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

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

Data on nutrients, pigments, suspended matter and secchi measurements from fixed stations on the Belgian Part of the North Sea.

• Partners: Flanders Marine Institute (VLIZ),Laboratory of Protistology and Aquatic Ecology (PAE) and Flemish Environment Agency (VMM). Former partners: Directorate Natural Environment (OD Natuur), Royal Netherlands Institute for Sea Research (NIOZ), National Oceanography Centre Southampton (NOCS), Marine Biology Research Group (MARBIOL)
• Period: since April 2001
• Geographical coverage: Belgian Exclusive Economic Zone
• Taxonomic coverage: Abiotic data only
• Moratorium: None
• Data quality: Research-grade. Pigment, nutrients and spm are subjected to an automated QC while the CTD data is not.

How to interpret this dataset

Query options

• Timeframe: Starting and stopping date for the query.
• Parameter categories: Type of parameters to request. Available: SPM, CTD, Nutrients, Secchi, Pigments.

Available columns

• Station: Name or code of sampling station or receiver code.
• Time: Time in UTC, beginning of sample timeperiod.
• Latitude: Center latitude in decimal degrees, WGS84.
• Longitude: Center longitude in decimal degrees, WGS84.

Click to see all the columns available:

• X19But_Fucoxanthin(µg/L): Concentration of 19'-butanoyloxyfucoxanthin per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); BUTAHPP1.
• X19Hex_Fucoxanthin(µg/L): Concentration of 19'-hexanoyloxyfucoxanthin {CAS 60147-85-5} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); HEXOHPP1.
• Alloxanthin(µg/L): Concentration of alloxanthin {CAS 28380-31-6} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); ALLOHPP1.
• Ammonium_NH4(µmol.N_NH4/L): Concentration of ammonium {NH4+ CAS 14798-03-9} per unit volume of the water body by filtration and colorimetric autoanalysis; AMONAAD5.
• Antheraxanthin(µg/L): Concentration of antheraxanthin {CAS 640-03-9} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); ANTHHPP1.
• Anthoxanthin(µg/L): Concentration of anthoxanthins {flavones+flavonols} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); ATHXHPP1.
• Astaxanthine(µg/L): Concentration of astaxanthin {CAS 472-61-7} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); ASTAXHP1.
• Beta_Carotene(µg/L): Concentration of beta, beta-carotene {beta-carotene CAS 7235-40-7} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); BBCAHPP1.
• Chlorophyll_a(µg/L): Concentration of chlorophyll-a {chl-a CAS 479-61-8} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); CPHLHPP1.
• Chlorophyll_b(µg/L): Concentration of chlorophyll-b {chl-b CAS 519-62-0} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); CHLBHPP1.
• Chlorophyll_c2c1(µg/L): Concentration of chlorophyll-c2 {chl-c2} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); CLC2HPP1.
• Chlorophyll_c2(µg/L): Concentration of chlorophyll-c1+c2 per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); C1C2HPP1.
• Chlorophyll_c3(µg/L): Concentration of chlorophyll-c3 {chl-c3} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); CLC3HPP1.
• Chlorophyllide_a(µg/L): Concentration of chlorophyllide-a {CAS 14897-06-4} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); CIDAHPP1.
• Conductivity(µS/cm): Electrical conductivity standard deviation of the water body by CTD, expressed in degrees µS/cm.
• CPAR: Corrected Photosynthetic Active Radiation of the water body.
• Density(kg/m3): The density of the water body, expressed in kg/m³.
• Diadinoxanthin(µg/L): Concentration of diadinoxanthin {CAS 18457-54-0} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); DIADHPP1.
• Diatoxanthin(µg/L): Concentration of diatoxanthin {CAS 31063-73-7} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); DIATHPP1.
• Echinenone(µg/L): Concentration of echinenone {CAS 432-68-8} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); ECHNHPP1.
• Fluorescence(mg/m³): Fluorescence of the water body, expressed in mg/m³.
• Fucoxanthin(µg/L): Concentration of fucoxanthin {CAS 3351-86-8} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); FUCXHPP1.
• Lutein(µg/L): Concentration of lutein {CAS 127-40-2} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); LUTNHPP1.
• Neoxanthin(µg/L): Concentration of neoxanthin {CAS 30743-41-0} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); NEOXHPP1.
• Nitrate_Nitrite(µmolN_NO3-NO2/L): Concentration of nitrates+ nitrites in the water body, expressed in µmol N_NO3-NO2/L; NTRZAAD5.
• Nitrate_NO3(µmolN_NO3/L): Concentration of nitrate in the water body, expressed in µmol N_NO3/L; ODSDM2UM.
• Nitrite_NO2(µmolN_NO2/L): Concentration of nitrites in the water body, expressed in µmol N_NO2/L; NTRIAAD5.
• OBS(NTU): Optical backscatter as turbidity of the water body, expressed in Nephelometric Turbidity Units.
• PAR: Photosynthetic Active Radiation.
• Peridinin(µg/L): Concentration of peridinin {CAS 33281-81-1} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); PERIHPP1.
• Ph: Acidity of the water body.
• Pheophorbide_a(µg/L): Concentration of phaeophorbide-a {pheophorbide-a CAS 15664-29-6} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); PBAXHPP1.
• Pheophytin_a(µg/L): Concentration of phaeophytin-a {pheophytin-a CAS 603-17-8} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); PTAXHPP1.
• Pheophytin_b(µg/L): Concentration of phaeophytin-b {pheophytin-b CAS 3147-18-0} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); PTBXHPP1.
• Phosphate_PO4(µmolP_PO4/L): Concentration of phosphate in the water body, expressed in µmol P_P04/L; PHOSAAD5.
• Prasinoxanthin(µg/L): Concentration of prasinoxanthin {CAS 94705-97-2} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); PRSXHPP1.
• Pressure(db): Pressure of the water body, expressed in decibel.
• Salinity(PSU): Salinity of the water body, expressed in Practical Salinity Units.
• Secchi_Depth(cm): Visibility in the water body by Secchi disk, expressed cm.
• Silicate_SiO4(µmolSi_SiO4/L): Concentration of silicate in the water body, expressed in µmol Si_SiO4/L; SLCAAAD5.
• SoundVelocity(m/s): The velocity of sound through the water body, expressed in m/s.
• SPAR: Surface photosynthetically Active Radiation.
• SPM(mg/l): Concentration of Suspended Particulate Matter in the water body, expressed in mg/L.
• Temperature(degC): Temperature of the water body, expressed in degrees Celcius.
• Violaxanthin(µg/L): Concentration of violaxanthin {CAS 126-29-4} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); VILXHPP1.
• Zeaxanthin(µg/L): Concentration of zeaxanthin {CAS 144-68-3} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC); ZEOXHPP1.

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)

The full methodology is described in a datapaper:

Mortelmans, J.; Deneudt, K.; Cattrijsse, A.; et al. (2019). Nutrient, pigment, suspended matter and turbidity measurements in the Belgian part of the North Sea. Scientific Data 6(1): 22. https://hdl.handle.net/10.1038/s41597-019-0032-7

How to cite these data

library(jsonlite)

# Set base url 5251 4688
url <- "https://www.vliz.be/en/imis?module=dataset&dasid=4685"
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 MARBIOL, NIOZ, NOCS, PAE, VMM and 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.