| title | date | output | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
Bird Survey Around Mida Creek |
2021-06-09 |
|
Raphaël Nussbaumer1,
1A Rocha Kenya, Watamu, Kenya
Corresponding author: Raphaël Nussbaumer (raphael.nussbaumer@arocha.org)
The initial goal of these surveys was to collect information about the location of Mangrove Kingfishers (Halcyon senegaloides) for a geolocator study. However, as surveys provided richer information, it was decided to publish this dataset on its own.
Each survey refers to a complete presence-only species list (called "event" in the dataset), each recorded over ~1km and during ~1hr. Four surveys were performed successively over a morning from 6am to 10am covering a transect. Each of the 23 transects was repeated once a month (grouping called "session") from May 2020 to May 2021. The study area covers the habitat between Arabuko-Sokoke Forest and Mida Creek. Surveys were collected by bird guides from the area (Daniel Kazungu, Juma Badi, Kibwana Ali, Saddam Kailo and Mohammed Ali) and organized by Kirao Lennox, Raphaël Nussbaumer and Colin Jackson from A Rocha Kenya.
Summary of count statistics.
- Number of transects : 23
- Number of sessions: 11
- Number of events (surveys): 873
- Number of occurrences (sightings): 29195
- Number of species: 217
Purpose:
- Collect standardized data on common species between the forest habitat and the creek/coastal habitat.
- Collect baseline data with a reproducible protocol in order to assess the change of avifauna over time.
- Assess the impact of deforestation on the 'shambas' (fields/farms).
Type of data
This dataset is published as a Darwin Core Archive using a sampling event dataset type.
Data structure
- The raw data was collected on the field using the Birdlasser application, and stored in
data/birdlasser_files. data/metadata.xlsxcontains basic survey information.- The metadata and raw data are combined in
Process2GBIF.rmd - This script also produces the GBIF formatted output files
events.csvrecords information related to the surveys andoccurrences.csvcontains information about the individual sightings.
Table 1: Events (surveys) table structure
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Table 2: Occurrences (counts) table structure
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bird, ornithology, count, monitoring, survey, Kenya, Africa, East Africa, coast, Mida Creek, Arabuko-Sokoke Forest, habitat change, population, trend, Birdlasser, African Bird Atlas, Samplingevent
The surveys were performed between Arabuko-Sokoke Forest and Mida Creek, on the coast of Kenya. See for more information about the spatial extent of the dataset.
## NOTE: keeping only 23 wkbLineString of 23 features
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The bounding box is -3.46669° to -3.271515° latitude and 39.891823° to 40.044845° longitude.
We record all birds seen (Aves sp.) at the species level (with the exception of the Hybrid Lovebird Agapornis fischeri x personatus). We use the taxonomy from the Checklist of the Birds of Kenya (5th Edition) (ISBN: 9966-761-37-3) for the scientificName and vernacularName. The taxonID and taxonRank are taken from the eBird/Clements Checklist of Birds of the World: v2019. See section Sampling Description for explanations on how the taxons were initially recorded in the field and later filtered and matched to these taxonomy lists.
Our dataset contains 217 unique species belonging to 64 families.
Kingdom: Animalia (animals)
Phylum: Chordata
Class: Aves (birds)
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Bare-eyed Thrush","Black-headed Oriole","African Fish Eagle","African Golden Oriole","African Harrier Hawk (Gymnogene)","African Paradise Flycatcher","African Pygmy Kingfisher","African Palm Swift","African Pied Wagtail","African Cuckoo","African Cuckoo Hawk","African Goshawk","African Green Pigeon","African Jacana","African Open-billed Stork","Grassland Pipit","African Spoonbill","Alpine Swift","Amani Sunbird","Amethyst Sunbird","Ashy Flycatcher","Barn Swallow","Bat Hawk","Black-and-white Mannikin","Black-bellied Starling","Blue-cheeked Bee-eater","Black-crowned Night Heron","Bearded Scrub Robin","Grey Plover","Black-chested Snake Eagle","Black-crowned Tchagra","Black-headed Batis","Black-winged Stilt","Great (Black) Sparrowhawk","Black Heron","Black Kite","Black-backed Puffback","Black-collared Barbet","Black-headed Apalis","Black-headed Heron","Black Cuckooshrike","Blue-naped Mousebird","Black-necked Weaver","Broad-billed Roller","Brown-crowned Tchagra","Brown-headed Parrot","Bronze 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Flamingo","Greater Honeyguide","Green Wood-hoopoe","Grosbeak Weaver","Greater Sand Plover","Gull-billed Tern","Grey-headed Bush-Shrike","Grey-headed Kingfisher","Hadada Ibis","Helmeted Guineafowl","House Crow","House Sparrow","Yellow-billed Egret","Isabelline Shrike","Jameson's Firefinch","Klaas's Cuckoo","Lesser Grey Shrike","Lesser Flamingo","Lesser Honeyguide","Lesser Masked Weaver","Lesser Sand Plover","Lesser Striped Swallow","Lilac-breasted Roller","Little Egret","Little Grebe","Little Sparrowhawk","Little Stint","Little Swift","Lizard Buzzard","Long-crested Eagle","Long-tailed (Reed) Cormorant","Madagascar Bee-eater","Madagascar Pratincole","Malachite Kingfisher","Mangrove Kingfisher","Madagascar Pond Heron","Martial Eagle","Mouse-coloured Sunbird","Mombasa Woodpecker","Mottled Spinetail","Namaqua Dove","Narina Trogon","Northern Carmine Bee-eater","Northern Brownbul","Osprey","Parrot-billed Sparrow","East Coast (Pale) Batis","Pale Flycatcher","Pallid Honeyguide","Palm-nut Vulture","Peter's Twinspot","Pied Crow","Jacobin Cuckoo","Pied Kingfisher","Pin-tailed Whydah","Plain-backed Sunbird","Purple-banded Sunbird","Purple Heron","White-browed Scrub Robin","Red-capped Robin Chat","Red-billed Teal","Red-billed Firefinch","Red-billed Quelea","Red-backed Shrike","Red-cheeked Cordon-bleu","Red-eyed Dove","Red-fronted Tinkerbird","Retz's Helmetshrike","Ring-necked Dove","Feral Pigeon","Red-tailed Ant Thrush","Common Rock Thrush","Rufous Chatterer","Rufous Bush Chat","Sacred Ibis","Scaly Babbler","Scaly-throated Honeyguide","Forest Batis","Silvery-cheeked Hornbill","Slender-tailed Nightjar","Sombre (Zanzibar) Greenbul","Speckled Mousebird","Speckled Tinkerbird","Spectacled Weaver","Spotted Morning (Spotted Palm) Thrush","Spotted Flycatcher","Striated Heron","Striped Kingfisher","Tawny-flanked Prinia","Tambourine Dove","Terrestrial Brownbul","Three-banded Plover","Thrush Nightingale","Trumpeter Hornbill","Verreaux's Eagle Owl","Violet-backed Starling","Village Indigobird","Village Weaver","Wahlberg’s Eagle","Water Thick-knee","White-browed Robin Chat","Western Marsh Harrier","White-faced Whistling Duck","White-browed Coucal","White-fronted Plover","Whimbrel","Coastal Cisticola","Willow Warbler","Woolly-necked Stork","Wood Sandpiper","White-throated Bee-eater","Hybrid Lovebird","Yellow-bellied Greenbul","Yellow-billed Stork","Yellow-fronted Canary","Little Yellow Flycatcher","Western Yellowbill (Blue Malkoha)","Southern Yellowbill (Green Malkoha)","Yellow-throated Longclaw","Zanzibar Red Bishop","East Coast Boubou",null],["Turdus tephronotus","Oriolus larvatus","Haliaeetus vocifer","Oriolus auratus","Polyboroides typus","Terpsiphone viridis","Ispidina picta","Cypsiurus parvus","Motacilla aguimp","Cuculus gularis","Aviceda cuculoides","Accipiter tachiro","Treron calvus","Actophilornis africanus","Anastomus lamelligerus","Anthus cinnamomeus","Platalea alba","Tachymarptis melba","Anthodiaeta pallidigaster","Chalcomitra amethystina","Fraseria caerulescens","Hirundo rustica","Macheiramphus alcinus","Spermestes bicolor","Notopholia corusca","Merops persicus","Nycticorax nycticorax","Cercotrichas quadrivirgata","Pluvialis squatarola","Circaetus pectoralis","Tchagra senegalus","Batis minor","Himantopus himantopus","Accipiter melanoleucus","Egretta ardesiaca","Milvus migrans","Dryoscopus cubla","Lybius torquatus","Apalis melanocephala","Ardea melanocephala","Campephaga flava","Urocolius macrourus","Ploceus nigricollis","Eurystomus glaucurus","Tchagra australis","Poicephalus cryptoxanthus","Spermestes cucullata","Circaetus cinereus","Bubulcus ibis","Prionops scopifrons","Ploceus golandi","Delichon urbicum","Glareola pratincola","Anthodiaeta collaris","Pycnonotus barbatus","Cuculus canorus","Sarkidiornis melanotos","Tringa nebularia","Luscinia megarhynchos","Actitis hypoleucos","Estrilda astrild","Cichladusa arquata","Charadrius hiaticula","Rhinopomastus cyanomelas","Dromas ardeola","Dendroperdix sephaena","Guttera pucherani","Lophoceros alboterminatus","Estrilda rhodopyga","Calidris ferruginea","Amadina fasciata","Chrysococcyx caprius","Ixobrychus sturmii","Sheppardia gunningi","Cyanomitra olivacea","Nicator gularis","Motacilla flava","Alopochen aegyptiaca","Turtur chalcospilos","Merops apiaster","Oriolus oriolus","Coracias garrulus","Circaetus fasciolatus","Phyllastrephus fischeri","Tauraco fischeri","Ploceus bicolor","Dicrurus adsimilis","Lamprotornis chalybaeus","Plegadis falcinellus","Tmetothylacus tenellus","Ploceus bojeri","Ardea cinerea","Camaroptera brachyura","Cryptolybia olivacea","Ardea alba","Phoenicopterus roseus","Indicator indicator","Phoeniculus purpureus","Amblyospiza albifrons","Charadrius leschenaultii","Gelochelidon nilotica","Malaconotus blanchoti","Halcyon leucocephala","Bostrychia hagedash","Numida meleagris","Corvus splendens","Passer domesticus","Egretta intermedia","Lanius isabellinus","Lagonosticta rhodopareia","Chrysococcyx klaas","Lanius minor","Phoeniconaias minor","Indicator minor","Ploceus intermedius","Charadrius mongolus","Cecropis abyssinica","Coracias caudatus","Egretta garzetta","Tachybaptus ruficollis","Accipiter minullus","Calidris minuta","Apus affinis","Kaupifalco monogrammicus","Lophaetus occipitalis","Microcarbo africanus","Merops superciliosus","Glareola ocularis","Corythornis cristatus","Halcyon senegaloides","Ardeola idae","Polemaetus bellicosus","Cyanomitra veroxii","Campethera mombassica","Telacanthura ussheri","Oena capensis","Apaloderma narina","Merops nubicus","Phyllastrephus strepitans","Pandion haliaetus","Passer (griseus) gongonensis","Batis soror","Bradornis pallidus","Indicator meliphilus","Gypohierax angolensis","Hypargos niveoguttatus","Corvus albus","Clamator jacobinus","Ceryle rudis","Vidua macroura","Anthreptes reichenowi","Cinnyris bifasciatus","Ardea purpurea","Cercotrichas leucophrys","Cossypha natalensis","Anas erythrorhyncha","Lagonosticta senegala","Quelea quelea","Lanius collurio","Uraeginthus bengalus","Streptopelia semitorquata","Pogoniulus pusillus","Prionops retzii","Streptopelia capicola","Columba livia","Neocossyphus rufus","Monticola saxatilis","Argya rubiginosa","Cercotrichas galactotes","Threskiornis aethiopicus","Turdoides squamulata","Indicator variegatus","Batis mixta","Bycanistes brevis","Caprimulgus clarus","Andropadus importunus","Colius striatus","Pogoniulus scolopaceus","Ploceus ocularis","Cichladusa guttata","Muscicapa striata","Butorides striata","Halcyon chelicuti","Prinia subflava","Turtur tympanistria","Phyllastrephus terrestris","Charadrius tricollaris","Luscinia luscinia","Bycanistes bucinator","Bubo lacteus","Cinnyricinclus leucogaster","Vidua chalybeata","Ploceus cucullatus","Hieraaetus wahlbergi","Burhinus vermiculatus","Cossypha heuglini","Circus aeruginosus","Dendrocygna viduata","Centropus superciliosus","Charadrius marginatus","Numenius phaeopus","Cisticola haematocephalus","Phylloscopus trochilus","Ciconia episcopus","Tringa glareola","Merops albicollis","Agapornis fischeri x personatus","Chlorocichla flaviventris","Mycteria ibis","Crithagra mozambica","Erythrocercus holochlorus","Ceuthmochares aereus","Ceuthmochares australis","Macronyx croceus","Euplectes nigroventris","Laniarius sublacteus",null],["Turdidae","Oriolidae","Accipitridae","Oriolidae","Accipitridae","Monarchidae","Alcedinidae","Apodidae","Motacillidae","Cuculidae","Accipitridae","Accipitridae","Columbidae","Jacanidae","Ciconiidae","Motacillidae","Threskiornithidae","Apodidae","Nectariniidae","Nectariniidae","Muscicapidae","Hirundinidae","Accipitridae","Estrildidae","Sturnidae","Meropidae","Ardeidae","Muscicapidae","Charadriidae","Accipitridae","Malaconotidae","Platysteiridae","Recurvirostridae","Accipitridae","Ardeidae","Accipitridae","Malaconotidae","Rhamphastidae (Lybiinae)","Cisticolidae","Ardeidae","Campephagidae","Coliidae","Ploceidae","Coraciidae","Malaconotidae","Psittacidae","Estrildidae","Accipitridae","Ardeidae","Vangidae (Prionopinae)","Ploceidae","Hirundinidae","Glareolidae","Nectariniidae","Pycnonotidae","Cuculidae","Anatidae","Scolopacidae","Muscicapidae","Scolopacidae","Estrildidae","Muscicapidae","Charadriidae","Upupidae","Dromadidae","Phasianidae","Numididae","Bucerotidae","Estrildidae","Scolopacidae","Estrildidae","Cuculidae","Ardeidae","Muscicapidae","Nectariniidae","Nicatoridae","Motacillidae","Anatidae","Columbidae","Meropidae","Oriolidae","Coraciidae","Accipitridae","Pycnonotidae","Musophagidae","Ploceidae","Dicruridae","Sturnidae","Threskiornithidae","Motacillidae","Ploceidae","Ardeidae","Cisticolidae","Rhamphastidae (Lybiinae)","Ardeidae","Phoenicopteridae","Indicatoridae","Upupidae","Ploceidae","Charadriidae","Laridae","Malaconotidae","Alcedinidae","Threskiornithidae","Numididae","Corvidae","Passeridae","Ardeidae","Laniidae","Estrildidae","Cuculidae","Laniidae","Phoenicopteridae","Indicatoridae","Ploceidae","Charadriidae","Hirundinidae","Coraciidae","Ardeidae","Podicipedidae","Accipitridae","Scolopacidae","Apodidae","Accipitridae","Accipitridae","Phalacrocoracidae","Meropidae","Glareolidae","Alcedinidae","Alcedinidae","Ardeidae","Accipitridae","Nectariniidae","Picidae","Apodidae","Columbidae","Trogonidae","Meropidae","Pycnonotidae","Pandionidae","Passeridae","Platysteiridae","Muscicapidae","Indicatoridae","Accipitridae","Estrildidae","Corvidae","Cuculidae","Alcedinidae","Viduidae","Nectariniidae","Nectariniidae","Ardeidae","Muscicapidae","Muscicapidae","Anatidae","Estrildidae","Ploceidae","Laniidae","Estrildidae","Columbidae","Rhamphastidae (Lybiinae)","Vangidae (Prionopinae)","Columbidae","Columbidae","Turdidae","Muscicapidae","Leiothrichidae","Muscicapidae","Threskiornithidae","Leiothrichidae","Indicatoridae","Platysteiridae","Bucerotidae","Caprimulgidae","Pycnonotidae","Coliidae","Rhamphastidae (Lybiinae)","Ploceidae","Muscicapidae","Muscicapidae","Ardeidae","Alcedinidae","Cisticolidae","Columbidae","Pycnonotidae","Charadriidae","Muscicapidae","Bucerotidae","Strigidae","Sturnidae","Viduidae","Ploceidae","Accipitridae","Burhinidae","Muscicapidae","Accipitridae","Anatidae","Cuculidae","Charadriidae","Scolopacidae","Cisticolidae","Phylloscopidae","Ciconiidae","Scolopacidae","Meropidae","Psitaculidae","Pycnonotidae","Ciconiidae","Fringillidae","Scotocercidae","Cuculidae","Cuculidae","Motacillidae","Ploceidae","Malaconotidae",null],["species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","species","hybrid","species","species","species","species","species","species","species","species","species",null],[189,397,90,201,17,136,8,648,601,15,1,15,65,3,20,167,17,2,14,447,27,339,7,70,569,5,1,124,6,7,763,1,1,100,3,261,500,5,82,160,16,19,1,12,6,4,251,13,13,39,1,2,3,518,892,15,17,15,1,6,9,113,11,10,3,49,4,1,4,1,2,88,1,1,376,115,5,2,662,118,370,43,3,3,25,49,898,7,1,2,197,41,334,198,93,4,27,16,3,2,6,361,234,386,22,833,112,32,9,10,92,4,3,3,32,5,113,194,38,7,13,4,297,381,6,46,1,1,18,123,3,6,13,58,25,1,1,48,352,1,720,72,172,1,23,2,36,19,60,38,4,363,3,9,94,1,4,89,39,405,462,181,51,744,1,1,3,1,7,114,258,2,22,4,1,637,486,2,9,32,212,20,423,741,82,15,42,1,107,1,140,3,592,5,14,227,1,7,618,7,12,133,14,106,3,257,4,163,26,587,2,8,112,54,1,431,3139]],"container":"<table class=\"compact\">\n <thead>\n <tr>\n <th>taxonID<\/th>\n <th>vernacularName<\/th>\n <th>scientificName<\/th>\n <th>family<\/th>\n <th>taxonRank<\/th>\n <th>nbSightings<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"dom":"Bfrtip","columnDefs":[{"className":"dt-right","targets":5}],"order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true}},"evals":[],"jsHooks":[]}</script>
The temporal coverage is from 2020-05-19 to 2021-05-25.
- The surveys were designed by Raphaël Nussbaumer, Kirao Lennox and Colin Jackson
- The logistics were organized by Kirao Lennox
- The surveys were performed by Daniel Kazungu, Juma Badi, Kibwana Ali, Saddam Kailo and Mohammed Ali
- The data was collected, registered, cleaned, formated for GBIF and uploaded by Raphaël Nussbaumer
The Kenyan coast was once a large continuous forest called the Northern Zanzibar-Inhambane coastal forest mosaic, of which Arabuko-Sokoke Forest is the largest remainder of today. Extensively studied, this forest is an area of high endemism and was therefore gazetted as a National Park in the late 1980s. Since then, it has benefited from a hard protection from deforestation and human influence. However, the surrounding habitat has been strongly affected by human and agricultural extensions on what used to be forest land.
On the other side of our study area, Mida Creek is a 580 ha tidal marine multi-habitat ecosystem fringed with a diverse assemblage of mangrove species (Ceriops tagal, Rhizophora rnucronata, Bruguiera gyrnnorrhiza, Avicennia marina, Sonneratia alba and Xylocarpus benadirensis).
Surveys in this area allow us to study the distribution and abundance of common species not necessarily restricted to a specific habitat (such as forest or mangrove), as well as their association with certain habitats.
The transects were defined to cover all habitat types between Arabuko-Sokoke Forest, Mida Creek and the coast. They were designed such that the habitat remains relatively homogeneous during each 1hr survey (i.e. along the forest edge or mangrove edge). In addition, each survey starts and finishes near a main road to facilitate access and early start (6am). See for a map of the transects.
- Each survey is performed by 2 persons.
- Each survey is designed to last 1 hour, covering a transect of 1km.
- During a survey, each bird species seen and/or heard is recorded once upon the first encounter (i.e., no count data, just presence/absence)
- The data is collected with the Birdlasser app, allowing to record the GPS location of the observer at the moment of the observation (i.e., not the bird), the exact time of observation (date and hour) as well as any additional comment.
- Surveys can be paused if interrupted due to heavy rain or interaction with land owners, for instance. This information is recorded in the
dynamicPropertiesandeventRemarkscolumns inevents. - Surveys are performed in clusters of 4, starting at 6am up to 10am. Some remote transects (e.g. Kiperwe Island) required more time, thus surveys were performed until 12pm.
- The Birdlasser data is then exported in CSV format, collected on A Rocha infrastructure and available at
/data/birdlasser_files.
Quality control is performed in the Rmarkdown script Processe2GBIF.rmd.
Protocol Ok Surveys were discarded if the protocol was not properly followed. This happened mainly at the beginning, before the guides were fully trained. We also deleted surveys when the rain lasted longer than 30 minutes.
Spatial error
Phone GPS errors or sightings entered later at wrong locations were manually identified by plotting all sightings on a map. These locations were interpolated linearly between the surrounding sightings of the same survey.
The column georeferenceVerificationStatus indicates if such interpolation was performed and georeferenceRemarks provides the original coordinate.
Species list
All species recorded were manually verified by Raphaël Nussbaumer, Colin Jackson and checked with the guides by Kirao Lennox.
The spreadsheet species_lists_validation.xlsx was used to record the status (see table below) of each species. In general, each specie was either validated or flagged with an error code. Some errors could be corrected by providing the Equivalent specieID (e.g., taxonomic issue).
| Status code | Description |
|---|---|
| Unknown | Unsure if it is an error or not. |
| Error--certain | Erroneous species with unknown origin (typo, identification, taxonomy). |
| Error--typo | Typing error on the phone. Corrected when possible with Equivalent specieID. |
| Error--taxonomy | Issues with taxonomy (old/new name, split/merge, duplicate specieID etc…). ALWAYS enter Equivalent specieID. |
| Error--probable | Possible species in the area but not sufficiently confident in the identification. Entry will be removed. See individual comments. |
| Valid--known | Species known to occur here. |
| Valid--confirmed | Uncommon/rare species confirmed by Mida guides. See individual comments. |
| Valid--likely | Uncommon species but probable enough to keep the data. |
The events data was cleaned accordingly: kept if valid, changed to the Equivalent specieID or deleted if erroneous. The status code and original specieID were recorded in events under the columns identificationVerificationStatus and identificationRemarks.
All the processing steps from the original Birdlasser datafile to the GBIF formatted file are described in the Rmarkdown script Processe2GBIF.rmd.