softcoral_SQuads: Sample Quadrat Data (0.6m by 0.9m)
In quadcleanR: Cleanup and Visualization of Quadrat Data

softcoral_SQuads

R Documentation

Sample Quadrat Data (0.6m by 0.9m)

Description

A data_frame that can be used with the Simple Cleaning Quadrat Data and the Cleaning and Cropping Quadrat Data vignettes 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 (0.9m by 0.6m) which were randomly annotated with 54 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.

Usage

softcoral_SQuads

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.