source("XX_setup.R")
trans <- read_csv("Data/03_Final/transitions_final.csv") |>
left_join(read_csv("Data/03_Final/summary_birds.csv"),
by = c("tagDeployID", "english")) |>
filter(travelled) |>
mutate(month = month(mid_date)) |>
mutate(n = n_distinct(tagDeployID), .by = "english") |>
arrange(desc(n))Maps
This script produces maps by species and by individuals for birds who moved at least 100km (travelled, see Summaries).
Setup
Maps by species
Code
walk(unique(trans$speciesID), \(x) {
t1 <- filter(trans, speciesID == x)
g <- ggplot(t1, aes(x = lon1, y = lat1)) +
annotation_map_tile(type = "cartolight", zoomin = 0) +
geom_spatial_segment(
aes(xend = lon2, yend = lat2, colour = month),
arrow = arrow(length = unit(10, "pt"), type = "closed"), crs = 4326, na.rm = TRUE) +
scale_colour_viridis_c(option = "inferno",
begin = 0.20, end = 0.85) +
guides(colour = guide_colourbar(reverse = TRUE)) +
labs(title = t1$english[1],
subtitle = paste0("n = ", n_distinct(t1$tagDeployID), "; ", as_date(min(t1$b1)), " to ", as_date(max(t1$e2))))
cat(paste0("\n\n### ", t1$english[1], "\n\n"))
print(g)
})Swainson’s Thrush
Ovenbird
Hermit Thrush
Song Sparrow
Yellow-rumped Warbler (Myrtle)
Chestnut-collared Longspur
Purple Finch
Tennessee Warbler
Magnolia Warbler
Red-eyed Vireo
Sprague’s Pipit
Western Meadowlark
Gray Catbird
White-throated Sparrow
Golden-crowned Sparrow
Blue-headed Vireo
Pine Siskin
Spotted Towhee
Northern Cardinal
Lazuli Bunting
Baird’s Sparrow
Black-throated Blue Warbler
Common Yellowthroat
Northern Waterthrush
Horned Lark
Maps by individual
Code
walk(unique(trans$speciesID), \(x) {
cat(paste0("\n\n### ", trans$english[trans$speciesID == x][1], "\n\n"))
walk(unique(trans$tagDeployID[trans$speciesID == x]), \(y) {
t1 <- filter(trans, tagDeployID == y)
g <- plot_map(trans, y, pad = FALSE, lowres = TRUE) +
labs(title = paste0(t1$english[1], " - ", t1$tagDeployID[1]),
subtitle = paste0(min(t1$b1), " to ", max(t1$e2)))
cat(paste0("\n\n#### ", t1$tagDeployID[1], "\n\n"))
print(g)
})
})Swainson’s Thrush
13854
13850
14299
13844
13845
13847
13846
13852
14164
13859
14163
14162
14167
14161
18877
18916
17852
18548
19419
17854
19420
17856
18880
19412
18885
19421
19972
18894
18886
19973
18881
18897
17853
18899
19975
19410
18890
18912
18904
18902
17695
18903
19971
18900
19970
18901
18914
18910
17671
19414
17672
18913
19417
18915
18911
25876
26121
28168
29458
29547
25521
29548
30180
29549
30119
30142
33362
35290
35734
35737
35307
35740
29918
35731
35733
35732
35914
35915
36320
36319
35605
35916
36315
36317
35486
35485
36316
36995
36500
36311
36321
35911
36314
36318
36313
36994
35306
36998
36312
36993
36997
35739
42753
42755
42749
42751
41683
41826
42476
42756
42787
42474
42244
41580
41676
41673
42752
42750
42974
42970
42900
42899
42971
42902
42475
42896
43067
42973
43149
41657
41579
41700
42002
41678
41677
41682
43016
42975
43065
42898
43066
Warning: ggrepel: 4 unlabeled data points (too many overlaps). Consider
increasing max.overlaps
42969
42972
41674
42242
41680
42001
41675
43426
42243
43427
42241
43929
Warning: ggrepel: 7 unlabeled data points (too many overlaps). Consider
increasing max.overlaps
44111
45239
49421
Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider
increasing max.overlaps
49420
49578
49418
49423
49422
49424
49583
Warning: ggrepel: 6 unlabeled data points (too many overlaps). Consider
increasing max.overlaps
49585
49417
49419
49579
49779
49780
49581
49582
51086
Ovenbird
34663
35300
35301
35302
34279
34479
34473
34278
34267
34266
34269
34662
34476
34668
34658
34277
34477
34268
34671
34271
34491
34478
34490
34272
34276
35303
34672
34673
34667
34661
34480
34280
37515
39603
39593
39587
39606
39607
39571
39618
39614
39542
39570
39619
39625
39564
39613
39624
39617
39623
39584
39588
39599
39563
39546
39552
39585
39565
39119
39616
39601
39573
39560
39621
39612
39596
39605
39592
39567
39600
39569
39627
Hermit Thrush
43351
43456
43633
43634
43331
43329
43669
43333
43258
43635
43636
43330
43259
43261
43260
43516
43455
43517
44752
50714
50720
50719
50718
50626
50716
50717
51121
50944
51151
51122
51148
50930
50983
51152
50929
51147
51213
51214
51150
51238
51272
51149
51294
Song Sparrow
34484
34492
34741
34665
35295
34664
34740
34666
34656
39578
39539
39598
39568
39561
43253
39574
43000
42999
39553
42890
43250
39581
39586
39594
39611
39610
42487
39576
39595
42558
43670
43519
43721
Yellow-rumped Warbler (Myrtle)
42995
42996
42686
43346
43407
43459
43458
43409
43410
42998
43457
43249
43631
43408
43334
50935
50428
50612
50934
50939
50933
50713
50932
50941
51119
50936
50938
50984
50942
51131
50943
Chestnut-collared Longspur
40626
40623
40625
40635
40881
41188
40906
40638
40629
40475
41194
40846
40867
40894
40913
48763
40896
47954
48765
40884
47998
Purple Finch
38307
38303
38287
38297
38290
38309
38296
38289
38292
38291
38943
38951
38942
38944
38941
45370
45345
45367
45365
45363
Tennessee Warbler
19409
17845
18888
19418
18878
19407
18892
26765
26766
26771
35604
35793
36310
36502
41542
41539
41540
41578
41543
Magnolia Warbler
50234
50248
50239
50238
50249
50247
50237
50326
50244
50242
50245
50422
50327
50236
50421
50246
50723
Red-eyed Vireo
39551
39591
39572
39547
39554
39549
39555
39559
39558
39589
39556
39609
39615
39089
39620
39557
Sprague’s Pipit
41192
41197
40624
40850
41186
40636
48771
48762
48768
48758
48776
48772
48767
Western Meadowlark
40488
40712
41370
47334
47377
46158
47329
47324
47328
46532
47339
47322
Gray Catbird
26019
26120
29551
29767
29766
29572
29769
25846
29768
37506
White-throated Sparrow
34739
34474
44498
44485
44725
45603
45605
45604
44722
44723
Golden-crowned Sparrow
44345
44352
44355
44359
44350
44344
44343
44346
44358
44348
Blue-headed Vireo
50722
50919
50715
50931
50721
51123
50945
51153
Pine Siskin
4350
2661
29306
29772
29770
29074
Spotted Towhee
41242
45745
45747
Northern Cardinal
43978
43720
43779
Lazuli Bunting
35009
41371
Baird’s Sparrow
40628
40612
Black-throated Blue Warbler
37524
Common Yellowthroat
37525
Northern Waterthrush
45402
Horned Lark
47959
