Package: diathor 0.1.4

Joaquin Cochero

diathor: Calculate Ecological Information and Diatom Based Indices

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 \href{<https://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=PASCAL8060205402>}{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 \href{, <https://www.bafu.admin.ch/bafu/fr/home/themes/eaux/publications/publications-eaux/methodes-analyse-appreciation-cours-eau-diatomees.html>)}{(2007)} - IDP index by Gómez & Licursi (2001, <doi:10.1023/A:1011415209445>) - ILM index by Leclercq & Maquet \href{<https://www.vliz.be/imisdocs/publications/286641.pdf>}{(1987)} - IPS index by Coste \href{<https://www.oieau.org/eaudoc/notice/ETUDE-DES-METHODES-BIOLOGIQUES-DAPPRECIATION-QUANTITATIVE-DE-LA-QUALITE-DES-EAUX>}{(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-Kovácsa et al. (2018)

Authors:Maria Mercedes Nicolosi Gelis [aut], Maria Belen Sathicq [aut], Joaquin Cochero [cre]

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Peer review:

Bug tracker:https://github.com/limnolab/diathor/issues

On CRAN:

24 exports 2 stars 0.95 score 41 dependencies 2 scripts 426 downloads

Last updated 1 months agofrom:1b136b978d. Checks:OK: 1 WARNING: 6. Indexed: yes.

Exports:diat_cemfgs_rbdiat_checkNamediat_desdiat_dispdiat_diversitydiat_epiddiat_getDiatBarcodediat_guildsdiat_idapdiat_idchdiat_idpdiat_ilmdiat_ipsdiat_loadDatadiat_lobodiat_morphodiat_pbidwdiat_sizediat_sladiat_speardiat_taxaListdiat_tdidiat_vandamdiaThorAll

Dependencies:cliclustercolorspacecpp11data.tabledplyrfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepermutepillarpkgconfigpurrrR6RColorBrewerrlangscalesstringdiststringistringrtibbletidyrtidyselectutf8vctrsveganviridisLitewithr