A data_frame that can be used with the cleaning vignette
to show how quadrat data can be cleaned to produce easy to analyze data
frames. Data was collected by the Baum Lab
and Kiritimati Field Teams. Data is the uncleaned version of data found in
Maucieri and Baum 2021. Biological Conservation. doi:10.1016/j.biocon.2021.109328
The data are from photo quadrats (1m by 1m) which were randomly annotated
with 100 random points each. At each of these annotated points, the substrate
was identified. Photo quadrats were collected on Kiritimati Island in the
Republic of Kiribati and document coral cover over time and space. The
annotations and output of the data_frame were produced using
CoralNet and all annotations were done manually,
by trained researchers.
Format
A data_frame with 135 columns, which are:
- Image.ID
Photo quadrat image ID from CoralNet.
- Image.name
The photo quadrat image name.
- Annotation.status
If the quadrat has been completely annotated, or if there are more annotations to occur.
- Points
The total number of annotation points in the quadrat.
- AcCor
Percent of total annotated points annotated for Acropora (corymbose morphology).
- AcDig
Percent of total annotated points annotated for Acropora (digitate morphology).
- Acr_arb
Percent of total annotated points annotated for Acropora (arborescent morphology).
- Acrop
Percent of total annotated points annotated for Acropora.
- AcroTab
Percent of total annotated points annotated for Acropora (tabulate morphology).
- Astreo
Percent of total annotated points annotated for Astreopora.
- B_Acr_arb
Percent of total annotated points annotated for bleached Acropora (arborescent morphology)
- B_Acro
Percent of total annotated points annotated for bleached Acropora.
- B_Astre
Percent of total annotated points annotated for bleached Astreopora.
- BAT
Percent of total annotated points annotated for bleached Acropora (tabulate morphology).
- B_Cosc
Percent of total annotated points annotated for bleached Coscinarea.
- B_Echin
Percent of total annotated points annotated for bleached Echinophyllia.
- B_FavHal
Percent of total annotated points annotated for bleached Favites halicora.
- B_Favia
Percent of total annotated points annotated for bleached_Favia.
- B_FaviaM
Percent of total annotated points annotated for bleached Favia matthaii.
- B_FaviaS
Percent of total annotated points annotated for bleached Favia speciosa.
- B_FaviaSt
Percent of total annotated points annotated for bleached Goniastrea stelligera.
- B_Favites
Percent of total annotated points annotated for bleached Favites.
- B_FavPent
Percent of total annotated points annotated for bleached Favites pentagona.
- B_Fung
Percent of total annotated points annotated for bleached Fungia.
- BGard
Percent of total annotated points annotated for bleached Gardineroseris.
- B_GonEd
Percent of total annotated points annotated for bleached Goniastrea edwardsi.
- B_Herpo
Percent of total annotated points annotated for bleached Herpolitha.
- B_HYDNO
Percent of total annotated points annotated for bleached Hydnophora.
- B_HyExe
Percent of total annotated points annotated for bleached Hydnophora exesa.
- BlAcro-Cor
Percent of total annotated points annotated for bleached Acropora (corymbose morphology).
- B_Lepta
Percent of total annotated points annotated for bleached Leptastrea.
- B_Lepto
Percent of total annotated points annotated for bleached Leptoseris.
- Blisop
Percent of total annotated points annotated for bleached Isopora.
- B_Lobo
Percent of total annotated points annotated for bleached Lobophyllia.
- BlTurbFol
Percent of total annotated points annotated for bleached Turbinaria (foliose morphology).
- B_MOEN
Percent of total annotated points annotated for bleached Montipora (encrusting morphology).
- B_MOFO
Percent of total annotated points annotated for bleached Montipora (foliose morphology).
- B_Monta
Percent of total annotated points annotated for bleached Montastraea.
- B_Monti
Percent of total annotated points annotated for bleached Montipora.
- B_Oxyp
Percent of total annotated points annotated for bleached Oxypora.
- B_Paly
Percent of total annotated points annotated for bleached Palythoa.
- B_PaveDUER
Percent of total annotated points annotated for bleached Pavona duerdeni.
- B_Pavona
Percent of total annotated points annotated for bleached Pavona.
- B_PEYDO
Percent of total annotated points annotated for bleached Pocillopora eydouxi.
- B_Plat
Percent of total annotated points annotated for bleached Platygyra.
- B_PMEAN
Percent of total annotated points annotated for bleached Pocillopora meandrina.
- B_Pocillo
Percent of total annotated points annotated for bleached Pocillopora.
- B_Porit
Percent of total annotated points annotated for bleached Porites.
- B_Psam
Percent of total annotated points annotated for bleached Psammocora.
- B_PVAR
Percent of total annotated points annotated for bleached Pavona varians.
- B_Sando
Percent of total annotated points annotated for bleached Sandolitha.
- B_UnkCoral
Percent of total annotated points annotated for bleached unknown hard coral.
- Cirr
Percent of total annotated points annotated for Cirrhipathes.
- COSC
Percent of total annotated points annotated for Coscinaraea.
- ECHIN
Percent of total annotated points annotated for Echinophyllia.
- Fav
Percent of total annotated points annotated for Favites.
- FavHal
Percent of total annotated points annotated for Favites halicora.
- Favites halicora
Percent of total annotated points annotated for Favia.
- FaviaM
Percent of total annotated points annotated for Dipsastraea matthaii.
- FaviaS
Percent of total annotated points annotated for Favia speciosa.
- FaviaSt
Percent of total annotated points annotated for Favia stelligera.
- FavPent
Percent of total annotated points annotated for Favites pentagona.
- Fung
Percent of total annotated points annotated for Fungia.
- Gardin
Percent of total annotated points annotated for Gardineroseris.
- GonEd
Percent of total annotated points annotated for Goniastrea edwardsi.
- Herpo
Percent of total annotated points annotated for Herpolitha.
- HYDNO
Percent of total annotated points annotated for Hydnophora.
- HyExe
Percent of total annotated points annotated for Hydnophora exesa.
- Isopora
Percent of total annotated points annotated for Isopora.
- Lepta
Percent of total annotated points annotated for Leptastrea.
- Lepto
Percent of total annotated points annotated for Leptoseris.
- Lobo
Percent of total annotated points annotated for Lobophyllia.
- *MOEN
Percent of total annotated points annotated for Montipora (encrusting morphology).
- *MOFO
Percent of total annotated points annotated for Montipora (foliose morphology).
- Monta
Percent of total annotated points annotated for Montastraea.
- Monti
Percent of total annotated points annotated for Montipora.
- Oxyp
Percent of total annotated points annotated for Oxypora.
- Paly
Percent of total annotated points annotated for Palythoa.
- PaveDUER
Percent of total annotated points annotated for Pavona duerdeni.
- Pavon
Percent of total annotated points annotated for Pavona.
- PEYDO
Percent of total annotated points annotated for Pocillopora eydouxi.
- Plat
Percent of total annotated points annotated for Platygyra.
- Plero
Percent of total annotated points annotated for Plerogyra.
- PMEAN
Percent of total annotated points annotated for Pocillopora meandrina.
- Pocill
Percent of total annotated points annotated for Pocillopora.
- Porit
Percent of total annotated points annotated for Porites.
- Psam
Percent of total annotated points annotated for Psammocora.
- PVAR
Percent of total annotated points annotated for Pavona varians.
- Sando
Percent of total annotated points annotated for Sandolitha.
- Tuba
Percent of total annotated points annotated for Tubastrea.
- TURB
Percent of total annotated points annotated for Turbinaria.
- UnkCoral
Percent of total annotated points annotated for unknown hard coral.
- ANEM
Percent of total annotated points annotated for sea anemone.
- B_Clad
Percent of total annotated points annotated for bleached Cladiella.
- B_Sinu
Percent of total annotated points annotated for bleached Sinularia.
- Clad
Percent of total annotated points annotated for Cladiella.
- EncBry
Percent of total annotated points annotated for encrusting Bryozoan.
- EUR
Percent of total annotated points annotated for sea urchin.
- HYDCO
Percent of total annotated points annotated for Hydrocoral.
- Hydra
Percent of total annotated points annotated for Hydroid.
- Mille
Percent of total annotated points annotated for Millepora.
- MOBI
Percent of total annotated points annotated for bivalves.
- Sarco
Percent of total annotated points annotated for Sarcophyton.
- SECO
Percent of total annotated points annotated for sea cucumber.
- Sinu
Percent of total annotated points annotated for Sinularia.
- Sponge
Percent of total annotated points annotated for sponge.
- Stylas
Percent of total annotated points annotated for Stylaster.
- UnkTUN
Percent of total annotated points annotated for unknown Tunicate.
- XmasW
Percent of total annotated points annotated for Christmas Tree Worm.
- ZOAN
Percent of total annotated points annotated for Zoanthid.
- B_Sarco
Percent of total annotated points annotated for bleached Sarcophyton.
- Sand
Percent of total annotated points annotated for sand.
- Sediment
Percent of total annotated points annotated for sediment.
- SCRO
Percent of total annotated points annotated for consolidated rock.
- B_Loph
Percent of total annotated points annotated for bleached Lobophytum.
- CYAN
Percent of total annotated points annotated for Cyanobacteria films.
- Loph
Percent of total annotated points annotated for Lobophytum.
- Rubble
Percent of total annotated points annotated for broken coral rubble.
- SHAD
Percent of total annotated points annotated for shadow.
- Trans
Percent of total annotated points annotated for transect hardware.
- Unc
Percent of total annotated points annotated for unclear.
- AVRA
Percent of total annotated points annotated for Avrainvillea.
- Caul
Percent of total annotated points annotated for Caulerpa.
- CCA
Percent of total annotated points annotated for crustose coraline algae.
- Dict
Percent of total annotated points annotated for Dictyota.
- DICTY
Percent of total annotated points annotated for Dictyosphaeria.
- Hali
Percent of total annotated points annotated for Halimeda.
- Lobph
Percent of total annotated points annotated for Lobophora.
- Macro
Percent of total annotated points annotated for macroalgae.
- Mdict
Percent of total annotated points annotated for Microdictyon.
- Pad
Percent of total annotated points annotated for Padina.
- Peysson
Percent of total annotated points annotated for Peyssonnelia.
- Turf
Percent of total annotated points annotated for turf algae.
- TURFH
Percent of total annotated points annotated for turf algae on hard substrate.
- Unidentified
Percent of total annotated points annotated that were unidentified.