Selecting Projects

Author

Steffi LaZerte

Published

July 4, 2024

Here we explore a list of open or semi open Motus projects to select more project ids which we can use in our pilot study.

This data TagSpeciesProject.xlsx was given to us by Birds Canada but in future should be accessibly directly through the motus package.

Setup

source("XX_setup.R")
library(readxl)

Cleaning and Filtering

Cleaning

The species names (English and scientific) listed here aren’t always consistent, so we’ll omit them and use only the species IDs to match them with the NatureCounts metadata from XX_setup.

Then we consolidate the deployments in those projects as some listed some deployments under one species name and others under another (even if the species was the same)

Filtering

keep only access == 1 which are fully public projects
omit species ID 129470 which are listed as attached to a Human…(?)
omit projects with non-Canadian species

p_sp <- read_excel("Data/01_Raw/TagsSpeciesProject.xlsx") |>
  rename_with(.cols = contains("No column"), \(x) "access") |>
  filter(access == 1,             # Only completely open projects
         speciesID != 129470) |>  # Don't worry about Human tags :D
  select(-speciesName, -motusEnglishName, -access) |> # Species Names are not consistent
  summarize(across(everything(), sum), .by = c("tagProjectID", "speciesID")) |>
  left_join(select(species_list, "species_id", "scientific_name", "english_name"),
            by = c("speciesID" = "species_id")) |>
  mutate(good = !is.na(scientific_name),
         other = str_detect(english_name, "Eurasian|European|Elaenia")) |>
  group_by(tagProjectID) |>
  filter(all(!other | is.na(other))) |> # Omit projects with non-Canadian species
  mutate(good_tags = sum(num_deployments[good]),
         prop_good_tags =  good_tags / sum(num_deployments)) |>
  ungroup() |>
  select(-other) |>
  arrange(desc(prop_good_tags))

gt(p_sp) |>
  fmt_number("prop_good_tags", decimals = 2) |>
  gt_theme() |>
  tab_options(container.height = px(600),
              container.overflow.y = "auto")

tagProjectID	speciesID	num_deployments	scientific_name	english_name	good	good_tags	prop_good_tags
85	19250	112	Plectrophenax nivalis	Snow Bunting	TRUE	112	1.00
221	15580	2	Catharus ustulatus	Swainson's Thrush	TRUE	2	1.00
240	42218	39	Junco hyemalis	Dark-eyed Junco	TRUE	39	1.00
249	16610	53	Setophaga coronata	Yellow-rumped Warbler	TRUE	53	1.00
258	15600	10	Hylocichla mustelina	Wood Thrush	TRUE	20	1.00
258	16950	10	Parkesia motacilla	Louisiana Waterthrush	TRUE	20	1.00
259	18940	8	Ammospiza nelsoni	Nelson's Sparrow	TRUE	103	1.00
259	18950	39	Ammospiza caudacuta	Saltmarsh Sparrow	TRUE	103	1.00
259	18960	56	Ammospiza maritima	Seaside Sparrow	TRUE	103	1.00
306	15770	69	Turdus migratorius	American Robin	TRUE	71	1.00
306	15830	2	Ixoreus naevius	Varied Thrush	TRUE	71	1.00
308	15770	30	Turdus migratorius	American Robin	TRUE	30	1.00
310	14050	176	Progne subis	Purple Martin	TRUE	176	1.00
352	15580	75	Catharus ustulatus	Swainson's Thrush	TRUE	257	1.00
352	15900	30	Dumetella carolinensis	Gray Catbird	TRUE	257	1.00
352	18550	2	Pipilo maculatus	Spotted Towhee	TRUE	257	1.00
352	18830	10	Pooecetes gramineus	Vesper Sparrow	TRUE	257	1.00
352	18900	21	Ammodramus savannarum	Grasshopper Sparrow	TRUE	257	1.00
352	19450	23	Passerina amoena	Lazuli Bunting	TRUE	257	1.00
352	19610	31	Sturnella neglecta	Western Meadowlark	TRUE	257	1.00
352	19760	25	Molothrus ater	Brown-headed Cowbird	TRUE	257	1.00
352	20420	40	Spinus pinus	Pine Siskin	TRUE	257	1.00
360	14250	54	Hirundo rustica	Barn Swallow	TRUE	54	1.00
361	16920	11	Limnothlypis swainsonii	Swainson's Warbler	TRUE	11	1.00
363	16820	35	Setophaga striata	Blackpoll Warbler	TRUE	35	1.00
364	16820	1	Setophaga striata	Blackpoll Warbler	TRUE	55	1.00
364	20310	2	Pinicola enucleator	Pine Grosbeak	TRUE	55	1.00
364	20330	38	Haemorhous purpureus	Purple Finch	TRUE	55	1.00
364	20420	14	Spinus pinus	Pine Siskin	TRUE	55	1.00
370	15590	6	Catharus guttatus	Hermit Thrush	TRUE	6	1.00
371	36261	15	Locustella naevia	Common Grasshopper Warbler	TRUE	57	1.00
371	36271	22	Acrocephalus schoenobaenus	Sedge Warbler	TRUE	57	1.00
371	36475	20	Curruca communis	Greater Whitethroat	TRUE	57	1.00
377	16060	1	Toxostoma lecontei	LeConte's Thrasher	TRUE	8	1.00
377	16370	7	Phainopepla nitens	Phainopepla	TRUE	8	1.00
380	14250	44	Hirundo rustica	Barn Swallow	TRUE	84	1.00
380	35407	40	Riparia riparia	Bank Swallow	TRUE	84	1.00
387	40818	1	Melozone cabanisi	Cabanis's Ground-Sparrow	TRUE	1	1.00
388	15651	91	Turdus philomelos	Song Thrush	TRUE	91	1.00
391	16900	31	Protonotaria citrea	Prothonotary Warbler	TRUE	31	1.00
393	14040	24	Eremophila alpestris	Horned Lark	TRUE	130	1.00
393	16300	31	Anthus spragueii	Sprague's Pipit	TRUE	130	1.00
393	18910	14	Centronyx bairdii	Baird's Sparrow	TRUE	130	1.00
393	19130	5	Rhynchophanes mccownii	Thick-billed Longspur	TRUE	130	1.00
393	19160	56	Calcarius ornatus	Chestnut-collared Longspur	TRUE	130	1.00
408	18940	83	Ammospiza nelsoni	Nelson's Sparrow	TRUE	83	1.00
414	19500	137	Passerina ciris	Painted Bunting	TRUE	137	1.00
417	16930	81	Seiurus aurocapilla	Ovenbird	TRUE	226	1.00
417	18990	58	Melospiza melodia	Song Sparrow	TRUE	226	1.00
417	19030	63	Zonotrichia albicollis	White-throated Sparrow	TRUE	226	1.00
417	41384	24	Vireo olivaceus	Red-eyed Vireo	TRUE	226	1.00
424	14050	63	Progne subis	Purple Martin	TRUE	63	1.00
426	18830	36	Pooecetes gramineus	Vesper Sparrow	TRUE	37	1.00
426	18950	1	Ammospiza caudacuta	Saltmarsh Sparrow	TRUE	37	1.00
430	15590	2	Catharus guttatus	Hermit Thrush	TRUE	6	1.00
430	17310	4	Icteria virens	Yellow-breasted Chat	TRUE	6	1.00
438	36271	29	Acrocephalus schoenobaenus	Sedge Warbler	TRUE	91	1.00
438	36467	30	Sylvia borin	Garden Warbler	TRUE	91	1.00
438	36475	32	Curruca communis	Greater Whitethroat	TRUE	91	1.00
464	15550	1	Catharus fuscescens	Veery	TRUE	59	1.00
464	15580	28	Catharus ustulatus	Swainson's Thrush	TRUE	59	1.00
464	15900	4	Dumetella carolinensis	Gray Catbird	TRUE	59	1.00
464	16460	1	Leiothlypis peregrina	Tennessee Warbler	TRUE	59	1.00
464	16540	6	Setophaga americana	Northern Parula	TRUE	59	1.00
464	16600	1	Setophaga caerulescens	Black-throated Blue Warbler	TRUE	59	1.00
464	16660	1	Setophaga virens	Black-throated Green Warbler	TRUE	59	1.00
464	16800	5	Setophaga palmarum	Palm Warbler	TRUE	59	1.00
464	16880	2	Mniotilta varia	Black-and-white Warbler	TRUE	59	1.00
464	16890	2	Setophaga ruticilla	American Redstart	TRUE	59	1.00
464	16930	5	Seiurus aurocapilla	Ovenbird	TRUE	59	1.00
464	17000	3	Geothlypis trichas	Common Yellowthroat	TRUE	59	1.00
466	14250	91	Hirundo rustica	Barn Swallow	TRUE	113	1.00
466	35407	21	Riparia riparia	Bank Swallow	TRUE	113	1.00
466	40667	1	Hirundo rustica erythrogaster	Barn Swallow (American)	TRUE	113	1.00
469	35407	909	Riparia riparia	Bank Swallow	TRUE	909	1.00
475	18920	66	Centronyx henslowii	Henslow's Sparrow	TRUE	66	1.00
482	18880	135	Passerculus sandwichensis	Savannah Sparrow	TRUE	135	1.00
484	15830	2	Ixoreus naevius	Varied Thrush	TRUE	122	1.00
484	18550	61	Pipilo maculatus	Spotted Towhee	TRUE	122	1.00
484	19050	4	Zonotrichia leucophrys	White-crowned Sparrow	TRUE	122	1.00
484	19060	55	Zonotrichia atricapilla	Golden-crowned Sparrow	TRUE	122	1.00
489	19520	33	Dolichonyx oryzivorus	Bobolink	TRUE	33	1.00
496	15550	15	Catharus fuscescens	Veery	TRUE	54	1.00
496	15580	1	Catharus ustulatus	Swainson's Thrush	TRUE	54	1.00
496	15590	38	Catharus guttatus	Hermit Thrush	TRUE	54	1.00
497	19030	68	Zonotrichia albicollis	White-throated Sparrow	TRUE	68	1.00
499	18990	4	Melospiza melodia	Song Sparrow	TRUE	4	1.00
515	15590	1	Catharus guttatus	Hermit Thrush	TRUE	42	1.00
515	15770	7	Turdus migratorius	American Robin	TRUE	42	1.00
515	15900	6	Dumetella carolinensis	Gray Catbird	TRUE	42	1.00
515	15970	3	Toxostoma rufum	Brown Thrasher	TRUE	42	1.00
515	19030	25	Zonotrichia albicollis	White-throated Sparrow	TRUE	42	1.00
524	15770	1	Turdus migratorius	American Robin	TRUE	1	1.00
529	42067	74	Oenanthe oenanthe/seebohmi	Northern/Atlas Wheatear	TRUE	74	1.00
531	14120	2	Tachycineta bicolor	Tree Swallow	TRUE	5	1.00
531	18550	2	Pipilo maculatus	Spotted Towhee	TRUE	5	1.00
531	40824	1	Pipilo maculatus x erythrophthalmus	Spotted x Eastern Towhee (hybrid)	TRUE	5	1.00
536	15580	20	Catharus ustulatus	Swainson's Thrush	TRUE	20	1.00
537	15550	4	Catharus fuscescens	Veery	TRUE	6	1.00
537	17150	2	Cardellina canadensis	Canada Warbler	TRUE	6	1.00
545	15970	2	Toxostoma rufum	Brown Thrasher	TRUE	3	1.00
545	16620	1	Setophaga coronata coronata	Yellow-rumped Warbler (Myrtle)	TRUE	3	1.00
551	13420	9	Vireo solitarius	Blue-headed Vireo	TRUE	203	1.00
551	15590	45	Catharus guttatus	Hermit Thrush	TRUE	203	1.00
551	16580	24	Setophaga magnolia	Magnolia Warbler	TRUE	203	1.00
551	16620	42	Setophaga coronata coronata	Yellow-rumped Warbler (Myrtle)	TRUE	203	1.00
551	18990	17	Melospiza melodia	Song Sparrow	TRUE	203	1.00
551	19360	66	Cardinalis cardinalis	Northern Cardinal	TRUE	203	1.00
570	15580	2	Catharus ustulatus	Swainson's Thrush	TRUE	2	1.00
604	20910	2	Passer domesticus	House Sparrow	TRUE	2	1.00
607	15900	2	Dumetella carolinensis	Gray Catbird	TRUE	10	1.00
607	16930	1	Seiurus aurocapilla	Ovenbird	TRUE	10	1.00
607	16940	3	Parkesia noveboracensis	Northern Waterthrush	TRUE	10	1.00
607	17000	1	Geothlypis trichas	Common Yellowthroat	TRUE	10	1.00
607	17130	2	Setophaga citrina	Hooded Warbler	TRUE	10	1.00
607	17310	1	Icteria virens	Yellow-breasted Chat	TRUE	10	1.00
609	12172	7	Empidonax traillii extimus	Willow Flycatcher (Southwestern)	TRUE	7	1.00
612	35407	100	Riparia riparia	Bank Swallow	TRUE	100	1.00
617	16830	18	Setophaga cerulea	Cerulean Warbler	TRUE	18	1.00
619	15580	20	Catharus ustulatus	Swainson's Thrush	TRUE	41	1.00
619	16600	5	Setophaga caerulescens	Black-throated Blue Warbler	TRUE	41	1.00
619	16890	16	Setophaga ruticilla	American Redstart	TRUE	41	1.00
621	16560	8	Setophaga petechia	Yellow Warbler	TRUE	8	1.00
623	17690	1	Piranga ludoviciana	Western Tanager	TRUE	3	1.00
623	19410	1	Pheucticus melanocephalus	Black-headed Grosbeak	TRUE	3	1.00
623	40789	1	Icteria virens auricollis	Yellow-breasted Chat (auricollis)	TRUE	3	1.00
627	16420	40	Vermivora chrysoptera	Golden-winged Warbler	TRUE	40	1.00
634	19040	10	Zonotrichia querula	Harris's Sparrow	TRUE	10	1.00
645	15600	3	Hylocichla mustelina	Wood Thrush	TRUE	3	1.00
657	15580	7	Catharus ustulatus	Swainson's Thrush	TRUE	10	1.00
657	19050	3	Zonotrichia leucophrys	White-crowned Sparrow	TRUE	10	1.00
660	14120	10	Tachycineta bicolor	Tree Swallow	TRUE	10	1.00
661	35407	24	Riparia riparia	Bank Swallow	TRUE	24	1.00
678	15600	15	Hylocichla mustelina	Wood Thrush	TRUE	15	1.00
691	20480	1	Spinus psaltria	Lesser Goldfinch	TRUE	1	1.00
556	8040	2	NA	NA	FALSE	13	0.87
556	14230	2	Petrochelidon pyrrhonota	Cliff Swallow	TRUE	13	0.87
556	14280	1	Poecile atricapillus	Black-capped Chickadee	TRUE	13	0.87
556	15560	1	Catharus minimus	Gray-cheeked Thrush	TRUE	13	0.87
556	16330	3	Bombycilla cedrorum	Cedar Waxwing	TRUE	13	0.87
556	20330	1	Haemorhous purpureus	Purple Finch	TRUE	13	0.87
556	41384	3	Vireo olivaceus	Red-eyed Vireo	TRUE	13	0.87
556	45168	2	Junco hyemalis hyemalis/carolinensis	Dark-eyed Junco (Slate-colored)	TRUE	13	0.87
406	3570	23	NA	NA	FALSE	143	0.86
406	15580	14	Catharus ustulatus	Swainson's Thrush	TRUE	143	0.86
406	18760	24	Spizelloides arborea	American Tree Sparrow	TRUE	143	0.86
406	18920	57	Centronyx henslowii	Henslow's Sparrow	TRUE	143	0.86
406	19030	1	Zonotrichia albicollis	White-throated Sparrow	TRUE	143	0.86
406	42218	13	Junco hyemalis	Dark-eyed Junco	TRUE	143	0.86
406	45168	34	Junco hyemalis hyemalis/carolinensis	Dark-eyed Junco (Slate-colored)	TRUE	143	0.86
115	16610	1	Setophaga coronata	Yellow-rumped Warbler	TRUE	5	0.83
115	16920	1	Limnothlypis swainsonii	Swainson's Warbler	TRUE	5	0.83
115	16960	1	Geothlypis formosa	Kentucky Warbler	TRUE	5	0.83
115	18760	1	Spizelloides arborea	American Tree Sparrow	TRUE	5	0.83
115	19500	1	Passerina ciris	Painted Bunting	TRUE	5	0.83
115	31856	1	NA	NA	FALSE	5	0.83
520	4450	10	NA	NA	FALSE	18	0.62
520	4750	1	NA	NA	FALSE	18	0.62
520	16940	18	Parkesia noveboracensis	Northern Waterthrush	TRUE	18	0.62
282	3570	22	NA	NA	FALSE	33	0.60
282	19520	11	Dolichonyx oryzivorus	Bobolink	TRUE	33	0.60
282	19600	22	Sturnella magna/lilianae	Eastern/Chihuahuan Meadowlark	TRUE	33	0.60
582	45168	59	Junco hyemalis hyemalis/carolinensis	Dark-eyed Junco (Slate-colored)	TRUE	59	0.60
582	47282	40	NA	NA	FALSE	59	0.60
614	4980	28	NA	NA	FALSE	41	0.48
614	7871	17	NA	NA	FALSE	41	0.48
614	18570	41	Pipilo erythrophthalmus	Eastern Towhee	TRUE	41	0.48
4	3761	2	NA	NA	FALSE	64	0.30
4	3770	3	NA	NA	FALSE	64	0.30
4	3830	42	NA	NA	FALSE	64	0.30
4	4630	30	NA	NA	FALSE	64	0.30
4	4670	74	NA	NA	FALSE	64	0.30
4	19500	64	Passerina ciris	Painted Bunting	TRUE	64	0.30
193	7680	36	NA	NA	FALSE	13	0.25
193	7871	3	NA	NA	FALSE	13	0.25
193	15600	11	Hylocichla mustelina	Wood Thrush	TRUE	13	0.25
193	16960	2	Geothlypis formosa	Kentucky Warbler	TRUE	13	0.25
9	4690	52	NA	NA	FALSE	5	0.06
9	18940	1	Ammospiza nelsoni	Nelson's Sparrow	TRUE	5	0.06
9	18950	4	Ammospiza caudacuta	Saltmarsh Sparrow	TRUE	5	0.06
9	100190	4	NA	NA	FALSE	5	0.06
9	100250	9	NA	NA	FALSE	5	0.06
9	100420	3	NA	NA	FALSE	5	0.06
9	100450	1	NA	NA	FALSE	5	0.06
9	124422	1	NA	NA	FALSE	5	0.06
9	124430	3	NA	NA	FALSE	5	0.06
27	4070	24	NA	NA	FALSE	0	0.00
27	4100	6	NA	NA	FALSE	0	0.00
27	4180	14	NA	NA	FALSE	0	0.00
27	4630	14	NA	NA	FALSE	0	0.00
27	4690	32	NA	NA	FALSE	0	0.00
27	4760	58	NA	NA	FALSE	0	0.00
27	4800	1	NA	NA	FALSE	0	0.00
27	4820	6	NA	NA	FALSE	0	0.00
27	5010	21	NA	NA	FALSE	0	0.00
68	4070	32	NA	NA	FALSE	0	0.00
68	4100	2	NA	NA	FALSE	0	0.00
68	4180	16	NA	NA	FALSE	0	0.00
68	4630	10	NA	NA	FALSE	0	0.00
68	4680	47	NA	NA	FALSE	0	0.00
68	4690	9	NA	NA	FALSE	0	0.00
68	4750	13	NA	NA	FALSE	0	0.00
68	4760	21	NA	NA	FALSE	0	0.00
68	4780	2	NA	NA	FALSE	0	0.00
68	4870	1	NA	NA	FALSE	0	0.00
68	5000	5	NA	NA	FALSE	0	0.00
68	5010	19	NA	NA	FALSE	0	0.00
78	4070	5	NA	NA	FALSE	0	0.00
78	4180	212	NA	NA	FALSE	0	0.00
78	4420	4	NA	NA	FALSE	0	0.00
78	4450	46	NA	NA	FALSE	0	0.00
78	4530	5	NA	NA	FALSE	0	0.00
78	4630	13	NA	NA	FALSE	0	0.00
78	4670	1	NA	NA	FALSE	0	0.00
78	4680	75	NA	NA	FALSE	0	0.00
78	4690	475	NA	NA	FALSE	0	0.00
78	4750	72	NA	NA	FALSE	0	0.00
78	4760	126	NA	NA	FALSE	0	0.00
78	4780	1	NA	NA	FALSE	0	0.00
78	4800	2	NA	NA	FALSE	0	0.00
78	4820	54	NA	NA	FALSE	0	0.00
78	4890	37	NA	NA	FALSE	0	0.00
147	41600	119	NA	NA	FALSE	0	0.00
156	5520	120	NA	NA	FALSE	0	0.00
194	7720	104	NA	NA	FALSE	0	0.00
194	7871	149	NA	NA	FALSE	0	0.00
271	3110	14	NA	NA	FALSE	0	0.00
271	3570	33	NA	NA	FALSE	0	0.00
271	45581	2	NA	NA	FALSE	0	0.00
276	230	54	NA	NA	FALSE	0	0.00
307	125480	12	NA	NA	FALSE	0	0.00
349	4820	150	NA	NA	FALSE	0	0.00
356	4180	3	NA	NA	FALSE	0	0.00
356	4840	2	NA	NA	FALSE	0	0.00
356	40372	5	NA	NA	FALSE	0	0.00
357	1740	4	NA	NA	FALSE	0	0.00
357	2170	1	NA	NA	FALSE	0	0.00
357	2390	4	NA	NA	FALSE	0	0.00
357	4160	1	NA	NA	FALSE	0	0.00
357	4380	13	NA	NA	FALSE	0	0.00
357	4620	4	NA	NA	FALSE	0	0.00
357	4670	36	NA	NA	FALSE	0	0.00
357	4700	20	NA	NA	FALSE	0	0.00
357	4820	12	NA	NA	FALSE	0	0.00
357	4890	14	NA	NA	FALSE	0	0.00
357	5460	3	NA	NA	FALSE	0	0.00
357	41600	13	NA	NA	FALSE	0	0.00
368	4820	62	NA	NA	FALSE	0	0.00
382	360	75	NA	NA	FALSE	0	0.00
390	5280	3	NA	NA	FALSE	0	0.00
390	45581	1	NA	NA	FALSE	0	0.00
418	100430	22	NA	NA	FALSE	0	0.00
420	100430	19	NA	NA	FALSE	0	0.00
421	100390	1	NA	NA	FALSE	0	0.00
421	100430	3	NA	NA	FALSE	0	0.00
421	100450	2	NA	NA	FALSE	0	0.00
421	100520	2	NA	NA	FALSE	0	0.00
427	100250	3	NA	NA	FALSE	0	0.00
427	100450	1	NA	NA	FALSE	0	0.00
427	100580	1	NA	NA	FALSE	0	0.00
427	252456	15	NA	NA	FALSE	0	0.00
432	100430	16	NA	NA	FALSE	0	0.00
432	100450	2	NA	NA	FALSE	0	0.00
432	124470	1	NA	NA	FALSE	0	0.00
434	7680	56	NA	NA	FALSE	0	0.00
436	32990	4	NA	NA	FALSE	0	0.00
437	263371	191	NA	NA	FALSE	0	0.00
448	120210	31	NA	NA	FALSE	0	0.00
450	1260	192	NA	NA	FALSE	0	0.00
454	7680	23	NA	NA	FALSE	0	0.00
458	4750	6	NA	NA	FALSE	0	0.00
458	4820	101	NA	NA	FALSE	0	0.00
458	4900	18	NA	NA	FALSE	0	0.00
468	40261	8	NA	NA	FALSE	0	0.00
486	1650	3	NA	NA	FALSE	0	0.00
486	1660	1	NA	NA	FALSE	0	0.00
486	100190	7	NA	NA	FALSE	0	0.00
486	100550	2	NA	NA	FALSE	0	0.00
498	100190	1	NA	NA	FALSE	0	0.00
498	100230	1	NA	NA	FALSE	0	0.00
498	100250	1	NA	NA	FALSE	0	0.00
498	100270	1	NA	NA	FALSE	0	0.00
498	100430	3	NA	NA	FALSE	0	0.00
498	100450	1	NA	NA	FALSE	0	0.00
498	123940	4	NA	NA	FALSE	0	0.00
498	124470	4	NA	NA	FALSE	0	0.00
500	100400	20	NA	NA	FALSE	0	0.00
501	100430	24	NA	NA	FALSE	0	0.00
525	7810	6	NA	NA	FALSE	0	0.00
532	100190	4	NA	NA	FALSE	0	0.00
532	100230	5	NA	NA	FALSE	0	0.00
532	100270	3	NA	NA	FALSE	0	0.00
532	100420	6	NA	NA	FALSE	0	0.00
532	100430	63	NA	NA	FALSE	0	0.00
532	100450	1	NA	NA	FALSE	0	0.00
533	252456	38	NA	NA	FALSE	0	0.00
534	7680	3	NA	NA	FALSE	0	0.00
534	47282	2	NA	NA	FALSE	0	0.00
541	7680	6	NA	NA	FALSE	0	0.00
554	125480	55	NA	NA	FALSE	0	0.00
555	257061	8	NA	NA	FALSE	0	0.00
555	257202	1	NA	NA	FALSE	0	0.00
563	100190	3	NA	NA	FALSE	0	0.00
563	100250	2	NA	NA	FALSE	0	0.00
563	100380	5	NA	NA	FALSE	0	0.00
563	100560	1	NA	NA	FALSE	0	0.00
563	124432	1	NA	NA	FALSE	0	0.00
585	3580	2	NA	NA	FALSE	0	0.00
586	4990	15	NA	NA	FALSE	0	0.00
608	7720	2	NA	NA	FALSE	0	0.00
608	7871	46	NA	NA	FALSE	0	0.00
611	257184	1	NA	NA	FALSE	0	0.00
611	257201	1	NA	NA	FALSE	0	0.00
611	257216	5	NA	NA	FALSE	0	0.00
632	7871	20	NA	NA	FALSE	0	0.00
635	100190	1	NA	NA	FALSE	0	0.00
635	100230	2	NA	NA	FALSE	0	0.00
635	100430	1	NA	NA	FALSE	0	0.00
644	100300	1	NA	NA	FALSE	0	0.00
644	121401	1	NA	NA	FALSE	0	0.00
646	100430	10	NA	NA	FALSE	0	0.00
646	124470	10	NA	NA	FALSE	0	0.00
648	124240	2	NA	NA	FALSE	0	0.00
648	125480	14	NA	NA	FALSE	0	0.00
649	230	30	NA	NA	FALSE	0	0.00
651	100680	40	NA	NA	FALSE	0	0.00
664	7680	51	NA	NA	FALSE	0	0.00
667	4990	5	NA	NA	FALSE	0	0.00
672	7871	45	NA	NA	FALSE	0	0.00
674	200	75	NA	NA	FALSE	0	0.00
688	100240	3	NA	NA	FALSE	0	0.00
688	100270	5	NA	NA	FALSE	0	0.00
688	100430	8	NA	NA	FALSE	0	0.00
688	100530	2	NA	NA	FALSE	0	0.00
690	100430	10	NA	NA	FALSE	0	0.00
690	100460	7	NA	NA	FALSE	0	0.00

Summarize

Now we can summarize these projects by how many species, deployments (tags) and the average number of deployments per species.

We’ll aim to include projects with a bread of species but also reasonable coverage, so we exclude projects with less than 100% passerines and fewer than three species.

p <- p_sp |>
  filter(prop_good_tags == 1) |>
  group_by(tagProjectID) |>
  summarize(total_tags = sum(num_deployments),
            n_species = n_distinct(speciesID),
            mean_tags_per_species = mean(num_deployments),
            species = list(unique(english_name))) |>
  filter(n_species > 3) |>
  arrange(desc(mean_tags_per_species), desc(n_species), desc(total_tags))

gt(p) |>
  fmt_number(columns = "mean_tags_per_species", decimals = 1) |>
  gt_theme()

tagProjectID	total_tags	n_species	mean_tags_per_species	species
417	226	4	56.5	Ovenbird, Song Sparrow, White-throated Sparrow, Red-eyed Vireo
551	203	6	33.8	Blue-headed Vireo, Hermit Thrush, Magnolia Warbler, Yellow-rumped Warbler (Myrtle), Song Sparrow, Northern Cardinal
484	122	4	30.5	Varied Thrush, Spotted Towhee, White-crowned Sparrow, Golden-crowned Sparrow
352	257	9	28.6	Swainson's Thrush, Gray Catbird, Spotted Towhee, Vesper Sparrow, Grasshopper Sparrow, Lazuli Bunting, Western Meadowlark, Brown-headed Cowbird, Pine Siskin
393	130	5	26.0	Horned Lark, Sprague's Pipit, Baird's Sparrow, Thick-billed Longspur, Chestnut-collared Longspur
364	55	4	13.8	Blackpoll Warbler, Pine Grosbeak, Purple Finch, Pine Siskin
515	42	5	8.4	Hermit Thrush, American Robin, Gray Catbird, Brown Thrasher, White-throated Sparrow
464	59	12	4.9	Veery, Swainson's Thrush, Gray Catbird, Tennessee Warbler, Northern Parula, Black-throated Blue Warbler, Black-throated Green Warbler, Palm Warbler, Black-and-white Warbler, American Redstart, Ovenbird, Common Yellowthroat
607	10	6	1.7	Gray Catbird, Ovenbird, Northern Waterthrush, Common Yellowthroat, Hooded Warbler, Yellow-breasted Chat

Data sizes

Now, we can check the amount of data per project (see what we’re in for!)

For reference, 7,006,847,799 bytes is ~ 7 GB

dir.create("Data/Temp")
status <- map(
  set_names(p$tagProjectID), 
  \(x) tellme(x, dir = "Data/Temp",  new = TRUE)) |>
  list_rbind(names_to = "proj_id")
unlink("Data/Temp", recursive = TRUE)

So this, isn’t too bad, data-wise, I think we could use all projects.

status |> 
  mutate(Megabytes = numBytes / 1000000) |>
  arrange(desc(numBytes)) |>
  gt() |>
  fmt_number(decimals = 0)  |>
  gt_theme()

proj_id	numHits	numBytes	numRuns	numBatches	numGPS	Megabytes
551	74,368,213	7,006,847,799	1,283,286	3,059	386,210	7,007
352	70,567,612	6,655,989,412	1,053,008	39,044	659,503	6,656
417	47,585,940	4,500,299,234	1,007,044	2,647	379,951	4,500
484	25,653,624	2,470,082,118	1,076,391	3,515	495,525	2,470
515	2,198,407	256,103,381	425,980	4,517	572,886	256
393	1,444,599	160,645,217	80,053	4,799	447,871	161
364	94,467	25,729,831	17,000	1,888	330,579	26
464	80,673	21,734,415	34,752	1,873	253,377	22
607	939	1,544,997	456	147	29,634	2

Reproducibility

Session Info

devtools::session_info()

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.0 (2024-04-24)
 os       Ubuntu 22.04.4 LTS
 system   x86_64, linux-gnu
 ui       X11
 language en_CA:en
 collate  en_CA.UTF-8
 ctype    en_CA.UTF-8
 tz       America/Winnipeg
 date     2024-07-04
 pandoc   3.1.1 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 ! package       * version  date (UTC) lib source
 P arrow         * 16.1.0   2024-05-25 [?] CRAN (R 4.4.0)
 P assertr       * 3.0.1    2023-11-23 [?] CRAN (R 4.4.0)
 P assertthat      0.2.1    2019-03-21 [?] CRAN (R 4.4.0)
 P bit             4.0.5    2022-11-15 [?] CRAN (R 4.4.0)
 P bit64           4.0.5    2020-08-30 [?] CRAN (R 4.4.0)
 P blob            1.2.4    2023-03-17 [?] CRAN (R 4.4.0)
 P cachem          1.1.0    2024-05-16 [?] CRAN (R 4.4.0)
 P cellranger      1.1.0    2016-07-27 [?] CRAN (R 4.4.0)
 P class           7.3-22   2023-05-03 [?] CRAN (R 4.3.1)
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 P cli             3.6.2    2023-12-11 [?] CRAN (R 4.4.0)
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 P colorspace      2.1-0    2023-01-23 [?] CRAN (R 4.4.0)
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 P dbplyr          2.5.0    2024-03-19 [?] CRAN (R 4.4.0)
 P devtools        2.4.5    2022-10-11 [?] CRAN (R 4.4.0)
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 P e1071           1.7-14   2023-12-06 [?] CRAN (R 4.4.0)
 P ebirdst       * 3.2022.3 2024-03-05 [?] CRAN (R 4.4.0)
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 P evaluate        0.23     2023-11-01 [?] CRAN (R 4.4.0)
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 P ggspatial     * 1.1.9    2023-08-17 [?] CRAN (R 4.4.0)
 P globals         0.16.3   2024-03-08 [?] CRAN (R 4.4.0)
 P glue            1.7.0    2024-01-09 [?] CRAN (R 4.4.0)
 P gt            * 0.10.1   2024-01-17 [?] CRAN (R 4.4.0)
 P gtable          0.3.5    2024-04-22 [?] CRAN (R 4.4.0)
 P hms             1.1.3    2023-03-21 [?] CRAN (R 4.4.0)
 P htmltools       0.5.8.1  2024-04-04 [?] CRAN (R 4.4.0)
 P htmlwidgets     1.6.4    2023-12-06 [?] CRAN (R 4.4.0)
 P httpuv          1.6.15   2024-03-26 [?] CRAN (R 4.4.0)
 P httr            1.4.7    2023-08-15 [?] CRAN (R 4.4.0)
 P jsonlite        1.8.8    2023-12-04 [?] CRAN (R 4.4.0)
 P KernSmooth      2.23-22  2023-07-10 [?] CRAN (R 4.3.1)
 P knitr           1.47     2024-05-29 [?] CRAN (R 4.4.0)
 P later           1.3.2    2023-12-06 [?] CRAN (R 4.4.0)
 P lifecycle       1.0.4    2023-11-07 [?] CRAN (R 4.4.0)
 P listenv         0.9.1    2024-01-29 [?] CRAN (R 4.4.0)
 P lubridate     * 1.9.3    2023-09-27 [?] CRAN (R 4.4.0)
 P lutz          * 0.3.2    2023-10-17 [?] CRAN (R 4.4.0)
 P magrittr        2.0.3    2022-03-30 [?] CRAN (R 4.4.0)
 P memoise         2.0.1    2021-11-26 [?] CRAN (R 4.4.0)
 P mime            0.12     2021-09-28 [?] CRAN (R 4.4.0)
 P miniUI          0.1.1.1  2018-05-18 [?] CRAN (R 4.4.0)
 P motus         * 6.1.0    2024-05-02 [?] Github (motuswts/motus@a53a8b8)
 P munsell         0.5.1    2024-04-01 [?] CRAN (R 4.4.0)
 P naturecounts    0.4.0    2024-05-02 [?] Github (birdscanada/naturecounts@a6e52da)
 P parallelly      1.37.1   2024-02-29 [?] CRAN (R 4.4.0)
 P patchwork     * 1.2.0    2024-01-08 [?] CRAN (R 4.4.0)
 P pillar          1.9.0    2023-03-22 [?] CRAN (R 4.4.0)
 P pkgbuild        1.4.4    2024-03-17 [?] CRAN (R 4.4.0)
 P pkgconfig       2.0.3    2019-09-22 [?] CRAN (R 4.4.0)
 P pkgload         1.3.4    2024-01-16 [?] CRAN (R 4.4.0)
 P profvis         0.3.8    2023-05-02 [?] CRAN (R 4.4.0)
 P promises        1.3.0    2024-04-05 [?] CRAN (R 4.4.0)
 P proxy           0.4-27   2022-06-09 [?] CRAN (R 4.4.0)
 P purrr         * 1.0.2    2023-08-10 [?] CRAN (R 4.4.0)
 P R6              2.5.1    2021-08-19 [?] CRAN (R 4.4.0)
 P Rcpp            1.0.12   2024-01-09 [?] CRAN (R 4.4.0)
 P readr         * 2.1.5    2024-01-10 [?] CRAN (R 4.4.0)
 P readxl        * 1.4.3    2023-07-06 [?] CRAN (R 4.4.0)
 P remotes         2.5.0    2024-03-17 [?] CRAN (R 4.4.0)
   renv            1.0.7    2024-04-11 [1] CRAN (R 4.4.0)
 P rlang           1.1.3    2024-01-10 [?] CRAN (R 4.4.0)
 P rmarkdown       2.27     2024-05-17 [?] CRAN (R 4.4.0)
 P rnaturalearth * 1.0.1    2023-12-15 [?] CRAN (R 4.4.0)
 P RSQLite         2.3.6    2024-03-31 [?] CRAN (R 4.4.0)
 P rstudioapi      0.16.0   2024-03-24 [?] CRAN (R 4.4.0)
 P sass            0.4.9    2024-03-15 [?] CRAN (R 4.4.0)
 P scales          1.3.0    2023-11-28 [?] CRAN (R 4.4.0)
 P sessioninfo     1.2.2    2021-12-06 [?] CRAN (R 4.4.0)
 P sf            * 1.0-16   2024-03-24 [?] CRAN (R 4.4.0)
 P shiny           1.8.1.1  2024-04-02 [?] CRAN (R 4.4.0)
 P stringi         1.8.4    2024-05-06 [?] CRAN (R 4.4.0)
 P stringr       * 1.5.1    2023-11-14 [?] CRAN (R 4.4.0)
 P terra           1.7-71   2024-01-31 [?] CRAN (R 4.4.0)
 P tibble        * 3.2.1    2023-03-20 [?] CRAN (R 4.4.0)
 P tidyr         * 1.3.1    2024-01-24 [?] CRAN (R 4.4.0)
 P tidyselect      1.2.1    2024-03-11 [?] CRAN (R 4.4.0)
 P timechange      0.3.0    2024-01-18 [?] CRAN (R 4.4.0)
 P tzdb            0.4.0    2023-05-12 [?] CRAN (R 4.4.0)
 P units         * 0.8-5    2023-11-28 [?] CRAN (R 4.4.0)
 P urlchecker      1.0.1    2021-11-30 [?] CRAN (R 4.4.0)
 P usethis         2.2.3    2024-02-19 [?] CRAN (R 4.4.0)
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 P xfun            0.44     2024-05-15 [?] CRAN (R 4.4.0)
 P xml2            1.3.6    2023-12-04 [?] CRAN (R 4.4.0)
 P xtable          1.8-4    2019-04-21 [?] CRAN (R 4.4.0)
 P yaml            2.3.8    2023-12-11 [?] CRAN (R 4.4.0)

 [1] /home/steffi/Projects/Business/Barbara Frei/urban_motus/renv/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu
 [2] /home/steffi/.cache/R/renv/sandbox/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu/9a444a72

 P ── Loaded and on-disk path mismatch.

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