diathor0.1.5 package

Calculate Ecological Information and Diatom Based Indices

diat_cemfgs_rb

Calculate the combined classification of ecological guilds and size cl...

diat_checkName

Searches all the taxa database for the input name

diat_ddi

Calculates the Duero Diatom Index (DDI)

diat_des

Calculates the Descy Index (DES)

diat_disp

Calculates the Diatom Index for Soda Pans (DISP)

diat_diversity

Calculate diversity parameters for diatoms using the vegan package

diat_edi

Calculates the Ecuador Diatom Index (EDI)

diat_epid

Calculates the EPID index (EPID)

diat_getDiatBarcode

Loads the 'Diat.Barcode' database into DiaThor in the correct format

diat_guilds

Calculate ecological guilds for diatoms

diat_idap

Calculates the Indice Diatomique Artois-Picardie (IDAP)

diat_idch

Calculates the Swiss Diatom Index (IDCH)

diat_idp

Calculates the Pampean Diatom Index (IDP)

diat_ilm

Calculates the ILM Index (ILM)

diat_ips

Calculates the Specific Polluosensitivity Index (IPS) index

diat_loadData

Loads the Data into DiaThor in the correct format

diat_lobo

Calculates the Lobo Index (LOBO)

diat_morpho

Calculate morphological parameters for diatoms

diat_pbidw

Calculates the PBIDW Index (PBIDW)

diat_pdise

Calculates the Swedish Phosphorus Diatom Index (PDIse)

diat_size

Calculate size classes for diatoms

diat_sla

Calculates the Sladecek Index (SLA)

diat_spear

Calculates the SPEAR(herbicides) Index (SPEAR)

diat_taxaList

Creates a single list with taxa names from all indices within DiaThor

diat_tdi

Calculates the Trophic (TDI) index

diat_vandam

Calculates ecological information for diatoms based on the Van Dam cla...

diathor-package

diathor: Calculate Ecological Information and Diatom Based Indices

diaThor

DiaThor: A package to calculate multiple diatom-based biotic indices

diaThorAll

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>).

  • Maintainer: Joaquin Cochero
  • License: GNU General Public License
  • Last published: 2024-12-20