,
Maria Belen Sathicq [aut] ,
Joaquin Cochero [cre] | Title: | Calculate Ecological Information and Diatom Based Indices |
|---|---|
| Description: | 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] |
| Maintainer: | Joaquin Cochero <[email protected]> |
| License: | GNU General Public License |
| Version: | 0.1.4 |
| Built: | 2024-10-15 05:46:19 UTC |
| Source: | https://github.com/limnolab/diathor |
Index values for diatom species combining their ecological guilds with their size classes
data(cemfgs_rb)data(cemfgs_rb)
A data frame with the ecological values for 495 species
https://www.sciencedirect.com/science/article/abs/pii/S1470160X1730420X
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.
Diatom database from the 'Diat.Barcode' project V9.0
data(dbc_offline)data(dbc_offline)
A data frame with ecological and morphological information for 8066 diatoms
https://www.kmae-journal.org/articles/kmae/abs/2012/03/kmae120025/kmae120025.html
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
Index values for diatom species included in the DES index
data(des)data(des)
A data frame with the ecological values for 622 species
https://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=PASCAL8060205402
Descy, J. P. 1979. A new approach to water qualityestimation using diatom. Beih. Nov Hedw. 64:305-323
The input for these functions is the resulting dataframe obtained from the diat_loadData() function, to calculate the ecological guilds for the diatoms Sample data in the examples 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. https://doi:10.1016/j.ecolind.2019.105951
Classification 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.
diat_cemfgs_rb(resultLoad)diat_cemfgs_rb(resultLoad)
resultLoad |
The resulting list obtained from the diat_loadData() function |
# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) guildsResults <- diat_cemfgs_rb(df)# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) guildsResults <- diat_cemfgs_rb(df)
Searches all the taxa database for the input name, returns a list with the results
diat_checkName(taxaname, byword = F)diat_checkName(taxaname, byword = F)
taxaname |
the name of the taxa (genus, species, variety) to be checked against the internal DB |
byword |
if byword = F (default), the input string will be searched without splitting words. If True, each word will be searched separately |
The input for all of these functions is the resulting dataframe (resultLoad) obtained from the diat_loadData() function A CSV or dataframe cannot be used directly with these functions, they have to be loaded first with the diat_loadData() function so the acronyms and species' names are recognized References for the index:
Descy, J. P. 1979. A new approach to water qualityestimation using diatom. Beih. Nov Hedw. 64:305-323
Sample data in the examples 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. https://doi:10.1016/j.ecolind.2019.105951
diat_des(resultLoad, maxDistTaxa = 2)diat_des(resultLoad, maxDistTaxa = 2)
resultLoad |
The resulting list obtained from the diat_loadData() function |
maxDistTaxa |
Integer. Number of characters that can differ in the species' names when compared to the internal database's name in the heuristic search. Default = 2 |
# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) desResults <- diat_des(df)# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) desResults <- diat_des(df)
The input for all of these functions is the resulting dataframe (resultLoad) obtained from the diat_loadData() function A CSV or dataframe cannot be used directly with these functions, they have to be loaded first with the diat_loadData() function so the acronyms and species' names are recognized References for the index:
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 in the examples 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. https://doi:10.1016/j.ecolind.2019.105951
diat_disp(resultLoad, maxDistTaxa = 2)diat_disp(resultLoad, maxDistTaxa = 2)
resultLoad |
The resulting list obtained from the diat_loadData() function |
maxDistTaxa |
Integer. Number of characters that can differ in the species' names when compared to the internal database's name in the heuristic search. Default = 2 |
# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) dispResults <- diat_disp(df)# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) dispResults <- diat_disp(df)
The input for these functions is the resulting dataframe obtained from the diat_loadData() function, to calculate diversity data using the vegan package Sample data in the examples 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. https://doi:10.1016/j.ecolind.2019.105951
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.)
diat_diversity(resultLoad)diat_diversity(resultLoad)
resultLoad |
The resulting list obtained from the diat_loadData() function |
The input for all of these functions is the resulting dataframe (resultLoad) obtained from the diat_loadData() function A CSV or dataframe cannot be used directly with these functions, they have to be loaded first with the diat_loadData() function so the acronyms and species' names are recognized References for the index:
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.
Sample data in the examples 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. <https://doi:10.1016/j.ecolind.2019.105951>
diat_epid(resultLoad, maxDistTaxa = 2)diat_epid(resultLoad, maxDistTaxa = 2)
resultLoad |
The resulting list obtained from the diat_loadData() function |
maxDistTaxa |
Integer. Number of characters that can differ in the species' names when compared to the internal database's name in the heuristic search. Default = 2 |
# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) epidResults <- diat_epid(df)# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) epidResults <- diat_epid(df)
The package downloads and installs a wrapper for the 'Diat.Barcode' project. Besides citing the DiaThor package, the Diat.Barcode project should also be cited, as follows:
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
diat_getDiatBarcode()diat_getDiatBarcode()
The input for these functions is the resulting dataframe obtained from the diat_loadData() function, to calculate the ecological guilds for the diatoms Sample data in the examples 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. https://doi:10.1016/j.ecolind.2019.105951
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
diat_guilds(resultLoad)diat_guilds(resultLoad)
resultLoad |
The resulting list obtained from the diat_loadData() function |
# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) guildsResults <- diat_guilds(df)# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) guildsResults <- diat_guilds(df)
The input for all of these functions is the resulting dataframe (resultLoad) obtained from the diat_loadData() function A CSV or dataframe cannot be used directly with these functions, they have to be loaded first with the diat_loadData() function so the acronyms and species' names are recognized References for the index:
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.
Sample data in the examples 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. https://doi:10.1016/j.ecolind.2019.105951
diat_idap(resultLoad, maxDistTaxa = 2)diat_idap(resultLoad, maxDistTaxa = 2)
resultLoad |
The resulting list obtained from the diat_loadData() function |
maxDistTaxa |
Integer. Number of characters that can differ in the species' names when compared to the internal database's name in the heuristic search. Default = 2 |
# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) idapResults <- diat_idap(df)# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) idapResults <- diat_idap(df)
The input for all of these functions is the resulting dataframe (resultLoad) obtained from the diat_loadData() function A CSV or dataframe cannot be used directly with these functions, they have to be loaded first with the diat_loadData() function so the acronyms and species' names are recognized References for the index:
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
Sample data in the examples 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. https://doi:10.1016/j.ecolind.2019.105951
diat_idch(resultLoad, maxDistTaxa = 2)diat_idch(resultLoad, maxDistTaxa = 2)
resultLoad |
The resulting list obtained from the diat_loadData() function |
maxDistTaxa |
Integer. Number of characters that can differ in the species' names when compared to the internal database's name in the heuristic search. Default = 2 |
# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) idchResults <- diat_idch(df)# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) idchResults <- diat_idch(df)
The input for all of these functions is the resulting dataframe (resultLoad) obtained from the diat_loadData() function A CSV or dataframe cannot be used directly with these functions, they have to be loaded first with the diat_loadData() function so the acronyms and species' names are recognized References for the index:
Gómez, N., & Licursi, M. (2001). The Pampean Diatom Index (IDP) for assessment of rivers and streams in Argentina. Aquatic Ecology, 35(2), 173-181.
Sample data in the examples 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. https://doi:10.1016/j.ecolind.2019.105951
diat_idp(resultLoad, maxDistTaxa = 2)diat_idp(resultLoad, maxDistTaxa = 2)
resultLoad |
The resulting list obtained from the diat_loadData() function |
maxDistTaxa |
Integer. Number of characters that can differ in the species' names when compared to the internal database's name in the heuristic search. Default = 2 |
# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) idpResults <- diat_idp(df)# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) idpResults <- diat_idp(df)
The input for all of these functions is the resulting dataframe (resultLoad) obtained from the diat_loadData() function A CSV or dataframe cannot be used directly with these functions, they have to be loaded first with the diat_loadData() function so the acronyms and species' names are recognized References for the index:
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.
Sample data in the examples 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. https://doi:10.1016/j.ecolind.2019.105951
diat_ilm(resultLoad, maxDistTaxa = 2)diat_ilm(resultLoad, maxDistTaxa = 2)
resultLoad |
The resulting list obtained from the diat_loadData() function |
maxDistTaxa |
Integer. Number of characters that can differ in the species' names when compared to the internal database's name in the heuristic search. Default = 2 |
# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) ilmResults <- diat_ilm(df)# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) ilmResults <- diat_ilm(df)
The input for all of these functions is the resulting dataframe (resultLoad) obtained from the diat_loadData() function A CSV or dataframe cannot be used directly with these functions, they have to be loaded first with the diat_loadData() function so the acronyms and species' names are recognized References for the index:
Coste, M. (1982). Étude des méthodes biologiques d’appréciation quantitative de la qualité des eaux. Rapport Cemagref QE Lyon-AF Bassin Rhône Méditerranée Corse.
Sample data in the examples 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. https://doi:10.1016/j.ecolind.2019.105951
diat_ips(resultLoad, maxDistTaxa = 2)diat_ips(resultLoad, maxDistTaxa = 2)
resultLoad |
The resulting list obtained from the diat_loadData() function |
maxDistTaxa |
Integer. Number of characters that can differ in the species' names when compared to the internal database's name in the heuristic search. Default = 2 |
# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) ipsResults <- diat_ips(df)# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) ipsResults <- diat_ips(df)
Loads the CSV or dataframe file, sets the Output folder for the package, and conducts both an exact and an heuristic search of the species' names.
The input file for the package is a dataframe or an external CSV file. Species should be listed as rows, with species' names in column 1 (column name should be "species") The other columns (samples) have to contain the abundance of each species (relative or absolute) in each sample. The first row of the file has to contain the headers with the sample names. Remember that a column named "species" is mandatory, containing the species' names If a dataframe is not specified as a parameter (species_df), the package will show a dialog box to search for the CSV file A second dialog box will help set up an Output folder, where all outputs from the package will be exported to (dataframes, CSV files, plots in PDF) The package also downloads and installs a wrapper for the 'Diat.Barcode' project. Besides citing the DiaThor package, the Diat.Barcode project should also be cited, as follows:
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
Sample data in the examples 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. https://doi:10.1016/j.ecolind.2019.105951
diat_loadData(species_df, isRelAb = FALSE, maxDistTaxa = 2, resultsPath)diat_loadData(species_df, isRelAb = FALSE, maxDistTaxa = 2, resultsPath)
species_df |
The data frame with your species data. Species as rows, Samples as columns. If empty, a dialog box will prompt to import a CSV file |
isRelAb |
Boolean. If set to 'TRUE' it means that your species' data is the relative abundance of each species per site. If FALSE, it means that it the data corresponds to absolute densities. Default = FALSE |
maxDistTaxa |
Integer. Number of characters that can differ in the species' names when compared to the internal database's name in the heuristic search. Default = 2 |
resultsPath |
String. Path for the output data. If empty (default), it will prompt a dialog box to select an output folder |
The input for all of these functions is the resulting dataframe (resultLoad) obtained from the diat_loadData() function A CSV or dataframe cannot be used directly with these functions, they have to be loaded first with the diat_loadData() function so the acronyms and species' names are recognized References for the index:
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.
Sample data in the examples 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. https://doi:10.1016/j.ecolind.2019.105951
diat_lobo(resultLoad, maxDistTaxa = 2)diat_lobo(resultLoad, maxDistTaxa = 2)
resultLoad |
The resulting list obtained from the diat_loadData() function |
maxDistTaxa |
Integer. Number of characters that can differ in the species' names when compared to the internal database's name in the heuristic search. Default = 2 |
# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) loboResults <- diat_lobo(df)# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) loboResults <- diat_lobo(df)
The input for these functions is the resulting dataframe obtained from the diat_loadData() function to calculate morphological parameters The morphological data (size classes, chlorophlasts) is obtained from the 'Diat.Barcode' project. Besides citing DiaThor, the Diat.Barcode project should also be cited if the package is used, as follows:
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
Sample data in the examples 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. https://doi:10.1016/j.ecolind.2019.105951
diat_morpho(resultLoad, isRelAb = FALSE)diat_morpho(resultLoad, isRelAb = FALSE)
resultLoad |
The resulting list obtained from the diat_loadData() function |
isRelAb |
Boolean. If set to 'TRUE' it means that your species' data is the relative abundance of each species per site. If FALSE, it means that it the data corresponds to absolute densities. Default = FALSE |
# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) morphoResults <- diat_morpho(df)# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) morphoResults <- diat_morpho(df)
The input for all of these functions is the resulting dataframe (resultLoad) obtained from the diat_loadData() function A CSV or dataframe cannot be used directly with these functions, they have to be loaded first with the diat_loadData() function so the acronyms and species' names are recognized References for the index:
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.
Sample data in the examples 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. https://doi:10.1016/j.ecolind.2019.105951
diat_pbidw(resultLoad, maxDistTaxa = 2)diat_pbidw(resultLoad, maxDistTaxa = 2)
resultLoad |
The resulting list obtained from the diat_loadData() function |
maxDistTaxa |
Integer. Number of characters that can differ in the species' names when compared to the internal database's name in the heuristic search. Default = 2 |
# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) pbidwResults <- diat_pbidw(df)# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) pbidwResults <- diat_pbidw(df)
This sample data is a dataset used in: 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.
data(diat_sampleData)data(diat_sampleData)
A data frame with the abundance of 164 diatoms in 108 sampled sites
https://www.sciencedirect.com/science/article/abs/pii/S1470160X1930946X
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.
The input for these functions is the resulting dataframe obtained from the diat_loadData() function to calculate size classes for diatoms Sample data in the examples 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. https://doi:10.1016/j.ecolind.2019.105951
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
diat_size(resultLoad)diat_size(resultLoad)
resultLoad |
The resulting list obtained from the diat_loadData() function |
# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) sizeResults <- diat_size(df)# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) sizeResults <- diat_size(df)
The input for all of these functions is the resulting dataframe (resultLoad) obtained from the diat_loadData() function A CSV or dataframe cannot be used directly with these functions, they have to be loaded first with the diat_loadData() function so the acronyms and species' names are recognized References for the index:
Sládeček, V. (1986). Diatoms as indicators of organic pollution. Acta hydrochimica et hydrobiologica, 14(5), 555-566.
Sample data in the examples 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. https://doi:10.1016/j.ecolind.2019.105951
diat_sla(resultLoad, maxDistTaxa = 2)diat_sla(resultLoad, maxDistTaxa = 2)
resultLoad |
The resulting list obtained from the diat_loadData() function |
maxDistTaxa |
Integer. Number of characters that can differ in the species' names when compared to the internal database's name in the heuristic search. Default = 2 |
# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) slaResults <- diat_sla(df)# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) slaResults <- diat_sla(df)
The input for all of these functions is the resulting dataframe (resultLoad) obtained from the diat_loadData() function A CSV or dataframe cannot be used directly with these functions, they have to be loaded first with the diat_loadData() function so the acronyms and species' names are recognized References for the index:
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.
Sample data in the examples 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. https://doi:10.1016/j.ecolind.2019.105951
diat_spear(resultLoad, maxDistTaxa = 2)diat_spear(resultLoad, maxDistTaxa = 2)
resultLoad |
The resulting list obtained from the diat_loadData() function |
maxDistTaxa |
Integer. Number of characters that can differ in the species' names when compared to the internal database's name in the heuristic search. Default = 2 |
# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) spearResults <- diat_spear(df)# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) spearResults <- diat_spear(df)
Creates a single list with taxa names from all indices within DiaThor
diat_taxaList()diat_taxaList()
The input for all of these functions is the resulting dataframe (resultLoad) obtained from the diat_loadData() function A CSV or dataframe cannot be used directly with these functions, they have to be loaded first with the diat_loadData() function so the acronyms and species' names are recognized References for the index:
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.
Sample data in the examples 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. https://doi:10.1016/j.ecolind.2019.105951
diat_tdi(resultLoad, maxDistTaxa = 2)diat_tdi(resultLoad, maxDistTaxa = 2)
resultLoad |
The resulting list obtained from the diat_loadData() function |
maxDistTaxa |
Integer. Number of characters that can differ in the species' names when compared to the internal database's name in the heuristic search. Default = 2 |
# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) tdiResults <- diat_tdi(df)# Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) tdiResults <- diat_tdi(df)
The input for these functions is the resulting dataframe obtained from the diat_loadData() function, to calculate ecological information for diatoms based on the Van Dam classification Sample data in the examples 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. https://doi:10.1016/j.ecolind.2019.105951
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.
diat_vandam(resultLoad, vandamReports = TRUE)diat_vandam(resultLoad, vandamReports = TRUE)
resultLoad |
The resulting list obtained from the diat_loadData() function |
vandamReports |
Boolean. If set to 'TRUE' the detailed reports for the Van Dam classifications will be reported in the Output. Default = TRUE |
## Not run: # Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) vandamResults <- diat_vandam(df) ## End(Not run)## Not run: # Example using sample data included in the package (sampleData): data("diat_sampleData") # First, the diat_loadData() function has to be called to read the data # The data will be stored into a list (loadedData) # And an output folder will be selected through a dialog box if resultsPath is empty # In the example, a temporary directory will be used in resultsPath df <- diat_loadData(diat_sampleData, resultsPath = tempdir()) vandamResults <- diat_vandam(df) ## End(Not run)
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
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.
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). ‘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: 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.
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() diat_pbidw() diat_disp() diat_idap() diat_cemfgs_rb() diat_checkName() diat_getDiatBarcode() diat_taxaList()
Maintainer: Joaquin Cochero [email protected] (ORCID)
Authors:
Maria Mercedes Nicolosi Gelis [email protected] (ORCID)
Maria Belen Sathicq [email protected] (ORCID)
The diaThorAll function is the master function of the package. It calculates all outputs from the data, and places them in the Output folder The input file for the package is a dataframe or an external CSV file. Species should be listed as rows, with species' names in column 1 (column name should be "species") The other columns (samples) have to contain the abundance of each species (relative or absolute) in each sample. The first row of the file has to contain the headers with the sample names. Remember that a column named "species" is mandatory, containing the species' names If a dataframe is not specified as a parameter (species_df), the package will show a dialog box to search for the CSV file A second dialog box will help set up an Output folder, where all outputs from the package will be exported to (dataframes, CSV files, plots in PDF) The package also downloads and installs a wrapper for the 'Diat.Barcode' project. Besides citing the DiaThor package, the Diat.Barcode project should also be cited, as follows:
Rimet, Frederic; Gusev, Evgenuy; Kahlert, Maria; Kelly, Martyn; Kulikovskiy, Maxim; Maltsev, Yevhen; Mann, David; Pfannkuchen, Martin; Trobajo, Rosa; Vasselon, Valentin; Zimmermann, Jonas; Bouchez, Agnès. 2018. "Diat.barcode, an open-access barcode library for diatoms". Scientific Reports,9, 15116. https://doi:10.15454/TOMBYZ
Sample data in the examples 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. https://doi:10.1016/j.ecolind.2019.105951
diaThorAll( species_df, isRelAb = FALSE, maxDistTaxa = 2, resultsPath, calculateguilds = TRUE, vandam = TRUE, vandamReports = TRUE, singleResult = TRUE, exportFormat = 3, exportName = "DiaThor_results", plotAll = TRUE, color = "#0073C2" )diaThorAll( species_df, isRelAb = FALSE, maxDistTaxa = 2, resultsPath, calculateguilds = TRUE, vandam = TRUE, vandamReports = TRUE, singleResult = TRUE, exportFormat = 3, exportName = "DiaThor_results", plotAll = TRUE, color = "#0073C2" )
species_df |
The data frame with your species data. Species as rows, Sites as columns. If empty, a dialog will prompt for a CSV file |
isRelAb |
Boolean. If set to 'TRUE' it means that your species' data is the relative abundance of each species per site. If FALSE, it means that it the data corresponds to absolute densities. Default = FALSE |
maxDistTaxa |
Integer. Number of characters that can differ in the species' names when compared to the internal database's name in the heuristic search. Default = 2 |
resultsPath |
String. Path to the output folder. If none specified (default), a dialog box will prompt to select it |
calculateguilds |
Boolean. If set to 'TRUE' the percentage of abundance of each diatom guild will be calculated. Default = TRUE |
vandam |
Boolean. If set to 'TRUE' the Van Dam classifications will be calculated in the Output. Default = TRUE |
vandamReports |
Boolean. If set to 'TRUE' the detailed reports for the Van Dam classifications will be reported in the Output. Default = TRUE |
singleResult |
Boolean. If set to 'TRUE' all results will go into a single output file. If FALSE, separate output files will be generated. Default = TRUE |
exportFormat |
Integer. If = 1: only a CSV (external file) will be generated with the output matrices; 2: only an internal R dataframe will be generated; 3: both a CSV and an internal R dataframe are generated. Default = 3 |
exportName |
String. Prefix for the CSV exported file. Default = "DiaThor_results" |
plotAll |
Boolean. If set to 'TRUE', plots will be generated for each Output in a PDF file. Default = TRUE |
color |
Color code (hex). Default color for bar charts and lolipop plots. Default = "#0073C2" |
# Example using sample data included in the package (sampleData): data("diat_sampleData") # In the example, a temporary directory will be used in resultsPath allResults <- diaThorAll(diat_sampleData, resultsPath = tempdir())# Example using sample data included in the package (sampleData): data("diat_sampleData") # In the example, a temporary directory will be used in resultsPath allResults <- diaThorAll(diat_sampleData, resultsPath = tempdir())
Index values for diatom species included in the DISP index
data(disp)data(disp)
A data frame with the ecological values for 143 species
https://www.sciencedirect.com/science/article/abs/pii/S1470160X18305478
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.
Index values for diatom species included in the EPID index
data(epid)data(epid)
A data frame with the ecological values for 1038 species
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.
Index values for diatom species included in the IDAP index
data(idap)data(idap)
A data frame with the ecological values for 194 species
https://link.springer.com/article/10.1007/BF00028033
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.
Index values for diatom species included in the IC-CH index
data(idch)data(idch)
A data frame with the ecological values for 550 species
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
Index values for diatom species included in the IDP index
data(idp)data(idp)
A data frame with the ecological values for 475 species
https://link.springer.com/article/10.1023/A:1011415209445
Gómez, N., & Licursi, M. (2001). The Pampean Diatom Index (IDP) for assessment of rivers and streams in Argentina. Aquatic Ecology, 35(2), 173-181.
Index values for diatom species included in the ILM index
data(ilm)data(ilm)
A data frame with the ecological values for 667 species
https://www.vliz.be/imisdocs/publications/286641.pdf
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
Index values for diatom species included in the IPS index
data(ips)data(ips)
A data frame with the ecological values for 6881 species
Coste, M. (1982). Étude des méthodes biologiques d’appréciation quantitative de la qualité des eaux. Rapport Cemagref QE Lyon-AF Bassin Rhône Méditerranée Corse.
Index values for diatom species included in the LOBO index
data(lobo)data(lobo)
A data frame with the ecological values for 297 species
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.
Index values for diatom species included in the PBIDW index
data(pbidw)data(pbidw)
A data frame with the ecological values for 79 species
https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.689.5469&rep=rep1&type=pdf#page=85
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.
Index values for diatom species included in the SLA index
data(sla)data(sla)
A data frame with the ecological values for 976 species
https://onlinelibrary.wiley.com/doi/abs/10.1002/aheh.19860140519
Sládeček, V. (1986). Diatoms as indicators of organic pollution. Acta hydrochimica et hydrobiologica, 14(5), 555-566.
Index values for diatom species included in the SPEAR(h) index
data(spear)data(spear)
A data frame with the ecological values for 285 species
https://www.sciencedirect.com/science/article/abs/pii/S1470160X18309683
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.
List of taxa names used in all indices. Gets updated user-end if a new DBC is found
data(taxaList)data(taxaList)
A data frame with names of 9806 taxa
Index values for diatom species included in the TDI index
data(tdi)data(tdi)
A data frame with the ecological values for 3445 species
https://link.springer.com/article/10.1007/BF00003802
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.
The package is a wrapper for the algaeClassify package from the 'AlgaeBase.org' database. Besides citing the DiaThor package, the Diat.Barcode project should also be cited, as follows:
Patil, V., Seltmann, T., Salmaso, N., Anneville, O., Lajeunesse, M., Straile, D. 2019. algaeClassify: Determine Phytoplankton Functional Groups Based on Functional Traits.
update_algaebase_list(listToUpdate, overwrite = T)update_algaebase_list(listToUpdate, overwrite = T)
listToUpdate |
the name of the taxa (genus, species, variety) to be checked against the internal DB |
overwrite |
if overwrite = T (default), if a new name is found, it replaces the original one. The corrected list is returned. Otherwise, a new list is returned, with the original taxon and the new name found |