{ "_id": "6a115f57acfb0bcc41ced1b8", "Package": "diathor", "Type": "Package", "Title": "Calculate Ecological Information and Diatom Based Indices", "Version": "0.1.6", "Authors@R": "c(\nperson(\"Maria Mercedes\", \"Nicolosi Gelis\", email = \"mercedesnicolosi@ilpla.edu.ar\", role = \"aut\", comment = c(ORCID = \"0000-0001-6324-7930\")),\nperson(\"Maria Belen\", \"Sathicq\", email = \"mbelen@ilpla.edu.ar\", role = \"aut\", comment = c(ORCID = \"0000-0002-3534-8950\")),\nperson(\"Joaquin\", \"Cochero\", email = \"jcochero@ilpla.edu.ar\", role = \"cre\", comment = c(ORCID = \"0000-0003-3957-6819\")))", "Maintainer": "Joaquin Cochero ", "Description": "Calculate multiple biotic indices using diatoms from\nenvironmental samples. Diatom species are recognized by their\nspecies' name using a heuristic search, and their ecological\ndata is retrieved from multiple sources. It includes\nnumber/shape of chloroplasts diversity indices, size classes,\necological guilds, and multiple biotic indices. It outputs both\na dataframe with all the results and plots of all the obtained\ndata in a defined output folder. - Sample data was taken from\nNicolosi Gelis, Cochero & Gómez (2020,\n). - The package uses the\n'Diat.Barcode' database to calculate morphological and\necological information by Rimet & Couchez (2012,\n),and the combined classification of\nguilds and size classes established by B-Béres et al. (2017,\n). - Current diatom-based\nbiotic indices include the DES index by Descy (1979) - EPID\nindex by Dell'Uomo (1996, ISBN: 3950009002) - IDAP index by\nPrygiel & Coste (1993, ) - ID-CH index\nby Hürlimann & Niederhauser (2007) - IDP index by Gómez &\nLicursi (2001, ) - ILM index by\nLeclercq & Maquet (1987) - IPS index by Coste (1982) - LOBO\nindex by Lobo, Callegaro, & Bender (2002, ISBN:9788585869908) -\nSLA by Sládeček (1986, ) - TDI\nindex by Kelly, & Whitton (1995, ) -\nSPEAR(herbicide) index by Wood, Mitrovic, Lim, Warne, Dunlop, &\nKefford (2019, ) - PBIDW\nindex by Castro-Roa & Pinilla-Agudelo (2014) - DISP index by\nStenger-Kovács et al. (2018,\n) - EDI index by Chamorro et\nal. (2024, ) - DDI index by\nÁlvarez-Blanco et al. (2013, )\n- PDISE index by Kahlert et al. (2023,\n).", "License": "GNU General Public License", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-23 07:59:41 UTC", "User": "root" }, "Author": "Maria Mercedes Nicolosi Gelis [aut]\n(), Maria Belen Sathicq\n[aut] (), Joaquin\nCochero [cre] ()", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://limnolab.r-universe.dev", "Date/Publication": "2025-11-24 15:13:07 UTC", "RemoteUrl": "https://github.com/limnolab/diathor", "RemoteRef": "HEAD", "RemoteSha": "1b058521e06fbde6ac20da324440c047e1777c3b", "MD5sum": "40d8a31d820171d7d51d95c543e486dc", "_user": "limnolab", "_type": "src", "_file": "diathor_0.1.6.tar.gz", "_fileid": "1a8be87d82ab82f317f700903cac5a2d208cf473214c61965a152bf760ba92c2", "_filesize": 1972734, "_sha256": "1a8be87d82ab82f317f700903cac5a2d208cf473214c61965a152bf760ba92c2", "_created": "2026-05-23T07:59:41.000Z", "_published": "2026-05-23T08:03:35.729Z", "_distro": "noble", "_jobs": [ { 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"https://github.com/limnolab/diathor", "_realowner": "limnolab", "_cranurl": true, "_releases": [ { "version": "0.0.1", "date": "2020-11-26" }, { "version": "0.0.4", "date": "2021-02-24" }, { "version": "0.0.5", "date": "2021-04-03" }, { "version": "0.0.6", "date": "2021-05-18" }, { "version": "0.0.9", "date": "2021-11-20" }, { "version": "0.1.0", "date": "2022-03-16" }, { "version": "0.1.4", "date": "2024-09-20" }, { "version": "0.1.5", "date": "2024-12-20" } ], "_exports": [ "diat_cemfgs_rb", "diat_checkName", "diat_ddi", "diat_des", "diat_disp", "diat_diversity", "diat_edi", "diat_epid", "diat_getDiatBarcode", "diat_guilds", "diat_idap", "diat_idch", "diat_idp", "diat_ilm", "diat_ips", "diat_loadData", "diat_lobo", "diat_morpho", "diat_pbidw", "diat_pdise", "diat_size", "diat_sla", "diat_spear", "diat_taxaList", "diat_tdi", "diat_vandam", "diaThorAll" ], "_datasets": [ { "name": "cemfgs_rb", "title": "CEMFGS_RB", "object": "cemfgs_rb", "class": [ "data.frame" ], "fields": [ "fullspecies", "cemfgs_rb" ], "rows": 495, "table": true, "tojson": true }, { "name": "dbc_offline", "title": "DBC (offline)", "object": "dbc_offline", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "sequence_id", "gen_bank_acc", "sequence", "amplified_region", "primer_names", "sequencing_project", "strain_or_sample_sampling_id", "short_sequence", "code_court_de_sequence_pour_fasta", "sequence_aligned_rbcl_only_aligned_june_2021", "sequence_aligned_rbcl_only_aligned_feb_2024", "specimen_id_labo_strain_number_sample_number", "name_of_the_sampler", "voucher_oui_non", "herbarium", "name_of_the_sampling_site", "country", "latitude_decimal_degrees", "longitude_decimal_degrees", "project_name", "tissu", "name_of_lab", "lab_for_extraction", "extraction_date", "lab_for_pcr", "pcr_date", "sequencing_lab", "sequencing_date", "collection_date", "original_taxon_name", "reference", "species", "genus", "family_following_round_crawford_mann_1990", "order_following_round_crawford_mann_1990", "class_following_round_crawford_mann_1990", "phylum_following_algaebase_2018", "subkingdom_following_algaebase_2018", "kingdom_following_algaebase_2018", "empire_following_algaebase_2018", "species_authority", "genus_authority", "curator", "curation_date", "family_following_adl_et_al_2019", "order_following_adl_et_al_2019", "subclass_following_adl_et_al_2019", "class_following_adl_et_al_2019", "subphylum_following_adl_et_al_2019", "subkingdom_following_adl_et_al_2019", "kingdom_following_adl_et_al_2019", "ipss", "ipsvv", "kellys", "kellyv", "vdams", "vdamnh", "vdamo2", "vdamsap", "vdamtrop", "vdamaero", "hof_t", "hof_s", "td_is_modified_for_sweeden_kahlert_file_2015_04_01", "td_iv_modified_for_sweeden_kahlert_file_2015_04_01", "omnidia_code", "chloroplast_number", "chloroplast_shape", "reference_for_chloroplast", "longueur", "largeur", "epaisseur", "biovolume", "classe_de_taille_1_0_99_mm3_2_100_299_3_300_599_4_600_1499_5_1500_et", "forme", "longueur_largeur", "cf_v1", "cf_v2", "reference_biblio_tailles", "reference_biblio_formes_de_vie_1", "reference_biblio_formes_de_vie_2", "reference_biblio_formes_de_vie_3", "reference_biblio_formes_de_vie_4", "reference_biblio_formes_de_vie_5", "benthic", "planctonic", "epipsamic", "epipelic", "wet_soil_bryophytes_intertidal_zone", "marine", "mobile", "pioneer", "not_attached", "attached", "adnate", "pedunculate_stalk_or_pad_attached_to_substrate", "pad_attached_to_substrate", "stalk_attached_to_substrate", "colonial", "non_colonial", "mucous_tubule_colony", "chain_colony", "zig_zag_colony", "rosette_colony", "ribbon_colony", "stellate_colony", "arbuscular_colony_0_pas_observe_mais_possible_1_deja_observe", "other_kind_of_colony", "high_profile_guild_adapted_from_passy_2007_v2", "low_profile_guild_adapted_from_passy_2007_v2", "motile_guild_adapted_from_passy_2007_mobiles_rapides_jamais_accrochees_et_biraphidees_naviculales_bacillariales_sauf_diadesmis_et_diploneis_v2", "euplanctonic_guild_v2_centrics" ], "rows": 9233, "table": true, "tojson": true }, { "name": "ddi", "title": "DDI", "object": "ddi", "class": [ "data.frame" ], "fields": [ "fullspecies", "ddi_s", "ddi_v" ], "rows": 137, "table": true, "tojson": true }, { "name": "des", "title": "DES", "object": "des", "class": [ "data.frame" ], "fields": [ "fullspecies", "des_s", "des_v" ], "rows": 528, "table": true, "tojson": true }, { "name": "diat_sampleData", "title": "Sample Data", "object": "diat_sampleData", "class": [ "data.frame" ], "fields": [ "species", "S1_LI1_DAY0", "S1_LI2_DAY0", "S1_LI3_DAY0", "S1_X1_DAY0", "S1_X2_DAY0", "S1_X3_DAY0", "S1_HI1_DAY0", "S1_HI2_DAY0", "S1_HI3_DAY0", "S1_LI1_DAY15", "S1_LI2_DAY15", "S1_LI3_DAY15", "S1_X1_DAY15", "S1_X2_DAY15", "S1_X3_DAY15", "S1_HI1_DAY15", "S1_HI2_DAY15", "S1_HI3_DAY15", "S1_LI1_DAY30", "S1_LI2_DAY30", "S1_LI3_DAY30", "S1_X1_DAY30", "S1_X2_DAY30", "S1_X3_DAY30", "S1_HI1_DAY30", "S1_HI2_DAY30", "S1_HI3_DAY30", "S1_LI1_DAY45", "S1_LI2_DAY45", "S1_LI3_DAY45", "S1_X1_DAY45", "S1_X2_DAY45", "S1_X3_DAY45", "S1_HI1_DAY45", "S1_HI2_DAY45", "S1_HI3_DAY45", "S2_LI1_DAY0", "S2_LI2_DAY0", "S2_LI3_DAY0", "S2_X1_DAY0", "S2_X2_DAY0", "S2_X3_DAY0", "S2_HI1_DAY0", "S2_HI2_DAY0", "S2_HI3_DAY0", "S2_LI1_DAY15", "S2_LI2_DAY15", "S2_LI3_DAY15", "S2_X1_DAY15", "S2_X2_DAY15", "S2_X3_DAY15", "S2_HI1_DAY15", "S2_HI2_DAY15", "S2_HI3_DAY15", "S2_LI1_DAY30", "S2_LI2_DAY30", "S2_LI3_DAY30", "S2_X1_DAY30", "S2_X2_DAY30", "S2_X3_DAY30", "S2_HI1_DAY30", "S2_HI2_DAY30", "S2_HI3_DAY30", "S2_LI1_DAY45", "S2_LI2_DAY45", "S2_LI3_DAY45", "S2_X1_DAY45", "S2_X2_DAY45", "S2_X3_DAY45", "S2_HI1_DAY45", "S2_HI2_DAY45", "S2_HI3_DAY45", "S3_LI1_DAY0", "S3_LI2_DAY0", "S3_LI3_DAY0", "S3_X1_DAY0", "S3_X2_DAY0", "S3_X3_DAY0", "S3_HI1_DAY0", "S3_HI2_DAY0", "S3_HI3_DAY0", "S3_LI1_DAY15", "S3_LI2_DAY15", "S3_LI3_DAY15", "S3_X1_DAY15", "S3_X2_DAY15", "S3_X3_DAY15", "S3_HI1_DAY15", "S3_HI2_DAY15", "S3_HI3_DAY15", "S3_LI1_DAY30", "S3_LI2_DAY30", "S3_LI3_DAY30", "S3_X1_DAY30", "S3_X2_DAY30", "S3_X3_DAY30", "S3_HI1_DAY30", "S3_HI2_DAY30", "S3_HI3_DAY30", "S3_LI1_DAY45", "S3_LI2_DAY45", "S3_LI3_DAY45", "S3_X1_DAY45", "S3_X2_DAY45", "S3_X3_DAY45", "S3_HI1_DAY45", "S3_HI2_DAY45", "S3_HI3_DAY45" ], "rows": 164, "table": true, "tojson": true }, { "name": "disp", "title": "DISP", "object": "disp", "class": [ "data.frame" ], "fields": [ "fullspecies", "disp_v", "disp_s" ], "rows": 141, "table": true, "tojson": true }, { "name": "edi", "title": "EDI", "object": "edi", "class": [ "data.frame" ], "fields": [ "fullspecies", "edi_s", "edi_v" ], "rows": 147, "table": true, "tojson": true }, { "name": "epid", "title": "EPID", "object": "epid", "class": [ "data.frame" ], "fields": [ "fullspecies", "epid_s", "epid_v" ], "rows": 1070, "table": true, "tojson": true }, { "name": "idap", "title": "IDAP", "object": "idap", "class": [ "data.frame" ], "fields": [ "fullspecies", "idap_s", "idap_v" ], "rows": 194, "table": true, "tojson": true }, { "name": "idch", "title": "ID-CH", "object": "idch", "class": [ "data.frame" ], "fields": [ "fullspecies", "idch_s", "idch_v" ], "rows": 551, "table": true, "tojson": true }, { "name": "idp", "title": "IDP", "object": "idp", "class": [ "data.frame" ], "fields": [ "fullspecies", "idp_v" ], "rows": 298, "table": true, "tojson": true }, { "name": "ilm", "title": "ILM", "object": "ilm", "class": [ "data.frame" ], "fields": [ "fullspecies", "ilm_s", "ilm_v" ], "rows": 495, "table": true, "tojson": true }, { "name": "ips", "title": "IPS", "object": "ips", "class": [ "data.frame" ], "fields": [ "fullspecies", "ips_s", "ips_v" ], "rows": 6914, "table": true, "tojson": true }, { "name": "lobo", "title": "LOBO", "object": "lobo", "class": [ "data.frame" ], "fields": [ "fullspecies", "lobo_v", "lobo_s" ], "rows": 297, "table": true, "tojson": true }, { "name": "pbidw", "title": "PBIDW", "object": "pbidw", "class": [ "data.frame" ], "fields": [ "fullspecies", "pbidw_v" ], "rows": 79, "table": true, "tojson": true }, { "name": "pdise", "title": "PDISE", "object": "pdise", "class": [ "data.frame" ], "fields": [ "fullspecies", "pdise_s", "pdise_v" ], "rows": 455, "table": true, "tojson": true }, { "name": "sla", "title": "SLA", "object": "sla", "class": [ "data.frame" ], "fields": [ "fullspecies", "sla_s", "sla_v" ], "rows": 976, "table": true, "tojson": true }, { "name": "spear", "title": "SPEAR(h)", "object": "spear", "class": [ "data.frame" ], "fields": [ "fullspecies", "spear_v" ], "rows": 300, "table": true, "tojson": true }, { "name": "taxaList", "title": "taxaList", "object": "taxaList", "class": [ "data.frame" ], "fields": [ "species" ], "rows": 9806, "table": true, "tojson": true }, { "name": "tdi", "title": "TDI", "object": "tdi", "class": [ "data.frame" ], "fields": [ "fullspecies", "tdi_s", "tdi_v" ], "rows": 4146, "table": true, "tojson": true } ], "_help": [ { "page": "cemfgs_rb", "title": "CEMFGS_RB", "topics": [ "cemfgs_rb" ] }, { "page": "dbc_offline", "title": "DBC (offline)", "topics": [ "dbc_offline" ] }, { "page": "ddi", "title": "DDI", "topics": [ "ddi" ] }, { "page": "des", "title": "DES", "topics": [ "des" ] }, { "page": "diat_cemfgs_rb", "title": "Calculate the combined classification of ecological guilds and size classes for diatoms", "topics": [ "diat_cemfgs_rb" ] }, { "page": "diat_checkName", "title": "Searches all the taxa database for the input name", "topics": [ "diat_checkName" ] }, { "page": "diat_ddi", "title": "Calculates the Duero Diatom Index (DDI)", "topics": [ "diat_ddi" ] }, { "page": "diat_des", "title": "Calculates the Descy Index (DES)", "topics": [ "diat_des" ] }, { "page": "diat_disp", "title": "Calculates the Diatom Index for Soda Pans (DISP)", "topics": [ "diat_disp" ] }, { "page": "diat_diversity", "title": "Calculate diversity parameters for diatoms using the vegan package", "topics": [ "diat_diversity" ] }, { "page": "diat_edi", "title": "Calculates the Ecuador Diatom Index (EDI)", "topics": [ "diat_edi" ] }, { "page": "diat_epid", "title": "Calculates the EPID index (EPID)", "topics": [ "diat_epid" ] }, { "page": "diat_getDiatBarcode", "title": "Loads the 'Diat.Barcode' database into DiaThor in the correct format", "topics": [ "diat_getDiatBarcode" ] }, { "page": "diat_guilds", "title": "Calculate ecological guilds for diatoms", "topics": [ "diat_guilds" ] }, { "page": "diat_idap", "title": "Calculates the Indice Diatomique Artois-Picardie (IDAP)", "topics": [ "diat_idap" ] }, { "page": "diat_idch", "title": "Calculates the Swiss Diatom Index (IDCH)", "topics": [ "diat_idch" ] }, { "page": "diat_idp", "title": "Calculates the Pampean Diatom Index (IDP)", "topics": [ "diat_idp" ] }, { "page": "diat_ilm", "title": "Calculates the ILM Index (ILM)", "topics": [ "diat_ilm" ] }, { "page": "diat_ips", "title": "Calculates the Specific Polluosensitivity Index (IPS) index", "topics": [ "diat_ips" ] }, { "page": "diat_loadData", "title": "Loads the Data into DiaThor in the correct format", "topics": [ "diat_loadData" ] }, { "page": "diat_lobo", "title": "Calculates the Lobo Index (LOBO)", "topics": [ "diat_lobo" ] }, { "page": "diat_morpho", "title": "Calculate morphological parameters for diatoms", "topics": [ "diat_morpho" ] }, { "page": "diat_pbidw", "title": "Calculates the PBIDW Index (PBIDW)", "topics": [ "diat_pbidw" ] }, { "page": "diat_pdise", "title": "Calculates the Swedish Phosphorus Diatom Index (PDIse)", "topics": [ "diat_pdise" ] }, { "page": "diat_sampleData", "title": "Sample Data", "topics": [ "diat_sampleData" ] }, { "page": "diat_size", "title": "Calculate size classes for diatoms", "topics": [ "diat_size" ] }, { "page": "diat_sla", "title": "Calculates the Sladecek Index (SLA)", "topics": [ "diat_sla" ] }, { "page": "diat_spear", "title": "Calculates the SPEAR(herbicides) Index (SPEAR)", "topics": [ "diat_spear" ] }, { "page": "diat_taxaList", "title": "Creates a single list with taxa names from all indices within DiaThor", "topics": [ "diat_taxaList" ] }, { "page": "diat_tdi", "title": "Calculates the Trophic (TDI) index", "topics": [ "diat_tdi" ] }, { "page": "diat_vandam", "title": "Calculates ecological information for diatoms based on the Van Dam classification", "topics": [ "diat_vandam" ] }, { "page": "diaThor", "title": "DiaThor: A package to calculate multiple diatom-based biotic indices", "topics": [ "diaThor", "diathor" ] }, { "page": "diathorAll", "title": "Runs all the DiaThor functions in a pipeline", "topics": [ "diaThorAll" ] }, { "page": "disp", "title": "DISP", "topics": [ "disp" ] }, { "page": "edi", "title": "EDI", "topics": [ "edi" ] }, { "page": "epid", "title": "EPID", "topics": [ "epid" ] }, { "page": "idap", "title": "IDAP", "topics": [ "idap" ] }, { "page": "idch", "title": "ID-CH", "topics": [ "idch" ] }, { "page": "idp", "title": "IDP", "topics": [ "idp" ] }, { "page": "ilm", "title": "ILM", "topics": [ "ilm" ] }, { "page": "ips", "title": "IPS", "topics": [ "ips" ] }, { "page": "lobo", "title": "LOBO", "topics": [ "lobo" ] }, { "page": "pbidw", "title": "PBIDW", "topics": [ 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