,
Research Institute for Nature and Forest (INBO) [cph, fnd]| Title: | Connect to and Retrieve Data from Databases on the INBO Server |
|---|---|
| Description: | A bundle of functions to connect to and retrieve data from databases on the INBO server, with dedicated functions to query some of these databases. |
| Authors: | Els Lommelen [aut, cre] (<https://orcid.org/0000-0002-3481-5684>,
Research Institute for Nature and Forest (INBO)),
Hans Van Calster [aut] (<https://orcid.org/0000-0001-8595-8426>,
Research Institute for Nature and Forest (INBO)),
Els De Bie [aut] (<https://orcid.org/0000-0001-7679-743X>, Research
Institute for Nature and Forest (INBO)),
Floris Vanderhaeghe [aut] (<https://orcid.org/0000-0002-6378-6229>,
Research Institute for Nature and Forest (INBO)),
Frederic Piesschaert [aut] (<https://orcid.org/0000-0002-5843-646X>,
Research Institute for Nature and Forest (INBO)),
Toon Westra [aut] (<https://orcid.org/0000-0003-2478-9459>, Research
Institute for Nature and Forest (INBO)),
Stijn Van Hoey [ctb] ,
Research Institute for Nature and Forest (INBO) [cph, fnd] |
| Maintainer: | Els Lommelen <[email protected]> |
| License: | GPL-3 |
| Version: | 0.0.6 |
| Built: | 2024-08-22 15:18:28 UTC |
| Source: | https://github.com/inbo/inbodb |
Connects to an INBO database by simply providing the database's name as an argument. The function can only be used from within the INBO network.
connect_inbo_dbase(database_name, autoconvert_utf8 = TRUE)connect_inbo_dbase(database_name, autoconvert_utf8 = TRUE)
database_name |
char Name of the INBO database you want to connect |
autoconvert_utf8 |
Should the encoding of the tables that are retrieved from the database be adapted to ensure correct presentation? Defaults to TRUE. |
For more information, refer to this tutorial.
odbc connection
Stijn Van Hoey [email protected]
Els Lommelen [email protected]
## Not run: connection <- connect_inbo_dbase("D0021_00_userFlora") connection <- connect_inbo_dbase("W0003_00_Lims") ## End(Not run)## Not run: connection <- connect_inbo_dbase("D0021_00_userFlora") connection <- connect_inbo_dbase("W0003_00_Lims") ## End(Not run)
This method is an adaptation to the INBO databases from the eponymous
function in the odbc package and is an implementation of the method
dbDisconnect defined in the DBI package.
## S4 method for signature 'OdbcConnection' dbDisconnect(conn, ...)## S4 method for signature 'OdbcConnection' dbDisconnect(conn, ...)
conn |
A DBIConnection object, as returned by
|
... |
Other parameters passed on to methods. |
This method is an adaptation from the eponymous function in the odbc
package and is an implementation of the method dbFetch defined in the
DBI package. Additional to the odbc package, it replaces a cryptic
error message by an informative error message.
## S4 method for signature 'OdbcResult' dbFetch(res, n = -1, ...)## S4 method for signature 'OdbcResult' dbFetch(res, n = -1, ...)
res |
An object inheriting from DBIResult, created by
|
n |
maximum number of records to retrieve per fetch. Use |
... |
Other arguments passed on to methods. |
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.
get_florabank_observations(connection, names, fixed = FALSE, collect = FALSE)get_florabank_observations(connection, names, fixed = FALSE, collect = FALSE)
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 |
A dataframe with the following variables:
NaamNederlands,
NaamWetenschappelijk,
Bron,
BeginDatum,
EindDatum,
hok,
Toponiem,
CommentaarTaxon,
CommentaarHabitat,
WaarnemingID,
X_waarneming,
Y_waarneming,
X_meting,
Y_meting
Other florabank:
get_florabank_taxon_ifbl_year(),
get_florabank_traits()
## 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("D0021_00_userFlora") # 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)## 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("D0021_00_userFlora") # 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)
This functions queries all validated observations of the florabank database
and returns unique combinations of taxon, IFBL-square and year.
Either a 1 km
by 1 km or a 4 km x 4 km resolution can be chosen and a begin year can be
set.
Observations of taxa at genus level or higher are excluded. The taxonomic
group can be chosen.
get_florabank_taxon_ifbl_year( connection, starting_year = 2010, ifbl_resolution = c("1km-by-1km", "4km-by-4km"), taxongroup = c("Vaatplanten", "Mossen", "Lichenen (korstmossen)", "Kranswieren"), collect = FALSE )get_florabank_taxon_ifbl_year( connection, starting_year = 2010, ifbl_resolution = c("1km-by-1km", "4km-by-4km"), taxongroup = c("Vaatplanten", "Mossen", "Lichenen (korstmossen)", "Kranswieren"), collect = FALSE )
connection |
A connection to the florabank database. See the example section for how to connect and disconnect to the database. |
starting_year |
Filter for observations that start from this year onwards. Default is 2010. |
ifbl_resolution |
The requested spatial resolution can be either
1km-by-1km |
taxongroup |
Choose for which taxonomic group you want the unique
combinations. One of |
collect |
If FALSE (the default), a remote |
A dataframe with one line for each combination of taxon,
IFBL-square
(either at 1 km x 1 km or 4 km x 4 km resolution) and year. In case the
resolution is 1 km x 1 km, a variable ifbl_4by4 gives the corresponding
ifbl_4by4 identifier within which the ifbl_1by1 square is located.
In case
the resolution is 4 km x 4 km, the variable ifbl_squares is a concatenation
of all nested squares with observations for the taxon in the corresponding
year. This can be nested 1 x 1 squares as well as the corresponding 4 x 4
square (the latter is the case if the original resolution of the observation
is at 4 x 4 resolution). In addition, the variable ifbl_number_squares
gives
the number of unique nested squares where the taxon was observed for that
year and 4 x 4 square combination.
Other florabank:
get_florabank_observations(),
get_florabank_traits()
## Not run: library(inbodb) # connect to florabank db_connectie <- connect_inbo_dbase("D0021_00_userFlora") # get records at 1 km x 1 km resolution for vascular plants from 2010 # (default) without collecting all data into memory (default). fb_kwartier <- get_florabank_taxon_ifbl_year(db_connectie) # to collect the data in memory set collect to TRUE or do fb_kwartier <- collect(fb_kwartier) # get records at 4 km x 4 km resolution starting from 2000 fb_uur <- get_florabank_taxon_ifbl_year(db_connectie, starting_year = 2000, ifbl_resolution = "4km-by-4km", taxongroup = "Mossen") # disconnect from florabank dbDisconnect(db_connectie) ## End(Not run)## Not run: library(inbodb) # connect to florabank db_connectie <- connect_inbo_dbase("D0021_00_userFlora") # get records at 1 km x 1 km resolution for vascular plants from 2010 # (default) without collecting all data into memory (default). fb_kwartier <- get_florabank_taxon_ifbl_year(db_connectie) # to collect the data in memory set collect to TRUE or do fb_kwartier <- collect(fb_kwartier) # get records at 4 km x 4 km resolution starting from 2000 fb_uur <- get_florabank_taxon_ifbl_year(db_connectie, starting_year = 2000, ifbl_resolution = "4km-by-4km", taxongroup = "Mossen") # disconnect from florabank dbDisconnect(db_connectie) ## End(Not run)
This function takes as input (part of) a taxon trait name, queries the florabank and returns the taxon trait values in a tidy data format
get_florabank_traits(connection, trait_name, collect = FALSE)get_florabank_traits(connection, trait_name, collect = FALSE)
connection |
A connection to the florabank database. See the example section for how to connect and disconnect to the database. |
trait_name |
A (part of) a trait name for which you want to get the associated taxon-specific trait values. If this is missing, the function returns an error and prints a message showing all possible trait names. |
collect |
If FALSE (the default), a remote |
A remote tbl object (collect = FALSE) or a tibble dataframe
(collect = TRUE) containing the trait values for each species and for all
partially matched traits. The dataframe contains the variables
TaxonID,
TaxonAfkorting,
TaxonWetenschappelijk,
TaxonNederlands,
Kenmerk,
Code,
Omschrijving,
Rekenwaarde,
Bron and
ExtraOmschrijving.
The first four variables identify the taxon, the latter five variables relate
to the taxon traits.
Other florabank:
get_florabank_observations(),
get_florabank_taxon_ifbl_year()
## Not run: library(inbodb) library(dplyr) # connect to florabank db_connectie <- connect_inbo_dbase("D0021_00_userFlora") # get all Ellenberg values via partial matching, return as lazy query fb_ellenberg <- get_florabank_traits(db_connectie, "llenberg") # collect the data fb_ellenberg <- fb_ellenberg %>% collect() # the same can be done by using the collect parameter fb_ellenberg <- get_florabank_traits(db_connectie, "llenberg", collect = TRUE) # get all red lists via partial matching fb_rodelijsten <- get_florabank_traits(db_connectie, "rode") # get only the red list for vascular plant species fb_rodelijstvaatplanten <- get_florabank_traits(db_connectie, "Rode lijst Vaatplanten") #if the trait_name argument is missing, a list of possible names is printed get_florabank_traits(db_connectie) #disconnect from florabank dbDisconnect(db_connectie) ## End(Not run)## Not run: library(inbodb) library(dplyr) # connect to florabank db_connectie <- connect_inbo_dbase("D0021_00_userFlora") # get all Ellenberg values via partial matching, return as lazy query fb_ellenberg <- get_florabank_traits(db_connectie, "llenberg") # collect the data fb_ellenberg <- fb_ellenberg %>% collect() # the same can be done by using the collect parameter fb_ellenberg <- get_florabank_traits(db_connectie, "llenberg", collect = TRUE) # get all red lists via partial matching fb_rodelijsten <- get_florabank_traits(db_connectie, "rode") # get only the red list for vascular plant species fb_rodelijstvaatplanten <- get_florabank_traits(db_connectie, "Rode lijst Vaatplanten") #if the trait_name argument is missing, a list of possible names is printed get_florabank_traits(db_connectie) #disconnect from florabank dbDisconnect(db_connectie) ## End(Not run)
This function queries the INBOVEG database for information on the field classification (N2000 or local vegetation type, e.g. BWK-code) of the relevé (recording) for one or more survey(s) by the name of the survey. See the examples for how to get information for all surveys.
get_inboveg_classification( connection, survey_name, classif, multiple = FALSE, collect = FALSE )get_inboveg_classification( connection, survey_name, classif, multiple = FALSE, collect = FALSE )
connection |
|
survey_name |
A character string or a character vector giving the name or names of the survey(s) for which you want to extract Classification information. If missing, all surveys are returned. |
classif |
A character vector giving the Classification code of the vegetation type for which you want to extract information. If missing, all classifications are returned. |
multiple |
If TRUE, survey_name can take a character vector with multiple survey names that must match exactly. If FALSE (the default), survey_name must be a single character string (one survey name) that can include wildcards to allow partial matches |
collect |
If FALSE (the default), a remote |
A remote tbl object (collect = FALSE) or a tibble dataframe
(collect = TRUE) with variables
Id,
SurveyName,
Classification-code,
vegetation type / BWK or N2000-list,
LocalClassification,
Description of the habitat type,
Cover-code,
Cover in percentage.
Other inboveg:
get_inboveg_header(),
get_inboveg_layer_cover(),
get_inboveg_layer_qualifier(),
get_inboveg_ppa(),
get_inboveg_qualifier(),
get_inboveg_recording(),
get_inboveg_relation_recording(),
get_inboveg_survey()
## Not run: library(inbodb) con <- connect_inbo_dbase("D0010_00_Cydonia") # get a specific classification from a survey and collect the data classif_info <- get_inboveg_classification(con, survey_name = "MILKLIM_Heischraal2012", classif = "4010", collect = TRUE) # get the classification from several specific surveys classif_info <- get_inboveg_classification(con, survey_name = c("MILKLIM_Heischraal2012", "NICHE Vlaanderen" ), multiple = TRUE) # get all surveys, all classifications, don't collect the data allecodes <- get_inboveg_classification(con) # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)## Not run: library(inbodb) con <- connect_inbo_dbase("D0010_00_Cydonia") # get a specific classification from a survey and collect the data classif_info <- get_inboveg_classification(con, survey_name = "MILKLIM_Heischraal2012", classif = "4010", collect = TRUE) # get the classification from several specific surveys classif_info <- get_inboveg_classification(con, survey_name = c("MILKLIM_Heischraal2012", "NICHE Vlaanderen" ), multiple = TRUE) # get all surveys, all classifications, don't collect the data allecodes <- get_inboveg_classification(con) # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)
This function queries the INBOVEG database for header information (metadata for a vegetation-recording or relevé) for one or more surveys and the recorder type. All records, also with 'work needed' are selected. See the examples for how to get information for all surveys.
get_inboveg_header( connection, survey_name, rec_type, additional_variables = character(0), multiple = FALSE, collect = FALSE )get_inboveg_header( connection, survey_name, rec_type, additional_variables = character(0), multiple = FALSE, collect = FALSE )
connection |
|
survey_name |
A character string or a character vector giving the name or names of the survey(s) for which you want to extract header information. If missing, all surveys are returned. |
rec_type |
A character vector giving the name of record type for which
you want to extract header information e.g. |
additional_variables |
Default character(0).
A character vector with names of additional variables to select from
|
multiple |
If TRUE, survey_name can take a character vector with multiple survey names that must match exactly. If FALSE (the default), survey_name must be a single character string (one survey name) that can include wildcards to allow partial matches |
collect |
If FALSE (the default), a remote |
A remote tbl object (collect = FALSE) or a tibble dataframe
(collect = TRUE) with variables
RecordingGivid,
SurveyName,
UserReference,
Observer,
LocationCode,
Latitude,
Longitude,
Area (in m2),
Length (in cm),
Width (in cm),
VagueDateType,
VagueDateBegin,
VagueDateEnd,
SurveyId,
RecTypeID,
RecTypeName.
Other inboveg:
get_inboveg_classification(),
get_inboveg_layer_cover(),
get_inboveg_layer_qualifier(),
get_inboveg_ppa(),
get_inboveg_qualifier(),
get_inboveg_recording(),
get_inboveg_relation_recording(),
get_inboveg_survey()
## Not run: library(inbodb) con <- connect_inbo_dbase("D0010_00_Cydonia") # get header information from a specific survey and a specific recording type # and collect the data header_info <- get_inboveg_header(con, survey_name = "OudeLanden_1979", rec_type = "Classic", collect = TRUE) # with additional variables header_info <- get_inboveg_header(con, survey_name = "OudeLanden_1979", rec_type = "Classic", additional_variables = c("Pq", "Homogenous"), collect = TRUE) # get header information from several specific surveys header_severalsurveys <- get_inboveg_header(con, survey_name = c("MILKLIM_Heischraal2012", "NICHE Vlaanderen"), multiple = TRUE) # get header information of all surveys, don't collect the data all_header_info <- get_inboveg_header(con) # close the connection when done dbDisconnect(con) rm(con) ## End(Not run)## Not run: library(inbodb) con <- connect_inbo_dbase("D0010_00_Cydonia") # get header information from a specific survey and a specific recording type # and collect the data header_info <- get_inboveg_header(con, survey_name = "OudeLanden_1979", rec_type = "Classic", collect = TRUE) # with additional variables header_info <- get_inboveg_header(con, survey_name = "OudeLanden_1979", rec_type = "Classic", additional_variables = c("Pq", "Homogenous"), collect = TRUE) # get header information from several specific surveys header_severalsurveys <- get_inboveg_header(con, survey_name = c("MILKLIM_Heischraal2012", "NICHE Vlaanderen"), multiple = TRUE) # get header information of all surveys, don't collect the data all_header_info <- get_inboveg_header(con) # close the connection when done dbDisconnect(con) rm(con) ## End(Not run)
This function queries the INBOVEG database for layer information (layer and cover) on recordings for one or more surveys.
get_inboveg_layer_cover(connection, survey_name, multiple = FALSE)get_inboveg_layer_cover(connection, survey_name, multiple = FALSE)
connection |
|
survey_name |
A character string or a character vector, depending on multiple parameter, giving the name or names of the survey(s) for which you want to extract recordings information. If missing, all surveys are returned. |
multiple |
If TRUE, survey_name can take a character vector with multiple survey names that must match exactly. If FALSE (the default), survey_name must be a single character string (one survey name) that can include wildcards to allow partial matches |
A dataframe with variables
Name (of the survey),
RecordingGivid (unique Id),
UserReference,
LayerCode,
LayerDescription,
CoverCode,
Coverpercentage and
Mean height (cm)
Other inboveg:
get_inboveg_classification(),
get_inboveg_header(),
get_inboveg_layer_qualifier(),
get_inboveg_ppa(),
get_inboveg_qualifier(),
get_inboveg_recording(),
get_inboveg_relation_recording(),
get_inboveg_survey()
## Not run: library(inbodb) con <- connect_inbo_dbase("D0010_00_Cydonia") # get the layer information from one survey layerinfo_heischraal2012 <- get_inboveg_layer_cover(con, survey_name = "MILKLIM_Heischraal2012") # get all layer qualifiers from MILKLIM surveys (partial matching) layerinfo_milkim <- get_inboveg_layer_cover(con, survey_name = "%MILKLIM%") # get layer qualifiers from several specific surveys layerinfo_severalsurveys <- get_inboveg_layer_cover(con, survey_name = c("MILKLIM_Heischraal2012", "NICHE Vlaanderen"), multiple = TRUE) # get all layer qualifiers of all surveys all_layerinfo <- get_inboveg_layer_cover(con) # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)## Not run: library(inbodb) con <- connect_inbo_dbase("D0010_00_Cydonia") # get the layer information from one survey layerinfo_heischraal2012 <- get_inboveg_layer_cover(con, survey_name = "MILKLIM_Heischraal2012") # get all layer qualifiers from MILKLIM surveys (partial matching) layerinfo_milkim <- get_inboveg_layer_cover(con, survey_name = "%MILKLIM%") # get layer qualifiers from several specific surveys layerinfo_severalsurveys <- get_inboveg_layer_cover(con, survey_name = c("MILKLIM_Heischraal2012", "NICHE Vlaanderen"), multiple = TRUE) # get all layer qualifiers of all surveys all_layerinfo <- get_inboveg_layer_cover(con) # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)
This function queries the INBOVEG database for layer qualifier information on recordings for one or more surveys.
get_inboveg_layer_qualifier(connection, survey_name, multiple = FALSE)get_inboveg_layer_qualifier(connection, survey_name, multiple = FALSE)
connection |
|
survey_name |
A character string or a character vector, depending on multiple parameter, giving the name or names of the survey(s) for which you want to extract information. If missing, all surveys are returned. |
multiple |
If TRUE, survey_name can take a character vector with multiple survey names that must match exactly. If FALSE (the default), survey_name must be a single character string (one survey name) that can include wildcards to allow partial matches |
A dataframe with variables
Name (of the survey),
RecordingGivid (unique Id),
UserReference,
LayerCode,
LayerDescription,
QualifierCode,
Qualifier Description,
Elucidation and
NotSure in case the qualifier is doubtful,
CoverCode and
Cover percentage
Other inboveg:
get_inboveg_classification(),
get_inboveg_header(),
get_inboveg_layer_cover(),
get_inboveg_ppa(),
get_inboveg_qualifier(),
get_inboveg_recording(),
get_inboveg_relation_recording(),
get_inboveg_survey()
## Not run: library(inbodb) con <- connect_inbo_dbase("D0010_00_Cydonia") # get the layer qualifiers from one survey layerqualifiers_Gagealutea <- get_inboveg_layer_qualifier(con, survey_name = "GageaLutea_1980") # get all layer qualifiers from MILKLIM surveys (partial matching) layerqualifiers_milkim <- get_inboveg_layer_qualifier(con, survey_name = "%MILKLIM%") # get layer qualifiers from several specific surveys layerqualifiers_severalsurveys <- get_inboveg_layer_qualifier(con, survey_name = c("MILKLIM_Overstroming", "NICHE Vlaanderen"), multiple = TRUE) # get all layer qualifiers of all surveys alllayerqualifiers <- get_inboveg_layer_qualifier(con) # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)## Not run: library(inbodb) con <- connect_inbo_dbase("D0010_00_Cydonia") # get the layer qualifiers from one survey layerqualifiers_Gagealutea <- get_inboveg_layer_qualifier(con, survey_name = "GageaLutea_1980") # get all layer qualifiers from MILKLIM surveys (partial matching) layerqualifiers_milkim <- get_inboveg_layer_qualifier(con, survey_name = "%MILKLIM%") # get layer qualifiers from several specific surveys layerqualifiers_severalsurveys <- get_inboveg_layer_qualifier(con, survey_name = c("MILKLIM_Overstroming", "NICHE Vlaanderen"), multiple = TRUE) # get all layer qualifiers of all surveys alllayerqualifiers <- get_inboveg_layer_qualifier(con) # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)
This function queries the INBOVEG database for
PPA-type relevé information (which species were recorded at what distance
from a point location) for one or more surveys,
or in combination with the unique ID (recordingGIVID) or user reference
Wildcards in survey_name, user_reference or recording_givid
should only be used if a character string (a length one character vector),
otherwise values are assumed to match exactly.
get_inboveg_ppa( connection, survey_name = "%", user_reference = "%", recording_givid = "%", collect = FALSE )get_inboveg_ppa( connection, survey_name = "%", user_reference = "%", recording_givid = "%", collect = FALSE )
connection |
|
survey_name |
A character string or a character vector, giving the name
or names of the survey(s) for which you
want to extract relevé information. As default ( |
user_reference |
A character string or a character vector giving the
name of a recording for which you want to extract relevé information.
As default ( |
recording_givid |
A character string or a character vector giving
the unique id of a recording for which you want to extract relevé
information.
As default ( |
collect |
If FALSE (the default), a remote |
A remote tbl object (collect = FALSE) or a tibble dataframe
(collect = TRUE) with variables
SurveyName,
RecordingGivid,
UserReference,
DateRecording,
LocationCode,
CoordinateRefSystem,
GivenLatitude,
GivenLongitude,
GivenLatitude2,
GivenLongitude2,
MaxSearchEffortUnit,
MaxSearchEffortLabel,
Indirect,
NotSure,
LayerCode,
LayerCover,
OriginalName,
ScientificName,
TaxonGroupCode,
PhenologyCode,
Distance,
Comment
DateIdentification,
RecordTypeName
Other inboveg:
get_inboveg_classification(),
get_inboveg_header(),
get_inboveg_layer_cover(),
get_inboveg_layer_qualifier(),
get_inboveg_qualifier(),
get_inboveg_recording(),
get_inboveg_relation_recording(),
get_inboveg_survey()
## Not run: library(inbodb) con <- connect_inbo_dbase("D0010_00_Cydonia") # get the recordings from one survey and collect the data specifieke_survey <- get_inboveg_ppa(con, survey_name = "LEN_sinusmaaiproject_ppa", collect = TRUE) # get all recordings from with partial matching, don't collect partial_match <- get_inboveg_ppa(con, survey_name = "%LEN%", collect = FALSE) # get recordings from several specific recordinggivid recording_severalgivids <- get_inboveg_ppa(con, recording_givid = c("IV2024040411243457","IV2024040411263782"), collect = TRUE) # get all PPA-type recordings of all surveys, don't collect the data all_ppa <- get_inboveg_ppa(con) # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)## Not run: library(inbodb) con <- connect_inbo_dbase("D0010_00_Cydonia") # get the recordings from one survey and collect the data specifieke_survey <- get_inboveg_ppa(con, survey_name = "LEN_sinusmaaiproject_ppa", collect = TRUE) # get all recordings from with partial matching, don't collect partial_match <- get_inboveg_ppa(con, survey_name = "%LEN%", collect = FALSE) # get recordings from several specific recordinggivid recording_severalgivids <- get_inboveg_ppa(con, recording_givid = c("IV2024040411243457","IV2024040411263782"), collect = TRUE) # get all PPA-type recordings of all surveys, don't collect the data all_ppa <- get_inboveg_ppa(con) # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)
This function queries the INBOVEG database for qualifier information (site qualifier or management qualifier)on recordings for one or more surveys.
get_inboveg_qualifier( connection, survey_name, qualifier_type, multiple = FALSE )get_inboveg_qualifier( connection, survey_name, qualifier_type, multiple = FALSE )
connection |
|
survey_name |
A character string or a character vector, depending on multiple parameter, giving the name or names of the survey(s) for which you want to extract recordings information. If missing, all surveys are returned. |
qualifier_type |
A character vector giving the name of qualifier type
for which you want to extract information e.g. |
multiple |
If TRUE, survey_name can take a character vector with multiple survey names that must match exactly. If FALSE (the default), survey_name must be a single character string (one survey name) that can include wildcards to allow partial matches |
A dataframe with variables
RecordingGivid (unique Id),
UserReference,
Observer,
QualifierType,
QualifierCode,
Description,
2nd QualifierCode,
2nd Description,
3rd QualifierCode,
3rd Description,
Elucidation, in case qualifier is 'NotSure',
ParentID,
QualifierResource
Other inboveg:
get_inboveg_classification(),
get_inboveg_header(),
get_inboveg_layer_cover(),
get_inboveg_layer_qualifier(),
get_inboveg_ppa(),
get_inboveg_recording(),
get_inboveg_relation_recording(),
get_inboveg_survey()
## Not run: library(inbodb) con <- connect_inbo_dbase("D0010_00_Cydonia") # get the qualifiers from one survey qualifiers_heischraal2012 <- get_inboveg_qualifier(con, survey_name = "MILKLIM_Heischraal2012") # get all site qualifiers (SQ) from MILKLIM surveys (partial matching) qualifiers_milkim <- get_inboveg_qualifier(con, survey_name = "%MILKLIM%", qualifier_type = "SQ") # get qualifiers from several specific surveys qualifiers_severalsurveys <- get_inboveg_qualifier(con, survey_name = c("MILKLIM_Heischraal2012", "NICHE Vlaanderen"), multiple = TRUE) # get all qualifiers of all surveys allqualifiers <- get_inboveg_qualifier(con) # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)## Not run: library(inbodb) con <- connect_inbo_dbase("D0010_00_Cydonia") # get the qualifiers from one survey qualifiers_heischraal2012 <- get_inboveg_qualifier(con, survey_name = "MILKLIM_Heischraal2012") # get all site qualifiers (SQ) from MILKLIM surveys (partial matching) qualifiers_milkim <- get_inboveg_qualifier(con, survey_name = "%MILKLIM%", qualifier_type = "SQ") # get qualifiers from several specific surveys qualifiers_severalsurveys <- get_inboveg_qualifier(con, survey_name = c("MILKLIM_Heischraal2012", "NICHE Vlaanderen"), multiple = TRUE) # get all qualifiers of all surveys allqualifiers <- get_inboveg_qualifier(con) # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)
This function queries the INBOVEG database for
relevé information (which species were recorded in which plots and in
which vegetation layers with which cover) for one or more surveys,
or in combination with the unique ID (recordingGIVID) or user reference
Wildcards in survey_name, user_reference or recording_givid
should only be used if a character string (a length one character vector),
otherwise values are assumed to match exactly.
get_inboveg_recording( connection, survey_name = "%", user_reference = "%", recording_givid = "%", collect = FALSE, multiple = deprecated() )get_inboveg_recording( connection, survey_name = "%", user_reference = "%", recording_givid = "%", collect = FALSE, multiple = deprecated() )
connection |
|
survey_name |
A character string or a character vector, giving the name
or names of the survey(s) for which you
want to extract relevé information. As default ( |
user_reference |
A character string or a character vector giving the
name of a recording for which you want to extract relevé information.
As default ( |
recording_givid |
A character string or a character vector giving
the unique id of a recording for which you want to extract relevé
information.
As default ( |
collect |
If FALSE (the default), a remote |
multiple |
Deprecated. |
A remote tbl object (collect = FALSE) or a tibble dataframe
(collect
= TRUE) with variables
RecordingGivid (unique ID),
User reference,
LayerCode,
CoverCode,
OriginalName,
ScientificName,
TaxonGroupCode,
PhenologyCode,
Comment,
CoverageCode,
PctValue (percentage coverage),
RecordingScale (name of the scale of coverage)
Other inboveg:
get_inboveg_classification(),
get_inboveg_header(),
get_inboveg_layer_cover(),
get_inboveg_layer_qualifier(),
get_inboveg_ppa(),
get_inboveg_qualifier(),
get_inboveg_relation_recording(),
get_inboveg_survey()
## Not run: library(inbodb) con <- connect_inbo_dbase("D0010_00_Cydonia") # get the recordings from one survey and collect the data recording_heischraal2012 <- get_inboveg_recording(con, survey_name = "MILKLIM_Heischraal2012", collect = TRUE) # get all recordings from MILKLIM surveys (partial matching), don't collect recording_milkim <- get_inboveg_recording(con, survey_name = "%MILKLIM%", collect = FALSE) # get recordings from several specific surveys recording_severalsurveys <- get_inboveg_recording(con, survey_name = c("MILKLIM_Heischraal2012", "NICHE Vlaanderen"), collect = TRUE) # get recordings from several specific recordinggivid recording_severalgivids <- get_inboveg_recording(con, recording_givid = c("IV2012081609450300","IV2012081610204607"), collect = TRUE) # get all recordings of all surveys, don't collect the data allrecordings <- get_inboveg_recording(con) # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)## Not run: library(inbodb) con <- connect_inbo_dbase("D0010_00_Cydonia") # get the recordings from one survey and collect the data recording_heischraal2012 <- get_inboveg_recording(con, survey_name = "MILKLIM_Heischraal2012", collect = TRUE) # get all recordings from MILKLIM surveys (partial matching), don't collect recording_milkim <- get_inboveg_recording(con, survey_name = "%MILKLIM%", collect = FALSE) # get recordings from several specific surveys recording_severalsurveys <- get_inboveg_recording(con, survey_name = c("MILKLIM_Heischraal2012", "NICHE Vlaanderen"), collect = TRUE) # get recordings from several specific recordinggivid recording_severalgivids <- get_inboveg_recording(con, recording_givid = c("IV2012081609450300","IV2012081610204607"), collect = TRUE) # get all recordings of all surveys, don't collect the data allrecordings <- get_inboveg_recording(con) # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)
This function queries the INBOVEG database for relation information on recordings for one or more surveys based on Parent (classic-chain/bucket) and Child (classic) relationship.
get_inboveg_relation_recording( connection, survey_name, multiple = FALSE, collect = FALSE )get_inboveg_relation_recording( connection, survey_name, multiple = FALSE, collect = FALSE )
connection |
|
survey_name |
A character string or a character vector, depending on multiple parameter, giving the name or names of the survey(s) for which you want to extract recordings information. If missing, all surveys are returned. |
multiple |
If TRUE, survey_name can take a character vector with multiple survey names that must match exactly. If FALSE (the default), survey_name must be a single character string (one survey name) that can include wildcards to allow partial matches |
collect |
If FALSE (the default), a remote |
A dataframe with variables
RecordingId,
Child_GIVID (unique RecordingGIVID),
Child_UserRef (UserReference),
ParentId (RecordingId),
Parent_GIVID (unique RecordingGIVID) and
Parent_UserRef (UserReference)
Other inboveg:
get_inboveg_classification(),
get_inboveg_header(),
get_inboveg_layer_cover(),
get_inboveg_layer_qualifier(),
get_inboveg_ppa(),
get_inboveg_qualifier(),
get_inboveg_recording(),
get_inboveg_survey()
## Not run: library(inbodb) con <- connect_inbo_dbase("D0010_00_Cydonia") # get the Parent-Child-relations from one survey relations_N2000meetnet_Grasland <- get_inboveg_relation_recording(con, survey_name = "N2000meetnet_Grasland") # get all Parent-Child-relations from N2000meetnet surveys (partial matching) relations_N2000meetnet <- get_inboveg_relation_recording(con, survey_name = "%N2000meetnet%") # get Parent-Child-relations from several specific surveys relations_severalsurveys <- get_inboveg_relation_recording(con, survey_name = c("DeBlankaart-1985-Beheer", "N2000meetnet_Grasland"), multiple = TRUE) # get all Parent-Child-relations of all relevant surveys allrelations <- get_inboveg_relation_recording(con) # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)## Not run: library(inbodb) con <- connect_inbo_dbase("D0010_00_Cydonia") # get the Parent-Child-relations from one survey relations_N2000meetnet_Grasland <- get_inboveg_relation_recording(con, survey_name = "N2000meetnet_Grasland") # get all Parent-Child-relations from N2000meetnet surveys (partial matching) relations_N2000meetnet <- get_inboveg_relation_recording(con, survey_name = "%N2000meetnet%") # get Parent-Child-relations from several specific surveys relations_severalsurveys <- get_inboveg_relation_recording(con, survey_name = c("DeBlankaart-1985-Beheer", "N2000meetnet_Grasland"), multiple = TRUE) # get all Parent-Child-relations of all relevant surveys allrelations <- get_inboveg_relation_recording(con) # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)
This function queries the INBOVEG database for survey information (metadata about surveys) for one or more survey(s) by the name of the survey. See the examples for how to get information for all surveys.
get_inboveg_survey(connection, survey_name, collect = FALSE)get_inboveg_survey(connection, survey_name, collect = FALSE)
connection |
|
survey_name |
A character vector giving the names of the surveys for which you want to extract survey information. |
collect |
If FALSE (the default), a remote |
A remote tbl object (collect = FALSE) or a tibble dataframe
(collect
= TRUE) with variables Id, Name, Description, Owner and Creator.
Other inboveg:
get_inboveg_classification(),
get_inboveg_header(),
get_inboveg_layer_cover(),
get_inboveg_layer_qualifier(),
get_inboveg_ppa(),
get_inboveg_qualifier(),
get_inboveg_recording(),
get_inboveg_relation_recording()
## Not run: library(inbodb) con <- connect_inbo_dbase("D0010_00_Cydonia") # get information of a specific survey and collect data survey_info <- get_inboveg_survey(con, survey_name = "OudeLanden_1979", collect = TRUE) # get information of all surveys and collect data allsurveys <- get_inboveg_survey(con) # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)## Not run: library(inbodb) con <- connect_inbo_dbase("D0010_00_Cydonia") # get information of a specific survey and collect data survey_info <- get_inboveg_survey(con, survey_name = "OudeLanden_1979", collect = TRUE) # get information of all surveys and collect data allsurveys <- get_inboveg_survey(con) # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)
This function queries the Meetnetten database for the locations and sublocations 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_locations(connection, scheme_name = NULL, species_group = NULL)get_meetnetten_locations(connection, scheme_name = NULL, species_group = NULL)
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 location 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 location data. Data from multiple species groups can be selected by providing a vector with the names of the species groups. |
Each monitoring scheme of the species monitoring programme of Flanders
Meetnetten consists of a fixed set of
locations.
A monitoring scheme for rare species includes all locations where the species
occurs.
For more common species a sample of locations is drawn and the the selected
locations are included in the monitoring scheme.
In some cases, the monitoring project in
Meetnetten also contains locations that are
not part of the sample. These locations can be counted optionally and are
indicated by (is_sample = FALSE).
It also occurs that a location becomes inaccessible or that the target
species disappears.
Then, a locations can be made inactive (is_active = FALSE),
which means that no observations can be recorded any more.
When the sf package is installed, a list with two sf
objects is returned:
main_locations: the main locations of the
selected monitoring schemes, with following attribute variables:
species_group
scheme: name of the monitoring scheme
location: name of the location
is_sample: whether the location belongs to the sample of
locations for the monitoring scheme (see details)
is_active: when a location is not suited for counting any
more, the location becomes inactive (is_active = FALSE)
sublocations: the sublocations (for example
the sections of a transect) for each of the selected main locations, with
following attribute variables:
species_group
scheme: name of the monitoring scheme
location: name of the main location
sublocation: name of the sublocation
is_active: whether the sublocation is counted or not
When the sf package is not installed, a list with two
tibble objects is returned, with the same attribute variables as above
and an additional variable geom that contains the geometry information
in wkt (well-known text) format.
Not all main locations are subdivided in sublocations. So in some cases the sublocations object is empty.
Other meetnetten:
get_meetnetten_observations(),
get_meetnetten_schemes(),
get_meetnetten_visits()
## Not run: library(inbodb) con <- connect_inbo_dbase("S0008_00_Meetnetten") # get locations for a specific monitoring scheme locations_heivlinder <- get_meetnetten_locations(con, scheme_name = "Heivlinder") locations_heivlinder$main_locations locations_heivlinder$sublocations # get locations for a specific species_group locations_dragonflies <- get_meetnetten_locations(con, species_group = "libellen") locations_dragonflies$main_locations locations_dragonflies$sublocations # Close the connection when done dbDisconnect(con) rm(con) rm(locations_heivlinder) rm(locations_dragonflies) ## End(Not run)## Not run: library(inbodb) con <- connect_inbo_dbase("S0008_00_Meetnetten") # get locations for a specific monitoring scheme locations_heivlinder <- get_meetnetten_locations(con, scheme_name = "Heivlinder") locations_heivlinder$main_locations locations_heivlinder$sublocations # get locations for a specific species_group locations_dragonflies <- get_meetnetten_locations(con, species_group = "libellen") locations_dragonflies$main_locations locations_dragonflies$sublocations # Close the connection when done dbDisconnect(con) rm(con) rm(locations_heivlinder) rm(locations_dragonflies) ## End(Not run)
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 )get_meetnetten_observations( connection, scheme_name = NULL, species_group = NULL, collect = FALSE )
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 |
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)
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
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.
Other meetnetten:
get_meetnetten_locations(),
get_meetnetten_schemes(),
get_meetnetten_visits()
## Not run: 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) ## End(Not run)## Not run: 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) ## End(Not run)
This function queries the Meetnetten database to give an overview of monitoring schemes that are included.
get_meetnetten_schemes(connection)get_meetnetten_schemes(connection)
connection |
dbconnection with the database 'S0008_00_Meetnetten' on the inbo-sql08-prd.inbo.be server. |
The species monitoring programme of Flanders (Meetnetten) consists of a series of monitoring schemes. In each monitoring scheme one or more target species are counted based on a specific protocol. For more details we refer to Maes et al. (2023)
A tibble dataframe with variables species_group, scheme and protocol.
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.
Other meetnetten:
get_meetnetten_locations(),
get_meetnetten_observations(),
get_meetnetten_visits()
## Not run: library(inbodb) con <- connect_inbo_dbase("S0008_00_Meetnetten") # get overview of monitoring schemes in meetnetten database meetnetten_schemes <- get_meetnetten_schemes(con) # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)## Not run: library(inbodb) con <- connect_inbo_dbase("S0008_00_Meetnetten") # get overview of monitoring schemes in meetnetten database meetnetten_schemes <- get_meetnetten_schemes(con) # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)
This function queries the Meetnetten database for visit data (data about a counting event) 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 visits of all monitoring schemes are returned.
get_meetnetten_visits( connection, scheme_name = NULL, species_group = NULL, collect = FALSE )get_meetnetten_visits( connection, scheme_name = NULL, species_group = NULL, collect = FALSE )
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. |
species_group |
the name of the species group for which you want to extract visit data. |
collect |
If |
A remote tbl object (collect = FALSE) or a
tibble dataframe (collect = TRUE) with following
variables:
species_group
scheme: the name of the monitoring scheme
protocol: the protocol used
location: the name of the location
visit_id: unique id for a count event
validation_status: validation status of the visit (visits
that are validated and not approved are not provided)
10: visit not validated
100: visit validated and approved
start_date: the start date of the visit
start_time: the start time of the visit
end_date: the end date of the visit
end_time: the end time of the visit
date_created: the date at which the data was imported in the
database
visit_status: the status of the visit (determined by
the observer) using following categories:
conform protocol: the protocol was applied
weersomstandigheden waren ongunstig: weather conditions
were unfavourable
telmethode uit handleiding niet gevolgd: the protocol
was not applied
geen veldwerk mogelijk - locatie ontoegankelijk:
counting was not possible because the location is inaccessible
geen veldwerk mogelijk - locatie is ongeschikt voor de
soort:
counting was not possible because the location is not suitable
for the species
for_analysis: whether the data is suited for analysis
(determined by the validator)
for_targets: every year targets are set in terms of the
number of locations that have to be counted per monitoring scheme; when
for_targets = TRUE the visit contributes to these targets
notes: notes by the observer
Other meetnetten:
get_meetnetten_locations(),
get_meetnetten_observations(),
get_meetnetten_schemes()
## Not run: library(inbodb) con <- connect_inbo_dbase("S0008_00_Meetnetten") # get visits for a specific monitoring scheme and collect data get_meetnetten_visits(con, scheme_name = "Boomkikker", collect = TRUE) # get visits for a specific species_group and collect data get_meetnetten_visits(con, species_group = "libellen", collect = TRUE) # get visits for all species and do not collect data visits_all <- get_meetnetten_visits(con) # Close the connection when done dbDisconnect(con) rm(con) rm(visits_all) ## End(Not run)## Not run: library(inbodb) con <- connect_inbo_dbase("S0008_00_Meetnetten") # get visits for a specific monitoring scheme and collect data get_meetnetten_visits(con, scheme_name = "Boomkikker", collect = TRUE) # get visits for a specific species_group and collect data get_meetnetten_visits(con, species_group = "libellen", collect = TRUE) # get visits for all species and do not collect data visits_all <- get_meetnetten_visits(con) # Close the connection when done dbDisconnect(con) rm(con) rm(visits_all) ## End(Not run)
D0156_00_Taxonlijsten
This function queries D0156_00_Taxonlijsten and gives an
overview of all the features associated with a TaxonlijstVersie (a red list
status or an annex of the Habitat Directive are examples of a feature). This
is an auxiliary function to check the accepted values (KenmerkwaardeCodes)
of the feature parameter in the core function get_taxonlijsten_items
get_taxonlijsten_features( connection, list = "%", version = c("latest", "old", "all"), collect = FALSE )get_taxonlijsten_features( connection, list = "%", version = c("latest", "old", "all"), collect = FALSE )
connection |
dbconnection with the database |
list |
name of the taxonlist that you want to retrieve. Wildcards % are allowed. Case insensitive. |
version |
A choice ('latest', 'old', 'all'). If 'latest' (the default) only the most recent version is returned. If 'old' all but the most recent version is returned. If 'all' all versions are returned. |
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. |
A remote tbl object (collect = FALSE) or a tibble dataframe (collect = TRUE) with variables Taxonlijst, Publicatiejaar, Version, Kenmerkcode, KenmerkBeschrijving, KenmerkwaardeCode, KenmerkwaardeBeschrijving
Other taxonlijsten:
get_taxonlijsten_items(),
get_taxonlijsten_lists()
## Not run: library(inbodb) con <- connect_inbo_dbase("D0156_00_Taxonlijsten") # get features of all versions of the 'Rode lijst van de Dagvlinders' get_taxonlijsten_features(con, version = 'all', list = '%rode%dagvlinders%' , collect = TRUE) # get features of Habitattypical fauna get_taxonlijsten_features(con, list = '%Habitattyp%fauna%') # use function with default values (all features of recent versions) get_taxonlijsten_features(con) # note that function also returns taxonlists without features get_taxonlijsten_features(con, list = '%SBP%') # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)## Not run: library(inbodb) con <- connect_inbo_dbase("D0156_00_Taxonlijsten") # get features of all versions of the 'Rode lijst van de Dagvlinders' get_taxonlijsten_features(con, version = 'all', list = '%rode%dagvlinders%' , collect = TRUE) # get features of Habitattypical fauna get_taxonlijsten_features(con, list = '%Habitattyp%fauna%') # use function with default values (all features of recent versions) get_taxonlijsten_features(con) # note that function also returns taxonlists without features get_taxonlijsten_features(con, list = '%SBP%') # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)
D0156_00_Taxonlijsten
This function queries D0156_00_Taxonlijsten and gives an
overview of the taxa that are on a given taxon list version. The interpreted
taxa are given by default, but it is possible to add taxa as they were
originally published. The taxa of the latest list version are shown
unless specified otherwise.
get_taxonlijsten_items( connection, list = "%", taxon = "%", feature = "%", version = c("latest", "old", "all"), original = FALSE, collect = FALSE )get_taxonlijsten_items( connection, list = "%", taxon = "%", feature = "%", version = c("latest", "old", "all"), original = FALSE, collect = FALSE )
connection |
dbconnection with the database |
list |
name of the taxonlist that you want to retrieve. Wildcards % are allowed. Case insensitive. |
taxon |
name of the taxon you want to retrieve. Scientific and vernacular (Dutch) names are allowed. Wildcards % are allowed. Case insensitive. |
feature |
name of the list feature (actually feature code) you want to retrieve. Wildcards % are allowed. Case insensitive. |
version |
A choice ('latest', 'old', 'all'). If 'latest' (the default) only the most recent version is returned. If 'old' all but the most recent version is returned. If 'all' all versions are returned. |
original |
If FALSE (the default), the function will only retrieve the interpreted taxa. If TRUE, columns with the original taxa will be added to the output. For example, if the originally published taxon on a taxonlist is 'Cicindela spec.', the interpretation will exist of all relevant Cicindela species |
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. |
A remote tbl object (collect = FALSE) or a tibble dataframe (collect = TRUE) with variables Lijst, Publicatiejaar, LaatsteVersie, Taxongroep, Naamwet_interpretatie, Auteur, NaamNed_interpretatie, Kenmerk, KenmerkwaardeCode, Kenmerkwaarde and extra variables Taxongroep_origineel, Naamwet_origineel, Naamned_origineel when requested (original = TRUE)
Other taxonlijsten:
get_taxonlijsten_features(),
get_taxonlijsten_lists()
## Not run: library(inbodb) library(tidyverse) con <- connect_inbo_dbase("D0156_00_Taxonlijsten") # Get all taxa from list 'Jachtdecreet' get_taxonlijsten_items(con, list = 'Jachtdecreet', collect = TRUE) # Get all taxa on category 2 of 'Soortenbesluit' get_taxonlijsten_items(con, list = 'soortenbesluit', feature = 'cat2') # Get all taxonlist that include 'Gentiaanblauwtje' get_taxonlijsten_items(con, taxon = 'Gentiaanblauwtje', collect = TRUE) # Get all taxa with red list status CR (critically endangered) get_taxonlijsten_items(con, feature = 'CR') # Get original and interpreted Cicindela taxa from list 'Soortenbesluit' get_taxonlijsten_items(con, list = 'Soortenbesluit', taxon = '%Cicindela%' , original = TRUE) %>% select('Naamwet_origineel', 'NaamNed_origineel', 'Naamwet_interpretatie' , 'NaamNed_interpretatie') # Compare red list status on multiple listversions get_taxonlijsten_items(con, version = 'all' , list = 'rode lijst van de dagvlinders') %>% select('Lijst', 'Publicatiejaar', 'Naamwet_interpretatie' , 'NaamNed_interpretatie', 'KenmerkwaardeCode') %>% pivot_wider(names_from = Publicatiejaar, values_from = KenmerkwaardeCode) # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)## Not run: library(inbodb) library(tidyverse) con <- connect_inbo_dbase("D0156_00_Taxonlijsten") # Get all taxa from list 'Jachtdecreet' get_taxonlijsten_items(con, list = 'Jachtdecreet', collect = TRUE) # Get all taxa on category 2 of 'Soortenbesluit' get_taxonlijsten_items(con, list = 'soortenbesluit', feature = 'cat2') # Get all taxonlist that include 'Gentiaanblauwtje' get_taxonlijsten_items(con, taxon = 'Gentiaanblauwtje', collect = TRUE) # Get all taxa with red list status CR (critically endangered) get_taxonlijsten_items(con, feature = 'CR') # Get original and interpreted Cicindela taxa from list 'Soortenbesluit' get_taxonlijsten_items(con, list = 'Soortenbesluit', taxon = '%Cicindela%' , original = TRUE) %>% select('Naamwet_origineel', 'NaamNed_origineel', 'Naamwet_interpretatie' , 'NaamNed_interpretatie') # Compare red list status on multiple listversions get_taxonlijsten_items(con, version = 'all' , list = 'rode lijst van de dagvlinders') %>% select('Lijst', 'Publicatiejaar', 'Naamwet_interpretatie' , 'NaamNed_interpretatie', 'KenmerkwaardeCode') %>% pivot_wider(names_from = Publicatiejaar, values_from = KenmerkwaardeCode) # Close the connection when done dbDisconnect(con) rm(con) ## End(Not run)
D0156_00_Taxonlijsten
This function queries D0156_00_Taxonlijsten and gives an
overview of all the taxon lists and list versions currently available in the
database. Only the latest version is shown unless specified otherwise
get_taxonlijsten_lists( connection, list = "%", version = c("latest", "old", "all"), collect = FALSE )get_taxonlijsten_lists( connection, list = "%", version = c("latest", "old", "all"), collect = FALSE )
connection |
dbconnection with the database |
list |
name of the taxonlist that you want to retrieve. Wildcards % are allowed. Case insensitive. |
version |
A choice ('latest', 'old', 'all'). If 'latest' (the default) only the most recent version is returned. If 'old' all but the most recent version is returned. If 'all' all versions are returned. |
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. |
A remote tbl object (collect = FALSE) or a tibble dataframe (collect = TRUE) with variables TaxonlijstType, TaxonlijstCode, Taxonlijst, Publicatiejaar, Version, ReferentieURL, Criteria, Validering, Vaststelling.
Other taxonlijsten:
get_taxonlijsten_features(),
get_taxonlijsten_items()
## Not run: library(inbodb) con <- connect_inbo_dbase("D0156_00_Taxonlijsten") # get the most recent version of the 'Rode lijst van de Dagvlinders' get_taxonlijsten_lists(con, version = 'latest', list = '%rode%dagvlinders%', collect = FALSE) # get all recent red lists get_taxonlijsten_lists(con, list = '%rode lijst%') # get all taxonlist versions in the database get_taxonlijsten_lists(con, version = 'all', collect = TRUE) # use function with default values (only most recent versions) get_taxonlijsten_lists(con) # status of red lists rl <- get_taxonlijsten_lists(con, list = '%rode lijst%') select(rl,"Taxonlijst", "PublicatieJaar", "Criteria", "Validering", "Vaststelling") # Close the connection when done dbDisconnect(con) rm(con, rl) ## End(Not run)## Not run: library(inbodb) con <- connect_inbo_dbase("D0156_00_Taxonlijsten") # get the most recent version of the 'Rode lijst van de Dagvlinders' get_taxonlijsten_lists(con, version = 'latest', list = '%rode%dagvlinders%', collect = FALSE) # get all recent red lists get_taxonlijsten_lists(con, list = '%rode lijst%') # get all taxonlist versions in the database get_taxonlijsten_lists(con, version = 'all', collect = TRUE) # use function with default values (only most recent versions) get_taxonlijsten_lists(con) # status of red lists rl <- get_taxonlijsten_lists(con, list = '%rode lijst%') select(rl,"Taxonlijst", "PublicatieJaar", "Criteria", "Validering", "Vaststelling") # Close the connection when done dbDisconnect(con) rm(con, rl) ## End(Not run)