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 Descy Index (DES)
Calculates the Diatom Index for Soda Pans (DISP)
Calculate diversity parameters for diatoms using the vegan package
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)
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 identified by their species names through a heuristic search, and ecological data is retrieved from multiple sources. The package includes the calculation of chloroplast diversity indices, size classes, ecological guilds, and various biotic indices. It outputs both a dataframe with all the results and plots of the obtained data in a specified output folder. Sample data is sourced from Nicolosi Gelis, Cochero, & Gómez (2020, <doi:10.1016/j.ecolind.2019.105951>). The package utilizes the 'Diat.Barcode' database for morphological and ecological information by Rimet & Couchez (2012, <doi:10.1051/kmae/2012018>), along with the combined classification of guilds and size classes from B-Beres et al. (2017, <doi:10.1016/j.ecolind.2017.07.007>). Currently supported diatom-based biotic indices include DES index (Descy, 1979); EPID index (Dell'Uomo, 1996); IDAP index (Prygiel & Coste, 1993); ID-CH index (Hürlimann & Niederhauser, 2007); IDP index (Gómez & Licursi, 2001); ILM index (Leclercq & Maquet, 1987); IPS index (Coste, 1982); LOBO index (Lobo, Callegaro, & Bender, 2002); SLA index (Sladecek, 1986); TDI index (Kelly & Whitton, 1995); SPEAR(herbicide) index (Wood et al., 2019); PBIDW index (Castro-Roa & Pinilla-Agudelo, 2014); DISP index (Stenger-Kovácsa et al., 2018).