Package 'ritalic' reference manual

Title:	Interface to the ITALIC Database of Lichen Biodiversity
Description:	A programmatic interface to the Web Service methods provided by ITALIC (<https://italic.units.it>). ITALIC is a database of lichen data in Italy and bordering European countries. 'ritalic' includes functions for retrieving information about lichen scientific names, geographic distribution, ecological data, morpho-functional traits and identification keys. More information about the data is available at <https://italic.units.it/?procedure=base&t=59&c=60>. The API documentation is available at <https://italic.units.it/?procedure=api>.
Authors:	Matteo Conti [aut, cre] (ORCID: <https://orcid.org/0009-0003-4917-2639>), Luana Francesconi [aut], Alice Musina [aut], Luca Di Nuzzo [aut], Gabriele Gheza [aut], Chiara Pistocchi [aut], Juri Nascimbene [aut], Pier Luigi Nimis [aut], Stefano Martellos [aut]
Maintainer:	Matteo Conti <[email protected]>
License:	MIT + file LICENSE
Version:	0.13.1
Built:	2026-10-13 12:07:14 UTC
Source:	https://github.com/plant-data/ritalic

Get species names in the checklist of the lichens of Italy

Description

Retrieves the complete list of accepted scientific names from the Checklist of the Lichens of Italy in ITALIC. The function returns all accepted names of species occurring in Italy. If the parameter include_bordering_countries is set to TRUE the function returns all the accepted names of species in ITALIC occurring both in Italy and in bordering countries.

Usage

italic_checklist(
  include_bordering_countries = FALSE,
  genus = NULL,
  family = NULL,
  order = NULL,
  class = NULL,
  phylum = NULL
)
italic_checklist(
  include_bordering_countries = FALSE,
  genus = NULL,
  family = NULL,
  order = NULL,
  class = NULL,
  phylum = NULL
)

Arguments

include_bordering_countries

Optional. Default FALSE. If TRUE the result includes also taxa occurring in bordering countries.

genus

Optional. A genus name to filter the checklist.

family

Optional. A family name to filter the checklist.

order

Optional. An order name to filter the checklist.

class

Optional. A class name to filter the checklist.

phylum

Optional. A phylum name to filter the checklist.

Value

A character vector containing all accepted scientific names from the checklist of ITALIC.

References

ITALIC - The Information System on Italian Lichens: checklist https://italic.units.it/index.php?procedure=checklist

Examples

## Not run: 
# Get the complete checklist of Italy
italic_checklist()
# Get the complete checklist of Italy and bordering countries
italic_checklist(include_bordering_countries=TRUE)
# Get the checklist of the species of genus Lecanora
italic_checklist(genus ="Lecanora")

## End(Not run)

## Not run: 
# Get the complete checklist of Italy
italic_checklist()
# Get the complete checklist of Italy and bordering countries
italic_checklist(include_bordering_countries=TRUE)
# Get the checklist of the species of genus Lecanora
italic_checklist(genus ="Lecanora")

## End(Not run)

Get descriptions of lichen taxa

Description

Retrieves morphological descriptions and additional taxonomic or ecological notes about lichen taxa present in the Checklist of the Lichens of Italy. Only accepts names that exist in the database of ITALIC.

Usage

italic_description(sp_names)
italic_description(sp_names)

Arguments

sp_names

Character vector of accepted names

Value

A data frame with columns:

scientific_name: The scientific name provided as input
description: Morphological description
notes: Additional taxonomic or ecological information

Note

Before using this function with a list of names, first obtain their accepted names using italic_match(). Example workflow:

      names_matched <- italic_match(your_names)
      descriptions <- italic_description(names_matched$accepted_name)

Examples

## Not run: 
italic_description("Cetraria islandica (L.) Ach. subsp. islandica")

## End(Not run)


## Not run: 
italic_description("Cetraria islandica (L.) Ach. subsp. islandica")

## End(Not run)

Create distribution map of a lichen taxon

Description

Creates a distribution map for a given lichen species based on its commonness/rarity status across Italian ecoregions and presence/absence across administrative regions. The map visually represents the data obtained from italic_ecoregions_distribution() and italic_regions_distribution().

Usage

italic_distribution_map(sp_name, plot_map = TRUE)
italic_distribution_map(sp_name, plot_map = TRUE)

Arguments

sp_name

Character string representing the accepted scientific name of a lichen species. If multiple names are provided, a list is returned.

plot_map

If TRUE (default) the function returns a ggplot graph, if FALSE returns a sf object

Details

The function internally utilizes italic_ecoregions_distribution() and italic_regions_distribution() to retrieve the commonness/rarity status across Italian ecoregions and presence/absence across administrative regions data for the provided species. It then joins this data with a geospatial dataset of Italian regions and ecoregions (included in the package) to generate the map.

Commonness/rarity categories are visualized with a color scale, where each color corresponds to a different level of commonness/rarity ("extremely common", "very common", "common", "rather common", "rather rare", "rare", "very rare", "extremely rare", "absent").

Value

If one name is provided: if plot_map = TRUE (default), a ggplot object; if plot_map = FALSE, the sf object used to create the plot. If multiple names are provided, a named list of ggplot or sf objects, one for each input name.

Note

Before using this function, ensure that you have obtained the accepted name of the lichen using italic_match(). Example workflow:

      name_matched <- italic_match("Cetraria islandica")
      map <- italic_distribution_map(name_matched$accepted_name)

References

For more information about Italian ecoregions see ITALIC ecoregions distribution https://italic.units.it/?procedure=base&t=59&c=60#commonness and the scientific publication describing the ecoregions used in ITALIC doi:10.3390/d12080294

Examples

## Not run: 
italic_distribution_map("Flavoparmelia caperata (L.) Hale")
italic_distribution_map("Anisomeridium biforme (Schaer.) R.C. Harris")

## End(Not run)

## Not run: 
italic_distribution_map("Flavoparmelia caperata (L.) Hale")
italic_distribution_map("Anisomeridium biforme (Schaer.) R.C. Harris")

## End(Not run)

Get ecology data and morphological traits of lichen taxa

Description

Retrieves morpho-functional traits, ecological indicators, altitudinal distribution, and poleotolerance data for lichen taxa. Only accepts names that exist in the database of ITALIC.

Usage

italic_ecology_traits(sp_names)
italic_ecology_traits(sp_names)

Arguments

sp_names

Character vector of accepted names

Value

A data frame with:

scientific_name: The scientific name provided as input
substrata: Substrate
photobiont: Type of photosynthetic partner
growth_form: Growth form
phytoclimatic_range: Distribution in vegetation zones
special_requirements_for_water: Water requirements
reproductive_strategy: Main reproductive methods
ph_of_the_substrata_min: Minimum pH value (1-5 scale)
ph_of_the_substrata_max: Maximum pH value (1-5 scale)
solar_irradiation_min: Minimum light requirements (1-5 scale)
solar_irradiation_max: Maximum light tolerance (1-5 scale)
aridity_min: Minimum aridity tolerance (1-5 scale)
aridity_max: Maximum aridity tolerance (1-5 scale)
eutrophication_min: Minimum nutrient requirements (1-5 scale)
eutrophication_max: Maximum nutrient tolerance (1-5 scale)
altitudinal_distribution_min: Minimum altitude zone (1-6 scale)
altitudinal_distribution_max: Maximum altitude zone (1-6 scale)
poleotolerance_min: Minimum poleotolerance level (1-5 scale)
poleotolerance_max: Maximum poleotolerance level (1-5 scale)

Note

Before using this function with a list of names, first obtain their accepted names using italic_match(). Example workflow:

      names_matched <- italic_match(your_names)
      data <- italic_ecology_traits(names_matched$accepted_name)

References

ITALIC - The Information System on Italian Lichens: data about taxa https://italic.units.it/?procedure=base&t=59&c=60#otherdata

Examples

## Not run: 
italic_ecology_traits("Cetraria islandica (L.) Ach. subsp. islandica")

## End(Not run)

## Not run: 
italic_ecology_traits("Cetraria islandica (L.) Ach. subsp. islandica")

## End(Not run)

Get distribution of lichen taxa across Italian ecoregions

Description

Returns the distribution and commonness status of lichen taxa across Italian ecoregions. Only accepts names that exist in the database of ITALIC.

Usage

italic_ecoregions_distribution(sp_names, result_data = "rarity")
italic_ecoregions_distribution(sp_names, result_data = "rarity")

Arguments

sp_names

Character vector of accepted names

result_data

Character string specifying the output format: "rarity" (default) returns commonness/rarity categories, "presence-absence" returns only values for presence/absence (0/1)

Value

A data frame with:

scientific_name: The scientific name provided as input
alpine: Status in alpine belt (extremely common to absent)
subalpine: Status in subalpine belt (extremely common to absent)
oromediterranean: Status in oromediterranean belt (extremely common to absent)
montane: Status in montane belt (extremely common to absent)
dry_submediterranean: Status in dry submediterranean belt (extremely common to absent)
padanian: Status in padanian belt (extremely common to absent)
humid_submediterranean: Status in humid submediterranean belt (extremely common to absent)
humid_mediterranean: Status in humid mediterranean belt (extremely common to absent)
dry_mediterranean: Status in dry mediterranean belt (extremely common to absent)

The possible values of commonness/rarity are: "extremely common", "very common", "common", "rather common", "rather rare", "rare", "very rare", "extremely rare", "absent"

Note

Before using this function with a list of names, first obtain their accepted names using italic_match(). Example workflow:

      names_matched <- italic_match(your_names)
      ecoregions_distribution <- italic_ecoregions_distribution(names_matched$accepted_name)

References

Examples

## Not run: 
# Get commonness/rarity categories
italic_ecoregions_distribution("Cetraria ericetorum Opiz")

# Get presence/absence data
italic_ecoregions_distribution("Cetraria ericetorum Opiz", result_data="presence-absence")

## End(Not run)

## Not run: 
# Get commonness/rarity categories
italic_ecoregions_distribution("Cetraria ericetorum Opiz")

# Get presence/absence data
italic_ecoregions_distribution("Cetraria ericetorum Opiz", result_data="presence-absence")

## End(Not run)

Generate interactive identification keys for lichen taxa

Description

Creates a URL link to a custom interactive dichotomous key for identifying the specified lichen taxa using the KeyMaker system of ITALIC. Only accepts names that exist in the database of ITALIC.

Usage

italic_identification_key(sp_names)
italic_identification_key(sp_names)

Arguments

sp_names

Character vector of accepted names

Value

Character string containing the URL to a web-based interactive identification key. The key is uniquely generated for the input taxa and allows step-by-step identification through dichotomous choices.

Note

Before using this function with a list of names, first obtain their accepted names using italic_match(). Example workflow:

      names_matched <- italic_match(your_names)
      key_url <- italic_identification_key(names_matched$accepted_name)

References

ITALIC - The KeyMaker https://italic.units.it/key-maker/

Examples

## Not run: 
# Generate key for two species
italic_identification_key(c("Cetraria ericetorum Opiz","Xanthoria parietina (L.) Th. Fr."))

## End(Not run)

## Not run: 
# Generate key for two species
italic_identification_key(c("Cetraria ericetorum Opiz","Xanthoria parietina (L.) Th. Fr."))

## End(Not run)

Match scientific names of lichens against the database of ITALIC

Description

Aligns scientific names of lichens against the Checklist of the Lichens of Italy available in ITALIC database. The function handles infraspecific ranks (subspecies, varieties, forms) and returns detailed matching information including nomenclatural status and matching scores.

Usage

italic_match(sp_names, subsp_marks = c(), var_marks = c(), form_marks = c())
italic_match(sp_names, subsp_marks = c(), var_marks = c(), form_marks = c())

Arguments

sp_names

A character vector of scientific names to match

subsp_marks

Character vector of markers used to indicate uncommon subspecies rank in the input names (different from "subsp.", "ssp."). For example, to match "Pseudevernia furfuracea b) ceratea", you need to pass "b)" as subsp_mark

var_marks

Character vector of markers used to indicate uncommon variety rank in the input names (different from "var.", "v."). For example, to match "Acarospora sulphurata varietas rubescens", you need to pass "varietas" as var_mark

form_marks

Character vector of markers used to indicate uncommon form rank in the input names (different from "f.", "form"). For example, to match "Verrucaria nigrescens fo. tectorum", you need to pass "fo." as form_mark

Value

A data frame with the following columns:

input_name: Original scientific name provided
matched_name: Name matched in ITALIC database
status: Nomenclatural status ("accepted" or "synonym")
accepted_name: Currently accepted name in ITALIC
name_score: Matching score for the name part (0-100)
auth_score: Matching score for the authority part (0-100)

Examples

## Not run: 
# Simple name match
italic_match("Cetraria islandica")

# Name match where the name contains spelling mistakes
italic_match("Xantoria parietina")

# Match where the name contains uncommon marker
italic_match("Acarospora sulphurata varietas rubescens",
                      var_marks = "varietas")

# Match multiple names
italic_match(c("Cetraria islandica", "Xanthoria parietina"))

## End(Not run)
## Not run: 
# Simple name match
italic_match("Cetraria islandica")

# Name match where the name contains spelling mistakes
italic_match("Xantoria parietina")

# Match where the name contains uncommon marker
italic_match("Acarospora sulphurata varietas rubescens",
                      var_marks = "varietas")

# Match multiple names
italic_match(c("Cetraria islandica", "Xanthoria parietina"))

## End(Not run)

Run the ITALIC MCP server

Description

Runs a local MCP server that lets AI assistants (Claude, Cursor, ...) work with ITALIC through the functions of ritalic: aligning names, retrieving the data of the taxa, searching taxa and creating identification keys. The tools are listed in italic_mcp_tools().

The server communicates over stdin/stdout and is meant to be started by the MCP client, not in an interactive session. Requires the packages mcptools and ellmer.

Usage

italic_mcp_server(...)
italic_mcp_server(...)

Arguments

...

Further arguments passed to mcptools::mcp_server().

Value

Does not return: it serves the tools until the client closes the connection.

Connecting an assistant

Claude Code:

claude mcp add ritalic -- Rscript -e "ritalic::italic_mcp_server()"

Claude Desktop, in claude_desktop_config.json:

{
  "mcpServers": {
    "ritalic": {
      "command": "Rscript",
      "args": ["-e", "ritalic::italic_mcp_server()"]
    }
  }
}

Use the full path of Rscript if it is not found (e.g. the output of file.path(R.home("bin"), "Rscript")).

Tools of the ITALIC MCP server

Description

Returns the functions of ritalic as tools for AI assistants, created with ellmer::tool(). They can be served to Claude, Positron or other MCP clients with italic_mcp_server(), or registered in an ellmer chat with chat$register_tools(italic_mcp_tools()).

The tools are:

italic_match: Aligns scientific names to ITALIC, dropping the matches below a minimum score
italic_taxon_data: Taxonomy, ecology and traits, distribution in regions and ecoregions, description and functional traits of the taxa, as a table
italic_search: Searches the taxa by distribution, ecology, traits and taxonomy
italic_search_filters: Lists the filters of the search and the meaning of their values
italic_identification_key: Creates an interactive identification key with the KeyMaker
italic_checklist: Lists the accepted names of the checklist

Each tool returns JSON text; errors are returned as {"error": "..."}.

Usage

italic_mcp_tools()
italic_mcp_tools()

Value

A list of ellmer tool definitions.

Examples

## Not run: 
# Use the tools in an ellmer chat
chat <- ellmer::chat_anthropic()
chat$register_tools(italic_mcp_tools())
chat$chat("Which saxicolous lichens with cyanobacteria grow in Sardegna?")

## End(Not run)

## Not run: 
# Use the tools in an ellmer chat
chat <- ellmer::chat_anthropic()
chat$register_tools(italic_mcp_tools())
chat$chat("Which saxicolous lichens with cyanobacteria grow in Sardegna?")

## End(Not run)

Get details of species names

Description

Retrieves information for a scientific name used in ITALIC, including name id, taxonomic status, Index Fungorum id and related taxon id.

Usage

italic_name_usage(sp_names)
italic_name_usage(sp_names)

Arguments

sp_names

Character vector of matched names or accepted names

Value

A data frame with columns:

input_name: The scientific name provided as input
scientific_name_id: Unique identifier of ITALIC for the scientific name
index_fungorum_id: Corresponding Index Fungorum identifier
scientific_name_full: Complete scientific name including authority
scientific_name: Scientific name without authority
authorship: Author of the name
notes: Additional notes about the taxon, if any
rank: Taxonomic rank of the name
status: Taxonomic status ('accepted', 'synonym' or 'basionym')
related_accepted_name_id: ID of the currently accepted name related to the input name in ITALIC
related_accepted_name: Full accepted name
related_taxon_id: ID of the related taxon in ITALIC

Note

Before using this function with a list of names, first obtain their matched names or accepted names using italic_match(). Example workflow:

      names_matched <- italic_match(your_names)
      name_data <- italic_name_usage(names_matched$matched_name)
      # or
      accepted_name_data <- italic_name_usage(names_matched$accepted_name)

Examples

## Not run: 
italic_name_usage(c("Cetraria islandica (L.) Ach. subsp. islandica", "Secoliga annexa Arnold"))

## End(Not run)

## Not run: 
italic_name_usage(c("Cetraria islandica (L.) Ach. subsp. islandica", "Secoliga annexa Arnold"))

## End(Not run)

Get occurrence records for lichen taxa

Description

Retrieves occurrence records from Italian herbarium collections for specified lichen taxa. Only accepts names that exist in the database of ITALIC.

Usage

italic_occurrences(sp_names, result_data = "simple")
italic_occurrences(sp_names, result_data = "simple")

Arguments

sp_names

Character vector of accepted names

result_data

Character string specifying output detail level: "simple" (default) or "extended"

Value

A data frame with occurrence records. Column names follow the Darwin Core standard, with the additional column substratum, which is particularly relevant for lichens. For simple output:

scientificName: The scientific name provided as input
decimalLatitude: Latitude in decimal degrees
decimalLongitude: Longitude in decimal degrees
coordinatesUncertaintyInMeters: Spatial uncertainty of the coordinates
substratum: Substrate on which the specimen was found
institutionCode: Code of the herbarium holding the specimen
eventDate: Collection date

Extended output adds:

locality: Collection locality
catalogNumber: Specimen identifier in the collection
minimumElevationInMeters: Lower limit of the elevation range
maximumElevationInMeters: Upper limit of the elevation range
verbatimIdentification: Scientific name reported on the original label
identifiedBy: Person who identified the specimen

Note

Before using this function with a list of names, first obtain their accepted names using italic_match(). Example workflow:

      names_matched <- italic_match(your_names)
      occ <- italic_occurrences(names_matched$accepted_name)

References

ITALIC - The Information System on Italian Lichens https://italic.units.it

Examples

## Not run: 
# Get simple occurrence data
italic_occurrences("Cetraria ericetorum Opiz")

# Get extended occurrence data
occ_ext <- italic_occurrences("Cetraria ericetorum Opiz", result_data = "extended")

# Then get citations for the retrieved occurrences
italic_occurrences_references(occ_ext)

## End(Not run)

## Not run: 
# Get simple occurrence data
italic_occurrences("Cetraria ericetorum Opiz")

# Get extended occurrence data
occ_ext <- italic_occurrences("Cetraria ericetorum Opiz", result_data = "extended")

# Then get citations for the retrieved occurrences
italic_occurrences_references(occ_ext)

## End(Not run)

Get scientific references for occurrence data

Description

Retrieves bibliographic references and DOIs for scientific publications describing occurrence datasets from specific herbarium collections.

Usage

italic_occurrences_references(occurrences_dataframe)
italic_occurrences_references(occurrences_dataframe)

Arguments

occurrences_dataframe

Data frame containing occurrence records, obtained from italic_occurrences(). Must include an 'institutionCode' column

Value

A data frame with two columns:

reference: Full bibliographic citation of the publication
doi: Digital Object Identifier URL

Examples

## Not run: 
# Get occurrences first
occurrences <- italic_occurrences("Cetraria ericetorum Opiz")

# Then get associated references
italic_occurrences_references(occurrences)

## End(Not run)

## Not run: 
# Get occurrences first
occurrences <- italic_occurrences("Cetraria ericetorum Opiz")

# Then get associated references
italic_occurrences_references(occurrences)

## End(Not run)

Get distribution of lichen taxa in Italy

Description

Retrieves presence/absence data (1/0) for lichen taxa across all the Italian administrative regions. Only accepts accepted names from the ITALIC database.

Only accepts names that exist in the database of ITALIC.

Usage

italic_regions_distribution(sp_names)
italic_regions_distribution(sp_names)

Arguments

sp_names

Character vector of accepted names from ITALIC database

Value

A data frame with columns:

scientific_name: The scientific name provided as input
abruzzo: Presence (1) or absence (0) in Abruzzo
basilicata: Presence (1) or absence (0) in Basilicata
calabria: Presence (1) or absence (0) in Calabria
campania: Presence (1) or absence (0) in Campania
emilia_romagna: Presence (1) or absence (0) in Emilia Romagna
friuli_venezia_giulia: Presence (1) or absence (0) in Friuli Venezia-Giulia
lazio: Presence (1) or absence (0) in Lazio
liguria: Presence (1) or absence (0) in Liguria
lombardia: Presence (1) or absence (0) in Lombardia
marche: Presence (1) or absence (0) in Marche
molise: Presence (1) or absence (0) in Molise
piemonte: Presence (1) or absence (0) in Piemonte
puglia: Presence (1) or absence (0) in Puglia
sardegna: Presence (1) or absence (0) in Sardegna
sicilia: Presence (1) or absence (0) in Sicilia
toscana: Presence (1) or absence (0) in Toscana
trentino_alto_adige: Presence (1) or absence (0) in Trentino Alto-Adige
umbria: Presence (1) or absence (0) in Umbria
valle_d_aosta: Presence (1) or absence (0) in Valle d'Aosta
veneto: Presence (1) or absence (0) in Veneto

Note

Before using this function with a list of names, first obtain their accepted names using italic_match(). Example workflow:

      names_matched <- italic_match(your_names)
      distribution <- italic_regions_distribution(names_matched$accepted_name)

Examples

## Not run: 
# First match names
matched <- italic_match("Cetraria islandica")
# Then get distribution in administrative regions
italic_regions_distribution(matched$accepted_name)

## End(Not run)

## Not run: 
# First match names
matched <- italic_match("Cetraria islandica")
# Then get distribution in administrative regions
italic_regions_distribution(matched$accepted_name)

## End(Not run)

Search lichen taxa by distribution, ecology, traits and taxonomy

Description

Returns the taxa of ITALIC that satisfy a set of filters: administrative regions and ecoregions of Italy, commonness-rarity, substratum, photobiont, growth form, reproductive strategy, ecological indicators (pH, solar irradiation, aridity, eutrophication, poleotolerance, altitudinal distribution) and taxonomy. Different filters are combined with AND, multiple values of the same filter with OR.

Use italic_search_filters() to list the filters, their allowed values and what each value means.

Usage

italic_search(...)
italic_search(...)

Arguments

...

Filters as named arguments. Values are readable words (e.g. substrata = "saxicolous"), case-insensitive, with spaces and hyphens equivalent. The filters are:

List filters: region, ecoregion, substrata, photobiont, growth_form, reproductive_strategy, phytoclimatic_range, special_requirements_for_water, genus, family, order, class, phylum: a character vector, the taxa matching any of the values are returned
Range filters: commonness, ph_of_the_substrata, solar_irradiation, aridity, eutrophication, poleotolerance, altitudinal_distribution: pass ⁠<filter>_min⁠ and/or ⁠<filter>_max⁠ with a single value (for the ecological indicators also its number, e.g. ph_of_the_substrata_min = 4); the taxa whose range overlaps the requested one are returned
Logical filters: in_italy, coastal, parasitic, pioneer, metal_rich, lichenized: TRUE returns only those taxa, FALSE excludes them

Value

A data frame with one row per taxon and columns:

taxon_id: Identifier of the taxon in ITALIC
scientific_name: Accepted name, that can be passed to the other functions of the package
family: Family of the taxon

References

ITALIC - The Information System on Italian Lichens https://italic.units.it

Examples

## Not run: 
# Saxicolous lichens of Friuli Venezia Giulia with cyanobacteria
italic_search(region = "friuli-venezia-giulia",
              substrata = "saxicolous",
              photobiont = "cyanobacteria")

# Epiphytic species of slightly basic substrata in the alpine or subalpine ecoregions
italic_search(substrata = "epiphytic",
              ph_of_the_substrata_min = "slightly-basic",
              ecoregion = c("alpine", "subalpine"))

# Rare species of the family Teloschistaceae
italic_search(family = "Teloschistaceae", commonness_max = "rare")

# Then get the data of the taxa found
found <- italic_search(genus = "Peltigera", region = "sardegna")
italic_taxon_data(found$scientific_name)

## End(Not run)

## Not run: 
# Saxicolous lichens of Friuli Venezia Giulia with cyanobacteria
italic_search(region = "friuli-venezia-giulia",
              substrata = "saxicolous",
              photobiont = "cyanobacteria")

# Epiphytic species of slightly basic substrata in the alpine or subalpine ecoregions
italic_search(substrata = "epiphytic",
              ph_of_the_substrata_min = "slightly-basic",
              ecoregion = c("alpine", "subalpine"))

# Rare species of the family Teloschistaceae
italic_search(family = "Teloschistaceae", commonness_max = "rare")

# Then get the data of the taxa found
found <- italic_search(genus = "Peltigera", region = "sardegna")
italic_taxon_data(found$scientific_name)

## End(Not run)

List the filters of the taxa search

Description

Lists the filters accepted by italic_search(), with their allowed values and the meaning of each value as explained on the ITALIC website.

Usage

italic_search_filters(filter = NULL)
italic_search_filters(filter = NULL)

Arguments

filter

Optional. Name of a filter (e.g. "substrata") or of one of its parameters (e.g. "ph_of_the_substrata_min"): only this filter is returned.

Value

A data frame with one row per allowed value of each filter, and columns:

filter: Name of the filter
type: list (one or more values), range (⁠_min⁠ / ⁠_max⁠ parameters) or boolean (TRUE / FALSE)
parameters: Arguments of italic_search() for this filter
value: Allowed value (NA for boolean filters and for genus, whose values are too many to be listed)
number: Numeric level of the value, accepted in place of the value by the ranges of the ecological indicators
label: Meaning of the value
description: Description of the filter

Examples

## Not run: 
# All the filters
italic_search_filters()

# Values of the pH of the substrata
italic_search_filters("ph_of_the_substrata")

## End(Not run)

## Not run: 
# All the filters
italic_search_filters()

# Values of the pH of the substrata
italic_search_filters("ph_of_the_substrata")

## End(Not run)

Get data of lichen taxa

Description

This function returns a dataframe containing taxonomy, ecology_traits, regions_distribution, ecoregions_distribution of the lichen species passed as input. For more info about these parameters see https://italic.units.it/?procedure=base&t=59&c=60#otherdata Only accepts names that exist in the database of ITALIC.

Usage

italic_taxon_data(sp_names)
italic_taxon_data(sp_names)

Arguments

sp_names

A vector containing the scientific names of the lichen species.

Value

A data frame with one row for each name in sp_names (in the same order) and the columns:

scientific_name: The scientific name provided as input
phylum, class, order, family, genus: Taxonomy, see italic_taxonomy()
substrata, ..., poleotolerance_max: Ecology and traits, see italic_ecology_traits()
abruzzo, ..., veneto: Presence (1) or absence (0) in the Italian administrative regions, see italic_regions_distribution()
alpine, ..., dry_mediterranean: Commonness/rarity in the Italian ecoregions, see italic_ecoregions_distribution()

Note

Before using this function with a list of names, first obtain their accepted names using italic_match(). Example workflow:

      names_matched <- italic_match(your_names)
      italic_taxon_data(names_matched$accepted_name)

References

ITALIC - The Information System on Italian Lichens: data about taxa https://italic.units.it/?procedure=base&t=59&c=60#otherdata

Examples

## Not run: 
italic_taxon_data(c("Cetraria ericetorum Opiz", "Lecanora salicicola H. Magn."))

## End(Not run)

## Not run: 
italic_taxon_data(c("Cetraria ericetorum Opiz", "Lecanora salicicola H. Magn."))

## End(Not run)

Get taxonomic classification of lichen taxa

Description

Retrieves the complete taxonomic classification of lichen taxa from the ITALIC database. Only accepts names that exist in the database of ITALIC.

Usage

italic_taxonomy(sp_names)
italic_taxonomy(sp_names)

Arguments

sp_names

Character vector of accepted names

Value

A data frame with:

scientific_name: The scientific name provided as input
phylum: Phylum
class: Class
order: Order
family: Family
genus: Genus

Note

Before using this function with a list of names, first obtain their accepted names using italic_match(). Example workflow:

      names_matched <- italic_match(your_names)
      taxonomy <- italic_taxonomy(names_matched$accepted_name)

Examples

## Not run: 
italic_taxonomy("Cetraria islandica (L.) Ach. subsp. islandica")

## End(Not run)

## Not run: 
italic_taxonomy("Cetraria islandica (L.) Ach. subsp. islandica")

## End(Not run)

Get a presence-absence matrix of lichen traits

Description

This function returns morphological traits of the lichen species passed as input. Only accepts names that exist in the database of ITALIC.

Usage

italic_traits_pa(sp_names)
italic_traits_pa(sp_names)

Arguments

sp_names

A vector containing scientific names of lichens.

Value

A dataframe containing a series of traits for the lichen species passed as input.

Note

Before using this function with a list of names, first obtain their accepted names using italic_match(). Example workflow:

      names_matched <- italic_match(your_names)
      traits <- italic_taits_pa(names_matched$accepted_name)

Examples

## Not run: 
italic_traits_pa("Cetraria ericetorum Opiz")

## End(Not run)
## Not run: 
italic_traits_pa("Cetraria ericetorum Opiz")

## End(Not run)

Package 'ritalic'

Help Index

Get species names in the checklist of the lichens of Italy

Description

Usage

Arguments

Value

References

Examples

Get descriptions of lichen taxa

Description

Usage

Arguments

Value

Note

Examples

Create distribution map of a lichen taxon

Description

Usage

Arguments

Details

Value

Note

References

Examples

Get ecology data and morphological traits of lichen taxa

Description

Usage

Arguments

Value

Note

References

Examples

Get distribution of lichen taxa across Italian ecoregions

Description

Usage

Arguments

Value

Note

References

Examples

Generate interactive identification keys for lichen taxa

Description

Usage

Arguments

Value

Note

References

Examples

Match scientific names of lichens against the database of ITALIC

Description

Usage

Arguments

Value

Examples

Run the ITALIC MCP server

Description

Usage

Arguments

Value

Connecting an assistant

See Also

Tools of the ITALIC MCP server

Description

Usage

Value

See Also

Examples

Get details of species names

Description

Usage

Arguments

Value

Note

Examples

Get occurrence records for lichen taxa

Description

Usage

Arguments

Value