VORTEX Population Viability Analysis Software
This page provides access to the VORTEX Population Viability
Analysis software produced by Bob Lacy
(Department of Conservation Biology,
Chicago Zoological Society,
Brookfield, Illinois, USA).
VORTEX is copyrighted, but is distributed without cost for the purpose of furthering conservation and research. Individuals and not-for-profit organizations are hereby given licenses for using VORTEX in research and conservation.
Distribution of VORTEX is restricted to:
Redistribution of VORTEX, in whole or in part, by any for-profit organization or for any profit-making purposes, is expressly forbidden.
A note about cost
Vortex is provided free of charge because of the commitment of the Chicago Zoological Society to making it widely
available to further biodiversity conservation. Similarly, the manual, developed by the CBSG, is provided
for downloading because the CBSG cares about saving species and their habitats. However, the initial development
and continuing improvement of the software and manual do represent a significant commitment by these conservation
organizations. The rate at which improvements can be made is determined by the resources available
to support that work.
If your budget allows it, please consider making a donation to support the further development of Vortex.
If you find the software to be especially valuable to you, consider donating perhaps US$100
(a wild guess about the investment of resources per user that have gone into Vortex),
or more or less as you feel is appropriate. If you find the manual to be especially helpful,
consider donating to the CBSG. As a side benefit to US tax-payers, donations to either the
Chicago Zoological Society or the CBSG are tax-deductible.
Donations to the Chicago Zoological Society should be as a check written to the Chicago Zoological Society,
sent to
"Vortex donation, Department of Conservation Biology, Brookfield Zoo, Brookfield, IL 60513 USA".
Donations to the CBSG should be sent to
"Vortex donation, CBSG, 12101 Johnny Cake Ridge Road, Apple Valley, MN 55124, USA".
To download the current version (9.73 14 April 2008) of VORTEX, go to
http://www.vortex9.org/vortex973install.zip (about 11 MB).
After downloading the above file, unzip it into a temporary directory on your hard drive.
(Do not unzip it into the directory into which you plan to install Vortex.) Then run the SETUP.EXE program.
If you receive a warning message asking whether to keep newer system files that are already on your computer,
answer yes (the default).
If you encounter problems with installing or running a new version of Vortex, go to the Microsoft web site (www.microsoft.com) and make sure that your version of Windows is up-to-date with the latest service pack and upgrades.
Using Vortex as a linked meta-model with other programs requires that you have XML capabilities installed on your computer.
The XML installation file can be downloaded from the Microsoft website or from http://www.vortex9.org/msxml.msi (about 5 MB).
Using Vortex with the Spatial or Outbreak modeling programs can require that you have the .Net framework installed on your system.
The .Net Framework installation file can be obtained from the Microsoft website or from http://www.vortex9.org/dotnetfx.exe (about 23 MB).
To download the (somewhat out-of-date) manual go to
v950manual.pdf (about 5 MB).
The 175-page manual is also available in printed form for purchase from the CBSG. (See information below.)
Note: If you have trouble downloading the manual
(for example, if only part of the pdf loads), there are two ways to fix a problem
between the Adobe Reader and your browser software:
(1) instead of opening v950manual.pdf in your browser, right-click on the link,
save it to your computer, and then open the saved copy of the pdf on your computer; or
(2) before downloading the manual, open Adobe Reader on your computer, go to the File menu,
select Preferences, and then within the Internet preferences uncheck the box that
allows Adobe to "Display PDF in Browser".
Recent changes and bug fixes include:
- Version 9.73 fixes a bug that used the wrong severity of inbreeding depression if you specified that none of the inbreeding depression was due to recessive lethal alleles, and fixes a bug that caused the program to crash if the option for hermaphroditic breeding was selected.
- Version 9.72 fixes a bug that mis-handled ST scenarios if there was only one non-ST scenario in the project, and adds change in K as a variable that can be modified in ST.
- Version 9.71 fixes a missing label and fixes a bug that could cause a crash when the Translocation special option was chosen.
- Version 9.70 replaces a not very reliable (but MS standard) random number generator that would often have caused less than random results when a seeded random number generator was included in a function of demographic rates.
- Version 9.61 adds a new variable, PARITY (= the number of offspring produced by an individual, whether still living or not), to those variables available for use in functions.
- Version 9.60 fixes a significant bug that caused an entered Dispersal Modifer Function to sometimes not be used.
- Version 9.59 fixes a few obscure bugs (not ones that most people would encounter)
that caused incorrect tallies of numbers of males (WW) and females (XX) in other populations when these variables were used in functions,
and that sometimes lost Notes that were entered if they were not saved immediately.
This version also includes some minor improvements,
such as retention of Graphs and Graph Options when that screen is exited and then you return, and
a change in the way that mortality rates are listed in the Sensitivity Testing Set-up (so that, for example, the variable for mortality between age 0 and 1 is now displayed as FemaleMortality_Pop1_Age0 rather than as ... _Age1).
- Version 9.58 fixes a bug in the use of IIS1, IIS2, etc. for Individual State variables in functions. It also fixes a problem that caused the screen shots not to appear when Help was invoked.
- Version 9.57 fixes a handful of problems that would have caused some data not to be displayed on graphs, and could have caused erroneous SDs of times to extinction if a Scenario was run, and then later resumed to add iterations. It also makes additional genetic data available to other programs that might be linked in a meta-model.
- Version 9.561 fixes a bug that would sometimes cause the y-axis of a graph to be scaled poorly.
- Version 9.56 (and the non-distributed versions between 9.51 and 9.56) fixes some obscure bugs (such as could have occurred if you used individual state variables within functions, and had supplementation), adds an option for screen text to be in Portuguese (in addition to Spanish and English as options), includes some enhancements to the internal coding to improve speed, adds some variables to the ones available for use in functions, and adds the ability to use functions for the numbers of animals to be harvested or supplemented.
- Version 9.51 added the ability to plot probability of extinction (in addition to probability of persistence), fixes a bug that caused problems if scenarios were added or deleted after Sensitivity Test analyses were created, and fixes a bug that would report incorrect probabilities of extinction if new iterations were added to a scenario with the 'Resume' command.
- Version 9.503 fixes a bug that could have caused the simulated populations to crash to 0 each iteration when EV was set to a very small, non-zero value.
- Version 9.50 implemented an automated sensitivity testing module, and a genetic management option.
- Version 9.42 fixes a problem with an incompatibility between versions of the Graphics Server that is used by Vortex. If you have already installed Vortex 9.41 on your system, you may need to do some manual changes before you can get it or any later version to work correctly. If you installed version 9.41 and are having problems with graphs, contact help@vortex9.org and we will give you further instructions.
- Version 9.41 fixes some more bugs, including some related to saving notes, and implements a few more options.
- Version 9.33 fixes some minor bugs, added back in Stop and Pause buttons, and handles abnormal progam terminations better
- Version 9.31 fixes a bug that caused problems for loading some input files from previous versions, and enables Vortex to work with a greater variety of Regional Language/Data settings
- Version 9.30 made a number of changes, including:
- some changes to the lay-out of the input screen for labels and state variables
- capability to create up to 10 Population State Variables for use in functions
- change of data transfer between Vortex and other programs to an xml file, thereby requiring installation of xml capabilities on your system if you intend to use Outbreak or other meta-model links
- simplification of the way Notes are entered for input fields
- ability to prevent matings that would result in inbreeding
- addition of optional labels for catastrophes
- removal of the buttons to Stop and Pause simulations (which did not work correctly on some systems)
- a number of other small fixes to screen formats and minor problems
- Version 9.23 fixes a bug that could cause the simulation to stop if an extinct population is recolonized with 1 supplemented individual
- Version 9.22 fixes various bugs that could have caused problems for some specific cases
(e.g., some cases with very large populations, and some cases using functions for demographic rates)
and fixes a few problems that could cause the program to use much more memory than was really needed.
Also, a change was made to limit the maximum population size to 5000 when using the
non-lethals model of inbreeding depression. Otherwise,
the program would likely use the hard disk to do inbreeding calculations,
leading to unacceptably slow analyses.
- Version 9.21 fixes a problem in version 9.20 that could set initial N to 0 for all populations after the first one.
- Version 9.20 fixes some bugs in the saving of Notes and otherwise.
It also includes a slightly improved lay-out of input screens for Dispersal.
- Version 9.17 uses InternetExplorer to display Help in a way that is
more consistently stable across versions of Windows.
- Between version 9.16 and 9.161, a bug was fixed that would cause the program to tie up all RAM
(and then start causing erratic behavior of the display) when multiple scenarios were run on computers
running Win95 or Win98.
Samples of VORTEX projects contributed by users will be made available to provide examples for teaching and experimentation,
and to provide public access to the full input data used in publications.
Users are encouraged to submit VORTEX project files for inclusion on this site.
To submit a project, send the project's .vpj file (preferably zipped) to help@vortex9.org,
with your name and affiliation, and a brief, 1-line description of the project.
It is helpful to include within your submitted project detailed Project Notes describing the nature of your project
and the citation for any publication reporting on your project results.
Sample projects currently available are:
- dugong.zip
(An analysis of the impacts of harvest of dugongs in the Torres Strait between Papua New Guinea and Australia
and along the Queensland coast. Submitted by Rob Heinsohn, Australian National University.)
- orangutan.zip
(Analyses of Orangutan populations in Sumatra and Borneo. Submitted by IUCN/SSC Conservation Breeding Specialist Group.)
- Amazonaleucocephala.zip
(Analyses of the Cuban amazon parrot (Amazona leucocephala) prepared by the Ministerio de Economia, Cuba, working with the CBSG.)
- Aratingaeuops.zip
(Analyses of the Cuban parakeet (Aratinga euops) prepared by the Ministerio de Economia, Cuba, working with the CBSG.)
- Colaptesfernandinae.zip
(Analyses of a Cuban flicker (Colaptes fernandinae) prepared by the Ministerio de Economia, Cuba, working with the CBSG.)
To subscribe to the VORTEX users Listserv (email discussion group), go to
VORTEX Listserv.
Information about the VORTEX Listserv discussion group is available at
listserv.net (2 KB).
If you think you discover a bug in VORTEX, please go to
VORTEX Bug Report.
The old DOS version of Vortex (version 8.4) is still available. To obtain the old version, download both
VORTXDOS.EXE and
DOS4GW.EXE.
VORTGRAF.EXE is an accessory DOS program which can
show screen plots of the results from previous VORTEX analyses.
I am not able to respond to all queries regarding uses of VORTEX, but I will respond when time permits.
I will not answer questions from users who have not yet obtained and read the users manual.
Queries about VORTEX should be directed to help@vortex9.org.
VORTEX on CD, with a printed manual, can be obtained for US$75 from:
IUCN SSC
Conservation Breeding Specialist Group
12101 Johnny Cake Ridge Road
Apple Valley, MN 55124 USA
Email address: office@cbsg.org
WWW: www.cbsg.org
VORTEX is copyrighted but not copy protected. Individuals and not-for-profit organizations can make copies of
VORTEX for use in their own research and conservation efforts or for others who have similar need for it.
You cannot legally sell the program to others or distribute it as your own work.
Good luck in your use of VORTEX and all your conservation efforts!
Links to related sites by Lacy
-
Intro to Bob Lacy
VORTEX Population Viability Analysis Software
OUTBREAK Modeling software for wildlife disease risk assessment
GENES DOS-based software for genetic analysis and management of pedigrees
PM2000 Windows-based software for genetic and demographic analysis and management of pedigrees
PARTINBR For calculating inbreeding and partial inbreeding coefficients
Publications by Lacy
Links to sites of related conservation organizations
-
Brookfield Zoo
CBSG Conservation Breeding Specialist Group
ISIS International Species Information System
Changes last made on: 14 April 2008