README.md

In RemkoDuursma/fitplc: Fit Hydraulic Vulnerability Curves

Fit Hydraulic Vulnerability Curves in R

This page describes the fitplc package, which can be used to fit curves to measurements of plant stem, leaf or root conductivity (or conductance) at varying water potentials (so called 'PLC curves'). The package either fits the Weibull curve as reparameterized by Ogle et al. (2009), or a sigmoidal model proposed by Pammenter and van Willigen (1998).

The package calculate confidence intervals for the parameters (e.g., P50, slope at P50) (using the bootstrap or normal approximations), make standard plots of 'relative conductivity' or the 'percentage embolized' vs. water potential (including a bootstrap 95% CI of the fit and the location of the P50).

Citation

Duursma R.A., Choat B. 2017. fitplc - an R package to fit hydraulic vulnerability curves. Journal of Plant Hydraulics. doi:10.20870/jph.2017.e002 (Open Access)

Help

Please read ?fitplc for more instructions, and the examples on that page.

To report bugs or suggest new features, please open a new issue by following this link.

Installation instructions

The fitplc package is now on CRAN, so just do

install.packages("fitplc")
library(fitplc)

To install the development version, use this command:

library(devtools)
install_bitbucket("remkoduursma/fitplc")
library(fitplc)

Windows users must have Rtools installed for this to work.

Model overview

Work in progress : options and implementation for the various models. 'when': is the confidence interval (via method 'ci') always calculated?

Model fitter ci when ------- ------- ------- ------- Weibull nls confint always boot bootci = TRUE nlme intervals always sigmoidal lm boot always lme intervals always loess loess boot always nls_sigmoidal nls boot bootci = TRUE

RemkoDuursma/fitplc documentation built on May 9, 2019, 9:39 a.m.