TPTdb

TPTdb provides access to a curated database of biological thermal performance curves across the tree of life. The package includes four machine-readable tables—taxonomy, temperature, response, and traits—and a Shiny explorer for subsetting, plotting, and exporting individual thermal performance curves.

Installation

For local peer review after downloading the repository or source folder:

install.packages("devtools")
devtools::install("path/to/TPTdb")

After the public GitHub repository is released:

install.packages("remotes")
remotes::install_github("amahury/TPTdb")

Usage

library(TPTdb)

# Load all tables
tpt <- TPTdb_data("all")
head(tpt$taxonomy)

# Load a single table
taxonomy <- TPTdb_data("taxonomy")

# Launch the interactive explorer
TPTdb_explorer()

Data files

The package stores the curated data in inst/extdata/:

• taxonomy.csv: curve identifiers, taxonomic information, binomial names, and source references.
• temperature.csv: temperature values in degrees Celsius for each curve.
• response.csv: performance-variable metadata and response values aligned to the temperature table.
• traits.csv: derived thermal traits for each curve.
• TPTdb_full.xlsx: reviewer-friendly Excel workbook containing the same four tables.

The CSV files are the canonical package inputs used by TPTdb_data() and TPTdb_explorer(). The Excel workbook is included as a convenient human-readable version of the same cleaned tables.

Shiny app

Run the app with:

TPTdb_explorer()

The app allows users to choose a curve, inspect taxonomy and available performance variables, plot the thermal performance curve, view thermal traits, and export the displayed temperature-response data as a CSV file.

License

Released under the MIT License (see LICENSE).