Package: ReLTER 2.1.1

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. [get_site_ODS](https://docs.ropensci.org/ReLTER/reference/get_site_ODS.html) 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_2.1.1.tar.gz
ReLTER_2.1.1.zip(r-4.5)ReLTER_2.1.1.zip(r-4.4)ReLTER_2.1.1.zip(r-4.3)
ReLTER_2.1.1.tgz(r-4.4-any)ReLTER_2.1.1.tgz(r-4.3-any)
ReLTER_2.1.1.tar.gz(r-4.5-noble)ReLTER_2.1.1.tar.gz(r-4.4-noble)
ReLTER_2.1.1.tgz(r-4.4-emscripten)
ReLTER.pdf |ReLTER.html✨
ReLTER/json (API)
NEWS

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

Peer review:

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

On CRAN:

biodiversity-informaticsdata-scienceecologyelterresearch-infrastructure

44 exports 12 stars 1.64 score 220 dependencies

Last updated 7 months agofrom:1715916c18 (on main)

Exports:%>%elter_write_rdataget_activity_infoget_dataset_infoget_deims_API_versionget_deims_base_urlget_ilter_envcharactsget_ilter_generalinfoget_ilter_observedPropertiesget_ilter_research_topicsget_network_envcharactsget_network_observedPropertiesget_network_related_resourcesget_network_research_topicsget_network_sitesget_sensor_infoget_sensor_observed_propertiesget_site_infoget_site_MODISget_site_ODSget_site_speciesOccurrencesget_sos_foiget_sos_obsget_sos_procedure_infoget_sos_procedurelistget_zenodo_datamap_occ_gbif2eltermap_occ_inat2eltermap_occ_obis2elterpackage_settingsproduce_network_points_mapproduce_site_mapproduce_site_observedProperties_pieproduce_site_observedProperties_waffleproduce_site_qrcodeproduce_zenodo_recordproduce_zenodo_record_from_elter_reportingreporting_compose_file_namereporting_produce_data_object_v1.3reporting_save_archivesave_occ_eLTER_reporting_Archiveset_deims_base_urltaxon_id_pesitaxon_id_worms

Dependencies:abindapeaskpassassertthatatom4Rbackportsbase64encbitbit64bitopsboldbrewbslibcachemcallrcheckmateclassclassIntclicliprclustercodetoolscolorspacecommonmarkcountrycodecpp11crayoncrosstalkcrulcurldata.tableDBIdescdichromatdigestdotCall64dplyrDTdtplyre1071evaluateextrafontextrafontdbfansifarverfastmapfastmatchfieldsfilelockfontawesomeforeachforeignFormulafsgdalUtilitiesgenericsgeodatageojsongeojsoniogeojsonsfgeometriesggforceggplot2gluegridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttpcodehttpuvhttrhttr2igraphisobanditeratorsjpegjqrjquerylibjsonifyjsonliteKernSmoothkeyringknitrlabelinglaterlatticelazyevalleafemleafletleaflet.providersleafsynclifecyclelubridatelwgeommagrittrmapsMASSMatrixmemoisemgcvmimeMODIStspmunsellnatservnlmennetoaiopensslpbapplyphangornpillarpkgbuildpkgconfigpkgloadplyrpngpolyclipprettyunitsprocessxprogresspromisesprotoliteproxypspurrrqrcodequadprogR6rapidjsonrrappdirsrasterratelimitrrbibutilsRColorBrewerRcppRcppEigenRCurlrdflibRdpackreadrrebirdredlandrentrezrexrgbifridigbioritisrlangrmarkdownrnaturalearthrnclrosmrotlroxygen2rpartrprojrootrredlistrstudioapiRttf2pt1rvertnetrworldmaps2sassscalessfsfheaderssodiumsolriumspspamspoccstarsstringistringrsyssystemfontstaxizeterratibbletidyrtidyselecttimechangetinytextmaptmaptoolstriebeardtweenrtzdbunitsurltoolsutf8V8vctrsviridisviridisLitevroomwafflewebshotwhiskerwidgetframeWikidataQueryServiceRWikidataRWikipediRwikitaxawithrwkworrmsxfunXMLxml2xsltxtsyamlzen4Rzipzoo

Readme and manuals

Help Manual

Help pageTopics
eLTER write Rdata dataelter_write_rdata
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 a list of all Environmental Characteristics of ILTER sites.get_ilter_envcharacts
Download information of all ILTER sites or a subset of ILTER sites.get_ilter_generalinfo
Obtain information about the observed properties collected of all sites ILTER.get_ilter_observedProperties
Obtain the information about the Research Topics of ILTER sites.get_ilter_research_topics
Obtain a list of all Environmental Characteristics of sites in an eLTER Network.get_network_envcharacts
Obtain a list of all the observed properties of sites in an eLTER Network.get_network_observedProperties
Obtain information about the Related Resources (dataset and activity) of a eLTER Network.get_network_related_resources
Obtain a list of Research Topics handled in an eLTER Network.get_network_research_topics
Retrieve a list of sites in an eLTER Network.get_network_sites
Obtain the information about of an eLTER sensor.get_sensor_info
Obtain the observed properties measured by a sensor.get_sensor_observed_properties
Obtain details about an eLTER site.get_site_info
Acquire a time series of MODIS satellite productsget_site_MODIS
Acquire various raster layers from ODS Europe and crops to an eLTER site boundary.get_site_ODS
Trims by eLTER site the species occurrence from different sourcesget_site_speciesOccurrences
Obtain the information about the feature of interest.get_sos_foi
Obtain the observations from a Sensor Observation Service (SOS).get_sos_obs
Obtain the information from a sensor.get_sos_procedure_info
List the procedures of a Sensor Observations Service (SOS).get_sos_procedurelist
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
Map of aggregated time series of MODIS imagesplot_agg_map
Plot a time series of averaged pixel values from MODIS images.plot_timeseries
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
Create a record in Zenodoproduce_zenodo_record
Create a record in Zenodo from eLTER data reporting formatproduce_zenodo_record_from_elter_reporting
eLTER reporting format naming convention for filesreporting_compose_file_name
Compose an eLTER Data Reporting Format objectreporting_produce_data_object_v1.3
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