diaThor
María Mercedes Nicolosi Gelis, Belén Sathicq, Joaquín Cochero
DiaThor calculates several diatom-based indices commonly used for water quality assesment, directly from your species’ data
Description
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. https://www.kmae-journal.org/articles/kmae/abs/2012/03/kmae120025/kmae120025.html
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. https://www.kmae-journal.org/articles/kmae/abs/2012/03/kmae120025/kmae120025.html
The combined classification of size classes and guilds is obtained from:
- B-Béres, V., Török, P., Kókai, Z., Lukács, Á., Enikő, T., Tóthmérész, B., & Bácsi, I. (2017). Ecological background of diatom functional groups: Comparability of classification systems. Ecological Indicators, 82, 183-188. https://www.sciencedirect.com/science/article/abs/pii/S1470160X1730420X
Ecological preferences are 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). ‘The Mathematical Theory of Communication.’ (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). Étude des méthodes biologiques d’appréciation quantitative de la qualité des eaux. Rapport Cemagref QE Lyon-AF Bassin Rhône Méditerranée 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: Gómez, 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: Hürlimann J., Niederhauser P. 2007: Méthodes d’analyse et d’appréciation des cours d’eau. Diatomées Niveau R (région). État de l’environnement n° 0740. Office fédéral de l’environnement, Berne. 132 p
ILM: Leclercq, L., & Maquet, B. (1987). Deux nouveaux indices diatomique et de qualité chimique des eaux courantes. Comparaison avec différents indices existants. Cahier de Biology Marine, 28, 303-310.
LOBO:
- Lobo, E. A., Callegaro, V. L. M., & Bender, E. P. (2002). Utilização de algas diatomáceas epilíticas como indicadoras da qualidade da água em rios e arroios da Região Hidrográfica do Guaíba, RS, Brasil. Edunisc.
- 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: Sládeček, 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–A new SPEcies At Risk (SPEARherbicides) index. Ecological Indicators, 99, 203-213.
PBIDW: Castro-Roa, D., & Pinilla-Agudelo, G. (2014). Periphytic diatom index for assessing the ecological quality of the Colombian Andean urban wetlands of Bogotá. Limnetica, 33(2), 297-312.
DISP: Stenger-Kovács, C., Körmendi, K., Lengyel, E., Abonyi, A., Hajnal, É., Szabó, B., Buczkó, K. & Padisák, J. (2018). Expanding the trait-based concept of benthic diatoms: Development of trait-and species-based indices for conductivity as the master variable of ecological status in continental saline lakes. Ecological Indicators, 95, 63-74.
Sample data included in the package is taken from:
- Nicolosi Gelis, María Mercedes; Cochero, Joaquín; Donadelli, Jorge; Gómez, 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.
Installation
You can install the released version of diathor from CRAN with:
install.packages("diathor")And the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("limnolab/DiaThor/")Example
To demonstrate the most common use of DiaThor, the package includes sample data with the abundance of 164 diatom species in 108 sampled sites (Nicolosi Gelis et al., 2020).
Install the package and load it into the R environment
> install.packages("diathor")
> library(diathor)Load the internally included sample data
> data("diat_sampleData")Run diaThorAll to get all the outputs from the sample data with the default settings, and store the results into the “results” object, to also retain the output within R
> results <- diaThorAll(diat_sampleData) #If the sample data was usedNote: The package will request the Input file an Output folder through a dialog box
[1] "Select Input file"
[1] "Select Results folder"After the Results folder is selected, all the calculations conducted will be shown in the console
Optionally, run each individual function with the results of the diat_loadData() function, for instance:
> loadedData <- diat_loadData() # load data with the diat_loadData() function
> results <- diat_ips(loadedData ) # use the diat_ips() function to calculate the IPS index with the loaded dataCRAN vs. GitHub package
The package available in the CRAN repository does not automatically update the internal diatom database from the ‘Diat.Barcode’ project. It uses the internal version of such database, which is currently v.9.0 published on 14-09-2020
The GitHub version of the package will update to the most recent database, if it is different to the current internal version.