Trait-Driven Models of Ecology and Evolution 🌲
C++ R Other
Switch branches/tags
Nothing to show
Latest commit 768344c Aug 6, 2017 @dfalster dfalster Update travis configuration (now with native R language support)
- also removed changes for C++11 support as these no longer seem to be needed

README.md

The Trait Ecology and Evolution (plant) model

Build Status Build status Coverage Status

Documentation

plant comes with a lot of documentation. Run library(help=plant) to see the index, and see vignettes:

Details of the modelling approaches:

  • vignette("demography"): Modelling demography of plants, patches and metapopulations online
  • vignette("physiology"): Plant physiological model online

Details of using plant from R:

  • vignette("plant"): Plant level properties online
  • vignette("cohort_spacing"): The cohort spacing algorithm online
  • vignette("equilibrium"): Finding demographic equilibrium online
  • vignette("patch"): Patch level dynamics online
  • vignette("emergent"): Patch level emergent properties online
  • vignette("fitness"): Calculating fitness online
  • vignette("parameters"): Modifying parameters of the physiological model online

Installation

Installation requires a C++11 compatible C compiler (OSX >= 10.10/Yosemite satisfies this, plus we've had success on Ubuntu 12.04 and 14.04).

Option 1, using drat

(install drat with install.packages("drat"))

drat:::add("traitecoevo")
install.packages("plant", dependencies=TRUE)

Answer "Yes", if you get asked whether you wish to "install these from sources?". Alternatively try install.packages("plant", type="source") here. The dependencies=TRUE installs some additional packages that are used in tests and some of the routines.

Option 2, using devtools::install_github

(install devtools with install.packages("devtools"))

The plant package can be installed from github using the devtools package. plant also requires the packages loggr and RcppR6 packages: install those with

devtools::install_github("smbache/loggr", dependencies=TRUE)
devtools::install_github("richfitz/RcppR6", dependencies=TRUE)

Then install plant:

devtools::install_github("traitecoevo/plant", dependencies=TRUE)

Windows

Installation on Windows is likely to be a challenge, because of the lack of a C++11 compiler. The current Windows toolchain uses gcc 4.6.3, which des not feature enough C++11 support to successfully compile plant. There is support coming for gcc 4.9.2, but that is under development. This should become available on Windows very soon (it was initially aimed for 3.2.0 but didn't quite make it). As soon as this is available we will provide Windows binaries.

Building vignettes

See docs/README.md for details. The vignettes are not built as part of the package installation as they take a couple of hours to build.