How long does it take to use Condatis, and what resources does it need?
Condatis is quick to use once the fundamentals are grasped; some of the calculations e.g. backwards optimisation, can take up a lot of processing time for large or high resolution rasters but this can be running in the background with no user input. Preparation of habitat rasters is likely to take more time, but this will depend on the software used and GIS expertise of the user
 

Do I need to be a GIS expert to use Condatis?
The condatis software itself requires no expertise in GIS. Preparation of the habitat layer raster maps, and merging exported maps onto other maps, may require GIS expertise but this will depend on the software used to create these layers
 

Will Condatis run on my computer or laptop?
Condatis software runs on Windows and Unix-like operating systems such as Mac OS X and Linux so should run on most pc’s or laptops without problems. Full instructions for installation are found on the downloads page of this website
 

Will this software run on 32bit machines?
There is a version available which will run on 32bit  machines, but the size of file you will be able to process will be reduced. Download 
 

Do I need to install Condatis on my computer, as our organisations policies will not allow this?
Condatis isn’t software that you install on your computer. You just unpack the zip file somewhere that you have access to (home folder for example) and run it by clicking the condatis.exe file. This was done because some organisations do not let you install software. So as long as your Condatis is unpacked in one of your own folders it should work
 

Not all of the Condatis files unzip on my computer, what can I do?
Windows Explorer does not always extract all the files required for Condatis to run properly. It is recommended that alternative software is used to unzip the files
 

Why do I have problems getting the program to start on my Windows computer?
Condatis has run on Windows versions from XP to 8. The requirement is to have the Visual C++ runtime installed, which can be downloaded from Microsoft. There have been problems on older installations of Windows that have not had updates installed. For example a Windows 7 installation from 3 or so  years ago that never had updates applied. The majority of Windows software requires the VC++ runtime, and most people already have it on their computers
 

Do I need a registration code to use Condatis?
When you first start Condatis it will present you with a registration box. You fill out and submit the form (ensure you have typed your email address correctly) and a registration code will be generated for you and sent by email. This is then entered in to Condatis (on the same registration box) to register your copy. You can also just close the registration box and continue to the application without registering, but the box will reappear every time you start Condatis until you register. An advantage of registering is that we can keep you up to date with Condatis news and updates
 

How do you get data out from Condatis for use in other mapping software?
Click on the Export menu bar, select which view you wish to export, and press ok. Condatis will export into a folder called Exports as a GeoTiff file which ARCGIS and most other GIS programs will be able to open
 

Can you use MAPINFO to provide the base habitat maps?
Condatis requires Raster maps for the habitat layer map, MAPINFO can provide these if the Virtual Mapper add on is used, or using MAPINFO Pro Advanced
 

How do I prepare a baseline habitat data map?
This will depend on your GIS software. Condatis will accept ESRI Grid format or TIFF files, most software will allow export to one of those formats. If using multiple layers the dimensions of each map layer should match. Instructions in doing this for ARCGIS can be found in the Condatis manual. Downloads
 

How do I choose what habitat to use as my base habitat layer?
Choice of habitat is very important as it provides the basic data Condatis needs. It should be matched to the specific habitat type, species or groups of species which are your conservation priority. Using several types of habitat together will show you routes applicable for generalist species which utilise all these habitats. Habitat needs to be manipulated in an appropriate GIS program to filter out unsuitable habitat. NB Condatis is designed to look at flow across landscapes which may require habitat being included which may be outside of nominal area boundaries to achieve valid results
 

Does the data you use affect the outcome?
Yes, the more accurate the habitat data is the more reliable the results will be. It is recommended to use at least phase 1 habitat data where possible. Including information like proportion of habitat present or area covered by habitat within each cell would add further precision and flexibility
 

What happens if my habitat data is imperfect?
Condatis is only as good as the data allows. Where habitat data is missing it will treat the space as a gap and attempt to jump it if dispersal distance allows, this means that even with missing data results are achievable. If habitat data is incorrect then the flow results and bottlenecks are likely to be incorrect as they will be using habitat cells which do not exist. In both cases, as missing habitat is filled in or more accurate habitat is identified, Condatis is quick enough to use that the analysis can be re-run swiftly and the results of both analyses can be compared
 

How does the software deal with gaps in the habitat i.e null values?
Condatis regards gaps or null values as not containing suitable habitat, and will attempt to jump across this if dispersal distance allows. As gaps are filled in the updated habitat raster can be imported into Condatis and the scenario re-run
 

Not all of each cell is suitable habitat, will this affect the results?
Depending on map resolution, individual cells may have a number of different habitats within them. When creating the raster file the amount of habitat within each cell can be recorded as a percentage, proportion, area or presence/absence value. The amount of useable habitat will be reflected in the conductance; more habitat increases the probability of immigration and production of emigrants
 

How big can my habitat map be?
Any size. The only limit is the processing power of your computer. Only active habitat cells affect performance (empty cells are not counted) and Condatis can process up to 20,000 of these before processing time becomes lengthy on a standard desktop computer. So a landscape map with relatively few scattered habitat patches can be much larger in area than one with frequent, densely packed habitat (but see resolution)
 

How much detail can my habitat map show?
Any amount of detail. The only limit is the processing power of your computer. Only active habitat cells affect performance(empty cells are not counted) and Condatis can process up to 20,000 of these before  processing time becomes lengthy on a standard desktop computer. So a landscape map with relatively few scattered habitat patches can have much more fine detail than one with frequent, densely packed habitat (but see resolution)
 

What resolution do I use on my baseline habitat map?
This is a trade off between detail of results and time spent processing. The best resolution will depend on the size of area being analysed e.g. several previous analyses have used 1km squares but larger than county sized areas may be more efficiently analysed at 2km resolution. The speed of the calculations depend on the number of cells containing habitat; a large area containing scattered fragments of habitat can use  quite a fine resolution, whereas an area containing a lot of useable habitat will need to be much smaller in extent or created at coarser resolution
 

How do I create a source and target raster?
This will depend on your GIS software. Condatis will accept ESRI Grid format or TIFF files, most software will allow export to one of those formats. Cells selected need to be denoted with specific integer values, ideally 1 for source cells and 2 for target cells. This raster file can then be imported into Condatis using the From File function in the add source and target menu. NB you should not create overlap between source and target cells and habitat cells
 

Why can't everywhere be source and target?
Condatis shows the flow of species across the landscape, and the majority of the flow will be concentrated in the shortest route between any source cell and any target cell. Making all suitable habitat cells as source and target will not show any flow
 

Source and Target - where should these be located?
Source and target are fundamental to the analysis and results can change dramatically when these are changed.  If you are looking at improving resilience to climate change then a South to North or Lowland to Upland direction of flow would be appropriate with source along south or lowland edge and target opposite. More generally, if you are interested in the functions of stepping stones you would chose the source and target to be two large ‘core’ patches which are distant from one another
 

How far apart must the source and target be?
Condatis assumes species absolutely have to colonise and reproduce in the intermediate patches – that there is no way one individual could traverse straight from the source to the target. Therefore to achieve reasonable results the distance between the source and target should be a minimum of ten times the average dispersal distance of the species
 

Source and Target - does size matter?
Condatis shows the flow of species across the landscape, and the majority of the flow will be concentrated in the shortest route between any source cell and any target cell. Having a large source / target area may make the results difficult to interpret but may be appropriate if you want to enable any flow in a general direction. Having too small a source / target may result in a restricted area of flow and show little of the effect in the wider landscape
 

Why would I click on Expand area in the assign source and target box?
If you leave this unchecked the source and target will be within the raster map so will show flow from the habitat present within the source edge to the habitat present within the target edge. If checked the source and target will be outside the raster map so will show flow across the whole range. This will affect speed of flow and likely bottlenecks. If there are habitat cells within the source / target zone then these cells will be deleted from the source / target. It is recommended that the box is checked unless little or no habitat is present within the source / target zones
 

What is the correct width to select in the assign source and target box?
The source is essentially created cells of habitat occupied at the start of the analysis. A wider source creates a larger pool of potential emigrants initially which may reduce the overall time of colonisation. The default width of 3 cells is recommended, but if the distance between source and target is small a narrower width may be more appropriate
 

Can Condatis be used to model colonisation of habitats for specific species?
Yes, it is possible to adjust parameters such as dispersal distance, rate of reproduction, selection of appropriate habitat and habitat extent to allow species specific outcomes to be tested where such information is known
 

What is the dispersal kernel parameter and what dispersal distance should I use?
The dispersal distance is the mean dispersal distance in km per generation of a species. This can be set for specific species where known, or as a general level to replicate dispersal patterns of short, medium and long distance dispersers. As a rule of thumb 2km or less will show movement of poor dispersers, 10km or more highly mobile dispersers. For less species specific analysis it may be necessary to run scenarios with several distances to see the how the flow may vary across a range of dispersal distances. Whichever distance is used, Condatis allows the possibility of dispersal over any distance but calculates the probability of this using a negative exponential distribution
 

Why do I get very odd results when I set a long dispersal parameter?
Condatis assumes species absolutely have to colonise and reproduce in the intermediate patches – that there is no way one individual could traverse straight from the source to the target. If the dispersal parameter is higher than the distance between source and target then effectively no range shift is required – either the dispersal distance needs reducing or the distance between source and target needs enlarging for Condatis to give meaningful results
 

What is the R parameter and what Rate of Reproduction (R) should I use?
R is the reproductive rate of the species of interest, where known, or a general level to replicate reproductive rates of slow, medium and fast reproducers. As a rule of thumb 10 or less will show movement of low fecundity species, 100 or more high fecundity species. This is effectively the number of emigrants leaving 1km² of suitable habitat every generation. As the speed of colonisation (and therefore time taken) is simply the flow results multiplied by R the speed of colonisation for any rate of reproduction can be easily calculated once the initial scenario has been run
 

How do I interpret Power?
Power is used to identify bottlenecks and is based on the flow between one cell and another combined with the distance between them. Broadly it can be considered the strain that each cell link is under. Condatis ranks the power of each link and the bottleneck threshold function can be used to show the links of highest power / strain
 

What bottlenecks threshold should I use?
The bottleneck threshold filters out link power across the habitat where 100% includes all links, 10% filters all but 10% highest power links. Adjust the figure until few links are left to see locations with the greatest potential for increasing flow
 

What does the progress map mean?
This shows the order in which cells are likely to be colonised over time, with the source being 1 and the target being 0 (the source representing 1 volt). Large areas of the same colour show linked up habitat where progress is relatively rapid and consistent. Small areas or strips of colours show gaps in the landscape where a longer period of time is required for colonisation
 

What does the isolated areas map mean?
This shows the discontinuities across the landscape, with the source being 1 and the target being 0 (the source representing 1 volt). Each layer represents a fairly well connected zone, changes between layers represent the seven biggest progress jumps. if you can connect the layers better, the landscape flow will increase
 

What does the speed figure in the solution box mean?
This is the overall flow speed across the landscape between the designated source and target for the species and landscape being considered. The higher the speed the greater the connectivity of the landscape. This is directly comparable across scenarios
 

What does the time figure in the solution box mean?
This is the number of generations (steps) a species needs to travel from source to target. If the number of generations per year is known this figure can be equated to an actual time period for a species
 

How do I interpret the resistance to extinction / metapopulation capacity result?
Resistance to extinction (Metapopulation capacity) is a measure of how easily species could survive in the landscape as metapopulations, and is based on the spatial arrangements of habitat. This is calculated for species which could only just survive due to low fecundity or high extinction rate, and a low score means low resistance to extinction, a high score means high resistance (i.e. more likely to survive)
 

Can I see what the effect of adding habitat in a particular location will be?
Yes, this can be done in two ways. Either use the inbuilt edit feature to add the habitat cell, or use another program to modify your habitat raster. It’s recommended to do this on a copy of your original scenario (but visible within the same project) as then once flow and bottlenecks have been re-run the original and the added habitat scenarios can be directly compared
 

What is backwards optimisation?
This is a method by which proposed restoration locations currently with no suitable habitat are tested in turn to rank their connectivity with suitable habitat. This will create a map of the locations which have the biggest potential effect on flow across the landscape and which therefore would be the best locations of those available to create new habitat. This would be used where constraints mean only a selected number of locations are likely to be viable for restoration effort
 

Where can I get further help?
A Condatis User manual is available for download @ downloads. A user forum can be found @ Discussion Forum or email your query to econets@liv.ac.uk
 

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