tests/testthat/testdata/db/Readme_dryad.md

In ButtR: Download and Extract Data from the 'OzButterflies' Database

OzButterflies database

This folder contains the OzButterflies database. It consists of this README.txt file, 2 spreadsheets (summary and specimen, each in 3 formats), reflectance spectra of the red, green and blue colour standards (standard-\<colour>.ProcSpec files) and specimen data files (photographs, spectra, and cytochrome C oxidase subunit 1 (CO1) sequence).

Specimen data file are stored in folders by family, species and specimen ID.

Summary spreadsheet

The summary spreadsheet, Oz_butterflies_summary.csv, .xslx or .json, contains a row for each species in the database and the following columns:

| Column | Description | |--------------------------|----------------------------------------------| | Family | Species family | | Species | Binomial species names | | Specimens | Number of specimens of the species in the database | | Females | Number of female specimens of the species in the database | | Males | Number of male specimens of the species in the database | | Dimorphic | "y" if clear sexual dimorphism in visible or UV, "n" if difficult to ID sexes in visible or UV | | Iridescent | "y" if obvious iridescent patches as measured in different angles, "n" if iridescence not clear |

Specimen spreadsheet

| Column | Description | |--------------------------|----------------------------------------------| | ID | Specimen identifier | | Family | Specimen family | | Genus | Specimen genus | | Species | Specimen specific name (i.e. not the binomial species name) | | Sex | "Female" or "Male" | | Body.damage | "y" or "n" if body has visible damage | | Forewing.dorsal.damage | "y" or "n" if dorsal forewing has visible damage | | Forewing.ventral.damage | "y" or "n" if ventral forewing has visible damage | | Hindwing.dorsal.damage | "y" or "n" if dorsal hindwing has visible damage | | Hindwing.ventral.damage | "y" or "n" if ventral hindwing has visible damage | | Site | Site code, see "Site Codes" below | | Latitude | Latitude of site | | Longitude | Longitude of site | | Climate | "Temperate", "Subtropical or"Tropical" | | Date | Date of collection in day/month/year format | | Collector | Initials of collector | | Binomial | Full species name | | Pinned | "y" if specimen is pinned (i.e. intact), "n" if wings are separated from body | | Spectra | "y" if colour patches on the specimen were measured by spectrophotometer, "n" if not | | DNA | "y" if specimen has CO1 sequence in the database, "n" if it does not | | Repo.zipname | Name of zip file in repository that contains specimen data |

Specimen data

Each specimen folder contains photographs of the specimen in Sony raw fomat (file extension .ARW). In the following file names, "\<ID>" represents the specimen identifier.

Pinned (intact) specimens have photographs named:

| File name | Description | |---------------------------------|---------------------------------------| | \<ID>-v-RGB.ARW | Ventral wing surfaces photographed in visible light | | \<ID>-d-RGB.ARW | Dorsal wing surfaces photographed in visible light | | \<ID>-v-UV.ARW | Ventral wing surfaces photographed in ultraviolet light | | \<ID>-d-UV.ARW | Dorsal wing surfaces photographed in ultraviolet light |

Photographs of non-pinned specimens (wings separated from body):

| File name | Description | |---------------------------------|---------------------------------------| | \<ID>-RGB.ARW | Dorsal and ventral wing surfaces photographed in visible light | | \<ID>-UV.ARW | Dorsal and ventral wing surfaces photographed in ultraviolet light |

Specimens with DNA include the following files:

| File name | Description | |--------------|-------------------------------------| | \<ID>-f.ab1 | CO1 gene gene sequenced forward (f) |

Spectroscoped specimens include the following files:

| File Name | Description | |--------------------------|----------------------------------------------| | <ID>-<side>.jpeg | Reference image indicating the locations where spectra were measured. The <side> parameter can be "d" (dorsal), "v" (ventral), or NULL (both sides in the same image). | | <ID>-<side>-<patch number>-<angle>.procspec | File containing processed spectral measurements. Parameters: <ID> (specimen number), <side> ("d", "v", or "b" for dorsal, ventral, or both, respectively), <patch number> (measured patch, referenced in the corresponding image), and <angle> ("s" for 45°, "a" for 60°, "a2" if 60° inclination was not enough to show iridescence). | | <ID>.csv | CSV file containing all processed spectral measurements. | | <ID>.png | Graph of the spectra measured at 45° and 60° or more. |

Site Codes

Sites with standardised collecting times

| Code | Place | City | |------|-------------------------------|----------| | BG | Cairns Botanic Gardens | Cairns | | JCU | James Cook University campus | Cairns | | GP | Gamboora Park | Cairns | | MR | Mossman River | Mossman | | BBG | Mt. Coot-tha Botanic Gardens | Brisbane | | CC | Cabbage Creek | Brisbane | | OC | Oxley Creek | Brisbane | | LSP | Lakeside Park | Brisbane | | MQ | Macquarie University campus | Sydney | | WPP | West Pymple Park | Sydney | | KRG | Ku-ring-gai Wildflower Garden | Sydney | | WLP | Westleigh Park | Sydney | | AO | Allan Small Oval | Sydney | | JB | Jubes Mountain Bike Track | Sydney | | WLR | Woo-La-Ra Park | Sydney | | PP | Parramatta park | Sydney |

Non-standardised collecting sites, i.e. haphazard collecting

| Code | Place | City | |------|----------------------|--------------| | PD | Port Douglas City | Port Douglas | | LG | Lisgar Gardens | Sydney | | CCF | Cabbage Creek Forest | Brisbane |

ButtR documentation built on April 22, 2026, 1:07 a.m.