Introduction

ritalic is an R package which gives you access to ITALIC mediated data via its RESTful API.

The ritalic package provides a series of function to:

How to install

The package can be installed from CRAN

# install from CRAN:
# install.packages("ritalic")

# load the library:
library(ritalic)
## Warning: package 'ritalic' was built under R version 4.3.3

For this guide we also load some other utility libraries

library(dplyr)
library(leaflet)

Available functions

italic_match

  • italic_match is the core function of ritalic:
  • It takes a vector of scientific names as input, aligns them against the ITALIC checklist, and retrieves the corresponding accepted scientific names.
  • These accepted names are very important, as they are used as input for most other functions in the package to retrieve data about specific taxa.
match <- ritalic::italic_match(c('Cetraria islandica L. subsp. islandica', 'Lecanora albela','Parmelia caperata (L.) Ach', 'Ramalina americana Hal' ))
match


! IMPORTANT: Now we can store the accepted names into a variable (accepted_names) to easily pass them to the other functions of the package

accepted_names <- match$accepted_name


italic_description

Returns the morphological description and any additional notes for the specified taxa.

descriptions <- ritalic::italic_description(accepted_names)
descriptions


italic_ecology_traits

Returns ecological and traits data for the specified taxa:

Substrata and morpho-functional traits:
substrata
  • saxicolous
  • on lignum
  • epiphytic
  • on soil, terricolous mosses, plant debris
  • foliicolous
photobiont
  • green algae other than Trentepohlia
  • trentepohlia
  • cyanobacteria, filamentous form, e.g. Nostoc, Scytonema
  • cyanobacteria, coccaceous form, e.g. Gloeocapsa, Xanthocapsa
growth_form
  • fruticose
  • fruticose filamentous
  • foliose
  • foliose broad-lobed, Parmelia type
  • foliose narrow-lobed, Physcia type
  • foliose umbilicate
  • crustose
  • crustose endolithic
  • crustose placodiomorph
  • leprose
  • squamulose
  • lichenicolous fungus
  • non-lichenized, non-lichenicolous fungus
phytoclimatic_range
  • oceanic
  • suboceanic
  • subcontinental
special_requirements_for_water
  • on otherwise dry surfaces with periodical seepage of water after rain
  • periodical submerged, e.g. in creeks or on coastal maritime rocks
  • on surface seldom wetted by rain, e.g. underhangs
reproductive_strategy
  • mainly sexual
  • mainly asexual, by soredia or soredia-like structures, e.g. blastidia
  • mainly asexual, by isidia or isidia-like structures, e.g. schizidia
  • mainly asexual, by thallus fragmentation
Ecological indicators, poleotolerance and altitudinal distribution:
ph_of_the_substrata
  • 1 - on very acid substrata, such as lignum and conifer bark
  • 2 - on acid substrata, such as on non-eutrophicated bark of Quercus
  • 3 - on subacid to subneutral substrata (e.g. on bark of Sambucus)
  • 4 - on slightly basic substrata, such as dust-covered bark
  • 5 - on basic substrata, e.g. pure limestone

solar_irradiation

  • 1 - in very shaded situations, e.g. deep gorges, closed evergreen forests
  • 2 - in shaded situations, such as on the northern side of boles in close-canopied deciduous forests
  • 3 - in sites with plenty of diffuse light but scarce direct solar irradiation, such as in rather open-canopied deciduous woodlands
  • 4 - in sun-exposed sites, but avoiding extreme solar irradiation
  • 5 - in sites with very high direct solar irradiation, such as on the southern side of isolated boles

aridity

  • 1 - hydro- and hygrophytic, in aquatic or marine situations, or in sites with a very high frequency of fog
  • 2 - rather hygrophytic, intermediate between 1 and 2
  • 3 - mesophytic
  • 4 - xerophytic, but absent from extremely arid stands
  • 5 - very xerophytic

eutrophication

  • 1 - not resistant to eutrophication
  • 2 - resistant to a very weak eutrophication
  • 3 - resistant to a weak eutrophication
  • 4 - occurring in rather eutrophicated situations
  • 5 - occurring in highly eutrophicated situations

altitudinal_distribution

  • 1 - eu-Mediterranean belt (potential vegetation: evergreen Quercus ilex forest)
  • 2 - submediterranean belt (deciduous Quercus-Carpinus forests)
  • 3 - montane belt (Fagus forests, marking treeline in the Apennines)
  • 4 - subalpine and oroboreal belts of the Alps (natural Picea abies, and Larix-Pinus cembra stands)
  • 5 - above treeline (both Alpine and oromediterranean)
  • 6 - nival belt of the Alps
poleotolerance This value points to the tendency of a lichen to occur in areas with different degrees of human disturbance. It is expressed on 4 classes, as follows:
  • 3 - species occurring also in heavily disturbed areas, incl. large towns
  • 2 - species occurring also in moderately disturbed areas (agricultural areas, small settlements etc.).
  • 1 - species mostly occurring in natural or semi-natural habitats
  • 0 - species which exclusively occur on old trees in ancient, undisturbed forests. 
taxon_data <-  ritalic::italic_ecology_traits(accepted_names)
taxon_data


italic_taxonomy

Returns the taxonomic classification (Phylum to Genus) for the specified taxa.

systematics <- ritalic::italic_taxonomy(accepted_names)
systematics


italic_ecoregions_distribution

Returns the commonness/rarity status for the specified taxa within each Italian ecoregion.

How to read and understand the values:
ecoregions in Italy
ecoregions in Italy

Ecoregions in italy

  • A: Alpine (above treeline in the Alps and in Abruzzo)
  • A1: Subalpine (near treeline in the Alps, oroboreal belt)
  • B: Oromediterranean (above treeline outside the Alps except Abruzzo)
  • C: Montane (beech forests)
  • D: Dry submediterranean (deciduous oaks, excluding SmedH)
  • E: Padanian (the plains of the North): this is the only OGU which was not separated on the basis of climatical-biogeographical characters; it is the most heavily anthropised part of Italy, where several species do not occur because of pollution and/or almost total deforestation
  • F: Humid submediterranean (as SmedD, but restricted to areas with a warm-humid climate, mostly Tyrrhenian)
  • G: Humid Mediterranean (mostly Tyrrhenian)
  • H: Dry Mediterranean
      • Commonness/rarity values range from “extremely common” to “extremely rare” or “absent”. 
rarity <- ritalic::italic_ecoregions_distribution(accepted_names)
rarity


italic_regions_distribution

Returns the presence (1) or absence (0) of the specified taxa in each of the 20 administrative regions of Italy.

Administrative regions: 
distribution <- ritalic::italic_regions_distribution(accepted_names)
distribution


italic_distribution_map

Creates a distribution map for a given taxon based on its commonness/rarity status across Italian ecoregions and presence/absence across administrative regions.

By default, the function returns a ggplot object. Setting the optional parameter plot_map = FALSE retrieves the underlying sf (Simple Features) spatial object used to create the map.

distribution_map <- ritalic::italic_distribution_map(accepted_names[1])
distribution_map


italic_occurrences

Returns georeferenced occurrence records for the specified taxa from Italian herbaria stored in ITALIC.

occurrences <- ritalic::italic_occurrences(accepted_names[1])
occurrences <- occurrences %>%
  mutate(decimalLatitude = as.numeric(decimalLatitude)) %>%
  mutate(decimalLongitude = as.numeric(decimalLongitude)) %>%
  mutate(coordinatesUncertaintyInMeters = as.numeric(coordinatesUncertaintyInMeters))
nrow(occurrences)
## [1] 370
head(occurrences)

The retrieved occurrences, which include latitude and longitude, can be easily visualized using mapping packages like rleaflet:

occurrences %>%
  leaflet() %>%
  addTiles() %>%
  setView(lng = 9.0, lat = 42.0, zoom = 5) %>%
  #addMarkers(~decimalLongitude, ~decimalLatitude, popup = ~scientificName)
  addCircleMarkers(~decimalLongitude, ~decimalLatitude,
    radius = 3,
    color = "red",
    stroke = FALSE, fillOpacity = 1
  )


italic_identification_key

Generates a URL linking to a web-based, interactive identification key for the specified taxa, created using the ITALIC KeyMaker.

key <- ritalic::italic_identification_key(accepted_names)
key
## [1] "https://italic.units.it/key-maker/87078616-0e2c-11f0-a898-000c2978584b/nodes/1/interactive"

The web interface: web key


italic_checklist

Retrieves the complete checklist of accepted lichen names currently present in the checklist of the lichens Italy.

checklist <- ritalic::italic_checklist()
head(checklist)
## [1] "Absconditella annexa (Arnold) Vězda"  
## [2] "Absconditella lignicola Vězda & Pišút"
## [3] "Acarospora admissa (Nyl.) Kullh."     
## [4] "Acarospora atrata Hue"                
## [5] "Acarospora badiofusca (Nyl.) Th. Fr." 
## [6] "Acarospora bullata Anzi"
print(paste("n of taxa:", length(checklist)))
## [1] "n of taxa: 2827"


italic_traits_pa

Returns a presence/absence (1/0) matrix (as a dataframe) indicating specific morphological traits for the specified taxa. The traits included are based on those used in the ITALIC identification keys.

traits <- ritalic::italic_traits_pa(accepted_names)
traits