rnbn tutorial

for v1.0.3

The National Biodiversity Network (NBN) is an on-line repository for biodiversity data from the UK. At the time of writing, it contains over 100 million species records in over 900 datasets. Data can be accessed via web-services provided by the Gateway web-site (see documentation)

This package provides methods to interact with the NBN's web services and get species records and other supporting information.

Registering with the NBN gateway and logging in

To use data from the NBN gateway you must first register. This is an easy process and can be done by visiting https://data.nbn.org.uk/User/Register. Once registered you will be sent an email to verify your address, once verified you are ready to use rnbn.

When using rnbn you will be asked to login the first time you attempt to access occurrence data. Once logged in you will stay logged in for the remainder of your R session.

Installation

install.packages("rnbn")

Or development version from GitHub

install.packages("devtools")
devtools::install_github("ropensci/rnbn")
library("rnbn")

Usage

Getting species occurrence records

The getOccurrences function gets a data.frame of species occurrence records from the NBN Gateway. Columns include name, TVK, date and location of the observation as a minimum, and may include other columns depending what has been submitted by the data providers and what access they allow. The first time this function is used in an R session you will be asked to enter your username and password at the console. An alternative method for logging in is to use the nbnLogin function (see below)

The minimum information required to request species occurrences from the NBN Gateway is one of the following: a Taxon Version Key (TVK), a grid reference or the name of a species group.

Independent of which method you use there are three messages that will appear in your console:

# I could log in like this...
# nbnLogin(username = 'myUsername', password = 'myPassword')
# ...or let getOccurrences prompt me. The latter is more
# secure as I dont have to include my password in my scripts

Request occurrence data using taxon version key

occ <- getOccurrences(tvks = 'NBNSYS0000002010', acceptTandC = TRUE)
#> Requesting batch 1 of 1 
#> Requesting data providers' information

The first message returned to console details the batch number being processed. rnbn breaks down a data request into batches so that it does not overload the system. This is also useful for monitoring progress. The second message tells us that the function is retrieving the data providers for the data it just collected. These can be silenced by setting silent = TRUE. The third message is a warning that highlights the terms and conditions associated with using data from the NBN gateway. It is important that you read these terms and conditions since by using the rnbn package you are accepting them. This warning can be silenced by setting acceptTandC = TRUE.

Using Taxon Version Keys (TVKs)

TVKs are 16-character strings of (usually, upper-case) letters and numbers. For example, "NBNSYS0000007111".

TVKs can be found using the function getTVKquery. This function will take the name of a species and attempt to match it to a TVK using the NBN's search feature. For example if we wanted the TVK for "badger" (Meles meles):

Search for taxon information using the query 'badger'

dt <- getTVKQuery(query = "badger")

Display two columns of the data 'ptaxonVersionKey' and 'name'

dt[,c('ptaxonVersionKey','name')]
#>   ptaxonVersionKey            name
#> 1 NHMSYS0000080191          Badger
#> 2 NBNSYS0000013055     Badger Flea
#> 3 NHMSYS0000545919   a Badger flea
#> 4 NHMSYS0000080191 Eurasian Badger

You will notice that "Badger" and "Eurasian Badger" have the same "ptaxonVersionKey" (the 'p' stands for preferred). This is because the terms are synonyms, both referring to Meles meles (which would also share the same ptaxonVersionKey). By using this TVK in the getOccurrence function it ensures that you get data for all synonyms. If you don't wish to include synonyms you can instead use the TVK given in the column "taxonVersionKey".

The following example will get all publicly available observations of Tropidia scita from all datasets and for any date:

Get species TVK, using 'top = TRUE' returns only the best match

dt <- getTVKQuery(query = "Tropidia scita",
                  top = TRUE)

Retrieve data from NBN using a TVK

occ <- getOccurrences(tvks = dt$ptaxonVersionKey,
                      silent = TRUE,
                      acceptTandC = TRUE)

Print the first few rows and a selection of columns

occ[1:10,c("pTaxonName", "startDate",
           "latitude", "longitude")]
#>        pTaxonName  startDate latitude longitude
#> 1  Tropidia scita 1985-01-01 51.38139 -1.211093
#> 2  Tropidia scita 2005-06-28 52.72542  1.621644
#> 3  Tropidia scita 2005-06-27 52.72740  1.615881
#> 4  Tropidia scita 2005-06-28 52.72098  1.619794
#> 5  Tropidia scita 2005-06-27 52.72663  1.611374
#> 6  Tropidia scita 1985-07-01 51.14454 -1.465307
#> 7  Tropidia scita 1987-07-09 53.23143 -4.076401
#> 8  Tropidia scita 1983-06-04 52.56806 -1.189979
#> 9  Tropidia scita 1976-07-20 52.56806 -1.189979
#> 10 Tropidia scita 1975-06-20 52.56806 -1.189979

TVKs can also be found on the NBN gateway at https://data.nbn.org.uk/Taxa. Navigating to a species reveals additional information including the "Taxon Version Key"

Occurrences for more than one species can be obtained by passing a list of TVKs. Such lists can be created in two ways:

List TVKs manually

(tvks <- c("NHMSYS0000530420","NHMSYS0000530658"))
#> [1] "NHMSYS0000530420" "NHMSYS0000530658"

Retrieve a list of TVKs using the NBN search

species <- getTVKQuery('grouse')
(tvks <- unique(species$ptaxonVersionKey))
#> [1] "NHMSYS0000530420" "NHMSYS0000530658"

Using species group

Data can be retrieved by specifying a species group. Species groups are taxonomic groups that are predefined by the NBN. A list of available groups can be found using the listGroups function.

View some of the groups available

groups <- listGroups()
head(groups)
#>                        name              key
#> 1           acarine (Acari) NHMSYS0000629148
#> 2 acorn worm (Hemichordata) NHMSYS0000080031
#> 3                      alga NHMSYS0000080032
#> 4                 amphibian NHMSYS0000080033
#> 5                   annelid NHMSYS0000080034
#> 6                  archaean NHMSYS0000629143

Once you have decided which group you require the name is passed to getOccurrences in the following manner.

Retrieve data from NBN using a species group. Note this can take some time depending on the size of the species group

occ <- getOccurrences(group = 'quillwort',
                      acceptTandC = TRUE)

Filtering results

By Year

The range of years for which you want to extract data can be specified using the startYear and/or endYear parameters:

Get data for a specified species, from a specified dataset over a specified time period

head(getOccurrences(tvks = "NBNSYS0000007111",
               datasets = "SGB00001",
               startYear = 1990,
               endYear = 2006,
               silent = TRUE,
               acceptTandC = TRUE))
#>   observationID fullVersion datasetKey        surveyKey
#> 1     238422351       FALSE   SGB00001 ADS0000100000002
#> 2     238422399       FALSE   SGB00001 ADS0000100000002
#> 3     238422468       FALSE   SGB00001 ADS0000100000002
#> 4     238422577       FALSE   SGB00001 ADS0000100000002
#> 5     238423432       FALSE   SGB00001 DIPFOR0200000003
#> 6     238423523       FALSE   SGB00001 DIPFOR0200000003
#>                 sampleKey   observationKey featureID location resolution
#> 1 ADS0000100000002-SAMPLE ADS00001000005PJ    206735   SD5152        1km
#> 2 ADS0000100000002-SAMPLE ADS000010000043G    137826   SD4875        1km
#> 3 ADS0000100000002-SAMPLE ADS00001000006AH    371275   SD5151        1km
#> 4 ADS0000100000002-SAMPLE ADS00001000007AC    137824   SD4869        1km
#> 5 DIPFOR0200000003-SAMPLE DIPFOR0200000A9F    320779   TM4667        1km
#> 6 DIPFOR0200000003-SAMPLE DIPFOR02000001K5    230293   TM4974        1km
#>    taxonVersionKey pTaxonVersionKey     pTaxonName  pTaxonAuthority
#> 1 NBNSYS0000007111 NBNSYS0000007111 Tropidia scita (Harris, [1780])
#> 2 NBNSYS0000007111 NBNSYS0000007111 Tropidia scita (Harris, [1780])
#> 3 NBNSYS0000007111 NBNSYS0000007111 Tropidia scita (Harris, [1780])
#> 4 NBNSYS0000007111 NBNSYS0000007111 Tropidia scita (Harris, [1780])
#> 5 NBNSYS0000007111 NBNSYS0000007111 Tropidia scita (Harris, [1780])
#> 6 NBNSYS0000007111 NBNSYS0000007111 Tropidia scita (Harris, [1780])
#>    startDate    endDate sensitive absence publicAttribute dateTypekey
#> 1 1999-06-16 1999-06-16     FALSE   FALSE           FALSE          D 
#> 2 1999-06-13 1999-06-13     FALSE   FALSE           FALSE          D 
#> 3 1999-06-16 1999-06-16     FALSE   FALSE           FALSE          D 
#> 4 1999-06-18 1999-06-18     FALSE   FALSE           FALSE          D 
#> 5 2003-07-19 2003-07-19     FALSE   FALSE           FALSE          D 
#> 6 2003-07-15 2003-07-15     FALSE   FALSE           FALSE          D 
#>                     siteKey         siteName latitude longitude
#> 1                      <NA>             <NA> 53.96629 -2.740774
#> 2                      <NA>             <NA> 54.17269 -2.790416
#> 3 NBN-SITE-SGB00001-4295447 A West Lancaster 53.95730 -2.740614
#> 4                      <NA>             <NA> 54.11877 -2.789389
#> 5                      <NA>             <NA> 52.25042  1.609902
#> 6 NBN-SITE-SGB00001-4287099  Walberswick NNR 52.31187  1.658932

By Vice-county

If data from a specific vice-county is required then the VC argument can be used. This takes the name of a vicecounty, a list of which can be found using listVCs:

View some of the vice-counties available

VCs <- listVCs()
head(VCs)
#>             name identifier featureID
#> 1       Anglesey GA00034452   2583220
#> 2 Angus (Forfar) GA00034490   2583258
#> 3       Ayrshire GA00034475   2583243
#> 4     Banffshire GA00034494   2583262
#> 5   Bedfordshire GA00034430   2583198
#> 6      Berkshire GA00034422   2583190

Once you have decided the vice-county you wish to search within you can use the getOccurrence function like this:

Request data for one species from East Suffolk

occ <- getOccurrences(tvk = 'NBNSYS0000007111',
                      VC = 'East Suffolk',
                      silent = TRUE,
                      acceptTandC = TRUE)

Taxa list

It can sometimes be helpful to have a list of taxa that are recorded in a given dataset here is an example of how this can be done:

Get taxa list for the ladybird survey

taxalist <- datasetTaxa('GA000312')

A range of details are provided

names(taxalist)
#>  [1] "taxonVersionKey"      "name"                 "authority"           
#>  [4] "languageKey"          "taxonOutputGroupKey"  "taxonOutputGroupName"
#>  [7] "commonName"           "gatewayRecordCount"   "href"                
#> [10] "observationCount"     "datasetKey"           "ptaxonVersionKey"

Here are some of those species

head(taxalist$commonName)
#> [1] "2-spot Ladybird"     "10-spot Ladybird"    "Eyed Ladybird"      
#> [4] "Water Ladybird"      "Larch Ladybird"      "Cream-spot Ladybird"

Citing

To cite rnbn in publications use:


Stuart Ball & Tom August (2014). rnbn: Access NBN Data. R package version 1.0.3. https://cran.rstudio.com/package=rnbn

License and bugs

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