Guideline

Workflow

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

2) Select the ecological indicator value system to be used for the analysis (see Indicator Value Systems).

3) Species names are automatically standardized and matched to accepted names used in ecological indicator value databases. 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 systems) 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 vegetation plot, IndiCATor prompts users to choose how abundance values should be handled (summed or averaged; see Multiple taxa occurrences).

9) Unweighted mean, cover-weighted mean, square root-cover-weighted mean and inverse-niche-width-weighted mean indicator values (See Calculation of 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 systems

IndiCATor supports two ecological indicator value systems: the Combined Ellenberg-type indicator values database and Ecological Indicator Values for Europe (EIVE) 1.0.

The Combined Ellenberg-type indicator values database integrates several complementary datasets to maximize taxonomic coverage while preserving compatibility among indicator values. For vascular plants indicator values for the main abiotic environmental factors (light, temperature, moisture, reaction, nutrients, and salinity) were taken from Tichý et al. (2023). Disturbance indicator values (disturbance severity, disturbance severity of the herb layer, disturbance frequency, disturbance frequency of the herb layer, mowing frequency, grazing pressure, and soil disturbance) were taken from Midolo et al. (2023).

For bryophytes, indicator values for light, temperature, moisture, reaction, and continentality were taken from Düll (1991), while nutrient values were obtained from Simmel et al. (2021). Indicator values for lichens were taken from Wirth (2010). 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 (Jansen, 2024) taxonomic backbone (Version from 2024-11-03) 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.

Ecological Indicator Values for Europe (EIVE) 1.0 (Dengler et al., 2023) is a harmonized European-scale indicator value system developed by integrating and rescaling 31 existing regional indicator value systems. It provides indicator values for five major environmental gradients: light, temperature, soil moisture, soil reaction, and soil nitrogen.

Unlike traditional Ellenberg-type systems, EIVE provides estimates of both ecological niche position and ecological niche width for each species and environmental factor. Niche-width estimates enable alternative approaches to calculating community-level indicator values, such as weighting species by the inverse of their niche width. In addition, all indicator values are expressed on a continuous scale from 0 to 10 rather than on ordinal integer scales.

EIVE was specifically designed as a unified indicator value system applicable across the whole of Europe and is therefore recommended for continental-scale analyses and studies extending beyond Central Europe (Midolo et al., 2026).

Plant names database

Most tools that process vegetation plots using ecological indicator values require users to harmonize species nomenclature manually. IndiCATor performs this step automatically by matching submitted names to taxa used in the indicator values systems.

The plant names database is primarily based on the EuroSL (Jansen, 2024) 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.

Different taxonomic concepts may assign the same scientific name to taxa of different circumscriptions (Jansen & Dengler, 2010). The taxonomic concept used in IndiCATor is determined by the selected indicator value database. For each supported ecological indicator value system IndiCATor maintains a separate synonym database. The synonym databases differ in the accepted names, the circumscription of supra-specific taxa (e.g. aggregates and sensu lato taxa), and the treatment of taxa below the species level.

For the Combined Ellenberg-type indicator values database, taxa below the species level were generally reassigned to the corresponding species because infraspecific taxa are only rarely represented in the original indicator value datasets. 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.

The Ellenberg-type datasets contain indicator values for numerous supra-specific taxa (e.g. aggregates, sensu lato taxa, and sections), sometimes together with values for individual constituent species. The composition of these taxa was determined using FloraVeg.eu (https://floraveg.eu/). Species-level indicator values are always used preferentially when available. If a species lacks its own indicator values, the values assigned to the corresponding supra-specific taxon are applied. In cases where both a narrowly defined species and a homonymous aggregate are present in the database (for example Achillea millefolium and A. millefolium aggr.), IndiCATor prompts the user to select the intended taxonomic concept before analysis.

For Ecological Indicator Values for Europe (EIVE) 1.0, the treatment of infraspecific taxa, the circumscription of supra-specific taxa, and the accepted names were adopted directly from the original publication (Dengler et al., 2023), ensuring complete consistency between the nomenclature used by IndiCATor and the taxonomic concepts underlying the EIVE dataset.

The databases for both indicator values systems were 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.

Calculation of indicator values

IndiCATor supports the most commonly used approaches for calculating ecological indicator values: unweighted mean, cover-weighted mean, square root-cover-weighted mean, and inverse-niche-width-weighted mean. In species-rich communities without strongly dominant species, unweighted and weighted averages generally produce very similar results. In contrast, substantial differences may arise in species-poor communities dominated by one or a few species (Ostrowski et al., 2025).

The rationale behind abundance-weighted averaging is that more abundant species are assumed to indicate greater habitat favourability and should therefore contribute more strongly to the estimated indicator value. However, this assumption has important limitations because it directly compares the abundance of species with very different growth forms and sizes. Applying a square-root transformation to species cover partly resolved this problem.

An alternative approach is to assign greater weight to species with narrower ecological niches, as these species are expected to provide more precise information about environmental conditions. However, estimates of ecological niche width are available for only a few indicator value systems, including EIVE (Dengler et al., 2023). Comparative evaluations of different weighting approaches remain scarce. Ostrowski et al. (2025) reported that unweighted and inverse-niche-width-weighted averages both showed good agreement with direct environmental measurements and yielded very similar results.

The choice of weighting method is left to the user.

Filter options

Users may include or exclude major clades (vascular plants, bryophytes, and lichens) using the clade selection panel. The selection of clades is performed independently for ecological indicator value calculations and for diversity indices and similarity coefficients. For indicator value calculations, clade selection is available only for the Ellenberg-type indicator values dataset (see Indicator Value Systems). Only taxa belonging to the selected clades are retained for the corresponding analyses.

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. Moreover, because trees generally live much longer than herbaceous species, they may reflect past rather than present environmental conditions in forests undergoing successional change. Finally, in cover-weighted analyses, tree species often receive disproportionately high weights because their cover is usually much greater than that of other life forms (Diekmann, 2023).

Multiple taxa occurrences

IndiCATor automatically detects cases where the same taxon occurs more than once within a vegetation plot. 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 vegetation plots, 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.