 (2022-02-03)
- refactor: Change reference to some files in BioMonTools vignette
- flag section
- rebuild without vignettes
## Changes in Version 0.5.0.9105 (2022-02-18)
- refactor: Tweak error checking for bugs in metric.values()
## Changes in Version 0.5.0.9104 (2022-02-18)
- refactor: Tweak error checking for bugs in metric.values()
## Changes in Version 0.5.0.9103 (2022-02-18)
- refactor: Tweak error checking for bugs in metric.values()
## Changes in Version 0.5.0.9102 (2022-02-18)
- refactor: Update shiny app to use metric.values(…, verbose = TRUE)
- refactor: Update number of steps in verbose for metric.values()
- refactor: Update fill missing columns metric.values()
- NA to NA_character\_
## Changes in Version 0.5.0.9101 (2022-02-18)
- refactor: Refine message output of metric.values() for use in Shiny
- refactor: Add verbose paramters to metric.values()
- refactor: Tweak Notes worksheet for metric Excel output
## Changes in Version 0.5.0.9100 (2022-02-11)
- refactor: Add new metric to MetricNames.xlsx
## Changes in Version 0.5.0.9099 (2022-02-11)
- refactor: Shiny add ‘tab’ as acceptable text file upload format.
- refactor: Add new bug metric to metric.values()
- pi_SphaerCorb
## Changes in Version 0.5.0.9098 (2022-02-07)
- refactor: Modify debugging messages to metric.values() for Shiny log
## Changes in Version 0.5.0.9097 (2022-02-07)
- refactor: Add debugging messages to metric.values()
## Changes in Version 0.5.0.9096 (2022-02-07)
- fix: Update metric.values() for input data missing Index_Name and
Index_Region
## Changes in Version 0.5.0.9095 (2022-02-04)
- fix: Update metric.values() with more error checking for missing
columns
- At start for minimal required fields before community specific
sections
- After metric values calculated in bug section for NA to 0
## Changes in Version 0.5.0.9094 (2022-02-03)
- refactor: Update metvalgrpxl() for blank cells hiding text to left
## Changes in Version 0.5.0.9093 (2022-02-03)
- fix: Update to changes in metric.values()
## Changes in Version 0.5.0.9092 (2022-02-03)
- fix: Remove redundant code in metric.values()
- Causing failures on Shiny.io with missing required columns
## Changes in Version 0.5.0.9091 (2022-02-03)
- refactor: Update metvalgrpxl() to use input parameter for groupings
## Changes in Version 0.5.0.9090 (2022-02-02)
- refactor: Small edits to Shiny app
- Text edits to help pages
- Update links for TaxaMaps
- refactor: Update metvalgrpxl() to use formulas in output
## Changes in Version 0.5.0.9089 (2022-02-01)
- refactor: Edits to help pages in Shiny app
- Update links to download files
## Changes in Version 0.5.0.9088 (2022-02-01)
- refactor: Shiny app updates
- Calculate Metrics
- Update help/notes for each function
- RMD in data-raw
- Add download files to www folder
- refactor: Define global variables in functions
- metric.values
- refactor: Define imported function
- MapTaxaObs
- markExcluded
- metric.stats2
- feature: Update MetricNames.xlsx with Sort_Group
- feature: Add new function, metvalgrpxl(), Issue \#68
## Changes in Version 0.5.0.9087 (2022-01-12)
- fix: Correct spelling of file name in global.R
- ShinyApps.io is Linux and is case-sensitive
## Changes in Version 0.5.0.9086 (2022-01-12)
- refactor: Reorganize -raw folder with subfolders
- Keep only the scripts to be run at the root
- Will have to update scripts at later date to use the new structure
- feature: Added HTML creation scripts for text in shiny app to -raw
- feature: Updates to Shiny app to include help text for each function
- feature: Add runShiny() to launch shiny app from console
- docs: Removed XLConnect from DESCRIPTION Suggests package list
- Not used
- docs: Added writexl package to DESCRIPTIOn Suggest for upcoming change
, Issue \# 68
## Changes in Version 0.5.0.9085 (2022-01-10)
- docs: Update GitHub default branch from “master” to “main”
## Changes in Version 0.5.0.9083 (2022-01-10)
- refactor: Added global variable bindings to fish metrics
metric.values()
- Only BCG_Attr