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Field-campaign management for fish trait digitization — photographs, specimens, provenance.
FishInTrait is the field-campaign side of the toolkit: it organises a digitization
campaign — the photographs of a survey, their import into a project folder, the specimens and
their determinations — and hands the resulting measurements to intraitR
(analysis) and Rfishmorph (FISHMORPH database). It keeps a
campaign journal (record, specimen, field, value) from which the provenance of every photograph
can be recovered, and provides a Shiny explorer of the campaign, including an Absent from FISHMORPH view
for species that still need to be added to the database.
DESCRIPTION, README and reference index once the repository is published.
A FishInTrait project is a folder with a fixed layout, auto-detected by the companion packages:
<project>/
├── photos/ # specimen photographs (stay local)
├── measurements/ # landmark workbooks (.xlsx) read by intraitR
└── journal/ # append-only import journals (provenance)intraitR::read_landmarks_xlsx() reads the provenance keys of this layout automatically, so that
a workbook keeps the link to the original photograph of each specimen even after files are renamed.
| Family | Functions |
|---|---|
| Exploration | launch_fishintrait_explorer() — Shiny explorer of a campaign (specimens, determinations, species absent from FISHMORPH) |
| Journal | campaign import journal (record_id, timestamp, operator, app_version, action, specimen, field, value) |
# install.packages("remotes")
remotes::install_github("FunTraits/FishInTrait") # once the repository is public
library(FishInTrait)