Query observation data from Meetnetten

Source: R/get_meetnetten_observations.R

This function queries the Meetnetten database for observation data (standardized counts) for a specified monitoring scheme or for all monitoring schemes within a specified species group. When no monitoring scheme or species group is specified, the observations of all monitoring schemes are returned.

get_meetnetten_observations(
  connection,
  scheme_name = NULL,
  species_group = NULL,
  collect = FALSE
)

Arguments

connection

dbconnection with the database 'S0008_00_Meetnetten' on the inbo-sql08-prd.inbo.be server

scheme_name

the name of the monitoring scheme for which you want to extract visit data. Data from multiple schemes can be selected by providing a vector with the names of the schemes.

species_group

the name of the species group for which you want to extract visit data. Data from multiple species groups can be selected by providing a vector with the names of the species groups.

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 remote tbl object (collect = FALSE) or a tibble dataframe (collect = TRUE) with following variables:

  • species_group

  • scheme

  • protocol: the protocol used

  • visit_id: unique id for a count event

  • start_date:date of the observation

  • location: the name of the location

  • sublocation: the name of the sublocation

  • not_counted: TRUE when the sublocation is not counted

  • sample_id: unique id for a count subevent (see details)

  • target_species: TRUE when the observed species is the target species, FALSE when the observed species is a secondary species (another species than the target species that can be counted with the same protocol, see details)

  • checklist_complete: whether all secondary species, defined in the monitoring scheme, are counted

  • name_nl: Dutch name of the observed species

  • scientific_name: scientific name of the observed species

  • sex: M (male), F (female), U (undefined)

  • activity: activity of the observed species

  • life_stage: live stage of the observed species

  • count: number of individuals counted

  • count_type: most of the time the number of individuals are counted (count_type = exact count), however for some monitoring schemes different type of counts are performed. Check the protocol for more information when this is the case.

  • notes: notes of the observed

  • x and y: when the Meetnetten-app is used, GPS coordinates (longitude and latitude, crs = WGS84) of each observation is recorded

Details

The species monitoring programme of Flanders (Meetnetten) consists of a series of monitoring schemes in which one or more target species are counted based on a specific protocol. Optionally, other species, that can be counted using the same protocol, can be recorded as well. When checklist_complete = TRUE, all secondary species were counted, and we can assume that the secondary species that were not recorded are absent.

Depending on the protocol, counting has to be done at the location or the sublocation level. Sublocations are, for example, different sections of a transect. For some monitoring schemes, it is necessary to record several count subevents at the location level. This is, for example, the case for the crested newt fyke count protocol, where two fykes are used per location and the counts are recorded per fyke. For every count subevent a unique sample_id is created.

The protocol of a monitoring scheme also defines for which combinations of sex, life stage, and activity type the counts have to be recorded. For example, for the crested newt fyke counts the number of female adults, male adults and juveniles (sex undefined) are counted. Another example: in the alcon blue monitoring scheme only the number of eggs are counted.

It is also important to know that counts can be recorded in the Meetnetten website or by using the Meetnetten app. When using the Meetnetten app, the GPS coordinates of all observations are recorded and the observations are assigned to a location or sublocation based on the coordinates. For example, when you record a butterfly transect count in the website, you will enter the total number of individuals per species for each section (the sublocation) of the transect. When you use the app, you can record the position of every individual separately in the Meetnetten database. So when you want to know the total number of individuals per section, you will have to aggregate the data.

To conclude, it is important to understand how the data is organised for a certain monitoring scheme, before you start analysing the data. For more details on the monitoring schemes we refer to Maes et al. (2023)

References

  • Maes D, Piesschaert F, Ledegen H, Van De Poel S, Adriaens T, Anselin A, Belpaire C, Breine J, Brosens D, Brys R, De Bruyn L, Decleer K, De Knijf G, Devos K, Driessens G, Feys S, Gouwy J, Gyselings R, Herremans M, Jacobs I, Lewylle I, Leyssen A, Louette G, Onkelinx T, Packet J, Provoost S, Quataert P, Ruyts S, Scheppers T, Speybroeck J, Steeman R, Stienen E, Thomaes A, Van Den Berge K, Van Keer K, Van Landuyt W, Van Thuyne G, Veraghtert W, Verbelen D, Verbeylen G, Vermeersch G, Westra T, Pollet M (2023). Monitoring schemes for species of conservation concern in Flanders (northern Belgium). An overview of established schemes and the design of an additional monitoring scheme. Reports of the Research Institute for Nature and Forest (INBO) 2023 (15). Research Institute for Nature and Forest (INBO), Brussels. doi:10.21436/inbor.93332112 .

Examples

if (FALSE) { # \dontrun{
library(inbodb)
con <- connect_inbo_dbase("S0008_00_Meetnetten")

# get observations for a specific monitoring scheme and collect data
get_meetnetten_observations(con, scheme_name = "Boomkikker", collect = TRUE)

# get observations for a specific species_group and collect data
get_meetnetten_observations(con, species_group = "libellen", collect = TRUE)

# get observations for all species and do not collect data
observations_all <- get_meetnetten_observations(con)

# Close the connection when done
dbDisconnect(con)
rm(con)
rm(observations_all)
} # }