CaryotAtlas

An interactive R Shiny app for exploring the global distribution of the palm genus Caryota (the fishtail palms). Users pick a species, a year range, and a data-cleaning level, and the app draws an occurrence map and lets them download the underlying dataset.

▶ Live app: https://ben-york.shinyapps.io/CaryotAtlas/

Developed as part of the Plant Evolutionary Biology group at Aarhus University.

Features

• Species selection across the Caryota genus.
• Year-range filter (1750–2020).
• Data-cleaning levels — Original, Partial, or Full — switching between three increasingly filtered occurrence datasets.
• Interactive Leaflet map: TDWG level-3 botanical regions shaded by species presence, with occurrence points plotted on top.
• Download the filtered occurrence dataset as a CSV.

Running locally

Requires R (4.x). Install the runtime packages:

install.packages(c("shiny", "shinydashboard", "leaflet",
                   "dplyr", "magrittr", "sf", "htmltools"))

Then, from this directory:

shiny::runApp(".")

Project structure

global.R            # loads libraries + data (datasets, shapefile, CSVs)
ui.R                # shinydashboard UI
server.R            # reactive logic: filtering, map rendering, CSV download
caryota_data.rds    # the Original / Partial / Full occurrence datasets
Caryota.csv         # species list for the dropdown
Caryotalist.csv     # per-region presence/abundance values
tdwg_level3_shp/    # TDWG level-3 region shapefile (Leaflet basemap)
dffolder/           # data-preparation scripts (provenance; not needed at runtime)

Data preparation

The occurrence data in caryota_data.rds was assembled offline from several biodiversity databases. The scripts under dffolder/ document how the raw records were pulled and cleaned; they are kept for provenance and are not run by the app.

Source databases: ALA, BIEN, BISON, GBIF, iDigBio, iNaturalist.

Deployment

The app is hosted on shinyapps.io. To redeploy after changes:

rsconnect::deployApp(
  appName  = "CaryotAtlas",
  appFiles = c(
    "global.R", "ui.R", "server.R",
    "caryota_data.rds", "Caryota.csv", "Caryotalist.csv",
    "tdwg_level3_shp/level3.shp", "tdwg_level3_shp/level3.shx",
    "tdwg_level3_shp/level3.dbf", "tdwg_level3_shp/level3.prj",
    "tdwg_level3_shp/level3.sbn", "tdwg_level3_shp/level3.sbx"
  )
)

The explicit appFiles list keeps the bundle to just the files the app needs at runtime.

Contact

Questions or suggestions: [email protected]