# 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