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")
#> - Query mode: Post request to OpenCPU server
#> No encoding supplied: defaulting to UTF-8.
#> - Query parameters:
#> - daterange: c("2021-03-19", "2021-04-21")
#> - stationlist: All
#> - type: Buoy data
as_tibble(df)
#> # A tibble: 2,384 x 20
#> Station Time Latitude Longitude `Air temperature~ `AtmPress(mBar)`
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 Buoy in Spu~ 2021-03-1~ 51.2 2.95 6.35 1022.
#> 2 Ostend Rese~ 2021-03-1~ 51.2 2.92 6.10 1019.
#> 3 Spuikom Slu~ 2021-03-1~ 51.2 2.94 NA NA
#> 4 Spuikom Slu~ 2021-03-1~ 51.2 2.94 NA NA
#> 5 Buoy in Spu~ 2021-03-1~ 51.2 2.95 5.66 1023.
#> 6 Ostend Rese~ 2021-03-1~ 51.2 2.92 5.56 1019.
#> 7 Buoy in Spu~ 2021-03-1~ 51.2 2.95 5.40 1024.
#> 8 Ostend Rese~ 2021-03-1~ 51.2 2.92 5.25 1019.
#> 9 Spuikom Slu~ 2021-03-1~ 51.2 2.94 NA NA
#> 10 Spuikom Slu~ 2021-03-1~ 51.2 2.94 NA NA
#> # ... with 2,374 more rows, and 14 more variables:
#> # Avg Wind direction (deg) <dbl>, Avg Wind speed (m/s) <dbl>,
#> # RelHumidity (%) <dbl>, SolarEnergy (W/m²) <dbl>, Voltage (V) <dbl>,
#> # Level Harbour (mTAW) <dbl>, Level Spuikom (mTAW) <dbl>, Rain15 (mm) <dbl>,
#> # NO3 (ppb) <dbl>, SiO2 (ppb) <dbl>, Rain (mm) <dbl>, DO (mg/l) <int>,
#> # Salinity (PSU) <int>, Water temperature (°C) <int>Note that the functions naming includes always the get word, followed by the data type.
# Functions available in the package
ls("package:lwdataexplorer")
#> [1] "getBatsData" "getBuoyData" "getCpodData" "getEtnData"
#> [5] "getFlowcamData" "getMvbData" "getStationData" "getUnderwayData"
#> [9] "getUvaBirdData" "getZooscanData" "listEtnProjects" "listMvbStations"
#> [13] "listUvaTags" "lwdata" "lwdata2"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)
#> - Query mode: Post request to OpenCPU server
#> No encoding supplied: defaulting to UTF-8.
#> Warning in lw_warning_empty(): No data returned
#> - Your query:
#> - daterange: c("2020-01-01", "2020-12-31")
#> - type: MVB data
#> - stations: All
#> - calc: none
#> - binSize: 10min
#> - parameters: All
#> - Server query:
#> - daterange: c("2021-11-03", "2020-12-31")
#> - type: MVB data
#> - stations: All
#> - calc: none
#> - binSize: day
#> - parameters: Tide TAW
#> Warning in lw_compare_parameters(input, par): The query applied on the server differ from the parameters you used.
#> Hint: You may need an account to fully access the data under moratorium.
#> Hint: Request access at: https://rshiny.lifewatch.be/account?p=registerGet 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)
#> - Query mode: Post request to OpenCPU server
#> No encoding supplied: defaulting to UTF-8.
#> - Query parameters:
#> - daterange: c("2021-03-19", "2021-04-21")
#> - stationlist: All
#> - type: Buoy data
# Check object type
class(data_with_params)
#> [1] "list"
# What are the elements of the list?
names(data_with_params)
#> [1] "mdf" "par"
# Get query parameters as a list
data_with_params$par
#> $daterange
#> [1] "2021-03-19" "2021-04-21"
#>
#> $stationlist
#> [1] "All"
#>
#> $type
#> [1] "Buoy data"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')
#> - Query mode: Post request to OpenCPU server
#> No encoding supplied: defaulting to UTF-8.
as_tibble(etn)
#> # A tibble: 192 x 2
#> name type
#> <chr> <chr>
#> 1 2004_Gudena network
#> 2 2011_Loire network
#> 3 2011_Warnow network
#> 4 2013_Foyle network
#> 5 2013_Maas network
#> 6 2014_Nene network
#> 7 2015_PhD_Gutmann_Roberts network
#> 8 2016_Diaccia_Botrona network
#> 9 2017_Fremur network
#> 10 2019_Grotenete network
#> # ... with 182 more rowsBoost 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:
Francisco Hernandez, Nick Dillen and Salvador Fernández-Bejarano (2021). lwdataexplorer: Access to data from the LifeWatch Data Explorer. R package version 0.0.0.9000. https://lifewatch.github.io/lwdataexplorer/
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")
#> [1] "MIT + file LICENSE"