vignettes/get_data_inboveg.Rmd
get_data_inboveg.RmdThe Flemish vegetation database, INBOVEG, is an application developed to provide a repository of relevés and makes the relevés available for future use. More information? Check out https://www.vlaanderen.be/inbo/en-gb/data-applications/inboveg/
INBOVEG supports different types of recordings: BioHab
recordings (protocol of Natura 2000 monitoring) and the classic relevés.
The classic relevés can stand alone, be an element of a collection or
element of a chain where the linkage is used to give information about
the relative position of recording within a series. Ample selection and
export functions toward analysis tools are provided. It also provides
standardized lists of species, habitats, life forms, scales … Original
observations are preserved and a full history of subsequent
identifications is saved.
More information? Check out INBOVEG-website
We make functions available to query data directly from the INBOVEG SQL-server database. This avoids writing your own queries or to copy/paste them from the access-frontend for INBOVEG.
We have provided functions to query
The main functions that we will use in this tutorial all start with
get_inboveg_*. These functions are made available by
loading the inbodb package.
These functions will only work for people with access to the INBO network. As an INBO employee, you should make sure you have reading-rights for CYDONIA, otherwise place an ICT-call.
The following R-code can be used to establish a connection to INBOVEG
by using connect_inbo_dbase of the inbodb-package with the
database ‘Cydonia’ on the inbo-sql07-prd server:
con <- connect_inbo_dbase("D0010_00_Cydonia")The function get_inboveg_survey queries the INBOVEG
database for survey information (metadata about surveys) for one or more
survey(s) by the name of the survey.
Three examples are given, this can be used as base to continue selecting the data you require.
Get information of a specific survey and collect data.
survey_info <- get_inboveg_survey(
con,
survey_name = "OudeLanden_1979",
collect = TRUE)
survey_info
#> # A tibble: 1 × 5
#> Id Name Description Owner creator
#> <int> <chr> <chr> <chr> <chr>
#> 1 172 OudeLanden_1979 Verlinden A, Leys G en Slembrouck J (1979… NA els_de…Get information of all surveys. This time we will not use
collect = TRUE, which will return a lazy
query:
allsurveys <- get_inboveg_survey(con)
class(allsurveys)
#> [1] "tbl_Microsoft SQL Server" "tbl_dbi"
#> [3] "tbl_sql" "tbl_lazy"
#> [5] "tbl"If only a part of the survey name is known, you can make use of
wildcards such as %.
partsurveys <- get_inboveg_survey(
con,
survey_name = "%MILKLIM%",
collect = TRUE)
partsurveys
#> # A tibble: 31 × 5
#> Id Name Description Owner creator
#> <int> <chr> <chr> <chr> <chr>
#> 1 4 MILKLIM_Alopecurion Standplaatsonder… MILK… maud_r…
#> 2 5 MILKLIM_WZ_AalstTeralfene Opnamen van PQ's… MILK… floris…
#> 3 6 MILKLIM_Hei(schraal)herstel PQ's in kader va… MILK… floris…
#> 4 7 MILKLIM_Heide Standplaatsonder… MILK… jan_wo…
#> 5 8 MILKLIM_W&Z_Leiebermen_2010_2013 Evaluatie maaibe… MILK… maud_r…
#> 6 9 MILKLIM_W&Z_Geraardsbergen Vegetatieopnames… MILK… luc_va…
#> 7 10 MILKLIM_Heischraal2012 Vegetatieopnames… MILK… cecile…
#> 8 11 MILKLIM_W&Z_Varia Losse opnamen in… MILK… floris…
#> 9 12 MILKLIM_W&Z_Bermen_AfleidingskanaalLeie Ecologische opvo… MILK… els_de…
#> 10 14 MILKLIM_W&Z_OeversLeie Oeveropnamen lan… Maud… luc_va…
#> # ℹ 21 more rowsThe function get_inboveg_header queries the INBOVEG
database for header information (metadata for a vegetation-relevé) for
one or more survey by the name of the survey(s) and the recorder type
(classic, classic-emmer,
classic-ketting, biohab, ppa).
All relevés are selected, also those with ‘needs work’ indicated (0 = no
work needed, 1 = needs work). It is important to realize that the relevé
is not finished yet, species lists can be incomplete, or not all species
have been identified yet. For certain analysis these relevés can better
be excluded (by using dplyr -> filter).
Three examples are given, this can be used as base to continue selecting the data you require.
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)
head(header_info, 10)
#> # A tibble: 10 × 17
#> RecordingGivid NeedsWork SurveyName UserReference Observer LocationCode
#> <chr> <int> <chr> <chr> <chr> <chr>
#> 1 IV2016021012140632 0 OudeLanden_… 5 Alex Ve… Ekeren
#> 2 IV2016021014064327 0 OudeLanden_… 1 Alex Ve… Ekeren
#> 3 IV2016021014244819 0 OudeLanden_… 2 Alex Ve… Ekeren
#> 4 IV2016021015310781 0 OudeLanden_… 4 Alex Ve… Ekeren
#> 5 IV2016021015515026 0 OudeLanden_… 81 Alex Ve… Ekeren
#> 6 IV2016021016074544 0 OudeLanden_… 20 Alex Ve… Ekeren
#> 7 IV2016021016140673 0 OudeLanden_… 17 Alex Ve… Ekeren
#> 8 IV2016021016201725 0 OudeLanden_… 19 Alex Ve… Ekeren
#> 9 IV2016021016335063 0 OudeLanden_… 18 Alex Ve… Ekeren
#> 10 IV2016021016484882 0 OudeLanden_… 23 Alex Ve… Ekeren
#> # ℹ 11 more variables: Latitude <dbl>, Longitude <dbl>, Area <dbl>,
#> # Length <int>, Width <int>, VagueDateType <chr>, VagueDateBegin <chr>,
#> # VagueDateEnd <chr>, SurveyId <int>, RecTypeID <int>, RecTypeName <chr>Get header information from several specific surveys by using
multiple = TRUE.
header_severalsurveys <- get_inboveg_header(
con,
survey_name = c("MILKLIM_Heischraal2012", "NICHE Vlaanderen"),
multiple = TRUE)Get header information of all surveys without collecting the data:
all_header_info <- get_inboveg_header(con)The function get_inboveg_recording() 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.
Several examples are given, this can be used as base to continue selecting the data you require.
First, we show how to get the relevés from one survey and collect the data:
recording_heischraal2012 <- get_inboveg_recording(
con,
survey_name = "MILKLIM_Heischraal2012",
collect = TRUE)
recording_heischraal2012
#> # A tibble: 3,288 × 13
#> Name RecordingGivid UserReference LayerCode CoverCode OriginalName
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 MILKLIM_Heisch… IV20120816113… HS_1001 M 5 Rhytidiadel…
#> 2 MILKLIM_Heisch… IV20120816113… HS_1001 M 5 Pseudoscler…
#> 3 MILKLIM_Heisch… IV20120816113… HS_1001 K 90 Juncus acut…
#> 4 MILKLIM_Heisch… IV20120816113… HS_1001 K 90 Nardus stri…
#> 5 MILKLIM_Heisch… IV20120816113… HS_1001 K 90 Potentilla …
#> 6 MILKLIM_Heisch… IV20120816113… HS_1001 K 90 Anthoxanthu…
#> 7 MILKLIM_Heisch… IV20120816113… HS_1001 K 90 Molinia cae…
#> 8 MILKLIM_Heisch… IV20120816113… HS_1001 K 90 Lysimachia …
#> 9 MILKLIM_Heisch… IV20120816113… HS_1001 K 90 Luzula mult…
#> 10 MILKLIM_Heisch… IV20120816113… HS_1001 K 90 Carex pilul…
#> # ℹ 3,278 more rows
#> # ℹ 7 more variables: ScientificName <chr>, TaxonGroupCode <chr>,
#> # PhenologyCode <chr>, Comment <chr>, CoverageCode <chr>, PctValue <dbl>,
#> # RecordingScale <chr>Here is how to get the relevé for a specific
RecordingGivid:
recording_specific_givid <- get_inboveg_recording(
con,
recording_givid = "IV2012080609161322",
collect = TRUE)Or for multiple RecordingGivid:
recording_specific_givid <- get_inboveg_recording(
con,
recording_givid = c("IV2012080609161322", "IV2012081611384756"),
collect = TRUE)The above is very useful in tandem with
get_inboveg_header() to first search for all relevés
belonging to one or more surveys and further filter these records to
only the relevés you require based on the relevé metadata (such as date,
observer, …).
Or based on a user reference:
recording_specific_userref <- get_inboveg_recording(
con,
user_reference = "HS_1001",
collect = TRUE)Get all recordings from MILKLIM surveys (partial matching), without collecting the data:
recording_milkim <- get_inboveg_recording(
con,
survey_name = "%MILKLIM%")Get recordings from several specific surveys:
recording_severalsurveys <- get_inboveg_recording(
con,
survey_name = c("MILKLIM_Heischraal2012", "NICHE Vlaanderen"),
collect = TRUE)Get all relevés of all surveys, without collecting the data:
allrecordings <- get_inboveg_recording(con)The function get_inboveg_ppa() is similar in use as
get_inboveg_recording(), but can be used specifically to
get point to plant distance type data (PPA) from the INBOVEG
database.
allppa <- get_inboveg_ppa(con)The function get_inboveg_classification queries the
INBOVEG database for information on the field classification (N2000 or
BWK-code) of the relevé for one or more survey(s) by the name of the
survey.
Two examples are given, this can be used as base to continue selecting the data you require.
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)
classif_info
#> # A tibble: 1 × 9
#> RecordingGivid Name Classif ActionGroup ListName LocalClassification
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 IV2013031814425352 MILKLIM_H… 4010 N2k Habitat… NA
#> # ℹ 3 more variables: Habitattype <chr>, Cover <chr>, PctValue <dbl>Get the classification from several specific surveys
classif_info <- get_inboveg_classification(
con,
survey_name = c("MILKLIM_Heischraal2012", "NICHE Vlaanderen"),
multiple = TRUE)
classif_infoGet all surveys, all classifications without collecting the data:
all_codes <- get_inboveg_classification(con)The function get_inboveg_qualifier()queries the INBOVEG
database for qualifier information on recordings for one or more
surveys. These qualifiers give information on management (management
qualifier MQ) or location description (site qualifier
SQ).
Get the qualifiers from one survey:
qualifiers_heischraal2012 <- get_inboveg_qualifier(
con,
survey_name = "MILKLIM_Heischraal2012")
head(qualifiers_heischraal2012)
#> Name RecordingGivid UserReference
#> 1 MILKLIM_Heischraal2012 IV2012081615083167 HS_008
#> 2 MILKLIM_Heischraal2012 IV2012081613133274 HS_009
#> 3 MILKLIM_Heischraal2012 IV2013041614525228 HS_035
#> 4 MILKLIM_Heischraal2012 IV2012081609450300 HS_036
#> 5 MILKLIM_Heischraal2012 IV2012081610204607 HS_037
#> 6 MILKLIM_Heischraal2012 IV2012081610393743 HS_044
#> Observer QualifierType Q1Code
#> 1 Cécile Herr en Robin Guelinckx MQ A
#> 2 Cécile Herr en Robin Guelinckx MQ A
#> 3 Cécile Herr, Patrik Oosterlynck, Robin Guelinckx MQ A
#> 4 Cécile Herr en Robin Guelinckx MQ A
#> 5 Cécile Herr, Robin Guelinckx, Patrik Oosterlynck MQ A
#> 6 Cécile Herr en Robin Guelinckx MQ A
#> Q1Description Q2Code Q2Description Q3Code Q3Description Elucidation NotSure
#> 1 <NA> PBuis Peilbuizen GUPP042A <NA> 0
#> 2 <NA> PBuis Peilbuizen GUPP043B <NA> 0
#> 3 Active PBuis Peilbuizen WALP161X <NA> 0
#> 4 <NA> PBuis Peilbuizen WALP157X <NA> 0
#> 5 <NA> PBuis Peilbuizen WALP117X <NA> 0
#> 6 <NA> PBuis Peilbuizen WALP162X <NA> 0
#> ParentID QualifierResource
#> 1 NA <NA>
#> 2 NA <NA>
#> 3 NA RS2012060811060080
#> 4 NA <NA>
#> 5 NA <NA>
#> 6 NA <NA>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 with
multiple = TRUE:
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)The function get_inboveg_layer_cover queries the INBOVEG
database for cover information per layer on recordings for one or more
surveys.
Get the layer cover information from one survey
layerinfo_heischraal2012 <- get_inboveg_layer_cover(
con,
survey_name = "MILKLIM_Heischraal2012")Get all layer cover information from MILKLIM surveys (partial matching)
layerinfo_milkim <- get_inboveg_layer_cover(
con,
survey_name = "%MILKLIM%")Get layer cover information from several specific surveys
layerinfo_severalsurveys <- get_inboveg_layer_cover(
con,
survey_name = c("MILKLIM_Heischraal2012", "NICHE Vlaanderen"),
multiple = TRUE)Get all layer cover information of all surveys
all_layerinfo <- get_inboveg_layer_cover(con)The function get_inboveg_layer_qualifier()queries the
INBOVEG database for layer qualifier information on recordings for one
or more surveys.
Get the layer qualifiers from one survey
layerqualifier_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_Heischraal2012", "NICHE Vlaanderen"),
multiple = TRUE)Get all layer qualifiers of all surveys
alllayerqualifiers <- get_inboveg_layer_qualifier(con)The function get_inboveg_relation_recording() queries
the INBOVEG database for relational information on recordings for one or
more surveys based on parent (classic-chain/bucket) and Child (classic)
relationships.
Get all parent-child-relations from N2000meetnet surveys
(partial matching):
relations_n2000meetnet <- get_inboveg_relation_recording(
con,
survey_name = "%N2000meetnet%")
relations_n2000meetnet#> # Source: SQL [?? x 7]
#> # Database: Microsoft SQL Server 13.00.6419[INBO\toon_westra@INBO-SQL07-PRD\LIVE/D0010_00_Cydonia]
#> Name RecordingId Child_GIVID Child_UserRef ParentId Parent_GIVID
#> <chr> <int> <chr> <chr> <int> <chr>
#> 1 N2000meetnet_Dui… 44283 IV20190218… 13594417_2170 44282 IV201902180…
#> 2 N2000meetnet_Dui… 44285 IV20190218… 10334001_2190 44284 IV201902181…
#> 3 N2000meetnet_Dui… 44287 IV20190218… 10186545_213… 44286 IV201902181…
#> 4 N2000meetnet_Dui… 44290 IV20190218… 10186545_2170 44289 IV201902181…
#> 5 N2000meetnet_Dui… 44292 IV20190218… 13561649_2170 44291 IV201902181…
#> 6 N2000meetnet_Dui… 44294 IV20190218… 11595569_2170 44293 IV201902181…
#> 7 N2000meetnet_Dui… 44296 IV20190218… 1240881_2170 44295 IV201902181…
#> 8 N2000meetnet_Dui… 44298 IV20190218… 13823793_2170 44297 IV201902181…
#> 9 N2000meetnet_Dui… 44300 IV20190218… 12644145_2170 44299 IV201902181…
#> 10 N2000meetnet_Dui… 44302 IV20190218… 10260273_213… 44301 IV201902181…
#> # ℹ more rows
#> # ℹ 1 more variable: Parent_UserRef <chr>Get the parent-child-relations from several specific surveys:
relations_severalsurveys <- get_inboveg_relation_recording(
con,
survey_name = c("DeBlankaart-1985-Beheer", "N2000meetnet_Grasland"),
multiple = TRUE)When you have retrieved the data from INBOVEG using one of the
inbodb functions in the previous section, you can easily
work with these data in R or export the data.
We recommend to use the dplyr package for
basic as well as advanced data wrangling. For instance:
dplyr::mutate() adds new variables that are
functions of existing variables
dplyr::select() picks variables based on their
names.
dplyr::filter() picks cases (rows) based on their
values.
dplyr::summarise() reduces multiple values down to a
single summary.
dplyr::arrange() changes the ordering of the
rows.
For exporting the data we can make use of the readr package.
Here is a simple example:
library(inbodb)
library(dplyr)
library(readr)
# get the data
con <- connect_inbo_dbase("D0010_00_Cydonia")
recording_heischraal2012 <- get_inboveg_recording(
con,
survey_name = "MILKLIM_Heischraal2012",
collect = TRUE)
# close the connection
dbDisconnect(con)
rm(con)
# do some data wrangling with dplyr
# here we remove one column
output_heischraal2012 <- recording_heischraal2012 %>%
select(-OriginalName)
# export the data to a csv file that can be easily read by excel
write_excel_csv2(
x = output_heischraal2012,
file = "data/output_heischraal2012.csv"
)