source("XX_setup.R")
all_bad <- read_rds("Data/02_Datasets/bad_bouts.rds")
bouts <- read_rds("Data/02_Datasets/bouts_initial.rds")
dist <- read_rds("Data/02_Datasets/stn_dist.rds")Manual Adjustments
Here we’ll apply manual adjustments to the bouts and transitions we identified in the previous step.
Setup
Manual
Manually identified issues
Code
fix <- tribble(
~tagDeployID, ~stn_group, ~start, ~end, ~note,
17852, "4945", "2018", "", "",
17856, "4726-4790", "2018-09-18", "2018-10-15", "Based on this group",
18548, "4726-4790", "2018-09-15", "2018-10-15", "",
18880, "4726-4790", "2018-09-22", "2018-10-15", "",
# 18899 # Checked and probably good, despite reversal
18916, "4726-4790", "2018-09-15", "2018-10-15", "",
# 29770 # Checked and probably good, despite going north through BC
29919, "5418", "2020", "", "",
34266, "7908-7930-7934", "2021-09-11", "2021-09-15", "",
35290, "7624-8039", "2021-09-20", "2021-10-16", "",
35605, "7662", "2021", "", "Maybe?",
35914, "7624-8039-8045-8194", "2021-09-15", "2021-10-20", "",
36310, "7624-8039-8045-8194", "2021-09-20", "2021-10-16", "based on the above, but none look good",
39546, "8845", "2022", "", "",
39554, "9193", "2022", "", "",
39555, "8845", "2022", "", "",
39557, "8845-9036", "2022", "", "",
39557, "9194", "2022", "", "Also not sure about the 8279 or 8950",
39570, "9192-9194", "2022", "", "",
39585, "7905-7906-7930-7934-8760", "2022-09-19", "", "Not sure about 8190, but 8283 looks good",
39609, "9150-9192", "2022", "", "",
39612, "3454", "2022", "", "",
39615, "9036", "2022", "", "",
39615, "9193", "2022", "", "Also not really sure about 7662... 8593 is good though",
39618, "8769", "2022", "", "",
41242, "5511-8296-8415", "2022-10-01", "2022-12-01", "",
41657, "6115", "2022", "", "",
41674, "6115", "2022", "", "",
41700, "7624-8845-8857-9030-9036-9049", "2022-09-29", "", "",
41826, "8845-8847-9030-9036-9049", "2022-09-26", "", "",
42002, "7624-8845-8857-9030-9036-9049", "2022-10-01", "", "",
42474, "7624-8845-9021-9028-9030-9036-9049", "2022-09-23", "", "",
42476, "8845-9030-9036-9049", "2022-09-19", "", "",
42787, "8194-8845-9030-9036-9049", "2022-09-15 05:00:00", "2022-10-15", "",
42890, "8194-8845-9030-9036-9049", "2022-10-15", "2022-11-05", "",
42974, "8845-9030-9036-9049", "2022-09-29", "", "",
42996, "9193-9194", "2022", "", "",
43000, "8194-8845-9036-9049", "2022-10-15", "2022-11-01", "Not sure about 8193",
43016, "8544", "2023", "", "Probably not really all that bad, but just too far to be considered a group member, and only gets the odd ping",
43065, "8194-8845-9030-9036-9049", "2022-10-02", "2022-10-10", "",
43258, "8194-8845-9030-9036-9049", "2022-10-19 02:00:00", "", "",
43351, "8194-8845-9030-9036-9049", "2022-10-15", "2022-11-01", "",
43460, "5068", "2023", "", "Montreal to Indiana?",
43518, "5068", "2023", "", "Montreal to Indiana?",
43637, "5068", "2023", "", "Montreal to Indiana?",
43638, "5068", "2023", "", "Montreal to Indiana?",
43639, "5068", "2023", "", "Montreal to Indiana?",
43640, "5068", "2023", "", "Montreal to Indiana?",
43718, "5068", "2023", "", "Montreal to Indiana?",
43719, "5068", "2023", "", "Montreal to Indiana?",
43768, "5068", "2023", "", "Montreal to Indiana?",
43770, "5068", "2023", "", "Montreal to Indiana?",
43777, "5068", "2023", "", "Montreal to Indiana?",
43778, "5068", "2023", "", "Montreal to Indiana?",
43882, "5068", "2023", "", "Montreal to Indiana?",
43883, "5068", "2023", "", "Montreal to Indiana?",
43884, "5068", "2023", "", "Montreal to Indiana?",
43979, "5068", "2023", "", "Montreal to Indiana?",
43980, "5068", "2023", "", "Montreal to Indiana?",
44752, "8415", "2023", "", "",
48765, "8831", "2023", "", "Possibly fine, but dups from overlapping stns (8834 a stronger match)",
48765, "8876", "2023", "", "Possibly fine, but dups from overlapping stns",
#49419 checked and good
#49421 checked and good
50249, "8768-10128-10228", "2023-09-22", "2023-10-01", "",
50714, "10128-10228", "2023-10-23", "2023-11-01", "Possible but unlikely",
50715, "10128-10228", "2023-10-15", "2023-11-01", "Although 4206 not great either",
50718, "10128-10228-10299", "2023-10-16", "2023-11-01", "Although 8938 not great either",
50719, "10128-10228-10299", "2023-10-16", "2023-11-01", "",
50720, "10128-10228", "2023-10-16", "2023-11-01", "Although 7290 not great either",
50721, "10128-10228", "2023-10-16", "2023-11-01", "",
50722, "10128-10228", "2023-10-16", "2023-11-01", "Although 5146 not great either",
51213, "10128-10228-10299", "2023-10-30", "2023-11-05", "Although no others are great either",
) |>
mutate(problem_manual = TRUE,
start = ymd_hms(start, truncated = 5),
end = ymd_hms(end, truncated = 5),
end = if_else(is.na(end), ceiling_date(start + seconds(1), unit = "year"), end))
select(fix, -problem_manual) |>
gt() |>
gt_theme() |>
tab_options(container.height = px(600),
container.overflow.y = "auto")| tagDeployID | stn_group | start | end | note |
|---|---|---|---|---|
| 17852 | 4945 | 2018-01-01 | 2019-01-01 | |
| 17856 | 4726-4790 | 2018-09-18 | 2018-10-15 | Based on this group |
| 18548 | 4726-4790 | 2018-09-15 | 2018-10-15 | |
| 18880 | 4726-4790 | 2018-09-22 | 2018-10-15 | |
| 18916 | 4726-4790 | 2018-09-15 | 2018-10-15 | |
| 29919 | 5418 | 2020-01-01 | 2021-01-01 | |
| 34266 | 7908-7930-7934 | 2021-09-11 | 2021-09-15 | |
| 35290 | 7624-8039 | 2021-09-20 | 2021-10-16 | |
| 35605 | 7662 | 2021-01-01 | 2022-01-01 | Maybe? |
| 35914 | 7624-8039-8045-8194 | 2021-09-15 | 2021-10-20 | |
| 36310 | 7624-8039-8045-8194 | 2021-09-20 | 2021-10-16 | based on the above, but none look good |
| 39546 | 8845 | 2022-01-01 | 2023-01-01 | |
| 39554 | 9193 | 2022-01-01 | 2023-01-01 | |
| 39555 | 8845 | 2022-01-01 | 2023-01-01 | |
| 39557 | 8845-9036 | 2022-01-01 | 2023-01-01 | |
| 39557 | 9194 | 2022-01-01 | 2023-01-01 | Also not sure about the 8279 or 8950 |
| 39570 | 9192-9194 | 2022-01-01 | 2023-01-01 | |
| 39585 | 7905-7906-7930-7934-8760 | 2022-09-19 | 2023-01-01 | Not sure about 8190, but 8283 looks good |
| 39609 | 9150-9192 | 2022-01-01 | 2023-01-01 | |
| 39612 | 3454 | 2022-01-01 | 2023-01-01 | |
| 39615 | 9036 | 2022-01-01 | 2023-01-01 | |
| 39615 | 9193 | 2022-01-01 | 2023-01-01 | Also not really sure about 7662... 8593 is good though |
| 39618 | 8769 | 2022-01-01 | 2023-01-01 | |
| 41242 | 5511-8296-8415 | 2022-10-01 | 2022-12-01 | |
| 41657 | 6115 | 2022-01-01 | 2023-01-01 | |
| 41674 | 6115 | 2022-01-01 | 2023-01-01 | |
| 41700 | 7624-8845-8857-9030-9036-9049 | 2022-09-29 | 2023-01-01 | |
| 41826 | 8845-8847-9030-9036-9049 | 2022-09-26 | 2023-01-01 | |
| 42002 | 7624-8845-8857-9030-9036-9049 | 2022-10-01 | 2023-01-01 | |
| 42474 | 7624-8845-9021-9028-9030-9036-9049 | 2022-09-23 | 2023-01-01 | |
| 42476 | 8845-9030-9036-9049 | 2022-09-19 | 2023-01-01 | |
| 42787 | 8194-8845-9030-9036-9049 | 2022-09-15 05:00:00 | 2022-10-15 | |
| 42890 | 8194-8845-9030-9036-9049 | 2022-10-15 | 2022-11-05 | |
| 42974 | 8845-9030-9036-9049 | 2022-09-29 | 2023-01-01 | |
| 42996 | 9193-9194 | 2022-01-01 | 2023-01-01 | |
| 43000 | 8194-8845-9036-9049 | 2022-10-15 | 2022-11-01 | Not sure about 8193 |
| 43016 | 8544 | 2023-01-01 | 2024-01-01 | Probably not really all that bad, but just too far to be considered a group member, and only gets the odd ping |
| 43065 | 8194-8845-9030-9036-9049 | 2022-10-02 | 2022-10-10 | |
| 43258 | 8194-8845-9030-9036-9049 | 2022-10-19 02:00:00 | 2023-01-01 | |
| 43351 | 8194-8845-9030-9036-9049 | 2022-10-15 | 2022-11-01 | |
| 43460 | 5068 | 2023-01-01 | 2024-01-01 | Montreal to Indiana? |
| 43518 | 5068 | 2023-01-01 | 2024-01-01 | Montreal to Indiana? |
| 43637 | 5068 | 2023-01-01 | 2024-01-01 | Montreal to Indiana? |
| 43638 | 5068 | 2023-01-01 | 2024-01-01 | Montreal to Indiana? |
| 43639 | 5068 | 2023-01-01 | 2024-01-01 | Montreal to Indiana? |
| 43640 | 5068 | 2023-01-01 | 2024-01-01 | Montreal to Indiana? |
| 43718 | 5068 | 2023-01-01 | 2024-01-01 | Montreal to Indiana? |
| 43719 | 5068 | 2023-01-01 | 2024-01-01 | Montreal to Indiana? |
| 43768 | 5068 | 2023-01-01 | 2024-01-01 | Montreal to Indiana? |
| 43770 | 5068 | 2023-01-01 | 2024-01-01 | Montreal to Indiana? |
| 43777 | 5068 | 2023-01-01 | 2024-01-01 | Montreal to Indiana? |
| 43778 | 5068 | 2023-01-01 | 2024-01-01 | Montreal to Indiana? |
| 43882 | 5068 | 2023-01-01 | 2024-01-01 | Montreal to Indiana? |
| 43883 | 5068 | 2023-01-01 | 2024-01-01 | Montreal to Indiana? |
| 43884 | 5068 | 2023-01-01 | 2024-01-01 | Montreal to Indiana? |
| 43979 | 5068 | 2023-01-01 | 2024-01-01 | Montreal to Indiana? |
| 43980 | 5068 | 2023-01-01 | 2024-01-01 | Montreal to Indiana? |
| 44752 | 8415 | 2023-01-01 | 2024-01-01 | |
| 48765 | 8831 | 2023-01-01 | 2024-01-01 | Possibly fine, but dups from overlapping stns (8834 a stronger match) |
| 48765 | 8876 | 2023-01-01 | 2024-01-01 | Possibly fine, but dups from overlapping stns |
| 50249 | 8768-10128-10228 | 2023-09-22 | 2023-10-01 | |
| 50714 | 10128-10228 | 2023-10-23 | 2023-11-01 | Possible but unlikely |
| 50715 | 10128-10228 | 2023-10-15 | 2023-11-01 | Although 4206 not great either |
| 50718 | 10128-10228-10299 | 2023-10-16 | 2023-11-01 | Although 8938 not great either |
| 50719 | 10128-10228-10299 | 2023-10-16 | 2023-11-01 | |
| 50720 | 10128-10228 | 2023-10-16 | 2023-11-01 | Although 7290 not great either |
| 50721 | 10128-10228 | 2023-10-16 | 2023-11-01 | |
| 50722 | 10128-10228 | 2023-10-16 | 2023-11-01 | Although 5146 not great either |
| 51213 | 10128-10228-10299 | 2023-10-30 | 2023-11-05 | Although no others are great either |
- What’s up with the bunch of ids ~ 43882 etc. which all go from Indiana to Montreal?
Remove ’bad bouts
First remove manually defined ‘bad’ bouts, as well as previously identified “bad bouts” (these are those identified by super fast transitions).
bouts <- anti_join(bouts, fix,
by = join_by("tagDeployID", "stn_group",
within("timeBegin", "timeEnd", "start", "end"))) |>
filter(!id %in% all_bad)
overlaps <- create_overlapping(bouts)
trans <- create_trans(bouts, overlaps, dist)Now a quick check to make sure that the only remaining problems are those that we said were okay. If any on this list are not those, double check the manual fix list and adjust as needed.
check_trans <- id_problems(trans)
filter(check_trans, problem) |>
arrange(tagDeployID, b1) |>
select(tagDeployID, stn1, b1, e1, stn2, b2, e2, contains("problem")) |>
gt() |>
gt_theme()| tagDeployID | stn1 | b1 | e1 | stn2 | b2 | e2 | problem_manual | problem_fast | problem_short_bout | problem_direction | problem |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 18899 | 4030 | 2018-10-15 05:19:46.6936 | 2018-10-15 05:31:36.9747 | 4703 | 2018-10-17 02:45:11.8191 | 2018-10-17 02:48:02.5247 | FALSE | FALSE | FALSE | TRUE | TRUE |
| 29770 | 5232-6115-6154-6156-6175 | 2020-09-22 18:46:51.5033 | 2020-09-22 19:10:02.5629 | 5417 | 2020-11-01 12:26:49.7809 | 2020-11-01 12:32:11.0015 | FALSE | FALSE | FALSE | TRUE | TRUE |
| 49419 | 6115-8098-8387-8644-8662-8926-10024 | 2023-09-12 02:45:02.5567 | 2023-09-12 02:53:11.0275 | 9995 | 2023-09-12 10:21:10.0179 | 2023-09-12 10:31:26.953 | FALSE | FALSE | FALSE | TRUE | TRUE |
| 49419 | 9995 | 2023-09-12 10:21:10.0179 | 2023-09-12 10:31:26.953 | 9698-9699-9882 | 2023-09-13 11:28:42.4057 | 2023-09-13 12:23:57.5096 | FALSE | FALSE | FALSE | TRUE | TRUE |
| 49421 | 8110-8165-9859 | 2023-09-06 05:46:36.6914 | 2023-09-06 06:03:19.4855 | 8834 | 2023-09-06 11:52:49.215 | 2023-09-06 12:29:13.7646 | FALSE | FALSE | FALSE | TRUE | TRUE |
All good! The only remaining stations match those we check out as good:
- 18899
- 29770
- 49419
- 49421
Final data
At last! We have our final set of cleaned bouts and transitions
write_rds(bouts, "Data/02_Datasets/bouts_cleaned.rds")
write_rds(trans, "Data/02_Datasets/transitions_cleaned.rds")Final plots
Here we’ll re-plot the manually adjusted plots (note that we only plot ids with at least one transition).
Code
ids <- trans |>
semi_join(fix, by = "tagDeployID") |>
pull(tagDeployID) |>
unique()
walk(ids, \(x) {
g <- plot_bouts(trans, bouts = bouts, tagDeployID = x)
ggsave(paste0("Figs/check2_", x, "_map.png"), g, width = 3840*1.5, height = 1920*1.5, units = "px")
})Code
walk(ids, \(x) {
cat("\n\n#### ", x, " {#", x, "}\n\n", sep = "")
cat("\n![](Figs/check2_", x, "_map.png){out-width=100%}\n\n", sep = "")
cat("\n\n", sep = "")
})18916
17852
18548
17856
18880
35290
34266
35914
35605
36310
39554
39555
39618
39570
39609
39615
39557
41826
42476
42787
42474
39546
39585
42974
39612
41242
41657
41700
42002
42996
43016
43065
41674
43351
43000
42890
43258
44752
50249
48765
50722
50715
50721
50714
50720
50719
50718
51213
