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

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

Biodiversity data on microplankton in the Belgian part of the North Sea

• Partners: Flanders Marine Institute (VLIZ)
• Period: since May 2017
• Geographical coverage: Belgian Exclusive Economic Zone
• Taxonomic coverage: Microplankton, being a substantial part of phytoplankton. Find the complete list in this sheet
• Moratorium: None
• Data quality: Calibrated/Validated

How to interpret this dataset

Query options

• Timeframe: Starting and stopping date for the query.

Available columns

• Tripaction: Unique identifier to recognize actions taken aboard the RV Simon Stevin.
• Time: Time in UTC, beginning of sample timeperiod.
• Station: Name or code of sampling station or receiver code.
• Longitude: Center longitude in decimal degrees, WGS84.
• Latitude: Center latitude in decimal degrees, WGS84.
• Fluid Volume Imaged (ml): Total volume of subsample processed with the FlowCAM in mililitres.
• Sample Volume (ml): Total volume of the water sample in mililitres.
• Volume Filtered (l): Total volume of water filtered through the Apstein net in mililitres.
• Sample Dilution Factor: Dilution factor of the processed sample to obtain Particles Per Used Image (PPUI). Values between 1.10 to 1.20.
• Taxon: Taxonomic group of organisms or group of artefacts.
• Count: The exact number of specimens counted.
• Total Count: The exact number of specimens counted in the sample.
• Density (cell/l): Number of specimens per litre¹.
• ActionType: The type of sampling equipment.
• Project: Project in charge of receiver deployments.

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=4688&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)

Further information can be found in this link or in a Data Paper: LifeWatch observatory data: phytoplankton observations in the Belgian Part of the North Sea.

At the moment, corrections are being made to the FlowCAM dataset and pipeline. Most up-to-date information on sampling or processing protocols and taxonomic information of the classes used during validations can be found in the following links:

• Sampling and processing protocols
• Taxonomic information

How to cite these data

library(jsonlite)

# Set base url 5251 4688
url <- "https://www.vliz.be/en/imis?module=dataset&dasid=4688"
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.

¹ The formula linked in the datapaper that describes these data is not used anymore. The corrected formula used during the aggregations is:

Density = ConcentrationSample x SampleVolume(L) / VolumeFiltered(L)

Density = Count x SampleVolume(L) / FluidVolumeImaged(L) x VolumeFiltered(L) x SampleDilutionFactor

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