pyitalic 0.1.0

Interface to the ITALIC database of lichen biodiversity

pyitalic

pyitalic is a Python package that gives you access to ITALIC mediated data via its RESTful API.

It is a Python port of the R package ritalic, exposing the same functions (the R italic_* exports become pyitalic.match, pyitalic.taxonomy, ...).

ITALIC, the Information System on Italian Lichens, makes available information and resources about the lichens known to occur in Italy and bordering countries. It is maintained and updated by the Research Unit of Professor Pier Luigi Nimis, at the University of Trieste (NE Italy), Department of Life Sciences. Most of the data are derived from the Checklist of the Lichens of Italy by Nimis (2016), but nomenclatural and distributional data are being continuously updated.

Installation

pip install pyitalic

The distribution-map function (distribution_map) needs extra geospatial/plotting dependencies (geopandas + matplotlib). Install them with:

pip install "pyitalic[map]"

Usage

import pyitalic

# Match scientific names against the Checklist of the Lichens of Italy
matched = pyitalic.match("Cetraria islandica")
accepted = matched["accepted_name"]

# Retrieve data for accepted names
pyitalic.taxonomy(accepted)
pyitalic.ecology_traits(accepted)
pyitalic.regions_distribution(accepted)
pyitalic.ecoregions_distribution(accepted)

# Occurrence records and their references
occ = pyitalic.occurrences("Cetraria ericetorum Opiz")
pyitalic.occurrences_references(occ)

# The full checklist (optionally filtered)
pyitalic.checklist(genus="Lecanora")

# A distribution map (requires the [map] extra)
fig = pyitalic.distribution_map("Flavoparmelia caperata (L.) Hale")
fig.savefig("flavoparmelia.png")

Most functions accept a single name (str) or several names (list[str] / pandas.Series) and return a pandas.DataFrame.

Available functions

Function	Description
match	Match scientific names against the ITALIC checklist
checklist	Accepted names in the Checklist of the Lichens of Italy
taxonomy	Taxonomic classification
name_usage	Name metadata (IDs, status, authorship)
description	Morphological descriptions and notes
ecology_traits	Morpho-functional traits and ecological indicators
traits_pa	Presence/absence matrix of morphological traits
regions_distribution	Presence/absence across Italian administrative regions
ecoregions_distribution	Commonness/rarity across Italian ecoregions
occurrences	Herbarium occurrence records (Darwin Core)
occurrences_references	Bibliographic references for occurrence datasets
taxon_data	Combined taxonomy + ecology + distribution data
identification_key	URL to an interactive identification key
distribution_map	Distribution map (requires the [map] extra)

License

MIT