Workflow

1) Upload a table containing relevés (see Input format). The data are used only for the current analysis session and are not stored or used for any other purposes.

2) Species names are automatically standardized and matched to accepted names used in ecological indicator value databases.

3) If a species name is not found in the database (see Plant names database), IndiCATor suggests up to five similar names to help correct minor spelling errors during processing.

4) If the species cannot be matched, the user can indicate that it is absent from the database and specify its clade (vascular plants, bryophytes, or lichens). This information is required for later stages when calculating diversity indices and similarity coefficients.

5) For some taxa, indicator values are available only at the aggregate level rather than for narrowly defined species. In such cases, indicator values of the aggregate are applied to all included taxa. When both a sensu stricto species and a corresponding aggregate are present in the indicator value databases, IndiCATor prompts users to select which taxonomic concept should be used in the analysis.

6) IndiCATor automatically links standardized plant names to their corresponding indicator values (see Indicator value databases) and provides a processed table containing validated species names and indicator values. This table can be downloaded, manually edited if needed, and re-uploaded on the main page of the website to avoid repeating the name validation step.

7) Users can choose whether to include or exclude the tree layer, vascular plants, and bryophytes from the analysis (see Filter options).

8) If a species occurs multiple times within the same relevé, IndiCATor prompts users to choose how abundance values should be handled (summed or averaged; see Multiple taxa occurrences).

9) Mean and abundance-weighted mean indicator values are calculated automatically. Result tables can be downloaded at this step.

10) Users may proceed to the next step to calculate alpha diversity indices and species similarity coefficients between plots (see Indices and coefficients). At this step, different clades can be selected for inclusion (see Filter options). The table with alpha diversity metrics and similarity matrices can be downloaded at this step.

11) Meow-Meow!

Indicator value databases

Indicator values for vascular plants were taken from Tichý et al. (2023). Tables containing Ellenberg-type indicator values for the main ecological factors (light, temperature, moisture, reaction, nutrients, and salinity) as well as disturbance indicator values were merged into a single dataset.

Indicator values for bryophytes were compiled from two sources: light, temperature, moisture, reaction, and continentality from Düll (1991), and nutrients from Simmel et al. (2021). As all indicator values used are of the Ellenberg type, they were considered conceptually compatible and combined for joint use.

Species names were standardized according to current taxonomic concepts using the EuroSL taxonomic backbone for biological databases (eurosl.infinitenature.org), which is based on Euro+Med (2006+) for vascular plants and Hodgetts et al. (2020) for bryophytes. For taxa treated as synonyms, only shared indicator values were retained.

For supra-specific taxa (aggregates, sensu lato taxa, sections), all included taxa were identified using FloraVeg.eu (https://floraveg.eu/). Indicator values were assigned from the supra-specific taxon only when no separate indicator values were available for the species in the narrow sense, thereby preserving taxonomic resolution when species-level data exist.

Plant names database

Most tools that process vegetation relevés using ecological indicator values require users to harmonize species nomenclature manually. IndiCATor performs this step automatically by matching submitted names to accepted taxa and their synonyms.

The plant names database is primarily based on the EuroSL taxonomic backbone for biological databases (https://eurosl.infinitenature.org/downloads/), which incorporates Euro+Med (2006+) for vascular plants and Hodgetts et al. (2020) for bryophytes. Species names present in the ecological indicator value datasets but absent from EuroSL were added based on World Flora Online (The World Flora Online Consortium et al., 2025). When accepted names differed between Euro+Med and World Flora Online, the nomenclature of Euro+Med (2006+) was preferred.

The synonym database was further expanded to include lichen taxa using a species list for Russia (Urbanavichus, 2010; Index Fungorum, (2025)) and the Lichen Taxon Dictionary (The British Lichen Society, 2005). Each taxon in the database was assigned to one of three clades (vascular plants, bryophytes, or lichens), which allows subsequent filtering during analysis.

Within the database, the taxon name serves as the primary key and uniquely identifies each record. Although unambiguous identification of scientific names normally requires author citation, author names were omitted to simplify data entry. To minimize ambiguity, homonymous names were removed: if none of the homonyms represented an accepted name, both were excluded, whereas if one name was accepted, only that name was retained.

Because taxa below the species level are rarely used in ecological indicator values database, names below subspecies rank were reassigned to the corresponding species. If a taxon treated as a species in indicator values database is currently recognized as a subspecies or variety, the currently accepted infraspecific taxon was retained. Hybrids that are not formally recognized nothospecies or nothogenera were excluded.

Indicator value datasets may include assessments for supra-specific taxa (e.g. aggregates, sensu lato taxa, sections) as well as for some included species in the narrow sense. For such supra-specific taxa, all included taxa were identified using FloraVeg.eu (https://floraveg.eu/). Species-level indicator values are used preferentially whenever they exist. If both a narrowly defined species and a same-named aggregate are present in the database (for example Achillea millefolium and A. millefolium aggr.), IndiCATor prompts the user to specify which taxonomic concept should be applied. Species lacking their own indicator values are evaluated using the values assigned to the corresponding aggregate.

The database was additionally supplemented with species names and synonyms from the checklist of vascular plants of Russia and adjacent countries (Cherepanov, 1995), restricted to taxa recorded within Eastern Europe.

Filter options

Users may include or exclude major clades using the clade selection panel. For indicator values this applies to vascular plants and bryophytes, while calculations of indices and coefficients may include any of the three clades (vascular plants, bryophytes, or lichens). Only taxa belonging to the selected clades are retained for further calculations.

If the uploaded dataset contains information on vegetation layers (a column named "layer", where the tree layer is denoted as A or t1, t2, t3), users can also specify whether the tree layer should be included in the analysis. Excluding the tree layer may be ecologically meaningful because mature trees often experience environmental conditions that differ from those of species in lower vegetation layers. Trees usually occupy canopy positions with full light exposure and may access water and nutrients from deeper soil horizons due to their extensive root systems.

Multiple taxa occurrences

IndiCATor automatically detects cases where the same taxon occurs more than once within a relevé. Such duplicates may arise for two main reasons: (i) the species is recorded separately in different vegetation layers, in which case abundance values (e.g. cover estimates) should be summed; or (ii) the species is recorded multiple times within the same relevé due to data entry errors or alternative recordings, in which case averaging abundance values may be more appropriate. For each taxon with overlapping occurrences, the user is prompted to select whether abundance values should be combined by summation or averaging.

Indices and coefficients

To characterize species diversity within relevés, IndiCATor calculates several widely used diversity indices. All calculations are performed after applying user-defined taxonomic and clade-based filters.

Alpha-diversity indices

For each plot (relevé), the following metrics are calculated.

Species richness ($S$) is defined as the number of taxa with non-zero abundance in a plot:

where $n_i$ is the abundance of species $i$.

Species richness reflects how many taxa are present regardless of their relative abundances.

The Shannon diversity index ($H'$) is calculated as

where $p_i = \frac{n_i}{N}$ and $N = \sum n_i \$ is the total abundance in the plot.

The Shannon index measures the entropy of the abundance distribution, it combines information on both species richness and evenness, increasing when more species are present and when abundances are more evenly distributed.

The Margalef richness index ($d$) is calculated as

where $S$ is species richness and $N$ is total abundance.

This index standardises species richness by sampling intensity (total abundance), allowing comparisons between plots with different total cover or biomass. It emphasises richness while partially correcting for differences in community size.

Pielou's evenness index ($J'$) is calculated as

where $H'$ is the Shannon-Wiener diversity index and $S$ is the total number of species.

Pielou’s evenness index measures the consistency of species distribution in a community, with values ranging from 0 to 1, where 1 represents perfectly equal abundance across species. A lower value indicates high dominance by a few species.

The Simpson dominance index ($D$) is calculated as

The Simpson dominance index (D) is the weighted mean of the proportional abundances, it quantifies the probability that two randomly selected units of cover from a plot belong to the same species, with values closer to 1 indicating low diversity (high dominance) and closer to 0 indicating high diversity.

Similarity coefficients

To quantify compositional similarity between pairs of plots, IndiCATor computes several similarity coefficients based on both presence–absence and abundance data. All coefficients range from 0 (no similarity) to 1 (identical composition).

The abundance-based Sørensen–Čekanowski index is calculated as

where $x_i$ and $y_i$ are abundances of species $i$ in plots $x$ and $y$.

The classical Jaccard index based on presence–absence data is defined as

where $a$ is the number of species shared by both plots, and $b$ and $c$ are species unique to each plot.

The abundance-based Jaccard index, also known as the Růžička index, is calculated as

This formulation extends the classical Jaccard index to quantitative data.