The Trait Ecology and Evolution (plant) model
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 onlinevignette("physiology")
: Plant physiological model online
Details of using plant
from R:
vignette("plant")
: Plant level properties onlinevignette("cohort_spacing")
: The cohort spacing algorithm onlinevignette("equilibrium")
: Finding demographic equilibrium onlinevignette("patch")
: Patch level dynamics onlinevignette("emergent")
: Patch level emergent properties onlinevignette("fitness")
: Calculating fitness onlinevignette("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.