**NOTE: This is currently in development. **
Provides an R interface to the spatial analyses available in Biodiverse. Biodiverse is a tool for the spatial analysis of diversity using indices based on taxonomic, phylogenetic, trait and matrix-based (e.g. genetic distance) relationships, as well as related environmental and temporal variations. More information is available at its Github page.
This is a two step process. First, install the Biodiverse engine. Second, install the R package.
- Install the Biodiverse engine.
This currently requires a working perl interpreter in your path. (Future versions will provide self contained executables).
On Windows a perl interpreter can be obtained through the Strawberry perl project, and there is a function to do this for you. Note that this will take a while and send large amounts of text to the console.
devtools::load_all()
BiodiverseR::install_strawberry_perl()
Most unix-derived systems provide a perl interpreter but it is best to avoid this and use a system like perlbrew. Be sure to also install the cpanm utility (see perlbrew site for details).
Once you have a perl installed and in your path you can install the perl dependencies using cpanm at the command line. (Make sure to update the below code to use the correct path separator on Windows). Note that this requires that you have git installed on your system and in the path.
This code also assumes you have run a git clone of this repo and are at the top level of this repo.
cpanm https://github.com/shawnlaffan/biodiverse.git
cd inst/perl
cpanm --installdeps .Note that the above will take a while if you do not already have the GDAL development package installed on your system. This is because it will compile its own version if it is unable to find one on the system (but maybe this is not such a bad thing as then it will be isolated from system changes).
If you want to see things as they happen then add the verbose flag to
the cpanm calls (cpanm --verbose ...).
- Install the R code
(You might already have done this in one of the steps above).
You can install the R code like so:
devtools::install_github("shawnlaffan/BiodiverseR")However, it is currently best to work within the git repo.
devtools::load_all()Check that the Biodiverse service can be accessed. The analytical functions call this internally so this is just a check that the server can be started.
# It is critical that this be set to wherever you have downloaded the package
# as otherwise the system will not find the server code.
# It is an ugly and temporary hack and will not be needed in the future.
# This version assumes you are at the top level of the BiodiverseR repository.
Sys.setenv("Biodiverse_basepath" = getwd())
# library(BiodiverseR)
devtools::load_all() # for during development
cs = start_server()
cs$server_object$is_alive()
# cleanup
rm(cs)
gc() # server is not deleted until garbage collected