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config.yml
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config.yml
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default:
surveys:
selection:
- document_id
- location_id
- year
- month
- day
has_value:
- document_id
- location_id
- year
- month
- day
counts:
abundance: abundance
use_data_after: "01-01"
flb:
name: Farmland birds
taxa:
- code: MX.27328
binomial: Crex crex
start_year: 2006
- code: MX.27527
binomial: Vanellus vanellus
- code: MX.27613
binomial: Numenius arquata
- code: MX.32065
binomial: Alauda arvensis
- code: MX.32132
binomial: Hirundo rustica
- code: MX.32163
binomial: Delichon urbicum
- code: MX.32213
binomial: Anthus pratensis
- code: MX.32949
binomial: Saxicola rubetra
- code: MX.33936
binomial: Sylvia communis
- code: MX.37142
binomial: Corvus monedula
- code: MX.36817
binomial: Sturnus vulgaris
- code: MX.36589
binomial: Passer montanus
start_year: 2006
- code: MX.35154
binomial: Emberiza hortulana
filters:
date_range_ymd:
- "1979-01-01"
- ""
location_tag: farmland
collection:
- HR.157
- HR.61
counts:
abundance: pair_abundance
selection:
- document_id
- pair_abundance
has_value:
- document_id
- pair_abundance
combine: geometric_mean
use_data_after: "10-01"
model:
trim:
units: "Relative abundance"
base_year: 2000
surveys_process:
- pick_first_survey_in_year
- require_two_years
counts_process:
- zero_fill
- sum_by_event
- set_start_year
- remove_all_zero_locations
mrb:
name: Mire birds
taxa:
- code: MX.32213
binomial: Anthus pratensis
- code: MX.27704
binomial: Calidris falcinellus
start_year: 2006
- code: MX.27710
binomial: Calidris pugnax
- code: MX.27674
binomial: Lymnocryptes minimus
- code: MX.27610
binomial: Numenius phaeopus
- code: MX.27553
binomial: Pluvialis apricaria
- code: MX.27628
binomial: Tringa glareola
- code: MX.35165
binomial: Emberiza pusilla
start_year: 2006
- code: MX.35167
binomial: Emberiza rustica
- code: MX.27666
binomial: Gallinago gallinago
- code: MX.27214
binomial: Grus grus
- code: MX.32180
binomial: Motacilla flava
- code: MX.27619
binomial: Tringa erythropus
start_year: 2006
- code: MX.27622
binomial: Tringa nebularia
- code: MX.35182
binomial: Emberiza schoeniclus
- code: MX.26921
binomial: Lagopus lagopus
filters:
date_range_ymd:
- "1981-01-01"
- ""
location_tag: mire
collection:
- HR.157
- HR.61
counts:
abundance: pair_abundance
selection:
- document_id
- pair_abundance
has_value:
- document_id
- pair_abundance
combine: geometric_mean
use_data_after: "10-01"
model:
trim:
units: "Relative abundance"
base_year: 2000
surveys_process:
- pick_first_survey_in_year
- require_two_years
counts_process:
- zero_fill
- sum_by_event
- set_start_year
- remove_all_zero_locations
mtb:
name: Mountain birds
taxa:
- code: MX.26921
binomial: Lagopus lagopus
- code: MX.27553
binomial: Pluvialis apricaria
- code: MX.28715
binomial: Cuculus canorus
- code: MX.32213
binomial: Anthus pratensis
- code: MX.32821
binomial: Luscinia svecica
- code: MX.32895
binomial: Phoenicurus phoenicurus
- code: MX.32966
binomial: Oenanthe oenanthe
- code: MX.33118
binomial: Turdus iliacus
- code: MX.33873
binomial: Phylloscopus trochilus
- code: MX.36239
binomial: Fringilla montifringilla
- code: MX.36308
binomial: Carduelis flammea
- code: MX.35185
binomial: Calcarius lapponicus
filters:
date_range_ymd:
- "1996-01-01"
- ""
location_tag: mountain
collection:
- HR.157
- HR.61
counts:
abundance: pair_abundance
selection:
- document_id
- pair_abundance
has_value:
- document_id
- pair_abundance
combine: geometric_mean
use_data_after: "10-01"
model:
trim:
units: "Relative abundance"
base_year: 2000
surveys_process:
- pick_first_survey_in_year
- require_two_years
counts_process:
- zero_fill
- sum_by_event
- set_start_year
- remove_all_zero_locations
ftb:
name: Forest birds
taxa:
- code: MX.26639
binomial: Accipiter nisus
sti: 11.92
start_year: 2005
region: south
- code: MX.36308
binomial: Carduelis flammea
sti: 8.19
start_year: 1980
region: north
- code: MX.36287
binomial: Carduelis spinus
sti: 10.24
- code: MX.34616
binomial: Certhia familiaris
sti: 11.12
- code: MX.32801
binomial: Erithacus rubecula
sti: 12.0
- code: MX.34029
binomial: Ficedula parva
sti: 11.6
start_year: 2006
region: south
- code: MX.36237
binomial: Fringilla coelebs
sti: 12.3
- code: MX.36239
binomial: Fringilla montifringilla
sti: 7.03
region: north
- code: MX.34553
binomial: Lophophanes cristatus
sti: 11.71
region: south
- code: MX.36355
binomial: Loxia
sti: 10.49
- code: MX.33989
binomial: Muscicapa striata
sti: 12.15
- code: MX.34549
binomial: Periparus ater
sti: 11.9
region: south
- code: MX.37095
binomial: Perisoreus infaustus
sti: 5.77
start_year: 2006
region: north
- code: MX.32895
binomial: Phoenicurus phoenicurus
sti: 11.31
- code: MX.33874
binomial: Phylloscopus collybita
sti: 11.95
- code: MX.33878
binomial: Phylloscopus sibilatrix
sti: 11.38
region: south
- code: MX.33891
binomial: Phylloscopus trochiloides
sti: 9.76
region: south
- code: MX.30453
binomial: Picoides tridactylus
sti: 7.98
start_year: 2006
region: north
- code: MX.36351
binomial: Pinicola enucleator
sti: 5.01
start_year: 2006
region: north
- code: MX.34542
binomial: Poecile cinctus
sti: 4.47
start_year: 2006
region: north
- code: MX.34535
binomial: Poecile montanus
sti: 10.2
- code: MX.36366
binomial: Pyrrhula pyrrhula
sti: 10.76
- code: MX.33954
binomial: Regulus regulus
sti: 10.81
- code: MX.27649
binomial: Scolopax rusticola
sti: 10.6
region: south
- code: MX.26931
binomial: Tetrastes bonasia
sti: 9.74
- code: MX.26928
binomial: Tetrao urogallus
sti: 8.74
start_year: 1984
- code: MX.32696
binomial: Troglodytes troglodytes
sti: 12.24
start_year: 1984
region: south
- code: MX.33119
binomial: Turdus philomelos
sti: 11.4
- code: MX.33121
binomial: Turdus viscivorus
sti: 11.91
start_year: 1984
extra_taxa:
- code: MX.33651
binomial: Acrocephalus arundinaceus
sti: 13.88
- code: MX.33650
binomial: Acrocephalus dumetorum
sti: 9.51
- code: MX.33649
binomial: Acrocephalus palustris
sti: 12.25
- code: MX.33641
binomial: Acrocephalus schoenobaenus
sti: 11.39
- code: MX.33646
binomial: Acrocephalus scirpaceus
sti: 13.15
- code: MX.27634
binomial: Actitis hypoleucos
sti: 11.2
- code: MX.34505
binomial: Aegithalos caudatus
sti: 12.66
- code: MX.29038
binomial: Aegolius funereus
sti: 9.1
- code: MX.32065
binomial: Alauda arvensis
sti: 12.2
- code: MX.26382
binomial: Anas acuta
sti: 8.53
- code: MX.26394
binomial: Anas clypeata
sti: 11.76
- code: MX.26366
binomial: Anas crecca
sti: 10.07
- code: MX.26360
binomial: Anas penelope
sti: 6.68
- code: MX.26373
binomial: Anas platyrhynchos
sti: 11.81
- code: MX.26388
binomial: Anas querquedula
sti: 12.39
- code: MX.26364
binomial: Anas strepera
sti: 12.52
- code: MX.26289
binomial: Anser albifrons
sti: 1.4
- code: MX.32217
binomial: Anthus cervinus
sti: 3.13
- code: MX.32221
binomial: Anthus petrosus
sti: 11.68
- code: MX.32213
binomial: Anthus pratensis
sti: 9.95
- code: MX.32204
binomial: Anthus richardi
sti: .na.real
- code: MX.32214
binomial: Anthus trivialis
sti: 11.24
- code: MX.29324
binomial: Apus apus
sti: 12.45
- code: MX.26722
binomial: Aquila pomarina
sti: 12.68
- code: MX.26094
binomial: Ardea cinerea
sti: 12.69
- code: MX.27642
binomial: Arenaria interpres
sti: 7.74
- code: MX.29072
binomial: Asio flammeus
sti: 9.62
- code: MX.29068
binomial: Asio otus
sti: 12.29
- code: MX.26407
binomial: Aythya ferina
sti: 12.45
- code: MX.26415
binomial: Aythya fuligula
sti: 10.14
- code: MX.32608
binomial: Bombycilla garrulus
sti: 5.77
- code: MX.26164
binomial: Botaurus stellaris
sti: 13.11
- code: MX.26300
binomial: Branta bernicla
sti: -4.6
- code: MX.26298
binomial: Branta canadensis
sti: 9.55
- code: MX.26299
binomial: Branta leucopsis
sti: 9.28
- code: MX.26435
binomial: Bucephala clangula
sti: 8.47
- code: MX.26701
binomial: Buteo buteo
sti: 12.7
start_year: 1984
- code: MX.35185
binomial: Calcarius lapponicus
sti: 4.06
- code: MX.27699
binomial: Calidris alpina
sti: 7.07
- code: MX.27704
binomial: Calidris falcinellus
sti: 4.97
- code: MX.27710
binomial: Calidris pugnax
sti: 7.97
- code: MX.29172
binomial: Caprimulgus europaeus
sti: 13.11
- code: MX.36310
binomial: Carduelis cannabina
sti: 13.16
- code: MX.36306
binomial: Carduelis carduelis
sti: 13.45
- code: MX.36283
binomial: Carduelis chloris
sti: 12.6
- code: MX.36309
binomial: Carduelis flavirostris
sti: 6.95
- code: MX.73545
binomial: Carduelis hornemanni
sti: 3.09
- code: MX.36331
binomial: Carpodacus erythrinus
sti: 10.35
- code: MX.27855
binomial: Cepphus grylle
sti: 7.46
- code: MX.27562
binomial: Charadrius dubius
sti: 12.77
- code: MX.27559
binomial: Charadrius hiaticula
sti: 8.22
- code: MX.27597
binomial: Charadrius morinellus
sti: 5.39
- code: MX.26187
binomial: Ciconia ciconia
sti: 13.61
- code: MX.26182
binomial: Ciconia nigra
sti: 13.11
- code: MX.26427
binomial: Clangula hyemalis
sti: 3.39
- code: MX.36368
binomial: Coccothraustes coccothraustes
sti: 12.98
- code: MX.27903
binomial: Columba livia
sti: 12.79
- code: MX.27908
binomial: Columba oenas
sti: 12.44
- code: MX.27911
binomial: Columba palumbus
sti: 12.22
- code: MX.37178
binomial: Corvus corax
sti: 11.74
- code: MX.73566
binomial: Corvus corone
sti: 12.13
- code: MX.37156
binomial: Corvus frugilegus
sti: 12.73
- code: MX.37142
binomial: Corvus monedula
sti: 12.96
- code: MX.27058
binomial: Coturnix coturnix
sti: 13.6
- code: MX.27328
binomial: Crex crex
sti: 11.97
- code: MX.28715
binomial: Cuculus canorus
sti: 12.14
- code: MX.34574
binomial: Cyanistes caeruleus
sti: 12.74
- code: MX.26280
binomial: Cygnus cygnus
sti: 6.27
- code: MX.26277
binomial: Cygnus olor
sti: 12.19
- code: MX.32163
binomial: Delichon urbicum
sti: 12.35
- code: MX.30443
binomial: Dendrocopos major
sti: 12.12
- code: MX.30428
binomial: Dendrocopos minor
sti: 11.55
- code: MX.30504
binomial: Dryocopus martius
sti: 11.12
- code: MX.26105
binomial: Egretta alba
sti: .na.real
- code: MX.35169
binomial: Emberiza aureola
sti: 9.21
- code: MX.35146
binomial: Emberiza citrinella
sti: 11.55
- code: MX.35154
binomial: Emberiza hortulana
sti: 12.73
- code: MX.35165
binomial: Emberiza pusilla
sti: 4.66
- code: MX.35167
binomial: Emberiza rustica
sti: 6.34
- code: MX.35182
binomial: Emberiza schoeniclus
sti: 11.27
- code: MX.26808
binomial: Falco columbarius
sti: 6.82
- code: MX.26811
binomial: Falco subbuteo
sti: 12.68
- code: MX.26796
binomial: Falco tinnunculus
sti: 12.43
- code: MX.34022
binomial: Ficedula albicollis
sti: 13.06
- code: MX.34021
binomial: Ficedula hypoleuca
sti: 10.43
- code: MX.27381
binomial: Fulica atra
sti: 12.96
- code: MX.27666
binomial: Gallinago gallinago
sti: 10.27
- code: MX.27364
binomial: Gallinula chloropus
sti: 13.34
- code: MX.37090
binomial: Garrulus glandarius
sti: 12.47
- code: MX.25837
binomial: Gavia arctica
sti: 6.83
- code: MX.29011
binomial: Glaucidium passerinum
sti: 8.63
- code: MX.27214
binomial: Grus grus
sti: 9.5
- code: MX.27459
binomial: Haematopus ostralegus
sti: 10.47
- code: MX.33676
binomial: Hippolais icterina
sti: 11.39
- code: MX.32132
binomial: Hirundo rustica
sti: 12.43
- code: MX.27777
binomial: Hydrocoloeus minutus
sti: 9.36
- code: MX.30333
binomial: Jynx torquilla
sti: 11.88
- code: MX.26922
binomial: Lagopus muta
sti: 6.02
- code: MX.32561
binomial: Lanius collurio
sti: 12.62
- code: MX.32570
binomial: Lanius excubitor
sti: 11.2
- code: MX.32568
binomial: Lanius minor
sti: 14.85
- code: MX.27750
binomial: Larus argentatus
sti: 9.06
- code: MX.27748
binomial: Larus canus
sti: 8.57
- code: MX.27753
binomial: Larus fuscus
sti: 8.92
- code: MX.27759
binomial: Larus marinus
sti: 8.37
- code: MX.27774
binomial: Larus ridibundus
sti: 11.07
- code: MX.27605
binomial: Limosa lapponica
sti: 3.25
- code: MX.33634
binomial: Locustella fluviatilis
sti: 12.32
- code: MX.33629
binomial: Locustella lanceolata
sti: 6.38
- code: MX.33635
binomial: Locustella luscinioides
sti: 13.59
- code: MX.33630
binomial: Locustella naevia
sti: 11.77
- code: MX.32063
binomial: Lullula arborea
sti: 13.47
- code: MX.32819
binomial: Luscinia luscinia
sti: 11.84
- code: MX.32821
binomial: Luscinia svecica
sti: 10.16
- code: MX.27674
binomial: Lymnocryptes minimus
sti: 5.83
- code: MX.26431
binomial: Melanitta fusca
sti: 4.81
- code: MX.26429
binomial: Melanitta nigra
sti: 4.23
- code: MX.32020
binomial: Melanocorypha calandra
sti: 16.12
- code: MX.26442
binomial: Mergus merganser
sti: 7.91
- code: MX.26440
binomial: Mergus serrator
sti: 7.37
- code: MX.32183
binomial: Motacilla alba
sti: 11.99
- code: MX.32180
binomial: Motacilla flava
sti: 12.14
- code: MX.37135
binomial: Nucifraga caryocatactes
sti: 10.73
- code: MX.27613
binomial: Numenius arquata
sti: 10.05
- code: MX.27610
binomial: Numenius phaeopus
sti: 5.89
- code: MX.32966
binomial: Oenanthe oenanthe
sti: 11.62
- code: MX.36871
binomial: Oriolus oriolus
sti: 13.47
- code: MX.33492
binomial: Panurus biarmicus
sti: 13.88
- code: MX.34567
binomial: Parus major
sti: 12.34
- code: MX.36573
binomial: Passer domesticus
sti: 12.26
- code: MX.36589
binomial: Passer montanus
sti: 13.07
- code: MX.36816
binomial: Pastor roseus
sti: 15.88
- code: MX.27048
binomial: Perdix perdix
sti: 12.85
- code: MX.26043
binomial: Phalacrocorax carbo
sti: 12.47
- code: MX.27646
binomial: Phalaropus lobatus
sti: 4.71
- code: MX.27152
binomial: Phasianus colchicus
sti: 12.87
- code: MX.32894
binomial: Phoenicurus ochruros
sti: 13.24
- code: MX.33890
binomial: Phylloscopus borealis
sti: 5.47
- code: MX.33873
binomial: Phylloscopus trochilus
sti: 10.46
- code: MX.37122
binomial: Pica pica
sti: 12.16
- code: MX.30530
binomial: Picus canus
sti: 12.06
- code: MX.35189
binomial: Plectrophenax nivalis
sti: 4.04
- code: MX.27553
binomial: Pluvialis apricaria
sti: 7.0
- code: MX.25861
binomial: Podiceps auritus
sti: 8.3
- code: MX.25860
binomial: Podiceps cristatus
sti: 12.69
- code: MX.25859
binomial: Podiceps grisegena
sti: 11.94
- code: MX.34532
binomial: Poecile palustris
sti: 12.33
- code: MX.27342
binomial: Porzana parva
sti: 13.5
- code: MX.27345
binomial: Porzana porzana
sti: 12.41
- code: MX.27343
binomial: Porzana pusilla
sti: 15.35
- code: MX.32772
binomial: Prunella modularis
sti: 10.91
- code: MX.27276
binomial: Rallus aquaticus
sti: 13.32
- code: MX.27486
binomial: Recurvirostra avosetta
sti: 14.58
- code: MX.32120
binomial: Riparia riparia
sti: 11.96
- code: MX.32949
binomial: Saxicola rubetra
sti: 11.3
- code: MX.32953
binomial: Saxicola rubicola
sti: 13.99
- code: MX.36242
binomial: Serinus serinus
sti: 13.88
- code: MX.34586
binomial: Sitta europaea
sti: 12.79
- code: MX.26419
binomial: Somateria mollissima
sti: 8.17
- code: MX.27731
binomial: Stercorarius longicaudus
sti: 3.57
- code: MX.27730
binomial: Stercorarius parasiticus
sti: 5.96
- code: MX.27801
binomial: Sterna hirundo
sti: 11.44
- code: MX.27802
binomial: Sterna paradisaea
sti: 6.72
- code: MX.27960
binomial: Streptopelia decaocto
sti: 12.92
- code: MX.28998
binomial: Strix aluco
sti: 12.87
- code: MX.36817
binomial: Sturnus vulgaris
sti: 11.8
- code: MX.29008
binomial: Surnia ulula
sti: 5.8
- code: MX.33934
binomial: Sylvia atricapilla
sti: 12.62
- code: MX.33935
binomial: Sylvia borin
sti: 11.32
- code: MX.33936
binomial: Sylvia communis
sti: 12.65
- code: MX.33937
binomial: Sylvia curruca
sti: 11.64
- code: MX.26323
binomial: Tadorna tadorna
sti: 12.04
- code: MX.32816
binomial: Tarsiger cyanurus
sti: 6.57
- code: MX.27403
binomial: Tetrax tetrax
sti: 16.16
- code: MX.27619
binomial: Tringa erythropus
sti: 4.77
- code: MX.27628
binomial: Tringa glareola
sti: 7.67
- code: MX.27622
binomial: Tringa nebularia
sti: 6.45
- code: MX.27626
binomial: Tringa ochropus
sti: 9.88
- code: MX.27620
binomial: Tringa totanus
sti: 11.04
- code: MX.33115
binomial: Turdus atrogularis
sti: .na.real
- code: MX.33118
binomial: Turdus iliacus
sti: 8.25
- code: MX.33106
binomial: Turdus merula
sti: 12.58
- code: MX.33117
binomial: Turdus pilaris
sti: 10.03
- code: MX.33104
binomial: Turdus torquatus
sti: 9.03
- code: MX.27527
binomial: Vanellus vanellus
sti: 11.53
filters:
date_range_ymd:
- "1979-01-01"
- ""
country: Finland
collection:
- HR.157
- HR.61
counts:
abundance: pair_abundance
selection:
- document_id
- pair_abundance
has_value:
- document_id
- pair_abundance
combine: geometric_mean
use_data_after: "10-01"
model:
trim:
units: "Relative abundance"
base_year: 2000
surveys_process:
- pick_first_survey_in_year
- require_two_years
counts_process:
- zero_fill
- sum_by_event
- set_start_year
- remove_all_zero_locations
sbcti:
name: Summer birds community temperature index
from: ftb
combine: cti
model:
lmer:
units: "Degrees Celsius"
surveys_process:
- pick_first_survey_in_year
counts_process:
- combine_with_surveys
- sum_by_event
wb:
name: Winter birds
taxa:
- code: MX.34535
binomial: Poecile montanus
sti: -7.51
- code: MX.33954
binomial: Regulus regulus
sti: -4.23
- code: MX.34553
binomial: Lophophanes cristatus
sti: -5.90
- code: MX.26931
binomial: Tetrastes bonasia
sti: -9.64
- code: MX.26928
binomial: Tetrao urogallus
sti: -9.78
- code: MX.26926
binomial: Lyrurus tetrix
sti: -9.96
- code: MX.34616
binomial: Certhia familiaris
sti: -6.89
- code: MX.30504
binomial: Dryocopus martius
sti: -7.59
- code: MX.36358
extra_codes: MX.36355
subtaxa: false
binomial: Loxia curvirostra
sti: -7.53
- code: MX.29011
binomial: Glaucidium passerinum
sti: -9.86
- code: MX.36351
binomial: Pinicola enucleator
sti: -12.49
- code: MX.30453
binomial: Picoides tridactylus
sti: -10.52
- code: MX.36356
binomial: Loxia pytyopsittacus
sti: -10.67
- code: MX.29008
binomial: Surnia ulula
sti: -12.25
- code: MX.34542
binomial: Poecile cinctus
sti: -13.70
- code: MX.37095
binomial: Perisoreus infaustus
sti: -12.56
extra_taxa:
- code: MX.26639
binomial: Accipiter nisus
sti: 2.79
- code: MX.27634
binomial: Actitis hypoleucos
sti: 23.39
- code: MX.34505
binomial: Aegithalos caudatus
sti: -5.07
- code: MX.29038
binomial: Aegolius funereus
sti: -9.79
- code: MX.32065
binomial: Alauda arvensis
sti: 2.39
- code: MX.27850
binomial: Alca torda
sti: 1.96
- code: MX.27848
binomial: Alle alle
sti: -2.69
- code: MX.26382
binomial: Anas acuta
sti: 19.01