Rex Software

ABC Rex is a user-friendly computer program for estimating parameters in a range expansion problem. The problem is common to many ecological studies where a geographical region has been generalized by a grid and a population count of a species has been recorded for each grid element to form a pattern called a dispersal pattern. While direct inference methods can be applied to infer some important parameters from a single dispersal pattern, the inference of range expansion parameters in this context; for example, point of invasion, time since invasion, intrinsic rate of growth, probability of emigration, probability of long distance dispersal, etc., would require methods that can infer parameters without directly evaluating parameter likelihoods, as those likelihoods are unknown. Recently, a family of likelihood-free Bayesian inference methods, called approximate Bayesian computation (ABC), have emerged with the inference power to accurately infer parameters where the parameter likelihoods are unknown. ABC has been applied widely to genetic data, but more recently to demographic data expressed in dispersal patterns for estimating range expansion parameters.

An example of a dispersal pattern from a field study of an invading species.

Given the inference power of ABC, ABC Rex is a computer program that provides ecologists with a graphical user interface to easily apply ABC and to estimate some important range expansion parameters from a dispersal pattern.

Rune Rasmussen and Grant Hamilton. An approximate Bayesian computation approach for estimating parameters of complex environmental processes in a Cellular Automata. Environmental Modelling and Simulation.29(1): 1-10. (http://dx.doi.org/10.1016/j.envsoft.2011.10.005).

Click here to download: The ABC Rex operating manual

System Requirements

ABC Rex requires an Apple Mac computer with Mac OS X version 10 or later operating system with at least 2GB RAM.

 Download ABC Rex

The download process involves two forms, where the first form “ABC Rex Download” is embedded in this page and requires your name, institution and email address for our download records, the “Submit” button of this form opens a second form that provides a link to the ABC Rex install (‘.dmg’) file.

Terms of use

The copyright for ABC Rex belongs to the creators, Dr Rune Rasmussen & Dr Grant Hamilton, under the common title of “Hamilton Labs” and must not be altered in any documentation that may accompany this software. This software (ABC Rex) is available free of charge and must not be sold, promoted or used for marketing or profit in any way by any third party, organisation or business without the expressed written permission of the copyright holders. This software must not be reversed engineered or modified in any way, nor should the “about” notice or the opening “splash” image or any file, binary or text or otherwise characterised, of the software be modified in any instance or version of the program. You have permission to use this software to generate results in your research and publications provided that you cite or reference this software. You have permission to pass the software free of charge on to other users.

Disclaimer

This software (ABC Rex) is provided by the copyright holders and contributors “as is” and free of charge, and any express or implied warranties, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose are disclaimed. In no event shall the copyright owner or contributors be liable for any direct, indirect, incidental, special, exemplary, or consequential damages (including, but not limited to, procurement of substitute goods or services; loss of use, data, or profits; or business interruption) however caused and on any theory of liability, whether in contract, strict liability, or tort (including negligence or otherwise) arising in any way out of the use of this software, even if advised of the possibility of such damage. You express your agreement to the terms of use and this disclaimer when you supply your details and click on the “Submit” button in the “ABC Rex Download” form (coming soon).

Install ABC Rex

Once you have downloaded ABC Rex you will find the ABC Rex ‘dmg’ file in the Downloads directory. Double clicking on this file will open a Finder window to the ABC Rex program (see Figure below).

download rex

You can drag-and-drop the ABC Rex program in any preferred directory, however, the standard location for programs is the Applications directory (see Figure below).

download rex2

Finally, once ABC Rex has been installed into the desired directory, eject the ‘dmg’ file by clicking on the eject icon (see Figure below).

download rex3

Utilities

The following utilities have been provided in open-source C++, to extend the range of conventional tool chains for ABC Rex. These utilities are simple ANSI C++ programs, which are each completely defined by a single main.cpp file that can be compiled on any computer platform with any ANSI compliant C++ compiler. Once compiled, each utility runs in terminal as a command line tool. Executing a utility without inputs will provide user instructions.

The “field_data2ABC_Rex” utility: This utility takes as input a full-path file name to a carrying capacity distribution file in ESRI ASCII grid format, a carrying capacity distribution scaling factor, a full-path file name to an occurrence data file in CSV format and output file name. Provided that the occurrence data is a spreadsheet of occurrences involving two columns so that each row is a location in the same coordinate space as the carrying capacity distribution file, this utility returns a data file that can be accepted as input to ABC Rex. An executable for Mac OS X can be found in the zip folder at: buildDebugfield_data2ABC_Rex.

Usage:$ ./field_data2ABC_Rex [habitat_suit (ESRI Ascii)] [scale] [data_file (csv)] [out_file]