diat_morpho: Calculate morphological parameters for diatoms

In jcochero/DiaThor: Calculate Ecological Information and Diatom Based Indices

Calculate morphological parameters for diatoms

Description

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

Usage

diat_morpho(resultLoad, isRelAb = FALSE)

Arguments

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

Examples

# 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)

jcochero/DiaThor documentation built on Aug. 17, 2024, 6:23 p.m.