The package calculates 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. Morphological information about the species is retrieved from the 'Diat.Barcode' project:
Rimet F., Gusev E., Kahlert M., Kelly M., Kulikovskiy M., Maltsev Y., Mann D., Pfannkuchen M., Trobajo R., Vasselon V., Zimmermann J., Bouchez A., 2019. Diat.barcode, an open-access curated barcode library for diatoms. Scientific Reports. https://www.nature.com/articles/s41598-019-51500-6
Size class classification is obtained from:
Rimet F. & Bouchez A., 2012. Life-forms, cell-sizes and ecological guilds of diatoms in European rivers. Knowledge and management of aquatic ecosystems, 406: 1-14. DOI:10.1051/kmae/2012018
Guild classification is obtained from:
Rimet F. & Bouchez A., 2012. Life-forms, cell-sizes and ecological guilds of diatoms in European rivers. Knowledge and management of aquatic ecosystems, 406: 1-14. DOI:10.1051/kmae/2012018
Van Dam classification is obtained form:
Van Dam, H., Mertens, A., & Sinkeldam, J. (1994). A coded checklist and ecological indicator values of freshwater diatoms from the Netherlands. Netherland Journal of Aquatic Ecology, 28(1), 117-133.
Diversity index (Shannons H') is calculated using the vegan package, following:
Shannon, C. E., and Weaver, W. (1949). <U+2018>The Mathematical Theory of Communication.<U+2019> (University of Illinios Press: Urbana, IL, USA.)
Species tolerance and their ecological information to calculate each biotic index is retrieved from their original sources:
IPS: Coste, M. (1982). <U+00C9>tude des m<U+00E9>thodes biologiques d<U+2019>appr<U+00E9>ciation quantitative de la qualit<U+00E9> des eaux. Rapport Cemagref QE Lyon-AF Bassin Rh<U+00F4>ne M<U+00E9>diterran<U+00E9>e Corse.
TDI: Kelly, M. G., & Whitton, B. A. (1995). The trophic diatom index: a new index for monitoring eutrophication in rivers. Journal of Applied Phycology, 7(4), 433-444.
IDP: G<U+00F3>mez, N., & Licursi, M. (2001). The Pampean Diatom Index (IDP) for assessment of rivers and streams in Argentina. Aquatic Ecology, 35(2), 173-181.
DES: Descy, J. P. 1979. A new approach to water quality estimation using diatom. Beih. Nov Hedw. 64:305-323
EPID: Dell'Uomo, A. (1996). Assessment of water quality of an Apennine river as a pilot study for diatom-based monitoring of Italian watercourses. Use of algae for monitoring rivers, 65-72.
IDAP: Prygiel, J., & Coste, M. (1993). The assessment of water quality in the Artois-Picardie water basin (France) by the use of diatom indices. Hydrobiologia, 269(1), 343-349.
ID-CH: H<U+00FC>rlimann J., Niederhauser P. 2007: M<U+00E9>thodes d<U+2019>analyse et d<U+2019>appr<U+00E9>ciation des cours d<U+2019>eau. Diatom<U+00E9>es Niveau R (r<U+00E9>gion). <U+00C9>tat de l<U+2019>environnement n<U+00B0> 0740. Office f<U+00E9>d<U+00E9>ral de l<U+2019>environnement, Berne. 132 p
ILM: Leclercq, L., & Maquet, B. (1987). Deux nouveaux indices diatomique et de qualit<U+00E9> chimique des eaux courantes. Comparaison avec diff<U+00E9>rents indices existants. Cahier de Biology Marine, 28, 303-310.
LOBO: Lobo, E. A., Callegaro, V. L. M., & Bender, E. P. (2002). Utiliza<U+00E7><U+00E3>o de algas diatom<U+00E1>ceas epil<U+00ED>ticas como indicadoras da qualidade da <U+00E1>gua em rios e arroios da Regi<U+00E3>o Hidrogr<U+00E1>fica do Gua<U+00ED>ba, RS, Brasil. Edunisc.
LOBO: Lobo, E. A., Bes, D., Tudesque, L., & Ector, L. (2004). Water quality assessment of the Pardinho River, RS, Brazil, using epilithic diatom assemblages and faecal coliforms as biological indicators. Vie et Milieu, 54(2-3), 115-126.
SLA: Sl<U+00E1>de<U+010D>ek, V. (1986). Diatoms as indicators of organic pollution. Acta hydrochimica et hydrobiologica, 14(5), 555-566.
SPEAR(herbicides): Wood, R. J., Mitrovic, S. M., Lim, R. P., Warne, M. S. J., Dunlop, J., & Kefford, B. J. (2019). Benthic diatoms as indicators of herbicide toxicity in rivers<U+2013>A new SPEcies At Risk (SPEARherbicides) index. Ecological Indicators, 99, 203-213.
Sample data included in the package is taken from:
Nicolosi Gelis, Mar<U+00ED>a Mercedes; Cochero, Joaqu<U+00ED>n; Donadelli, Jorge; G<U+00F3>mez, Nora. 2020. "Exploring the use of nuclear alterations, motility and ecological guilds in epipelic diatoms as biomonitoring tools for water quality improvement in urban impacted lowland streams". Ecological Indicators, 110, 105951.
diat_loadData() diat_morpho() diat_size() diat_diversity() diat_guilds() diat_vandam() diat_loadData() diat_ips() diat_tdi() diat_idp() diat_des() diat_epid() diat_idch() diat_ilm() diat_lobo() diat_sla() diat_spear()