From 31c59b2b37368225595d969aed6d0074c3fce1c8 Mon Sep 17 00:00:00 2001 From: Gonzalo Date: Wed, 10 Oct 2018 10:16:29 -0400 Subject: [PATCH] update README file. Maxnet implementation --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 0d75dedc..60fb47f8 100644 --- a/README.md +++ b/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 (Mac OS, Windows) and RStudio (Mac OS / Windows: 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 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. +#### 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 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. ### 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 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. +#### 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 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. #### 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.