Calculate Ecological Information and Diatom Based Indices
Calculate the combined classification of ecological guilds and size cl...
Searches all the taxa database for the input name
Calculates the Duero Diatom Index (DDI)
Calculates the Descy Index (DES)
Calculates the Diatom Index for Soda Pans (DISP)
Calculate diversity parameters for diatoms using the vegan package
Calculates the Ecuador Diatom Index (EDI)
Calculates the EPID index (EPID)
Loads the 'Diat.Barcode' database into DiaThor in the correct format
Calculate ecological guilds for diatoms
Calculates the Indice Diatomique Artois-Picardie (IDAP)
Calculates the Swiss Diatom Index (IDCH)
Calculates the Pampean Diatom Index (IDP)
Calculates the ILM Index (ILM)
Calculates the Specific Polluosensitivity Index (IPS) index
Loads the Data into DiaThor in the correct format
Calculates the Lobo Index (LOBO)
Calculate morphological parameters for diatoms
Calculates the PBIDW Index (PBIDW)
Calculates the Swedish Phosphorus Diatom Index (PDIse)
Calculate size classes for diatoms
Calculates the Sladecek Index (SLA)
Calculates the SPEAR(herbicides) Index (SPEAR)
Creates a single list with taxa names from all indices within DiaThor
Calculates the Trophic (TDI) index
Calculates ecological information for diatoms based on the Van Dam cla...
diathor: Calculate Ecological Information and Diatom Based Indices
DiaThor: A package to calculate multiple diatom-based biotic indices
Runs all the DiaThor functions in a pipeline
Calculate multiple biotic indices using diatoms from environmental samples. Diatom species are recognized by their species' name using a heuristic search, and their ecological data is retrieved from multiple sources. It includes number/shape of chloroplasts diversity indices, size classes, ecological guilds, and multiple biotic indices. It outputs both a dataframe with all the results and plots of all the obtained data in a defined output folder. - Sample data was taken from Nicolosi Gelis, Cochero & Gómez (2020, <doi:10.1016/j.ecolind.2019.105951>). - The package uses the 'Diat.Barcode' database to calculate morphological and ecological information by Rimet & Couchez (2012, <doi:10.1051/kmae/2012018>),and the combined classification of guilds and size classes established by B-Béres et al. (2017, <doi:10.1016/j.ecolind.2017.07.007>). - Current diatom-based biotic indices include the DES index by Descy (1979) - EPID index by Dell'Uomo (1996, ISBN: 3950009002) - IDAP index by Prygiel & Coste (1993, <doi:10.1007/BF00028033>) - ID-CH index by Hürlimann & Niederhauser (2007) - IDP index by Gómez & Licursi (2001, <doi:10.1023/A:1011415209445>) - ILM index by Leclercq & Maquet (1987) - IPS index by Coste (1982) - LOBO index by Lobo, Callegaro, & Bender (2002, ISBN:9788585869908) - SLA by Sládeček (1986, <doi:10.1002/aheh.19860140519>) - TDI index by Kelly, & Whitton (1995, <doi:10.1007/BF00003802>) - SPEAR(herbicide) index by Wood, Mitrovic, Lim, Warne, Dunlop, & Kefford (2019, <doi:10.1016/j.ecolind.2018.12.035>) - PBIDW index by Castro-Roa & Pinilla-Agudelo (2014) - DISP index by Stenger-Kovács et al. (2018, <doi:10.1016/j.ecolind.2018.07.026>) - EDI index by Chamorro et al. (2024, <doi:10.1021/acsestwater.4c00126>) - DDI index by Álvarez-Blanco et al. (2013, <doi: 10.1007/s10661-012-2607-z>) - PDISE index by Kahlert et al. (2023, <doi:10.1007/s10661-023-11378-4>).