get_florabank_observations: Get all validated observations for one or more taxa from the...

In inbo/inbodb: Connect to and Retrieve Data from Databases on the INBO Server

Get all validated observations for one or more taxa from the florabank database

Description

This function takes as input a character vector with one or more names of species either as scientific names and/or Dutch names. By default (fixed = FALSE), partial matching will be used (the names are prepended and appended with %). The function queries the florabank, and returns a dataframe with observation level information about the matching taxa.

Usage

get_florabank_observations(connection, names, fixed = FALSE, collect = FALSE)

Arguments

connection	A connection to the florabank database. See the example section for how to connect and disconnect to the database.
names	Default missing. A character vector with scientific names and/or Dutch names. If fixed = TRUE, character strings are matched exactly and scientific names must include authorship in order to match.
fixed	Logical. If TRUE, names is to be matched as is (no partial matching) .
collect	If FALSE (the default), a remote tbl object is returned. This is like a reference to the result of the query but the full result of the query is not brought into memory. If TRUE the full result of the query is collected (fetched) from the database and brought into memory of the working environment.

Value

A dataframe with the following variables: NaamNederlands, NaamWetenschappelijk, AcceptedNaamWetenschappelijk, Bron, BeginDatum, EindDatum, Hok, Toponiem, CommentaarEvent, CommentaarWaarneming, EventID, X_event, Y_event, X_waarneming, Y_waarneming

See Also

Other florabank: get_florabank_taxon_ifbl_year(), get_florabank_traits()

Examples

## Not run: 
# code can only be run if a connection to the database is possible
library(inbodb)
# connect to florabank
db_connectie <- connect_inbo_dbase("D0152_00_Flora")

# query and collect the data using scientific name
succprat1 <-	get_florabank_observations(db_connectie,
names = 'Succisa pratensis Moench', collect = TRUE)

# the same species but using Dutch name
succprat2 <-	get_florabank_observations(db_connectie,
names = 'Blauwe knoop', collect = TRUE)

# providing both a Dutch name and scientific name will not duplicate records
# if they are the same species
succprat3 <- get_florabank_observations(db_connectie,
names = c("Succisa pratensis Moench", "Blauwe knoop"), collect = TRUE)

all.equal(succprat1, succprat2)
all.equal(succprat1, succprat3)

# passing dutch names and scientific names for different species
# is possible (records for each species is returned)
myspecies1 <- get_florabank_observations(db_connectie,
names = c('Succisa pratensis Moench', 'Gevlekte orchis'), collect = TRUE)

# passing multiple dutch names
myspecies2 <- get_florabank_observations(db_connectie,
names = c('Gevlekte orchis', 'Blauwe knoop'),
collect = TRUE)

all.equal(myspecies1, myspecies2)

# using default for collect will return a lazy query
# fixed = TRUE for exact matches only
myspecies3 <-	get_florabank_observations(db_connectie,
names = c('Succisa pratensis Moench', 'Gevlekte orchis'),
fixed = TRUE)

# to collect the data for a lazy query you can also use the collect()
# function:
myspecies3 <- dplyr::collect(myspecies3)

# disconnect from florabank
dbDisconnect(db_connectie)

## End(Not run)

inbo/inbodb documentation built on Feb. 21, 2025, 9:04 a.m.