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

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lwdataexplorer

Access to LifeWatch Belgium data hosted by the Flanders Marine Institute (VLIZ) in R.

See the package website: https://lifewatch.github.io/lwdataexplorer/

Installation

You can install the development version of deleteme from GitHub using devtools:

# install.packages("devtools")
devtools::install_github("lifewatch/lwdataexplorer", build_vignettes = TRUE)

Usage

The package lwdataexplorer retrieves biodiversity, environmental or genetic data from the projects supported by LifeWatch Belgium. These data is also available to explore and download through the LifeWatch Data Explorer: an R Shiny application that allows you to check and download data from your browser.

You can find more information about these projects and the LifeWatch Data Explorer in this link: - https://www.lifewatch.be/en/lifewatch-data-explorer

There is a function for each specific data type. For instance, to retrieve data from the moonitoring buoy on the Belgian Part of the North Sea:

library(lwdataexplorer)
library(tibble) # only for visualizing

df <- getBuoyData("2021-03-19", "2021-04-21", "All")

as_tibble(df)

Note that the functions naming includes always the get word, followed by the data type.

# Functions available in the package
ls("package:lwdataexplorer")

Query parameters

To find more information about the query parameters you can check the help page of each function which include some basic examples. For example, to see the help page of the function that retrieves data from the European Tracking Network (ETN):

# Open the help page and go over the examples
?getEtnData()

Data under moratorium

Some data types are temporarily under embargo due to the project requirements. To help you to know if the query you are applying was restricted, the query parameters are always printed in the console. If the query parameters you requested were restricted on the server side, a warning will be raised and both your query parameters and those applied in the server will be printed in the console.

The example below tries to request some data from the Meetnet Vlaams Banken (MVB). However, without an account some restrictions are applied: (1) parameter is 'Tide TAW', (2) Time grouping is day or hour and (3) dates are only between the last 30 days.

# This will raise a warning
mvb <- getMvbData("2020-01-01", "2020-12-31", parameters = 'All', 
                  stations = "All", by = "10min", calc = "none", 
                  params = TRUE)

Get data and query parameters in a list

You can request to get the parameters applied in the server by setting the argument params = TRUE. The get functions will return a list with both the data and another list with the query parameters applied in the server

# Request data but with parameters this time
data_with_params <- getBuoyData("2021-03-19", "2021-04-21", "All", params = TRUE)

# Check object type
class(data_with_params)

# What are the elements of the list?
names(data_with_params)

# Get query parameters as a list
data_with_params$par

Wrapper functions

Besides the functions that start with get, you can use the lwdata function. This is a wrapper for all the other get functions. You have to provide the data type as an argument and all the other query parameters for the specific data type. Find more info with ?lwdata()

For instance, You can request the list of ETN projects with its specific function listETNprojects() or using lwdata():

etn <- lwdata('listETNprojects')

as_tibble(etn)

Boost performance

If you are working in one of the LifeWatch Belgium RStudio server, for example https://rstudio.lifewatch.be/ or https://rstudio.vsc.lifewatch.be, you can make your queries run faster. For more information please contact the package maintainer to discuss permissions and configuration.

More information

Issues

If you find any problems please raise a new issue or contact the package maintainer:

# Run once the package is installed
maintainer("lwdataexplorer")

Citation

Please cite this software as:

cat(paste0("> ", citation("lwdataexplorer")$textVersion))

You must also cite the datasets retrieved by the lwdataexplorer. You can find more information and their individual citations in the vignettes. The vignettes are available online at: https://lifewatch.github.io/lwdataexplorer/articles/

License

See the license file.

packageDescription("lwdataexplorer", fields="License")

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