The Trait Ecology and Evolution (plant) model
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 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:::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
plant package can be installed from github using the
plant also requires the packages
RcppR6 packages: install those with
devtools::install_github("smbache/loggr", dependencies=TRUE) devtools::install_github("richfitz/RcppR6", dependencies=TRUE)
Then install plant:
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.
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.