Package: ReLTER 3.0.0

Alessandro Oggioni

ReLTER: An Interface for the eLTER Community

ReLTER provides access to DEIMS-SDR (https://deims.org/), and allows interaction with data and software implemented by eLTER Research Infrastructure (RI) thus improving data sharing among European LTER projects. ReLTER uses the R language to access and interact with the DEIMS-SDR archive of information shared by the Long Term Ecological Research (LTER) network. This package grew within eLTER H2020 as a major project that will help advance the development of European Long-Term Ecosystem Research Infrastructures (eLTER RI - https://elter-ri.eu). The ReLTER package functions in particular allow to: - retrieve the information about entities (e.g. sites, datasets, and activities) shared by DEIMS-SDR (see e.g. get_site_info function); - interact with the ODSEurope (maps.opendatascience.eu) starting with the dataset shared by DEIMS-SDR (https://deims.org/) (see e.g. the get_site_ODS() function); - use the eLTER site informations to download and crop geospatial data from other platforms (see e.g. get_site_ODS function()); - improve the quality of the dataset (see e.g. get_id_worms()). Functions currently implemented are derived from discussions of the needs among the eLTER users community. The ReLTER package will continue to follow the progress of eLTER-RI and evolve, adding new tools and improvements as required.

Authors:Alessandro Oggioni [aut, cre, fnd], Micha Silver [aut, ctb], Paolo Tagliolato [aut, ctb], Luigi Ranghetti [aut, ctb], Allison Horst [rev], Will Bolton [rev], Mauro Lepore [edt]

ReLTER_3.0.0.tar.gz
ReLTER_3.0.0.zip(r-4.6)ReLTER_3.0.0.zip(r-4.5)ReLTER_3.0.0.zip(r-4.4)
ReLTER_3.0.0.tgz(r-4.5-any)ReLTER_3.0.0.tgz(r-4.4-any)
ReLTER_3.0.0.tar.gz(r-4.6-any)ReLTER_3.0.0.tar.gz(r-4.5-any)
ReLTER_3.0.0.tgz(r-4.5-emscripten)
ReLTER.pdf |ReLTER.html
ReLTER/json (API)
NEWS

# Install 'ReLTER' in R:
install.packages('ReLTER', repos = c('https://packages.ropensci.org', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ropensci/relter/issues

Pkgdown/docs site:https://docs.ropensci.org

Datasets:

On CRAN:

Conda:

biodiversity-informaticsdata-scienceecologyelterresearch-infrastructure

5.41 score 13 stars 8 scripts 31 exports 102 dependencies

Last updated from:a6675fd79a (on main). Checks:2 NOTE, 3 OK, 5 ERROR. Indexed: yes.

TargetResultTotal timeArtifact
linux-devel-x86_64NOTE341
pkgdown docsOK396
source / vignettesOK387
linux-release-x86_64NOTE353
macos-release-arm64ERROR203
macos-oldrel-arm64ERROR205
windows-develERROR307
windows-releaseERROR346
windows-oldrelERROR394
wasm-releaseOK220

Exports:%>%get_activity_infoget_dataset_infoget_deims_API_versionget_deims_base_urlget_location_infoget_network_sitesget_sensor_infoget_site_EcoDataCubeget_site_infoget_site_speciesOccurrencesget_sites_interactiveget_sites_within_3d_bounding_boxget_sites_within_radiusget_zenodo_datamap_occ_gbif2eltermap_occ_inat2eltermap_occ_obis2elterpackage_settingsproduce_network_points_mapproduce_site_mapproduce_site_observedProperties_pieproduce_site_observedProperties_waffleproduce_site_qrcodereporting_produce_data_object_v1.3reporting_produce_data_object_v2.0reporting_save_archivesave_occ_eLTER_reporting_Archiveset_deims_base_urltaxon_id_pesitaxon_id_worms

Dependencies:abindaskpassassertthatbase64encbslibcachemclassclassIntclicpp11crayoncrosstalkcurldata.tableDBIdigestdplyrdtplyre1071evaluatefarverfastmapfontawesomefsgenericsgeojsonsfgeometriesggforceggplot2ggspatialgluegtablehighrhmshtmltoolshtmlwidgetshttr2isobandjpegjqrjquerylibjsonifyjsonliteKernSmoothknitrlabelinglatticelazyevalleafletleaflet.providerslifecyclelubridatemagrittrMASSmemoisemimeopensslpillarpkgconfigpngpolyclipprettyunitsprogressproxypurrrqrcodeR6rapidjsonrrappdirsrasterRColorBrewerRcpprlangrmarkdownrosms2S7sassscalessfsfheadersspstringistringrsyssystemfontsterratibbletidyrtidyselecttimechangetinytextweenrunitsutf8vctrsviridisLitewithrwkxfunxml2yaml

How to retrieve occurrence records by exploiting the {ReLTER} get_site_speciesOccurrences() function

Rendered fromoccurrences_into_site.Rmdusingknitr::knitron Sep 21 2025.

Last update: 2025-08-22
Started: 2022-12-22

Obtain information about one LTER Site using the DEIMS ID

Rendered fromsingle_site_information.Rmdusingknitr::knitron Sep 21 2025.

Last update: 2025-08-22
Started: 2025-08-22

Obtain list of contacts from several DEIMS ID's (in csv file)

Rendered frommulti_sites_contacts.Rmdusingknitr::knitron Sep 21 2025.

Last update: 2025-08-22
Started: 2025-08-22

Obtaining information about many LTER Sites

Rendered frommulti_sites_information.Rmdusingknitr::knitron Sep 21 2025.

Last update: 2025-08-22
Started: 2025-08-22

Run ReLTER in a Docker container

Rendered fromrocker_ReLTER.Rmdusingknitr::knitron Sep 21 2025.

Last update: 2025-08-22
Started: 2022-04-15

Readme and manuals

Help Manual

Help pageTopics
Construct full url for downloadEDC_construct_full_url
eLTER Data Reporting Format (DRF)eLTER_data_reporting_format
Obtain the information about of an eLTER activity.get_activity_info
Obtain the information about of an eLTER dataset.get_dataset_info
Get version of DEIMS-SDR APIget_deims_API_version
Get DEIMS-SDR base URLget_deims_base_url
Obtain the information about of an eLTER location.get_location_info
Retrieve a list of sites in an eLTER Network.get_network_sites
Obtain the information about of an eLTER sensor.get_sensor_info
Acquire various raster layers from EcoDataCube EU and crop to an eLTER site boundary.get_site_EcoDataCube
Obtain details about an eLTER site.get_site_info
Trims by eLTER site the species occurrence from different sourcesget_site_speciesOccurrences
Select sites by choosing a 3d bounding box through an interactive GUI.get_sites_interactive
select sites within a 3d bounding boxget_sites_within_3d_bounding_box
Get all sites within a given distance of a point locationget_sites_within_radius
Obtain the data from a dataset deposited in Zenodo record.get_zenodo_data
Harmonize outputs of get_site_speciesOccurrence and map them into eLTER reporting formatmap_occ_gbif2elter
Harmonize outputs of get_site_speciesOccurrence and map them into eLTER reporting formatmap_occ_inat2elter
Harmonize outputs of get_site_speciesOccurrence and map them into eLTER reporting formatmap_occ_obis2elter
Package settings that can be changed by the userpackage_settings
Provide a map (image) of sites in an eLTER Network.produce_network_points_map
Provide a map object of a sites LTER.produce_site_map
Produce a pie chart of the observed properties collected in a site LTER.produce_site_observedProperties_pie
Produce a waffle chart of the observed properties collected in a site LTER.produce_site_observedProperties_waffle
Obtain the QRCode of any DEIMS-SDR entities.produce_site_qrcode
Compose an eLTER Data Reporting Format objectreporting_produce_data_object_v1.3
Compose an eLTER Data Reporting Format objectreporting_produce_data_object_v2.0
Creates an archive with files following the eLTER reportingFormatreporting_save_archive
Creates an archive with files following the eLTER reportingFormatsave_occ_eLTER_reporting_Archive
Set DEIMS-SDR API base URLset_deims_base_url
Provide a taxon ID LSID to a taxon list.taxon_id_pesi
Enrich and certify a list of species names by comparing with WoRMS.taxon_id_worms