In lifewatch/lwdataexplorer: Access to data from the LifeWatch Data Explorer

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  warning = FALSE,
  message = FALSE
)

Data on CTD-profile data from LifeWatch sampling campaigns in the Belgian part of the North Sea.

• Partners: Flanders Marine Institute (VLIZ)
• Period: since April 2001
• Geographical coverage: Belgian Exclusive Economic Zone
• Taxonomic coverage: Abiotic data only
• Moratorium: None
• Data quality: Proof-of-concept

How to interpret this dataset

Query options

• Timeframe: Starting and stopping date for the query.
• Stations: Name or code of sampling station or receiver code.
• Bins: Number of measurements in a certain depth bin.

Available columns

• Station: Name or code of sampling station or receiver code.
• CastId: Unique identifier to specify a single CTD-cast.
• Depth: Bottom depth to surface from echosounder 200Hz in m.
• Status: An identifier to specify whether a specific measurement was taken in the up-cast, the down-cast, near the bottom, or during the calibration-phase at the surface.
• Latitude: Center latitude in decimal degrees, WGS84.
• Longitude: Center longitude in decimal degrees, WGS84.
• Time: Time in UTC, beginning of sample timeperiod.
• Obs3+: Turbidity measured by the CTD (expressed in NTU)
• AltM: Altimetry measured by the CTD (expressed in m).
• Par: Photosynthetic Active Radiation.
• FIECO-AFL: Fluorescence measured by the CTD (expressed in mg/m³).
• Oxigenvoltage: Oxygen measured by the CTD (expressed in V).
• Sbeox0Mg/L: Oxygen measured by CTD (expressed in mg/L).
• Sbeox0PS: Oxygen percentage measured by CTD.
• PrdM: Pressure measured by the CTD (expressed in db).
• Temperature: Temperature of air or the water body, expressed in degrees Celcius.
• C0uS/cm: Conducitivity of the water body, expressed in ms/cm.
• Salinity: Salinity of the water body, expressed in PSU.
• Soundspeed: The velocity of sound through the water body, expressed in m/s.
• Density: Calculated densities of zooplankton expressed in specimens/m³, by using the count, fraction, volumeM or volumeC.
• DescSpeed: The speed by which the CTD-carroussel was winched through the water column, expressed in m/s.
• Flag: A quality flag associated with a certain measurement.

Abstract

# Get the abstract and/or description from IMIS and print here
library(jsonlite)

dasid <- fromJSON("https://www.vliz.be/en/imis?module=dataset&dasid=4686&show=json")

abstract <- dasid[["datasetrec"]][["EngAbstract"]]
description <- dasid[["datasetrec"]][["EngDescr"]]

if (is.null(abstract) & is.null(description)){

} else if(is.null(abstract) & !is.null(description)){
  out <- description
} else if(!is.null(abstract) & is.null(description)){
  out <- abstract
} else if(!is.null(abstract) & !is.null(description)){
  out <- paste0(abstract, "</br>", description)
}

cat(out)

How to cite these data

library(jsonlite)

# Set base url
url <- "https://www.vliz.be/en/imis?module=dataset&dasid=4686"
dasid <- fromJSON(paste0(url, "&show=json"))

# Build citation. Get active DOI.
doi <- dasid[["dois"]]
doi <- subset(doi, doi$CurrentDOI == 1)$DOI
doi <- paste0("https://doi.org/", doi)
citation <- dasid[["datasetrec"]][["Citation"]]
citation <- paste0("> ", citation, " ", doi, 
                   ". Accessed through the LifeWatch Data Explorer / lwdataexplorer R package.")

# Get license
license <- dasid[["datasetrec"]][["AccConstrDisplay"]]

cat(citation)

cat(paste0("<b>Availability:</b>", license))

Please acknowledge as: This work makes use of the LifeWatch observation data and infrastructure (provided by VLIZ) funded by Research Foundation - Flanders (FWO) as part of the Belgian contribution to LifeWatch.

These data are also available in the R language with the lwdataxplorer package.

lifewatch/lwdataexplorer documentation built on Aug. 24, 2024, 12:35 a.m.