update README file. Maxnet implementation

README.md

@@ -26,13 +26,13 @@ run_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://www.rstudio.com/products/rstudio/download3/" target="_blank">Mac OS /  Windows</a>: choose the free version).
 
-#### Download maxent.jar
-*Wallace* uses 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 <a href="https://biodiversityinformatics.amnh.org/open_source/maxent/" target="_blank">here</a>, 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.
+#### How to run Maxent with maxent.jar
+*Wallace* v1.0.6 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 <a href="https://biodiversityinformatics.amnh.org/open_source/maxent/" target="_blank">here</a>, 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.
 
 ### Potential Issues
 
-#### rJava and Java versions
-*Wallace* uses the `rJava` package 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://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="http://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.xml" target="_blank">Mac</a> and <a href="https://www.java.com/en/download/help/windows_offline_download.xml" target="_blank">Windows</a>.
+#### 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://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="http://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.xml" target="_blank">Mac</a> and <a href="https://www.java.com/en/download/help/windows_offline_download.xml" 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.