wallace

[![R-CMD-check](https://github.com/wallaceEcoMod/wallace/workflows/R-CMD-check/badge.svg)](https://github.com/wallaceEcoMod/wallace/actions) [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) [![CRAN version](http://www.r-pkg.org/badges/version/wallace)](https://CRAN.R-project.org/package=wallace) [![downloads](https://cranlogs.r-pkg.org:443/badges/grand-total/wallace?color=orange)](https://cranlogs.r-pkg.org:443/badges/grand-total/wallace?color=orange)

# Wallace (v2.2.1)

*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.

```R
install.packages("wallace")
library(wallace)
run_wallace()
```

Development versions can be downloaded from Github with the following R code.

```R
install.packages("remotes")
remotes::install_github("wallaceEcoMod/wallace")
library(wallace)
run_wallace()
```

### Before using *Wallace*

#### Update R and RStudio versions
Please make sure you have installed the latest versions of both R (<a href= "https://cran.r-project.org/bin/macosx/" target="_blank">Mac OS</a>, <a href= "https://cran.r-project.org/bin/windows/base/" target="_blank">Windows</a>) and RStudio (<a href= "https://posit.co/download/rstudio-desktop" target="_blank">Mac OS /  Windows</a>: choose the free version).

#### How to run Maxent with maxent.jar
*Wallace* v2.2.1 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).

### Potential Issues

#### rJava and Java versions (just for maxent.jar option)
*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 <a href="https://www.java.com/en/download/manual.jsp" target="_blank">here</a>, 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 <a href="https://stackoverflow.com/questions/30738974/rjava-load-error-in-rstudio-r-after-upgrading-to-osx-yosemite" target="_blank">this StackOverflow post</a> 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 <a href="https://www.java.com/en/download/help/mac_install.html" target="_blank">Mac</a> and <a href="https://www.java.com/en/download/help/windows_offline_download.html" target="_blank">Windows</a>.

#### Problems viewing tables
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.

#### Windows Users: PDF download of session code
If PDF downloading of session code is not working for you, please follow the following instructions, taken from <a href="https://github.com/rstudio/shiny-examples/issues/34" target="_blank">here</a>:
     - 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:\Program Files\MiKTeX 2.9\miktex\bin\x64\pdflatex.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=";"))`.

#### Windows Users: Only for Github installation
If you are using Windows, please download and install <a href="https://cran.r-project.org/bin/windows/Rtools/" target="_blank">RTools</a> before installing the `devtools` package. After you install RTools, please make sure you add "C:\Rtools\bin" to your PATH variable (instructions <a href="https://stackoverflow.com/questions/29129681/create-zip-file-error-running-command-had-status-127/29480538#29480538" target="_blank">here</a>). Additionally, when using `devtools` on Windows machines, there is a known <a href="https://github.com/r-lib/devtools/issues/1298" target="_blank">bug</a> 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.

#### Any other problems with install_github()
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.