VORTEX Population Viability Analysis Software
page provides access to the VORTEX Population Viability Analysis
software produced by Bob Lacy
(Conservation Scientist, Chicago Zoological
Society, Brookfield, Illinois, USA).
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 Science,
Chicago Zoological Society, Brookfield, IL 60513 USA".
Donations to the CBSG should be sent to
"Vortex donation, CBSG, 12101 Johnny Cake Ridge Road, Apple Valley, MN
download the current version (9.99c 17 July 2012) of VORTEX, go to http://www.vortex9.org/vortex999install.zip
(about 15 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.
Some people have reported problems using Vortex with MS Vista, while other
people have encountered no such problems. It may be that the Vista system
settings on some computers block Vortex from being able to create directories
and files for storing results. If you encounter problems with using Vortex on
Vista, try to make sure that you have authorization for programs to create new
directories and files in any location that might the
program might specify.
somewhat out-of-date manual is included in the current installation zipfile. To download the manual separately, 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".
changes and bug fixes include:
- Version 9.99c fixes a bug that caused some males to not
be available for breeding when the breeding system was set to monogamy
(long-term or short-term) and females could produce more than one brood
per year. In addition, now monogamous females will stay with the same mate
for all of the multiple broods within each year (and across years if
long-term monogamy is specified).
Version 9.99c also fixes a bug that caused bad graphs of Prob.
Extinction from within the Sensitivity Testing module when used on
computers with European regional settings for numerical formats.
- As of 9 March 2012 (but still labeled as version 9.99b)
a bug was fixed that incorrectly implemented the option to specify that
only animals within a specified age range can disperse. For the test of
dispersal age, the program had been treating all adults as being the age
at which breeding begins (i.e., the beginning of adulthood). Thus, Vortex
was allowing too many animals disperse when the user specified that only
some adult age classes should be able to disperse.
- Version 9.99b fixes a bug that occurred if the maximum
number of broods per year was set to 1, but the probability of producing 1
brood was specified to be less than 100%. In such cases, all breeding
females would have produced 1 brood, rather than only some breeding
females producing a brood.
- Version 9.99 fixes a few bugs that caused difficulty in
entering some genetic management options and which prevented display of
graphs comparing sensitivity test results.
- Version 9.98 (and 9.97, which was never publicly
distributed) fixes a few problems with some graphs; addds
the ability to graph global state variables and population state
variables; allows specification of starting allele frequencies at
additional simulated loci; allows reporting of genetic summary statistics
based on all modeled loci; and adds a few new variables for use in
functions. A short description of these changes is available at www.vortex9.org/Vortexversion998.doc
- Version 9.96 provides an option to read annual rates
for an input variable from a file (one value per line), by specifying
"=FILE=filename" as the function. Also fixed a bug that caused
mortality to be 100% in very rare years.
- Version 9.95 adds a Special Option to output a list of
all animals created in the simulation. It also fixes a problem that caused
the population to start with one too many or too few animals in some
cases. Also fixed was a bug that caused miscalculation of KIN when used in
- Version 9.94 fixes a problem that caused program
crashes with some specifications of brood sizes.
- Version 9.93 fixes a problem that caused program
crashes at random points in some very big projects.
- Version 9.92 fixes a problem with the number of progeny
per brood in some cases.
- Version 9.91 fixes a problem that caused the input
screen to not display correctly the table with the distribution of number
- Version 9.90 now asks the user to specify in the input
the duration in days of a simulated Vortex "year" (the model timestep). This has no impact on the model results,
but it is helpful to document when a model is considering a
"year" to be of shorter or longer duration. Vortex also now
separates the annual reproduction into multiple possible litters (or
broods or clutches), so that the user enters both the probabilities of a
female producing 0, 1, 2, etc. broods and the distribution of the number
of offspring per brood. This will usually have no effect on demography, as
4 offspring in one brood is equivalent to 2 offspring in each of two
broods (Vortex forces all reproduction each year to occur in one
instantaneous breeding season), but it can change the genetics, as each
brood can have a different sire. Thus, reproduction each year is now
specified as a probability that a female will be paired for breeding, a
probability that a breeding female has each possible number of broods, and a distribution of the numbers of offspring
in the broods. Note that various combinations of these parameters can
result in functionally the same demographic model.
Vortex now provides the option to use Global State Variables and Population
State Variables, as well as Individual State variables. Version 9.90
removes some automated links to other simulation software, Outbreak and
Spatial, as the linkage between Vortex and these programs is now being
implemented with a MetaModel Manager program.
Vortex still provides a button to automatically create some Individual
State variables that are needed if it is to be linked to these other
- Various versions -- 9.80 through 9.85 -- that were
never widely distributed fixed a number of small bugs, including problems
that could cause a crash if notes or scenario names included a few
problematic characters, such as '#' or '/'
- 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
- 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 email@example.com 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
- 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
- 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
- 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
- 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
- Version 9.17 uses IExplorer
to display Help in a way that is more consistently stable across versions
- 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.
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 firstname.lastname@example.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:
(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
(Analyses of Orangutan populations in Sumatra and Borneo. Submitted by
IUCN/SSC Conservation Breeding Specialist Group.)
(Analyses of the Cuban amazon parrot (Amazona leucocephala)
prepared by the Ministerio de Economia, Cuba, working with the CBSG.)
(Analyses of the Cuban parakeet (Aratinga
euops) prepared by the Ministerio
de Economia, Cuba, working with the CBSG.)
(Analyses of a Cuban flicker (Colaptes
fernandinae) prepared by the Ministerio de Economia,
Cuba, working with the CBSG.)
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.
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 email@example.com.
on CD, with a printed manual, can be obtained for US$75 from:
IUCN SSC Conservation Breeding Specialist
12101 Johnny Cake Ridge Road
Apple Valley, MN 55124 USA
Email address: firstname.lastname@example.org
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.
luck in your use of VORTEX and all your conservation efforts!
Links to related
sites by Lacy
Intro to Bob
VORTEX Population Viability
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
Chicago Zoological Society
CBSG Conservation Breeding Specialist Group
ISIS International Species Information System
last made on: 17 July 2012