Wallace is a modular platform for reproducible modeling of species niches and distributions, written in R. The application guides users through a complete analysis, from the acquisition of data to visualizing model predictions on an interactive map, thus bundling complex workflows into a single, streamlined interface.
Install Wallace via CRAN and run the application with the following R code.
install.packages("wallace")
library(wallace)
run_wallace()Development versions can be downloaded from Github with the following R code.
install.packages("devtools")
devtools::install_github("wallaceEcoMod/wallace")
library(wallace)
run_wallace()Please make sure you have installed the latest versions of both R (Mac OS, Windows) and RStudio (Mac OS / Windows: choose the free version).
Wallace v2.1.3 includes two options to run Maxent models:
maxnet and maxent.jar. The former, which is an R implementation and fits
the model with the package glmnet, is now the default and
does not require the package rJava (see Phillips et
al. 2017). The latter, which is the Java implementation, runs the
maxent() function in the package dismo. This
function requires the user to place the maxent.jar file in
the /java directory of the dismo package root
folder. You can download Maxent
here,
and locate maxent.jar, which is the Maxent program itself,
in the downloaded folder. You can find the directory path to
dismo/java by running
system.file('java', package="dismo") at the R console.
Simply copy maxent.jar and paste it into this folder. If
you try to run Maxent in Wallace without the file in place, you
will get a warning message in the log window and Maxent will not
run.
Wallace uses the rJava package only to run the
program maxent.jar. The package rJava will not
load properly if the version of Java on your computer (32-bit or 64-bit)
does not match that of the R installation you are using. For example, if
you are running 64-bit R, please make sure your Java is also 64-bit, or
else rJava will be unable to load. Install the latest
version of Java
here,
and 64-bit Windows users should make sure to select “Windows Offline
(64-bit)”. There is currently only a 64-bit download for Mac OS. For Mac
users running OSX Yosemite and above with problems, see
this
StackOverflow post for some tips on how to get rJava
working again. If you need to install Java for the first time, you can
follow these instructions for
Mac
and
Windows.
If for some reason you are unable to view the tables in
Wallace, please install (force if necessary) the development
version of htmlwidgets by running this code:
devtools::install_github("ramnathv/htmlwidgets"). You
should be able to view tables now.
If PDF downloading of session code is not working for you, please
follow the following instructions, taken from
here:
- Step 1: Download and Install MiKTeX from http://miktex.org/2.9/setup -
Step 2: Run Sys.getenv("PATH") in R studio. This command
returns the path where Rstudio is trying to find pdflatex.exe. In
Windows (64-bit), it should return “C:Files.exe”. If pdflatex.exe is not
located in this location Rstudio gives this error code 41. - Step 3: To
set this path variable run:
Sys.setenv(PATH=paste(Sys.getenv("PATH"),"C:/Program Files/MiKTeX 2.9/miktex/bin/x64/",sep=";")).
If you are using Windows, please download and install
RTools
before installing the devtools package. After you install
RTools, please make sure you add “C:” to your PATH variable
(instructions
here).
Additionally, when using devtools on Windows machines,
there is a known
bug
that sometimes results in the inability to download all package
dependencies. If this happens to you, please install the packages and
their dependencies directly from CRAN.
Although the recommended way to install is through CRAN, if you are
trying to install the Github version and are having problems, follow
these steps. 1. Download the zip file from the repository page. 2. Unzip
and open the wallace.Rproj file in RStudio. 3. In the right-hand pane,
click Build, then Install & Restart. 4. Type
run_wallace() in the console and press Enter.