A Modular Platform for Reproducible Modeling of Species Niches and Distributions

The 'shiny' application 'wallace' is a modular platform for reproducible modeling of species niches and distributions. 'wallace' guides users through a complete analysis, from the acquisition of species occurrence and environmental data to visualizing model predictions on an interactive map, thus bundling complex workflows into a single, streamlined interface.


Build Status License: GPL v3 CRAN version downloads

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. Here is a link to the paper published in Methods in Ecology and Evolution that describes Wallace.

Install Wallace via CRAN and run the application with the following R code.

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

In the future, development versions can be downloaded from Github with the following R code. For now, please install via CRAN.

install.packages("devtools")
devtools::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 (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.

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.

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 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:\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 RTools before installing the devtools package. After you install RTools, please make sure you add "C:\Rtools\bin" 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 run this script to install the packages and their dependencies directly from CRAN, and then run the code below.

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 Build & Reload.
  4. Type run_wallace() in the console and press Enter.

News

wallace 1.0.3

  • Added error checks for when the coordinate reference system (CRS) of an input user raster is NA, and updated guidance text in the User-specified Environmental Data module with a guide on configuring the CRS of rasters in R.
  • Fixed a bug that prevented downloads of 30 arcsec Worldclim rasters.
  • Updated the intro screen tab module names.

wallace 1.0.2

  • There is now an option to download all the response curves at once in the same png.
  • Local path to dismo's maxent.jar is now printed inside the log window to avoid failure to word wrap in some browsers.
  • Component 2 module "Select Occs" now informs user of the occIDs of points removed, not of the ones retained.

wallace 1.0.1

  • Removed button used for development.

wallace 1.0.0

  • Biggest change: reprogrammed most of the software to integrate shiny modules. Now each module is a separate script in /inst/shiny/modules that contains both UI and server logic. This should make authorship and integration of new modules much easier.
  • Second biggest change: integrated leaflet draw toolbar functionality from leaflet.extras package, which replaces the previous code to draw and internally record polygons in comps 2 and 7. The code is much cleaner now and easier to make edits to.
  • By popular demand, added user-input environmental variables module. This is a work in progress, so please report bugs to Issues on Github.
  • Added buffer by points feature for background extent module (comp4).
  • Added cloglog output option for Maxent (updated for Maxent version 3.4x) in map prediction module (comp7).
  • Partition occurrences modules (comp5) now plot on the map with a legend showing the partition group per color.
  • Maxent models now show the evaluation statistics for all partition groups (ENMevaluate() option bin.output=TRUE) -- the partition group numbers correspond to the comp5 legend.
  • Unit tests are now available for all modules in two flavors: 1) control tests run automatically via Travis with each Github push, which test that the UI buttons, forms, etc. are functioning properly; and 2) function tests which run Wallace as a user would by pushing buttons and entering fields, and as these tests take more than 5 minutes to complete, they are not automatically run for now. Unit tests will be a signature part of module contribution.
  • Updated guidance text.

wallace 0.6.4

  • Added explicit package references to writeRaster() calls. Should work now without loading raster package first.
  • Fixed reference to required field names in component 1 User Occurrences module guidance text. Now reads "names" instead of "species" as first field.
  • Added checks for appropriate fields for VertNet and BISON, as not all downloads include all fields. Should avoid erroring due to missing fields now.

wallace 0.6.3

  • Added repmis and rgdal to package dependencies.
  • Turned off evaluation of chunk that loads packages in userReport.Rmd.
  • Added error catches to component 5 and 6 if rJava cannot load.

wallace 0.6.2

  • Turned off evaluation of code chunks in userReport.Rmd. Now the building of user session code is much, much faster.
  • Made code compatible with leaflet version 1.0.1. There was a mysterious problem with zooming to points before clearing markers and/or plotting points, which resulted in crashing as soon as points are plotted unless the user had the Github master version of leaflet installed. Thus the code was rearranged and cleaned to accomodate the current leaflet version on CRAN.
  • Fixed some errors in userReport.Rmd relating to the user .csv path and printing of a couple of headings.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("wallace")

1.0.4 by Jamie M. Kass, 4 months ago


https://wallaceEcoMod.github.io


Browse source code at https://github.com/cran/wallace


Authors: Jamie M. Kass [aut, cre], Bruno Vilela [aut], Matthew E. Aiello-Lammens [aut], Robert Muscarella [aut], Cory Merow [aut], Robert P. Anderson [aut]


Documentation:   PDF Manual  


GPL-3 license


Imports DT, shinyjs, spocc, RColorBrewer, dplyr, spThin, ENMeval, rgeos, maptools, dismo, raster, shinythemes, magrittr, rgdal, leaflet.extras

Depends on shiny, leaflet

Suggests knitr, rmarkdown, testthat, RSelenium


See at CRAN