seal-tool 0.11.0

A tool to perform richness-extent-grain analyses

seal

Perform richness-extent-grain analyses inspired by Palmer & White (doi:10.1086/285704, doi:10.17615/n84a-pd17)

Setup

Installation

From PyPI via pip:

pip install seal-tool

Or simply download seal from Codeberg releases or clone the repository using git.

First run

Done only when installing and running the tool for the first time and necessary only for non-PyPI installations.

Open the project directory in your command-line interface.

Linux

In POSIX-compatible shell run:

source ./src/firstrun.sh

Windows

In PowerShell Run:

./src/firstrun.ps1

If you encounter an error such as ./src/firstrun.ps1 cannot be loaded because running scripts is disabled on this system on Windows, it means the script was blocked by your security settings. In that case either unblock the script e.g. using the Unblock-File or Set-ExecutionPolicy cmdlets or run the necessary commands manually.

python -m venv ./venv
./venv/Scripts/Activate.ps1
pip install .[dev]

You should see (venv) before your shell prompt now and seal --help should run the tool without errors. Continue with Usage.

Subsequent runs

Done when running the tool any time after the first initial installation.

Linux:

source ./venv/bin/activate
seal <subcommand>

Windows PowerShell:

./venv/Scripts/activate.ps1
seal <subcommand>

Usage

One would generally want to use preprocess, analyse and plot subcommands in this order. misc subcommand contains several scripts that may be useful while converting or modifying either datasets or quadrat lists for analysis.

More detailed help can be accessed by seal --help or seal <subcommand> --help.

Preprocess

Preprocess will ensure given dataset is fit to be processed by the analyse command by e.g. sanitizing strings, warning for missing values or checking whether species column remains consistent with name, morph and phase.

Example:

seal preprocess --dataset ./datasets/raw.csv --output ./datasets/clean.csv

Analysis

analyse subcommand ingests a taskfile to perform analyses requested therein.

Example:

seal analyse --taskfile ./tasks/0-example-task.toml

More example taskfiles are available at our Codeberg repository along with some datasets.

Currently supported analyses are:

a1 - Overview

This analysis calculates per-quadrat species number and number of encountered individuals for each level.

The additional data contain general description of given dataset and various smaller statistics for each level. Such statistics include, for example, the most common value, mean, median, min and such for each data column.

This helps familiarize oneself with the data and serves as a basic check of the levels-creating strategy.

a2 - Species-area relationship

This analysis shows relationship between species richness and area sampled.

Species-area curve is calculated for each level by accumulating quadrats and tallying the number of species. Since this method is sensitive to order of the quadrats, number of permutations must be specified and their arithmetic mean is plotted.

The additional data contain statistics of the calculated results.

a3 - Distance-dependent species difference

This analysis creates pairwise difference of sets of encountered species in two quadrats.

Result is the difference as a function of distance of the quadrats.

a4 - Radius richness

This analysis calculates the number of species within various distance intervals (interval's width is set by the interval-step parameter) from each quadrat. The radius forms a belt of sorts with a specified width.

We recommend using the size of the smallest quadrat as the smallest possible step.

a5 - Ratio of observed and expected species

This analysis calculates the ratio of observed and expected number of species for each quadrat. The expected value is calculated as $$\sum_{}P_i * (1 - P_i)$$ where P_i is the proportion of quadrats occupied by species i and the summation is over all the species in the study grid.

a6 - Ratio of shared and unique species

This analysis calculates several ratios for pairs of quadrats based on their distance.

1. Ratio of shared species among the quadrats and exclusive species among the quadrats.
2. Ratio of shared species among the quadrats and all the species in the dataset.
3. Ratio of shared species among the quadrats and all the species in the study grid.

a7 - Jaccard dissimilarity

This analysis calculates Jaccard dissimilarity with regards to species between all possible pairs of quadrats.

Result is plotted as dissimilarity against the distance of the quadrats.

Jaccard dissimilarity between quadrats a and b is calculated as: $$J(a, b) = 1 - \frac{intersect_{ab}}{intersect_{ab} + exclusive_a + exclusive_b}$$

Plotting

plot subcommand ingests taskfile to detect results of previous analyses and present them as graphs.

Generated graphs will be saved to the same directory as analysis results.

Example:

seal plot --taskfile ./tasks/0-example-task.toml

Misc

misc subcommand is a kitchen sink of opinionated convenience tools.

Development

For unit tests run python -m doctest ./src/seal/<file>.

For functional tests run pytest.

License

The source code—including the tests and documentation—is licensed under GPLv3

./datasets/data-bmd-sl.csv is licensed under CC-BY-SA-4.0

aopk-fish.csv was provided under CC-BY-4.0 by AOPK ČR, Nálezová databáze ochrany přírody, on-line database portal.nature.cz. Downloaded 2024-02-05.