msk.macrophytes.2017.read.compile.evaluate: Function to read and compile data for macrophyte and...
In ecoval: Procedures for Ecological Assessment of Surface Waters

Description Usage Arguments Details Value References See Also

View source: R/msk.macrophytes.2017.read.compile.evaluate.R

Function to read and compile data for macrophyte and calculate river types and valuation.

msk.macrophytes.2017.read.compile.evaluate(file.site,
                                           pic.folder        = ".",
                                           file.species      = NA,
                                           file.typeplaus    = NA,
                                           sampling.protocol = "v2018",
                                           sampsize          = 10000,
                                           file.res          = NA,
                                           file.doc          = NA,
                                           file.taxa.used    = NA,
                                           file.taxa.removed = NA,
                                           file.check.msg    = NA,
                                           sep               = "\t",
                                           sep.in            = NA,
                                           sep.out           = NA,
                                           language          = "English",
                                           dictionaries      = NA)

`file.site`	name of text file with site characteristics.
`pic.folder`	(optional) name of folder to search for site pictures (pictures found will be displayed).
`file.species`	(optional) name of text file with species observations.
`file.typeplaus`	(optional) name of text file with plausibilized river types.
`sampling.protocol`	(optional) sampling protocol ("v2018" or "v2009").
`sampsize`	(optional) sample size for Monte Carlo calculation of probabilities of macrophyte river types (default is 10000).
`file.res`	Name of text file for results.
`file.doc`	Name of text file for documentation of sites.
`file.taxa.used`	(optional) name of text file for taxa used for assessment.
`file.taxa.removed`	(optional) name of text file for taxa that were removed because of insufficient determination or because they are not on the taxa list.
`file.check.msg`	(optional) name of text file for warnings and error messages from compilation of species data.
`sep`	Column separator for input and output text files (see also arguments `sep.in` and `sep.out` below).
`sep.in`	Column separator for input files (only needed if different for input and output files; default is the argument `sep` above).
`sep.out`	Column separator for output files (only needed if different for input and output files; default is the argument `sep` above).
`language`	Language to be used to denote nodes, attributes and attribute levels. Must be a column name of the table provided by the second argument.
`dictionaries`	Matrix of dictionaries with the languages provided by the column names and the original words provided as the row names. If dictionary is NA, the default dictionary `ecoval.dictionaries.default` is loaded.

The tasks and ouput depends on the input provided. For sampsize = 0, only checking of the input files is done. For sampsize > 0, in addition, Monte Carlo simulation is done to get the probabilities of all river types. If the file file.species is provided (and sampsize > 0), in addition, the valuations of all sites are performed. If also the file file.typeplaus is provided, an additional valuation is calculated for the plausibilized river types. In addition to the list of outputs (see Value) the output is written to the text file file.res and to pdf site documentation files with names constructed from file.doc and the identifiers of the sites, if these file names are provided. In addition, diagnostics and error messages are written to the files file.taxa.used, file.taxa.removed and file.check.msg. See https://modul-stufen-konzept.ch for more details regarding the methodology.

Named list of outputs dependent on tasks performed (see Details).

Langhans, S.D., Lienert, J., Schuwirth, N. and Reichert, P. How to make river assessments comparable: A demonstration for hydromorphology, Ecological Indicators 32, 264-275, 2013. doi: 10.1016/j.ecolind.2013.03.027

Langhans, S.D., Reichert, P. and Schuwirth, N. The method matters: indicator aggregation in ecological river assessment. Ecological Indicators 45, 494-507, 2014. doi: 10.1016/j.ecolind.2014.05.014

Reichert, P., Schuwirth, N. and Langhans, S. Constructing, evaluating and visualizing value and utility functions for decision support, Environmental Modelling & Software 46, 283-291, 2013. doi: 10.1016/j.envsoft.2013.01.017

Reichert, P., Langhans, S., Lienert, J. and Schuwirth, N. The conceptual foundation of environmental decision support. Journal of Environmental Management. 154, 316-332, 2015. doi: 10.1016/j.jenvman.2015.01.053

Reichert, P., Borsuk, M., Hostmann, M., Schweizer, S., Sporri, C., Tockner, K. and Truffer, B. Concepts of decision support for river rehabilitation, Environmental Modelling and Software 22, 188-201, 2007. doi: 10.1016/j.envsoft.2005.07.017

Kaenel, B., Michel, C., Reichert, P. Methoden zur Untersuchung und Beurteilung der Fliessgewaesser. Makrophyten - Stufe F (flaechendeckend) und Stufe S (systembezogen). Entwurf. Bundesamt fuer Umwelt, Bern. 119 S. 2017. https://modul-stufen-konzept.ch/