plantecophys-package {plantecophys}

Modelling and Analysis of Leaf Gas Exchange Data

Description

Coupled leaf gas exchange model, A-Ci curve simulation and fitting, Ball-Berry stomatal conductance models, leaf energy balance using Penman-Monteith, Cowan-Farquhar optimization, humidity unit conversions. See Duursma (2015) <doi:10.1371/journal.pone.0143346>.

Details

The DESCRIPTION file:

Package:	plantecophys
Type:	Package
Title:	Modelling and Analysis of Leaf Gas Exchange Data
Version:	1.4-6
Authors@R:	person("Remko", "Duursma", role = c("aut", "cre"),email = "[e-mail]")
Description:	Coupled leaf gas exchange model, A-Ci curve simulation and fitting, Ball-Berry stomatal conductance models, leaf energy balance using Penman-Monteith, Cowan-Farquhar optimization, humidity unit conversions. See Duursma (2015) <doi:10.1371/journal.pone.0143346>.
URL:	https://bitbucket.org/remkoduursma/plantecophys
BugReports:	https://bitbucket.org/remkoduursma/plantecophys/issues
Depends:	R (>= 3.3.0)
Suggests:	nlstools, testthat, knitr, rmarkdown, DT
License:	GPL
LazyData:	yes
RoxygenNote:	7.1.1
VignetteBuilder:	knitr
Author:	Remko Duursma [aut, cre]
Maintainer:	Remko Duursma <[e-mail]>

Index of help topics:

AciC4                   C4 Photosynthesis
FARAO                   FARquhar And Opti
Photosyn                Coupled leaf gas exchange model
PhotosynEB              Coupled leaf gas exchange model with energy
                        balance
PhotosynTuzet           Coupled leaf gas exchange model with Tuzet
                        stomatal conductance
RHtoVPD                 Conversions between relative humidity, vapour
                        pressure deficit and dewpoint
acidata1                An example A-Ci curve
findCiTransition        Calculate transition points for fitted A-Ci
                        curves
fitBB                   Fit Ball-Berry type models of stomatal
                        conductance
fitBBs                  Fit Ball-Berry type models of stomatal
                        conductance to many groups at once
fitaci                  Fit the Farquhar-Berry-von Caemmerer model of
                        leaf photosynthesis
fitacis                 Fit multiple A-Ci curves at once
manyacidat              An example dataset with multiple A-Ci curves
plantecophys-package    Modelling and Analysis of Leaf Gas Exchange
                        Data

The following functions are the main tools in plantecophys:

1. fitaci (and fitaci) fits A-Ci curves to data.

2. Photosyn can be used to simulate A-Ci curves (or Aci), and simulate from a coupled leaf gas exchange model.

3. fitBB fits Ball-Berry-type stomatal conductance models to data.

4. FARAO is an implementation of a numeric solution to Cowan-Farquhar optimization of stomatal conductance.

5. RHtoVPD converts relative humidity to vapour pressure deficit (and more similar functions on that help page).

The package also includes the following example datasets:

1. acidata1 A dataset with a single A-Ci curve.

2. manyacidat A dataset with many A-Ci curves.

Author(s)

Remko Duursma

Maintainer: Remko Duursma

References

Duursma, R.A., 2015. Plantecophys - An R Package for Analysing and Modelling Leaf Gas Exchange Data. PLoS ONE 10, e0143346. doi:10.1371/journal.pone.0143346