Subcommands

preprocess

Preprocessing 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.

Default checks suitable for any data are performed by default with several others available provided the input has specific columns to be checked.

Example:

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

analyse

The command that does the heavy lifting and analyses given data according to configuration set in taskfile.

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

plot

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

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

Warning

Plotting is not the main focus of seal, it’s the data resulting from analysis. While we try our best, it is not feasible to ensure every possible combination of grid size and species renders correctly and without overlaps. Users are encouraged to simply load the CSV output from the analyse subcommand into their favorite tool to create their own visualizations or to modify the code of plotting to fit their needs.

Example:

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

misc

misc subcommand is a kitchen sink of helpers and opinionated convenience tools originating from our needs. These may or may not be useful to others.

seal misc --help

a2-quantify

Quantify spp. difference between levels based on results from species-area relationship analysis and plot the results.

seal misc a2-quantify ./results/a2-aux-data.csv ./results/a2-quant.csv

rtm

Pass to to indicate that a2-aux-data was generated using repeated transect merging strategy.

adjust-grid

adjust-grid will crop grid edges as necessary to be suitable for chosen strategy and levels. It will not, however, adjust the grid to fit every analysis (notably a5, we strongly recommend adjusting the grid manually before running this analysis).

Adjustments that minimize loss of encounters, species and area will be preferred in this order.

seal misc adjust-grid --taskfile ./tasks/example-task.toml --output ./adjusted

check-quadrat-list

Check quadrat list for duplicates, malformed coordinates, missing values, and unrecognized columns.

seal misc check-quadrat-list ./tests/datasets/qlists/invalid.csv

convert-aopk

Convert an AOPK dataset (from https://portal.nature.cz/nd/) for preprocessing and analysis.

Columns expected in the input: DRUH, DATI_INSERT, SITMAP, POCET

seal misc convert-aopk ./datasets/aopk-raw.csv ./expected/aopk-conv.csv

Output columns: coord_x,coord_y,species,date,individuals

convert-biolib

Convert a BioLib dataset (from https://www.biolib.cz/cz/speciesmappings) for preprocessing and analysis.

Columns expected in the input: CREATED, DAY, LATIN, MONTH, SUBSQ, SQUARE, QUANTITY, YEAR

seal misc convert-biolib ./datasets/biolib-raw.csv ./tests/expected/biolib-conv.csv

Output columns: species,individuals,date,coord_x,coord_y

Note

Quadrat list with KFME coordinates for Czechia is available in our repository.