Distribution of VORTEX is restricted to:

• distribution by the Chicago Zoological Society;
• distribution by the IUCN/SSC Conservation Breeding Specialist Group;
• downloading of the program from the Internet (vortex999install.zip) by individuals and not-for-profit organizations for their own research and conservation applications;
• redistribution without charge of the unmodified executable program for the purposes described above.

Redistribution of VORTEX, in whole or in part, by any for-profit organization or for any profit-making purposes, is expressly forbidden.

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 55124, USA".

• 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 functions.
• 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 of broods.
• 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 (Voretx 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 programs.
• 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 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.

• 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.)

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

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

Chicago Zoological Society
CBSG Conservation Breeding Specialist Group
ISIS International Species Information System