{"id":"https://openalex.org/W4407250907","doi":"https://doi.org/10.1016/j.ecoinf.2026.103803","title":"Rarefy: An R Package for the Calculation of Taxonomic, Functional and Phylogenetic Sample-Based Spatially Explicit Rarefaction Curves","display_name":"Rarefy: An R Package for the Calculation of Taxonomic, Functional and Phylogenetic Sample-Based Spatially Explicit Rarefaction Curves","publication_year":2025,"publication_date":"2025-01-01","ids":{"openalex":"https://openalex.org/W4407250907","doi":"https://doi.org/10.1016/j.ecoinf.2026.103803"},"language":"en","primary_location":{"id":"doi:10.1016/j.ecoinf.2026.103803","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.ecoinf.2026.103803","pdf_url":null,"source":{"id":"https://openalex.org/S195809937","display_name":"Ecological Informatics","issn_l":"1574-9541","issn":["1574-9541","1878-0512"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Ecological Informatics","raw_type":"journal-article"},"type":"preprint","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1016/j.ecoinf.2026.103803","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069287753","display_name":"Elisa Thouverai","orcid":null},"institutions":[{"id":"https://openalex.org/I142444530","display_name":"University of Trieste","ror":"https://ror.org/02n742c10","country_code":"IT","type":"education","lineage":["https://openalex.org/I142444530"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Elisa Thouverai","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063114135","display_name":"Sandrine Pavoine","orcid":"https://orcid.org/0000-0003-2767-6484"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sandrine Pavoine","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027832690","display_name":"Enrico Tordoni","orcid":"https://orcid.org/0000-0002-9722-6692"},"institutions":[{"id":"https://openalex.org/I56085075","display_name":"University of Tartu","ror":"https://ror.org/03z77qz90","country_code":"EE","type":"education","lineage":["https://openalex.org/I56085075"]}],"countries":["EE"],"is_corresponding":false,"raw_author_name":"Enrico Tordoni","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080212261","display_name":"Alessandro Chiarucci","orcid":"https://orcid.org/0000-0003-1160-235X"},"institutions":[{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alessandro Chiarucci","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038145095","display_name":"Carlo Ricotta","orcid":"https://orcid.org/0000-0003-0818-3959"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Carlo Ricotta","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053455920","display_name":"Duccio Rocchini","orcid":"https://orcid.org/0000-0003-0087-0594"},"institutions":[{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Duccio Rocchini","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5036259500","display_name":"Giovanni Bacaro","orcid":"https://orcid.org/0000-0003-0946-4496"},"institutions":[{"id":"https://openalex.org/I142444530","display_name":"University of Trieste","ror":"https://ror.org/02n742c10","country_code":"IT","type":"education","lineage":["https://openalex.org/I142444530"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giovanni Bacaro","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5069287753"],"corresponding_institution_ids":["https://openalex.org/I142444530"],"apc_list":{"value":2510,"currency":"USD","value_usd":2510},"apc_paid":{"value":2510,"currency":"USD","value_usd":2510},"fwci":1.7561,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.80025279,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"96","issue":null,"first_page":"103803","last_page":"103803"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10005","display_name":"Ecology and Vegetation Dynamics Studies","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/2309","display_name":"Nature and Landscape Conservation"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10005","display_name":"Ecology and Vegetation Dynamics Studies","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/2309","display_name":"Nature and Landscape Conservation"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11354","display_name":"Evolution and Paleontology Studies","score":0.9937000274658203,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10895","display_name":"Species Distribution and Climate Change","score":0.9930999875068665,"subfield":{"id":"https://openalex.org/subfields/2302","display_name":"Ecological Modeling"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/rarefaction","display_name":"Rarefaction (ecology)","score":0.8270608186721802},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.633003830909729},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6317757964134216},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.594890296459198},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.37834423780441284},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.344235897064209},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.32970547676086426},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.262911856174469},{"id":"https://openalex.org/keywords/paleontology","display_name":"Paleontology","score":0.22320556640625},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.18990680575370789},{"id":"https://openalex.org/keywords/species-richness","display_name":"Species richness","score":0.07451680302619934},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.07281443476676941},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.06996715068817139}],"concepts":[{"id":"https://openalex.org/C132705693","wikidata":"https://www.wikidata.org/wiki/Q7294543","display_name":"Rarefaction (ecology)","level":3,"score":0.8270608186721802},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.633003830909729},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6317757964134216},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.594890296459198},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.37834423780441284},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.344235897064209},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.32970547676086426},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.262911856174469},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.22320556640625},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.18990680575370789},{"id":"https://openalex.org/C53565203","wikidata":"https://www.wikidata.org/wiki/Q17146659","display_name":"Species richness","level":2,"score":0.07451680302619934},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.07281443476676941},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.06996715068817139},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1016/j.ecoinf.2026.103803","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.ecoinf.2026.103803","pdf_url":null,"source":{"id":"https://openalex.org/S195809937","display_name":"Ecological Informatics","issn_l":"1574-9541","issn":["1574-9541","1878-0512"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Ecological Informatics","raw_type":"journal-article"},{"id":"doi:10.2139/ssrn.5128618","is_oa":true,"landing_page_url":"https://doi.org/10.2139/ssrn.5128618","pdf_url":null,"source":{"id":"https://openalex.org/S4210172589","display_name":"SSRN Electronic Journal","issn_l":"1556-5068","issn":["1556-5068"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1318003438","host_organization_name":"RELX Group (Netherlands)","host_organization_lineage":["https://openalex.org/I1318003438"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},{"id":"pmh:oai:arts.units.it:11368/3132758","is_oa":false,"landing_page_url":"https://hdl.handle.net/11368/3132758","pdf_url":null,"source":{"id":"https://openalex.org/S4306400480","display_name":"ArTS Archivio della ricerca di Trieste (University of Trieste https://www.units.it/)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I142444530","host_organization_name":"University of Trieste","host_organization_lineage":["https://openalex.org/I142444530"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:cris.unibo.it:11585/1063077","is_oa":true,"landing_page_url":"https://www.sciencedirect.com/science/article/pii/S1574954126002098","pdf_url":null,"source":{"id":"https://openalex.org/S4306402579","display_name":"Archivio istituzionale della ricerca (Alma Mater Studiorum Universit\u00e0 di Bologna)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210117483","host_organization_name":"Istituto di Ematologia di Bologna","host_organization_lineage":["https://openalex.org/I4210117483"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1016/j.ecoinf.2026.103803","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.ecoinf.2026.103803","pdf_url":null,"source":{"id":"https://openalex.org/S195809937","display_name":"Ecological Informatics","issn_l":"1574-9541","issn":["1574-9541","1878-0512"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Ecological Informatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.46000000834465027,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W74614967","https://openalex.org/W1542024621","https://openalex.org/W1971083126","https://openalex.org/W1983874169","https://openalex.org/W2002303396","https://openalex.org/W2022825068","https://openalex.org/W2026094939","https://openalex.org/W2032683107","https://openalex.org/W2039516620","https://openalex.org/W2093701054","https://openalex.org/W2103336148","https://openalex.org/W2104022455","https://openalex.org/W2107794977","https://openalex.org/W2109052809","https://openalex.org/W2116601594","https://openalex.org/W2118502404","https://openalex.org/W2129802470","https://openalex.org/W2132853588","https://openalex.org/W2149765389","https://openalex.org/W2162873750","https://openalex.org/W2166655850","https://openalex.org/W2168603378","https://openalex.org/W2171783890","https://openalex.org/W2343536809","https://openalex.org/W2411824431","https://openalex.org/W2460850757","https://openalex.org/W2605088440","https://openalex.org/W2735342869","https://openalex.org/W2901806538","https://openalex.org/W2911335739","https://openalex.org/W2913278882","https://openalex.org/W2969744633","https://openalex.org/W3001531191","https://openalex.org/W3033953255","https://openalex.org/W6603038438","https://openalex.org/W6767822661"],"related_works":["https://openalex.org/W2104022455","https://openalex.org/W2066769347","https://openalex.org/W2095378770","https://openalex.org/W2136325639","https://openalex.org/W2398357795","https://openalex.org/W2159973045","https://openalex.org/W2164787828","https://openalex.org/W2144958703","https://openalex.org/W2080410528","https://openalex.org/W2529820324"],"abstract_inverted_index":{"AbstractRarefaction":[0],"methods":[1,28,53],"are":[2,29,73],"statistical":[3],"techniques":[4],"used":[5],"to":[6,35,93,122,146,183],"estimate":[7],"diversity":[8,20,41,89,126,143,195,213],"for":[9,59,104,185],"an":[10,78,163,215],"incremental":[11],"number":[12],"of":[13,24,86,98,127,155,168,203],"samples,":[14],"generating":[15],"rarefaction":[16,52,138,189],"curves":[17],"that":[18,81,217],"depict":[19],"as":[21,57],"a":[22,178],"function":[23],"sample":[25,106],"size.":[26],"These":[27,160],"widely":[30],"applied":[31,119],"in":[32,171,188,220],"ecological":[33],"research":[34],"compare":[36],"taxonomic,":[37,99],"functional,":[38,100],"and":[39,65,180,210],"phylogenetic":[40,102],"across":[42],"samples":[43],"with":[44],"varying":[45],"collection":[46],"efforts.":[47],"However,":[48],"incorporating":[49],"spatially":[50,109,136,156],"explicit":[51,137],"has":[54],"become":[55],"essential,":[56],"accounting":[58],"spatial":[60,169,186],"autocorrelation":[61,170],"substantially":[62],"influences":[63],"results":[64],"alters":[66],"how":[67],"biodiversity":[68],"hotspots":[69],"or":[70,101],"conservation":[71],"priorities":[72],"identified.This":[74],"paper":[75],"describes":[76],"Rarefy,":[77],"R":[79],"package":[80,121,175],"introduces":[82],"novel":[83],"functions":[84,139],"capable":[85],"handling":[87],"any":[88],"metric,":[90],"allowing":[91],"users":[92],"compute":[94],"the":[95,120,124,131,151,172,201],"expected":[96],"values":[97,144],"indices":[103],"reduced":[105],"sizes":[107],"under":[108],"constrained,":[110],"distance-based":[111],"sampling":[112],"unit":[113],"arrangements.To":[114],"demonstrate":[115],"its":[116],"utility,":[117],"we":[118],"assess":[123],"functional":[125,152],"plant":[128,158],"communities":[129],"along":[130],"northern":[132],"Adriatic":[133],"coastline.":[134],"The":[135],"consistently":[140],"produced":[141],"lower":[142],"compared":[145],"their":[147],"non-spatial":[148],"counterparts,":[149],"reflecting":[150],"redundancy":[153],"typical":[154],"adjacent":[157],"communities.":[159],"differences":[161],"provide":[162],"indirect":[164],"yet":[165],"effective":[166],"measure":[167],"dataset.The":[173],"Rarefy":[174],"offers":[176],"ecologists":[177],"robust":[179],"straightforward":[181],"tool":[182],"account":[184],"constraints":[187],"analyses,":[190],"yielding":[191],"more":[192],"ecologically":[193],"meaningful":[194],"estimates.":[196],"Future":[197],"developments":[198],"will":[199],"include":[200],"integration":[202],"null":[204],"models,":[205],"enabling":[206],"comparisons":[207],"between":[208],"observed":[209],"randomized":[211],"community":[212],"patterns,":[214],"approach":[216],"is":[218],"exemplified":[219],"this":[221],"study.":[222]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-06-07T08:38:57.713557","created_date":"2025-10-10T00:00:00"}