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 Vortex FAQs

If you have a question about the use of Vortex, please read the manual, then search the FAQs below, and then -- if you don't find an answer, submit your question.


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Q:>  I'm trying to run ST Sampled and Factorial tests in Vortex. I can get the Sampled option to run and an STSUM file, but no graphs will display within Vortex. The Factorial test will only run the base model. I have BaseVal, Minimum, Maximum and Increment values listed for both tests, plus a value list for the Factorial tets. What could I be doing wrong? Thanks.  Submit Answer

Q:>  I am just starting to look at using Vortex (I have a Mac, so haven’t actually downloaded it yet, but that’s another story) and was trying to work out whether it is possible to feed it scripts? I would like to run a pretty basic analysis for multiple species, and this would obviously be a lot quicker if it were possible just to feed in all of the relevant information in one go and get the outputs all at once. Is this possible?  Submit Answer

Q:>  Hello! I have a question about mean growth rate (rs)in Vortex. I ran a model (1000 iterations over 100 years). My N vs Yr data and graph suggest a positive growth rate. However, the rs value provided by Vortex is negative (-0.01). I hand calculated the r from the N vs Yr data, and got a different (positive) value. Is there a reason the rs would be different/possibly incorrect? I only caught this because of the obvious difference in the positive graph and negative rs value. This also occurs in models run over 10 and 20 years. Has anyone else gotten different rs values than Vortex provides? Thank you for any suggestions or help!  Submit Answer

Q:>  I'm trying to figure out the appropriate function that will gradually increase the dispersal rate between populations over time. I have two populations that are small and will eventually meet each other once they increase in number over a 10 year period. I assume I can adjust the rate of D for each Y or N I specify but I'm not sure how to create a function that will double the D rate each time.  Submit Answer

Q:>  Hello. I want to use the sensitivity test for analysis population dynamic with feral cat TNR(trap neuter return). I read the manual several times. But I still do not know how and where to input the data for TNR the sensitivity test. I understand from the manual of VORTEX is need to use state variables section for inputting data(GSvar etc). But I can not understand what kind of data I need to put in the variable, label, Initialization function and transition function(State variables) analysis TNR effect. Especially, I want to change the percentage of breeding of both sexes.  Submit Answer

Q:>  Hello, my sincere thanks for the prompt and informative answer to my last question. This question pertains to how Vortex implements carrying capacity, and what possibilities there may be to implement in other ways. I understand that Vortex truncates population by altering mortality rates at the end of each time step if the population has gone over carrying capacity. This creates a "hard ceiling" for the population, and doesn't really allow boom and bust dynamics (at least so far as my scenarios have shown). I am trying to assess extinction risk for a species that has large observed population fluctuations. Analysis of a time series of abundance for this population results in estimated K's that are quite a bit lower than the occasional booms that population experiences, but I am unable to simulate this effectively in Vortex because of population truncation if I set the carrying capacity to the independently estimates K. Is it best to simply set the Vortex K to some arbitrarily high number but have the populations start at a more realistic number, to give them freedom to boom and bust? Additionally, can anyone recommend a good way to implement density dependence in juvenile survival? We have evidence that nest success and juvenile survival may decrease for this species at high densities, but not adult mortality or possibly even the proportion of females breeding. Many thanks! URL:  Submit Answer

Q:>  I have a question about how Vortex calculates with standard deviation. For instance, if I assume 100% of adults females breeding and put a standard deviation due to EV of 10%, will the program calculate the 'biologically impossible 110%' does it only estimate up to 100% (90-100% in this example)? Thank you for any help!  Submit Answer

Q:>  Hi, I'm working with a specie of fish. However, even in simpler scenarios there were two types of error: error the calckinship and error the output.Apparently, the errors appear to increase the size of the "initial population size" and the "carrying capacity". scenarios more complex, including harvest information, also error presentation. What should I do?  Submit Answer

Q:>  Hi, I'm working with a specie of fish. However,even in simpler scenarios there were two types of error: erro the calckinship and erro the output.Apparently, the errors appear as I increased the size of the "initial population size" and the "carrying capacity". Larger scenarios more complex, including harvest information, also error presentation. What should I do?  Submit Answer

Q:>  Hi, I'm working with a specie of fish. However,even in simpler scenarios there were two types of error: erro the calckinship and erro the output.Apparently, the errors appear as I increased the size of the "initial population size" and the "carrying capacity". Larger scenarios more complex, including harvest information, also error presentation. What should I do?  Submit Answer

Q:>  Hi, I'm starting with Vortex. I would like to know how to introduce a function that specifies that for there to be male to female copulation the male must be larger than the female? Is this possible?.  Submit Answer

Q:>  I am running VORTEX with genetic data incorporated. The allele frequencies are in the correct format. I have re-downloaded the newest version but I receive the message "Error in Animal Contructor" back. What does this mean? Thanks.  Submit Answer

Q:>  Will the current version of the program run under old Windows XP?  Submit Answer

      A:>  Probably not. The .NET Framework that is a core part of current Windows (i.e., Win7 and up) is not compatible with Windows XP. Thus, many newer programs that are compiled for the current versions of Windows will not run under XP. Usually, the installation of the program will fail.

Q:>  Hi, I am working on vortex to model trout populations. I am very new at using vortex. I would like to know how to enter a function "age fecundity dependent" such as my 2 years old female produces X juveniles, my 3 years old produces 1.2X juveniles etc...". Regards  Submit Answer

Q:>  Hi, I am working on vortex to model trout populations. I am very new at using vortex. I would like to know how to enter a function "age fecundity dependent" such as my 2 years old female produces X juveniles, my 3 years old produces 1.2X juveniles etc...". Regards  Submit Answer

Q:>  Hey, I'm working with some species of alligator. We know that mortality is size dependent, thus is why we divide animals into classes of animal sizes for the population study. In vortex mortality is age-dependent, is there any way to write this parameter by "class-size"?  Submit Answer

Q:>  Hey, I'm working with some species of alligator. We know that mortality is size dependent, thus is why we divide animals into classes of animal sizes for the population study. In vortex mortality is age-dependent, is there any way to write this parameter by "class-size"?  Submit Answer

Q:>  Hello, I'm sending this question as a test. I've had trouble another time to writing my doubts here.  Submit Answer

Q:>  The catastrophe I would like to model is a parasite epizootic that effects the survival of age classes differently (high mortality in the 0-1 class and low effect on mortality of the 1+ class). Is there a way to do this in Vortex? Thank you.  Submit Answer

Q:>  I am interested in better understanding how Vortex uses certain parameters in the actual simulation. In particular, I am confused at the respective roles of "% Breeding at low density" in the Density dependent reproduction box of the Reproductive System tab, and "% adult females breeding" in the Reproductive Rates tab. In the manual, the latter of these (% Adult Females Breeding) is explained in terms of lengths of time between successive reproductive events, while the former is described as p(0), the probability of a female (attempting?) breeding in a given year under no density-dependent feedback. Are these two, then, multiplied together to give the probability of a female breeding in a given year at population size N? More specifically, if my study species breeds twice yearly and most females with a mate that have territory space (i.e., are not affected by density dependence) will breed, should %adult females breeding be very high? URL:  Submit Answer

      A:>  The Density Dependent reproduction box is simply a tool for automating the process of writing a function that describes the shape of a plausible density dependent curve. If you fill in the values in that box (and add the check mark so that the info in the box is enabled), then a density dependent function is inserted for you into the "% adult females breeding" box on the next page. You don't need to use the DD reproduction box at all if reproduction is not density dependent. Or, for that matter, even if it is density dependent, you can write your own function in the %females breeding box on the next page. Once you (or the automated DD tool) put a value or function into the %females breeding input, that value or function is used to define the breeding rate (and anything in the DD box is not used on top of what is specified). See the manual for some examples.

Q:>  I would like to use Vortex to create a model showing population size at specific varying rates of growth and decline, including a specific number of animals harvested every year, without having to enter a starting population. is this possible?  Submit Answer

      A:>  I don't understand how Vortex (or any model) could project population sizes if you do not specify the starting population. Would it work for you to simply specify some default starting N, such as 100 or 1000, and then proceed from there?

Q:>  I am modelling a safari hunting offtake and would like to specify in the Harvest option that only older males (>8) can be harvested. What is the formula I would need to use to overide the default 'number of males of each age to be harvested' categories?  Submit Answer

      A:>  I think that this would be easy to do, assuming that the males can start breeding by age 8 (so that the harvested males are all in the last age class). Just enter into the "Optional criteria for individuals" the function "=(A>8)". This will cause all harvested males to be more than 8 y old. (If you are also harvesting any females, then your function will need to be something like "=IF(S='M';(A>8);1)".)

Q:>  Dear all, I would like to develop a population viability analysis where supplemented individuals (captive-born) are present in the initial/starting population in addition to wild-born individuals. I know how to design an individual state for supplemented individuals ( ISvar1=IF(Y=0;1;2) ), but it only concerns individuals that are added in later supplementation. Do you have any advice on how to include supplemented individuals in the initial/starting population and keep track of them ? Thank you for your help and time LB  Submit Answer

      A:>  I am not certain what you need, in terms of what you want to track about these individuals, but ... One way to distinguish two sets or individuals in the starting population would be by their IDs. E.g., if you wanted half of the starting population to be "tagged" as being from the captive source, you could create an ISvar that is initialized as "=(ID%2)". This would label every other animal as IS1=0 and every other one as IS1=1. You could use slightly more complex ISvar functions to assign some other proportions. E.g., if you want, on average, 15% of the starting population to be tagged, then use IS1=(RAND<0.15).

Q:>  Hi, I am trying to create a new project on Vortex but once I have typed in the file name and pressed 'OK' it closes and an error message appears reading: 'Error in V10Project constructor'. I am not sure whether it is an error with the installation or what I am doing?  Submit Answer

      A:>  Most likely the problem is that the folder in which Vortex is trying to save your new project is a folder to which you do not have read&write access on your computer. The default folder was in the ProgramFiles folder, but often users who do not have Administrator rights on their computers cannot have files saved to that folder. Try changing the Folder Location when you create a new project to some folder where you do have read&write access -- such as a folder within MyDocuments. We will also change the default working directory for the Vortex10 shortcut to be Vortex10Projects, so as to avoid this problem.

Q:>  Dear all, I am working on a supplemented bird population. Every year 1 year old captive-born individuals are released in the wild. To develop accurate population viability models with vortex I need to keep track of supplemented individuals after the year of supplementation as mortality from age 1 to 2 and 2 to 3 is different between supplemented (captive-born) and wild-born individuals.I know that supplemented individuals can be specified (SUPPLEMENTS) in functions, but they only represents individuals supplemented that year, updated after each population is supplemented. Do you have any advice on how to keep track of supplemented individuals ? I thought of using "individual state variables", but I struggle to find a clear example useful for my study case. Thank you for your time and help.  Submit Answer

      A:>  The easiest way to track who was supplemented is to use an Individual State variable (as you suspected). Create IS1 with Initialization function "=(Y>0)", Birth fn "0" and Transition fn "=IS1". A supplemented individual will have IS1 initialized, and it will happen after Year 0, so it will have IS1=1. All other individuals will have IS1=0. You can then use this IS1 to modify mortality (or other) rates for individuals that were added as supplements.

Q:>  The Vortex Manual states (p23) that "In a population-based simulation, all genetic options and modeling (e.g., of inbreeding depression) are disabled, as is individual variation (demographic stochasticity)." Below this it states that "if N typically stays above about 1000, it might be more efficient to run as a population-based simulation." My question is, for clarification, if I have no inbreeding or genetic data input, will I get the same results using a population-based versus an individual based model if my sample size is high (Ninit 175,000)? I don't want to lose any important information from using population-based, but my population size is so large, the program is taking a very long time to run as individual based. I supposed the demographic stochasticity would be very small and therefore insignificant? Thank you for your time!  Submit Answer

      A:>  If population size stays above a few 1000, the results from a population based model should be almost identical to the individual-based model, except that the population based model will run a LOT faster. The exception to this would be if you are using individual state variables to create a complex model of individual variation in some trait -- but that would be an uncommon thing to do. A disadvantage to the population based model will be that you won't get genetic statistics, but for a population as large as 10,000 or more, genetic drift and loss of variation will be undetectably small anyway.

Q:>  I am trying to assess the impact of supplementing a population for N years on P(extinction). I set up a sensitivity test to vary the Last Year of Supplement, but when I set that =GS1 I get the error "Enter a Value greater than 0". Is Last Year of Supplement not allowed as a parameter that can be varied?  Submit Answer

      A:>  Indeed, Last Year of Supplement is not a parameter that can be set to be a function. It must be an integer. The easy way around this is to set the Optional Criteria for Supplements to be Y < GS1.

Q:>  HELP! I have been working in Vortex carrying out various ST and scenarios for over a week. I had an error stating "Error when processing." Next, it says"Unhandled exception has occurred in your application." Now all of my tests and results have disappeared, and there are no scenarios or ST's appearing in the file. Is there a way to retrieve all of the work I have done?  Submit Answer

      A:>  Something got corrupted in your input file, making it unreadable by Vortex. When this happens, the first thing that you should do (before even starting Vortex again!) is to make copies (in a different folder) of the .xml project file and the associated .xml.bak and .xml.bk2 files. You can then delete the bad .xml project file, rename the .bak (or maybe .bk2) file to be an .xml, and then see if it will open for you. Vortex tries to protect you by always making a backup copy of project files when you use them. You can then restore a project to an earlier state, if you rename files before you try multiple times to read a bad file. (If you do keep trying to use the bad file, often you will cause Vortex to over-write the backups with copies of the bad file.)

Q:>  Hello, I am working on Sensitivity tests using the ST tool in Vortex. Thanks to your previous response, I now am understanding how to use this tool. I am curious of how you would go about testing the distribution of two broods? I would like to test 0-90-10, 0-70-30, and 0-50-50. Do you have ideas of how to do this?  Submit Answer

      A:>  To do that, you can create an SV1 variable in the ST module, and assign to it values 90, 70, and 50. Then, in the distribution of broods, set 0 broods = "0", 1 brood = "SV1", and Vortex will take care of making the % with 2 broods be such that it adds to 100 when the model is run. It can get trickier if you want to simultaneously change the % for each of 0, 1, and 2 (or more) broods, but fortunately that isn't what you need!

Q:>  My question refers to the sensitivity testing within Vortex 10. I have created a baseline sensitivity scenario. I am reading the manual and as it states to go to each parameter and enter the appropriate SV number. This works for carrying capacity, but on the reproductive systems tab it will not let me enter a value other than 1. It comes up with an error message. What am i doing wrong? I want to alter the age of first breeding females, the max age of reproduction females and percentage of juvenile mortality. Thanks  Submit Answer

      A:>  Vortex cannot do sensitivity tests on the few variables that would alter the structure of data entry. E.g., age of first breeding is used to determine how many age classes are to be included in mortality rates, so changing age of first breeding within a ST causes structural problems for the model. The way to get around this is to set age of breeding at the lowest possible age, then control when individuals can breed via a function of age in the "%breeding" rate. Then, an SV from the sensitivity test can be used as a parameter in this function to change at which age females have >0 chance of breeding. E.g., use "=(A>=SV1)*50" for the percent breeding, and then SV1 can be set in the sensitivity test to be the age of first breeding.

Q:>  I tried to download the new installation, but I got a warning about a bad or missing certificate (or unknown publisher). Also, when I did download it, it crashes when I run the new version with an error about missing files. What is wrong?  Submit Answer

      A:>  You can safely ignore that warning. We cannot afford the cost and hassle of becoming a "known" publisher (in MS's eyes), but no one has ever encountered a virus in our software. If you get errors when trying to run a new version (or if the installation fails for whatever reason), then first uninstall the old version, then download and install the newest version, and then reboot. The problem often is that Windows doesn't fully install and recognize all the new files in the installation unless you go through these steps.

Q:>  Hello, I am trying to carry out ST (sensitivity tests) in Vortex 10. I am unsure of specifics for this, and how it recognizes the parameter you wish to test. Can anyone explain the SV (and GS synonym) and how Vortex recoginizes it? I have tried to google and find any information I can, and of course have read the manual several times, but I cannot seem to find specific instructions for how to carry out the ST. For example: If I want to test the sensitivity of the SD due to EV of the mortality rates, how do I go about this? Do I make several scenarios, each with a different SD? Please help or can you help lead me to a reference or instructions for how to run the ST? Thank you much!  Submit Answer

      A:>  Briefly ... To run a ST on, say, EV in mortality, there are several options. First, (as a brute force method) you can create multiple copies of your base scenario, and then change the EV (and the scenario label) for each one to cover the range of values that you want to test. Alternatively, you could create a GSvar that samples from the range of interest (e.g., perhaps EV = 5 to 25) at each iteration, by using an initialization function such as "=UNIFORM(5;25)", with Transition function "=GS1". Then, you would put "=GS1" into the input box for the EV. You would then need to analyze statistically the results in the .run output file to determine the importance of the variation in the EV rate. (This gets more complex if you want to vary all the EVs proportionally, but at the same time.) Finally, you can use the automated ST module by specifying that an SV (with label something like "EVvalue") is to be varied from 5 to 25. Vortex will then create a GSvar that samples from that range for you, and it will give it the synonym "SV1". You then put "=SV1" into the input box for EV. When the ST is then run, it will automatically create a series of scenarios that sample from that range. If you want to vary all mortality EVs up and down by, say, up to 10%, you could specify that the SV samples from 0.9 to 1.1, and then enter for each EV value the function "=base*SV1", in which "base" is the baseline EV for that age and sex. It takes some practice to get comfortable with all the options in the automated ST module, but it is quite powerful once you do get used to it.

Q:>  Under Table & Graphs / Custom Plot I can set "inbreeding" as variable. This is the inbreeding applied to populations (population mean homozygosity). However, I need to get the mean inbreeding of individuals (not populations) over time. How can I find this information in Vortex?  Submit Answer

      A:>  The mean homozygosity of the population will be a very good approximation of the mean inbreeding of individuals. If you want to get the exact inbreeding coefficient of individuals, you can: (1) create an IS1 variable that has Birth function =I and transition function of =IS1, (2) create a PS1 that has transition function = IMEAN1, (3) on the sequence of events, insert a PSupdate step after the UpdateVars (so that it is evaluated after IS1 is evaluated).

Q:>  I was hoping to download Vortex onto my personal computer, but when I tried the two different download options, both of them led to a message from my computer claiming there was a virus attached to them. Is there something within the program that a firewall or security program may mistake for a virus?  Submit Answer

      A:>  The problem is that the Vortex installation doesn’t have a digital signature identifying to Windows what company produced the file. Thus, some anti-virus programs grumble that the file might not be safe. Someday, I will find out what I need to do to add a digital signature to the installation file. No one has ever detected a virus or any kind of malware within the Vortex installation. To be extra safe, I would recommend downloading the installation, then ask your antivirus program to scan the file. When I do this, the download initially pops up a warning that the program “might” contain a virus, but the scan of the actual file reports no virus is embedded in the file.

Q:>  When doing sensitivity tests, would it be reasonable to just test the full range (0 to 100) of every parameter?  Submit Answer

      A:>  No! Not only would it take forever to run all those tests, but doing that would be essentially testing all possible life histories (and even many that are not possible). This would yield the non-informative result that any outcome is possible. The purpose of sensitivity tests is to determine how your results might be affected by plausible alternate values of parameters that are uncertain or might be manipulated. There is rarely any reason to test values outside of the range of what is plausible for your species. Somewhat related to this issue, a number of ecologists recently have pointed out that the common approach of testing the same range (e.g., + or – 1%) for each parameter varied in a sensitivity test makes little sense, and creates an artificial appearance of “standardization”. First, different parameters in a model are not on the same nor often even linearly related scales. E.g., a 1% change in the severity of inbreeding depression has no relationship to a 1% change in K, and neither has any relationship to a 1% change in fecundity. Second, even for parameters that might be considered to be scaled comparably, they might differ greatly in the uncertainty in the values and in the plausible range of values. E.g., if it would be easy to change fecundity by 10% but not feasible (or maybe even mathematically impossible) to change survival by more than 1%, there is no obvious usefulness of a test that compares the impact of an equal % change in the two parameters.

Q:>  How can I specify different dispersal rates for movements among multiple populations? E.g. pop1 to pop2, pop2 to pop3?  Submit Answer

      A:>  Simply enter the pairwise dispersal rates in the matrix on the Dispersal input tab.

Q:>  Can Vortex 10 be run on Windows 10 64 bits.  Submit Answer

      A:>  We have not heard about anyone having problems running Vortex on Windows 10. 64-bits is probably best for any intensive number-crunching software, but Vortex will run on either 32-bit or 64-bit machines.

Q:>  I am modelling with two catastrophes - drought, and fire. Can drought be modelled to occur in concert with fire - that is, when a drought occurs, can the occurrence of a fire that year also be linked? I believe this is possible, but I am struggling to understand the user-defined variables and operators as laid out in the manual. Also, fire has only a short-term impact - can the severity index associated with fire be limited to just part of one year, or must it be imposed over the entire year in which the catastrophe occurs? Any help much appreciated!  Submit Answer

Q:>  I am looking at the .het files for projections of heterozygosity. I assume this is expected heterozygosity? Anyway, some of my results (i.e., some of the iterations) in the 90th percentile are actually showing a slight (< 10%) increase in heterozygosity over time. This only occurs when I use starting allele frequencies from microsatellite data. When I use the default infinite alleles model this does not seem to happen. How is it possible to see a relative increase in genetic diversity for a closed population with no genetic management?  Submit Answer

      A:>  Although the mean expected heterozygosity is always expected to decrease in a closed population with no genetic management, and it must always decrease in an infinite alleles model (because it starts at 100%), when you enter starting allele frequencies there is a chance that random allele frequency shifts will be such that the heterozygosity actually increases. This is part of the stochasticity of Mendelian genetics. Averaged across many loci, or averaged across many iterations, you would not expect to see such an increase in heterozygosity.

Q:>  I am modelling a population with demographic data and allele frequency data generated from microsatellites. While reading the output gene diversity is showing different values inferred from allele frequency data. I would like to mainly understand, how vortex caliculates gene diversity from allele frequency data for the year 0 and so on...., Could you be please brief???  Submit Answer

      A:>  Being both brief and complete is not possible! Vortex simulates the Mendelian transmission of alleles through the generations (an approach referred to as a "gene drop"). Gene diversity and other genetic metrics (e.g., number of alleles, Fst, etc.) are then calculated for the living population each year using standard formulas for estimating these metrics from genotypic and allelic frequencies. I can only refer you to population genetics texts, as it would be beyond the scope of these FAQs and even the Vortex manual to provide all the details of the methods.

Q:>  While using genetic management option in vortex, will the file of allele frequencies alone calculated from microsatellite loci have an effect on the simulation???  Submit Answer

      A:>  Usually not. The option to enter allele frequencies is provided so that you can model how well genetic diversity at some loci is retained. However, it can affect the simulation if you make some demographic rates a function of the genotypes at the loci.

Q:>  Is there a way to specify that animals disperse only once carrying capacity has been reached?  Submit Answer

      A:>  Yes. Just enter for the optional Dispersal Modifier Function =D*(N>=K) This will set dispersal to 0 when N < K.

Q:>  How do you let one sex disperse earlier while keeping both sexes in the assesment?  Submit Answer

      A:>  Although the standard input only allows for the age of dispersal to be the same for the two sexes, there are two ways that you can make it sex-specific. First, you can enter a Dispersal Modifier function that includes sex, such as "=D*((S='M')OR(A>4)". This function would let males disperse at the ages specified, but let females disperse only after age 4. (You would modify this according to your needs.) Alternatively, you could enter a function of sex in the dispersal rate matrix, such as "=2*((S='M')OR(A>4)" to achieve 2% dispersal of males in the age range and females only if older than 4. This second method allows the sex-difference in dispersal ages to be set differently for different pairs of populations.

Q:>  What is error in gv states for while running vortex  Submit Answer

      A:>  It is hard to know without further information. Usually, this means that a function used to define the transition of a GS variable could not be calculated. For example, it may have tried to divide by 0 or take the log of a negative number. If you cannot determine what is wrong in your model (or if you think it may be somethnig wrong in the program), then send a bug report, with the xml project file that causes the error.
      A:>  As I observed is Vortex runs smooth with XP/Vista versions of Windows than with Windows-7

Q:>  Can allele frequency file format for vortex 10 be created by using any software???  Submit Answer

      A:>  Yes. The file should be a simple text file, with space, semi-colon, or tab delimiters. It can be created with NotePad or any text editor, or (especially if it is a big file) it can be created in Excel and then saved as a text file. However, it should not use commas as separators, because of problems that can cause for non-USA data formats.

Q:>  Please provide an example file of initial allele frequencies..., I have been trying different formats but could not be able to run the program  Submit Answer

      A:>  A sample allele frequency file has now been made available at Note that the newest version of the program (installation uploaded 11 Aug 2014)now allows comment lines to be inserted into the allele frequency file. (Otherwise, remove the comment lines from the sample file.) URL:
      A:>  Note also that if your computer uses non-American data formats (e.g., one half is 0,5 rather than 0.5), then in your allele frequency file you will probably need to use the comma as the decimal delimiter.

Q:>  When I type a function into the Function Editor window, the "Accept" button is greyed out and disabled, even though the editor says that the syntax is OK. Why won't it accept my function?  Submit Answer

      A:>  The reason that the Accept button on the function editor window was greyed out is that you must have entered that Function Editor window while your cursor wasn't currently on the data entry box. When you have clicked on a box that can accept a function, then when you enter the Function Editor you have the option to "Accept" that function (if its syntax is OK, as yours was) and it will be placed into the data box. But if the last place you clicked on the input screens wasn't a data entry box that can accept functions (e.g., you clicked on Notes), then you can still go to the Function Editor, but it won't allow you to Accept the function because it doesn't know into which input box to put the function. You can type (or cut and paste) the function directly into the appropriate input box, or you can go to that box before entering the Function Editor.

Q:>  I am modeling a bison population. I need the dominant and prime age males to do a disproportionate amount of breeding. Under Mate Monopolization I can use a function so that the 7-12 year olds have a higher probability of being in the breeding pool (minimum and maximum ages for breeding males is about 4-20). Is this a reasonable approach? However, within a cohort there are often dominant animals that do a disproportionate amount of breeding. I can use an Individual State Variable to tag individuals as dominant or subdominant, but where do I go from there? Its important that these "dominant" individuals retain that tag throughout their life as genetics is an import output for my project.  Submit Answer

Q:>  Just started migrating to VORTEX10 from version 9. My functions don't seem to work anymore, specifically, functions with population descriptors such as Y. When I use the Function Grapher in VORTEX10 it shows no response to the descriptors such as Y, N, or others. Are population descriptors working in VORTEX10?  Submit Answer

      A:>  To get the Function Grapher to display a plot against any variable, you need first to select that X-axis variable (from the dropdown box in the upper right) and then hit the "Plot" button. The population variables are working. (The submitter of the Question later discovered that he had an error in parentheses in his function -- and that is an easy mistake to make!)

Q:>  I work in IT at a University. We’ve had a request from one of our academics who’d like to teach using Vortex. Unfortunately we’re having difficulties deploying Vortex to a computer room (without manually installing one by one).  Submit Answer

      A:>  There is a “quiet” version of the installation that doesn’t require any user input (other than to start the msi), and it is available at A risk of using the quiet installation is that it will create and use the pre-defined default folders, and it may be that you would rather install the program elsewhere or set something different as the default working folder for projects. You could do one install from the normal installation msi, so that you see what are the default folder locations, and then – if all looks OK – do the rest of the installations from the quiet installation.

Q:>  Can Vortex take advantage of a multi-processor UNIX system to run multiple scenarios simultaneously on different processors?  Submit Answer

      A:>  The Vortex program itself cannot partition its scenarios among processors, but you can always start multiple instances of Vortex.exe and have each one run different scenarios. Windows could then run up to 8 Vortex's (I think) simultaneously, each using a different processor.

Q:>  Can vortex be used on Ubundu?  Submit Answer

      A:>  Yes, this is possible (at least in Ubuntu 12.04, 64 bit), just use "wine" to emulate windows. When I was doing this I had to install a certain windows file (dll?) (I do not remember which one but you will get an error message and if you google this error message you will get the answer!). The easiest way to install this file is by using "Winetricks" or "PlayOnLinux". But still you might experience some inconvenience using VORTEX in Ubuntu like a too small default font size in the plots or importing graphs to the "Project Report".
      A:>  Both Vortex 9.99 and Vortex 10.0 have specific Windows-only components. It means that they can only run under the Windows operating system. One solution I use is to install so-called emulator software on a Linux (Unix or Mac OS X) computer. The open source program VirtualBox is a good choice. You then install Windows in VirtualBox. Vortex 9.99 works fine with Windows XP and 2000. Version 10.0 seems to work fine too. Note that you need to download and install .NET software in Windows XP in order to run version 10.0. The WINE solution is already discussed in another answer

Q:>  If I install Vortex version 10 will my older vpj. files built up in Vortex 9.99 run in new version 10? If not, is it possible to have installed both versions of Vortex on one computer?  Submit Answer

      A:>  Usually, a vpj file created under version 9.99 will run also under version 10. This is very useful, because the user interface for making version 10 vpj files is not yet ready for distribution! However, if you use functions for input values, then there are some changes to the syntax that might require some modification to your functions. For example, in version 10, the order of precedence of operators follows common rules of arithmetic rather than being strictly left-to-right. (E.g., in version 9 functions: 3+2*2 = 10; whereas in version 10 that function evaluates to 7.) The changes from v9 are v10 are described in a Word document that is included with the version 10 installation. You can have both version 9 and version 10 installed on the same computer, although I would recommend that you install them into different program folders.

Q:>  Can this software be used in a computer lab at a University free of charge? If not, what are the licensing options for this product?  Submit Answer

      A:>  Yes, Vortex is distributed free-of-charge for any teaching, research, and conservation uses. (You can download it and the manual from .) Some universities have run into hassles loading Vortex on a network for use by students. It was compiled primarily for use on individual PCs, and there are no restrictions on installing it on multiple computers for student use. The problems that have arisen come from either university restrictions that don’t let students install software on lab computers (meaning that some lab administrator needs to do all the installations), or from restrictions set by the university network that limit into what folders students can store and manipulate files. Often, these problems can be bypassed by installing Vortex into its own folder on the C: drive (e.g., C:\Vortex) rather than within ProgramFiles, but it should work from any location as long as the program can create and edit files within the folder where it is placed and the folder(s) where students choose to store their Vortex projects. On some systems, this means that the program may need to be run in Administrator mode.

Q:>  Who paid for the development of Vortex?  Submit Answer

      A:>  The programming of Vortex was funded from the Chicago Zoological Society. Many of the ideas implemented into Vortex (and, indeed, the original idea to create Vortex) came from the IUCN/SSC Conservation Breeding Specialist Group.

Q:>  What changes have occurred between version 9 and version 10?  Submit Answer

      A:>  To see a short description of some of the new and changed features, go to the link. URL:
      A:>  An update to this answer: The most current version of "changes" document is always included in the Vortex 10 installation.

Q:>  Is Vortex version 10 ready for use?  Submit Answer

      A:>  Only in a very preliminary test version at this time. The simulation code is complete, and a simple user interface allows version 9 projects to be run with this new version 10 code. The full GUI for version 10 input and output will be available soon.
      A:>  And we expect that the full release of version 10 will occur by about June 2013. Even so, at the initial release we know that there will still be many bugs, and we will appreciate careful testing and reports of any bugs encountered.

Q:>  Is the code for Vortex available as open-source?  Submit Answer

      A:>  No. The community of people with the expertise in both population viability analyses and C# programming is too small to support an active open-source development of the tool. Moreover, the program is used globally for management of endangered populations, and the organizations using Vortex need to know that there is quality control of the distributed version. Resources are not available to support the testing and verification of changes to code made by a possible community of contributors. When researchers need to know exactly how Vortex is making its calculations, the code can be provided by special request.

Q:>  Can Vortex be used on a Mac?  Submit Answer

      A:>  Vortex was developed for Windows-based PCs. It can run on a Mac that is running a version of Windows OS or a Windows emulator. The details of how to do this will need to be provided by some Mac-user. (Anyone want to offer further information?)
      A:>  I successfully run Vortex on a late 2013 Macbook Pro Retina under Windows 7 virtual machine in the Parallels 10 emulation software. The only issue I had to resolve is the screen resolution to best display both graphics and tabular data. Since my Macbook Pro uses a 2880x1800 Retina display, it is important to set the Parallels video display resolution to 'Scaled', then in Windows I set the screen resolution to 1440x900 (half the native Retina resolution). This will ensure that tables of values in the inputs and outputs will have the correct vertical spacing. If not set this way, the individual cells of the tables will be half height, and nearly impossible to read without a cut-and-paste to another software such as Excel. Ironically, the display graphics look better under full 2880x1800 resolution, but the reduced resolution of 1440x900 is the best balance for everything concerned. I also ran Vortex on an earlier version of the MacBook Pro (also Windows 7 emulated under Parallels) without Retina display (native 1920x1200) and no such resetting of resolutions was necessary; in fact, the screen output was even clearer under the pre-Retina display since no rescaling was necessary. Other than that, I have had no problems running Vortex on Mac. Under Parallels Coherence mode, all files can be easily moved from Mac side to Windows side with no apparent difficulties. I have not tested whether Vortex runs faster or slower under emulation, so can offer no advice there.


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