My R Packages

PUBLISHED ON NOV 10, 2017 — R

A somewhat comprehensive list of the R packages that I have developed over the years.

plantecophys

Analysis of leaf gas exchange. Fit A-Ci curves, simulate from the coupled leaf gas exchange model, fit Ball-Berry models of stomatal conductance, and more. Read open-access publication describing plantecophys.

fitplc

Analysis and visualization of plant hydraulics data. Fit PLC curves to estimate P50 and related parameters, report uncertainty via bootstrap resampling, incorporate random effects, and more. Read open-access publication describing fitplc.

smatr

A very popular R package, the methods were developed by David Warton and described in this publication. Use the package to fit allometric relationships, used in many biological applications and even river networks on Mars.

speciesmap

Obtain species occurrence data from one of two web services, download corresponding climate data from WorldClim, rasterize occurrences, calculate climate envelopes. See here for an example demonstration.

YplantQMC

bitbucket

Implementation of a functional-structural plant model, coupling plant architecture (Y-Plant) to the QuasiMC ray-tracer (developed by Mik Cieslak). Calculate radiative transfer in 3D plant canopies, estimate photosynthesis and transpiration for each leaf. I used this package in this publication. The package was recently removed from CRAN, the registration of Fortran code in the package turned into a bit of an annoyance.

Maeswrap

Wrapper functions for the Maespa model, a detailed model to estimate vegetation water use and carbon uptake, and hydraulics of the soil-to-plant pathway. Read further on my website on the Maespa model.

phenora

bitbucket

Analysis of phenocam images for greenness. Uses the imager R package to calculate greenness indices, as used to record phenology of leaf growth and senescence, with convenient functions to analyze many images, extract time and date of images, etc.

bootpredictlme4

github

Calculate confidence intervals for predictions from linear mixed-effects models with the bootstrap, implemented as a wrapper around the bootMer function. Read further in this blog post.

HIEv

bitbucket

Collection of tools to interface with the API of a data management system at the HIE, the HIEv. Find and download files, upload files, tools for timeseries data, and more.

Last edited 2018-03-22