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1. This applies to both the dM and varM values calculated by Conefor as follows the total dlIC varliC dPC and varPC values will also be presented in addition to the partitioned fraction values dIIC dlICintra dllC flux diIlCconnector varlIC varlICintra varlICflux varlIlCconnector aPC dPCintra dPCflux dPCconnector varPC varPCintra varPC flux varPCconnector The three fractions will be calculated both for the existing nodes that can be lost standard analysis node removal and for the nodes that may be added in the landscape as a result of habitat restoration measures see option nodes to add in manual for version 2 2 While a habitat patch can contribute to connectivity through all these three fractions links corridors connectors can only contribute through the connector fraction see Saura and Rubio 2010 for details Baranyi et al 2011 have shown through cluster analysis and multidimensional scaling that the intra flux and connector fractions provide a non redundant and complementary information on the importance of a patch in a landscape network and that they capture most of the variability in patch conservation priorities that would derive from using a much larger set of connectivity metrics see figure 5 in that study perhaps complemented by a centrality metric see section 10 below The only exception for the dM and varM calculations in the node importance file as explained above are the va2. C and EC PC values respectively EC IIC and EC PC maintain all the desirable properties and good prioritization abilities of IIC and PC but have the following advantages as an overall index value compared to IIC and PC a they avoid the very low metric values that might be obtained for C and PC when the amount of habitat is very small compared to the total extent of the analyzed landscape since EC I IC and EC PC will not be smaller than the largest attribute e g habitat area for the patches in the landscape b EC IIC and EC PC have the same units as the attributes of the nodes which facilitates the interpretation and understanding of the resultant values c EC IIC and EC PC avoid the need of specifying any A value as is needed for IIC and PC which in some cases might not be straightforward and might be to some degree arbitrary and more importantly d the relative variation in EC IIC or EC PC after a particular spatial change or set of changes in the landscape can be directly compared with the variation in the total amount of habitat area in the landscape or any other considered node attribute after the same change with an easy interpretation and additional insights that can be gained from that comparison Saura et al 2011a 2011b This latter property makes EC IIC and EC PC quite convenient for quantifying changes in landscape connectivity and comparing them with the changes in the amount of habitat in the landscap
3. Carranza et al 2012 Landscape Ecology 27 281 290 Rubio et al in press Forest Systems The importance of a link for maintaining or improving connectivity is calculated in the same way as for the nodes see section 9 i e as the relative dM or absolute varM variation in the value of a given connectivity metric M after a certain change affecting one of the links in the landscape Note that links can only contribute to habitat connectivity and availability as measured by IIC and PC through the connector fraction Since a link is defined as a connecting element that contains no habitat area a link cannot contribute through the intra fraction For the same reason a link cannot be the final permanent destination for any dispersal flux Therefore both the intra and the flux fractions will be by definition equal to zero for any link in the landscape If a connecting element contains some habitat area this should be modeled as a node in the graph and its value as a connecting element or stepping stone will be anyway quantified through the connector fraction of the IIC or PC metrics together with its potential contribution through the intra and flux fractions The connector values for links can be directly compared with the connector values for nodes See Saura and Rubio 2010 for details In summary even when Conefor will express the results of the link importance values as d C varliC dPC and varPC depending on the metric and type of res
4. Conefor will calculate and show the dM values for each node and for each of the indices selected for analysis If you select the option Show vars Conefor will calculate and show the varM values for each node and for each of the indices selected for analysis You can also select both Show deltas and Show vars and then Conefor will calculate and show both dM and varM values Note however that this may generate a large number of columns in the node importance file and that the ranking of habitat patches nodes by their contribution to landscape connectivity is the same according to either dM or varM since both variables are proportional as given by varM dM M 100 Although in some cases dM values are easier to interpret this will depend on the selected indices and user preferences In some cases if the landscape network is very large dM values can be very low it is hard for a single node to have a large relative importance for connectivity if the network is made up by many thousands of nodes and hard to handle eventually indistinguishable from zero In these cases varM values might be a preferable option The index M can correspond to any of the following connectivity metrics included in Conefor 2 6 NL NC H LCP Chum F AWF PCnum Note that in Conefor the IC and PCrum values numerators of the IIC and PC metrics respectively see equations below are those used for computing the dlIC dPC varlIC and varPC values
5. PC and as varBC IIC and varBC PC Conefor 2 6 user manual The centrality metrics are calculated in the intact landscape and do not consider how the flows might change as a consequence of losing a particular patch Unlike the connector fraction of the IIC and PC metrics they do not deliver estimates of the impacts of a patch removal in terms of connectivity loss The pairs of values dBC IIC and dilCconnector for a given node k should be interpreted in the following way exactly the same applies to the pairs of values varBC IIC and varllCconnector dBC PC and dPCconnector and varBC PC and varPCconnector dBC IIC quantifies the amount of fluxes that are expected to go through k in the intact landscape the undisturbed landscape in which no habitat patch has been lost because k is part of the best shortest or most probable paths between other habitat patches However dBC IIC does not quantify how much the connectivity between other habitat areas depends on the presence of k in the landscape i e it does not measure how irreplaceable k is as a connecting element between other habitat areas This latter aspect is what is measured by d Cconnector It might happen that even if k is considerably involved in the fluxes occurring in the current landscape high dBC IIC the loss of k does not have a large impact in the connectivity between the other habitat areas low d iCconnector much smaller than dB IIC because the connectivity that was p
6. Science and Innovation through projects AGL2009 07140 and REN2003 01628 Sensinode 1 0 LandGraphs package was developed by Dean Urban Duke University 3 Scope of this manual This user manual only explains those new features that have been implemented in Conefor 2 6 and were not included in version 2 2 All the other functionalities and the basic functioning and instructions for this software package are the same as for version 2 2 See the manual of version 2 2 attached for the rest of most of the information on how to use Conefor Later on we plan to produce a single updated manual integrating the contents of these two manuals Check the Conefor website www conefor org for updates In that website you can also subscribe to an email list that will automatically notify you of any relevant news regarding Conefor 4 Key new features in version 2 6 compared to version 2 2 e The three fractions of the dPC and dlIC indices intra flux connector are computed see section 9 in addition to the total dPC dlIC values already provided by version 2 2 This allows separately evaluating the different ways in which habitat patches can contribute to habitat connectivity and availability in the landscape i e their different roles as connectivity providers Saura and Rubio 2010 e The importance for connectivity of individual links sensilink can be computed in addition to the importance of nodes sensinode that was already provided by versi
7. This makes unnecessary specifying any A value for calculating the node importances according to IIC or PC Even if the IIC and PC values for a particular A were used instead of IC OF PC ym to calculate the node importance values d iC and dPC would be exactly the same as those obtained using Cnum or PCnum respectively This is because A is a constant that does not vary by the removal of any node or link 5 Conefor 2 6 user manual from the landscape If you wish to obtain the varlIC or varPC values as they would result from using the IIC and PC values for a given A value you just need to divide the varlIC or varPC values that are calculated by Conefor 2 6 by A aj AG a Gj a ahid Seat gt a IIC e a Crum 1 nlij A A i 1 j 1 n n PC Dai a ph PCaum gt aiaj pi PC mum Bij G u i 1 j L L See manual for version 2 2 and the two related papers Pascual Hortal and Saura 2006 Saura and Pascual Hortal 2007 for further details on these metrics and formulas As shown by Saura and Rubio 2010 the importance values for the IIC and PC metrics can be partitioned in three different fractions intra flux connector considering the different ways in which a habitat patch node or link can contribute to overall habitat connectivity and availability in the landscape Conefor 2 6 will automatically calculate for each node the values of these three fractions separately whenever IIC and or PC are selected for analysis
8. connection file is a distance file when selecting BC and PC you will need to provide a distance threshold that will be used for calculating BC as for any other binary connectivity metric and a pair of probability distance values that will be used for calculating PC and BC PC The distance threshold value specified in the box for the binary indices does not affect at all the calculations for BC PC which are just based on the probability distance values specified for the probabilistic indices In the same way the calculations for BC are not at all affected by the probability distance values that are specified for the probabilistic indices The same applies if your input connection file is a probability file In this case a probability threshold will be requested for calculating BC but this will not affect at all the calculations for PC or BC PC which will run using directly the probability values in the connection file without requesting any additional distance or probability value in the probabilistic indices box See the manual for version 2 2 if you are not familiar with these latter considerations If you wish to calculate BC and PC but not BC PC then you should run Conefor two times one with only BC selected and the other with only PC selected 10 5 How do the generalized Betweenness Centrality metrics relate to the connector fraction of IIC and PC How should this relationship be interpreted If you select Show deltas the BC IIC an
9. the processing feasible In summary you can change to the standard precision only if either you do not need the separated fraction values i e you will just use the overall index value M or the total dM or varM value for each node or if your computer is not able to process the graph with the more demanding high precision mode 16 Other comments related to Conefor 2 6 The option to save DBF files is disabled in this new version but you may easily convert the text files the output format for the results in Conefor into DBF format with any other external software if needed Almost any software package GIS spreadsheet statistical etc is able to directly read the text files as produced by Conefor ArcGIS is able to directly open and work with them as tables as long as each column has an appropriate header some of the files produced by Conefor already include these headers for each column for the others you can easily add them in a new first line of text with any text editor In the particular case of ArcGIS some characters like parenthesis are not admitted in the names of the column headers this means that you should manually change the headers for the BC IIC or BC PC metrics in the node importance file e g to BC_IIC and BC_PC if this metrics have been selected for computation before you can open this result file in ArcGIS Finally in the PC gt More gt PC setup window in the Conefor interface you may notice that a new
10. the USA and from Brazil to Finland You can get more details on these applications and perhaps inspiration on the way you can use Conefor for the purposes of your own case study from the references listed in http www conefor org applications html and in the map of Conefor applications available here 19 Empirical support Several studies have evaluated and demonstrated the ability of the new habitat availability reachability metrics implemented in Conefor IIC PC etc to explain or predict ecological processes related to landscape connectivity including species distributions colonization events or genetic diversity patterns at the landscape scale Most of these studies have been performed by other research groups and institutions different from the one that developed Conefor and the metrics there implemented which provides an independent assessment and empirical support to these quantitative developments and metrics Some of these studies have evaluated the ability of IIC or PC to explain ecological processes and have compared it with the performance of other existing connectivity metrics When this has been done C or PC have been shown to outperform the other analyzed connectivity metrics by presenting a stronger relationship with the analyzed ecological processes and empirical data You can find more details on this empirical support and validation at http www conefor org empirical html 20 References For the C and PC metric
11. user interface for Conefor 2 6 Most of the new features in Conefor 2 6 are located within the red boxes indicated in the image below The rest is exactly as in version 2 2 The numbers next to each red box indicate in which section of this user manual you can find the description of that particular option or functionality See also section 12 for an additional new feature not indicated graphically in this image Conefor 2 6 NewProject1 txt Project Execution Results Help Node file C Example Nodes txt wel 7 There are nodes to add Connection file C Example Distances txt wel Full Partial Connection type Distances Connectivity indices Binary indices NL IV NC ite B V PC more gt gt gt 0 M LCP W IC M AWF Distance threshold 2250 Distance 2250 corresponds to probability 14 Link importances V Show deltas I Link Removal I Show vars Link Improvement Link Change Reduce calculations C Precision High C Standard Execution Events Processed indices NC IIC PC Indices processing started at 10 56 48 AM 18 4 2012 Processing time for indices v E View node importances 100 completed Conefor 2 6 user manual 9 Calculating the node importance values including the fractions of IIC or PC intra flux connector Unless you specify the only overall index option see section 11 below Conefor will calculate the importance of every node as the decrease in the connectivity met
12. CONEFOR 2 6 User manual Saura amp Torn April 2012 Quantifying the importance of habitat patches and links for maintaining or enhancing landscape connectivity through spatial graphs and habitat availability reachability metrics Table of contents De WINE tAS COMCTORS tnaa desc ohata a a an coca Ses dusield aa sacedan lt odetn sa A a aat ea aaa 1 2 AUH ORS ceii aeinn sya ciaatest Uae bests i i E E E AA EER A ai e 2 e osole KoI MAEA TALS E EE E E E E E T ET E E 2 4 Key new features in version 2 6 compared tO version 2 2 ccessssccccecessessneeceeeeecesseseneseeeessessessaeees 2 5 Installation operating system and computer configuration sssssssesssssssssereesrssssesereesrssssesereesnsseo 3 6 CONGITIONS OF USE ha ia Dass hack a a ae a a aa oe aeaa 3 7 Questions or further informations seritirs nesi ieeii eiia ie i aea ea EE a a ia ia aaaeaii 3 8 An overview of the new features in the graphical user interface for Conefor 2 6 cccsesssceeeeeees 4 9 Calculating node importance values including the fractions of IIC or PC intra flux connector 5 10 Generalized Betweenness Centrality Metrics ccccccsssscececesessssseaeeeceessesseseaeeeeeesseesssaeeeesensesees 7 11 Calculating only the overall index values for the entire lANdSCAPEC ccsesseccceceeessestaeeeeeeeseeses 10 12 Calculating the Equivalent Connectivity EC for the entire landscape overall index values 11 13 Calculatin
13. ak links with large distances or small probabilities will get dM 0 and varM 0 because they have not been evaluated in the analysis this does not mean that they would be zero if the Reduce calculations option would not have been selected 14 4 Link change how user defined changes in the links translate in connectivity gains or losses This is the most powerful and flexible modality for link importance analysis It however requires additional input information to be provided by the user compared to the link removal and link improvement options If the option Link change is selected Conefor will require the connection file to have four columns instead of three as in the usual case in fact this is the only processing option in which the connection file needs to have four instead of three columns The first three columns are the same as in any connection file for Conefor ID of node i ID of node j and a value typically some form of distance or a direct dispersal probability p characterizing the connection between nodes i and j in the initial landscape see manual for version 2 2 for further details The fourth column required by the Link change option will also contain a value characterizing the connection between nodes i and j but this value will correspond to the new distance or direct dispersal probability between nodes i and j that would result in a given change scenario This value in the fourth column will be in general d
14. alue after that change addition Master This may result in a connectivity gain as measured by metric M case in which dM lt 0 and varM lt 0 Note that the relative and absolute variations of the IIC and PC metrics dM and varM will have negative values in this case because Mafter is higher than M see the formula for dM and varM in section 9 but in fact these negative values mean that connectivity has improved Obviously for those pairs of patches that were already linked in the initial landscape the connectivity cannot increase by adding a link that in fact already existed and therefore dM 0 and varM 0 In the probabilistic connection model the one that applies for PC Conefor will calculate the potential positive impacts of improving as much as possible the direct connection link between each pair of patches only one at a time In this probabilistic model this translates in assigning a p 1 to each pair of patches which means that the strength or frequency of use of the direct connection between i and j as quantified by p will be improved for all the pairs of patches except for those that already had p 1 in the initial landscape For those pairs of patches with p 1 in the initial landscape the result will necessarily be dM 0 and varM 0 For the rest the increase in the p value for each link may result although not necessarily in an improvement in connectivity as quantified by dM or varM as said above such improvement will corres
15. ated using a different approach procedure than for the others 10 3 Which is the difference between the classical BC and the generalized BC IIC and BC PC metrics BC only considers the number of shortest paths between all pair of patches that go through a particular node regardless of the area or attributes of the patches being connected and of the length or strength of those paths BC IIC and BC PC however take into account the area or any other attribute of the patches that are being connected through a particular node considering more central those nodes that serve as stepping stones between large and high quality patches than those that sit in between patches with scarce or poor habitat resources BC IIC also takes into account the length number of links of the paths between patches in which a particular node is involved longer paths are considered less feasible for conducting effective movements and therefore they are given less weight in the centrality calculations Similarly BC PC takes into account the probability of movement through a particular path maximum product probability p ip see Pascual Hortal and Saura 2007 so that those paths with higher p j are given more weight in the centrality calculations See Bodin and Saura 2010 for further details Note that BC IIC and BC PC are the most computationally intensive of all the metrics implemented in Conefor You should therefore be cautious when trying to calculate the
16. d BC PC values will be scaled in the same way as for dlIC and aPC dllCconnector and dPCconnector and the resultant values for each node will be shown in two columns with names dBC I C and dBC PC In this case dBC IIC diiCconnector and dBC PC dPCconnector Note however that the names dBC IIC and dBC PC just indicate that the values are directly comparable with those for d iCconnector and dPCconnector It does not mean that the dBC IIC and dBC PC values are calculated as the relative variation in any connectivity metric value following any patch removal procedure See Bodin and Saura 2010 for details and equations If you select Show vars the BC IIC and BC PC values will be scaled in the same way as for varlIC and varPC varllCconnector and varPCconnector and the resultant values for each node will be shown in two columns with names varBC IIC and varBC PC In this case varBC IIC varllCconnector and varBC PC varPCconnector Note however that the names varBC IIC and varBC PC just indicate that the values are directly comparable with those for varllCconnector and varPCconnector It does not mean that dBC IIC and dBC PC values are calculated as the absolute variation in any connectivity metric value following any patch removal procedure If you select both Show deltas and Show vars then the values for BC IIC and BC PC in the node importance file will be respectively scaled and shown both as dBC I C and dBC
17. e as described in Saura et al 2011a 2011b See figure 1 in Saura et al 2011a and figure 1 in Saura et al 2011b 13 Calculating the importance only for the added nodes When the option Only added nodes is selected Conefor will make the calculations of the dM or varM values only for the potential nodes that may be added in the landscape as a result of potential habitat restoration actions that may improve connectivity and not for the nodes that already exist 11 Conefor 2 6 user manual in it the impact on connectivity of their potential loss will not be evaluated Selecting Only nodes to add will also deactivate any of the options for link importance analysis This option Only added nodes is active only when the option There are nodes to add has been previously selected in the box for the node file When There are nodes to add has been selected Conefor will expect a node file with three columns see section 4 2 in the manual for version 2 2 and will in general calculate a the dM or varM values representing the connectivity loss that would be caused by the removal of each of the nodes that exist in the current initial landscape and b the dM or varM values representing the connectivity improvement that would occur thanks to the addition of new nodes in the landscape as resulting from habitat restoration measures see manual for version 2 2 for details If the option Only added nodes is selec
18. e content in Baranyi et al 2011 11 Calculating only the overall index values for the entire landscape The option Only overall index first option in the Mode box should be selected when you are only interested in obtaining the overall index values for the whole landscape M and not in the importance values for each individual node or link dM or varM This option allows the user to save a lot of processing time when the interest is only in the M value This is because the overall index value M is much faster to compute than the dM or varM values for every node Obtaining M requires just one calculation of the metric value while obtaining dM or varM requires n additional calculations of the metric value one for each node where n is the total number of nodes in the landscape Much more calculations of the metric value in general n n 1 2 are required for obtaining dM or varM if any of the link importance analysis options if selected see section 14 below Obviously if the Only overall index is selected the dM or varM values node or link importance files will not be calculated As stated in the previous section the results for the overall index values 10 Conefor 2 6 user manual will not contain any value for the Betweenness Centrality metrics even if these have been selected for calculation 12 Calculating the Equivalent Connectivity EC for the entire landscape overall index values If you compute IIC o
19. e the same results as in the Link removal option while setting all the values in the fourth column to one will provide the same results as in the Link improvement option 16 Conefor 2 6 user manual The Reduce calculations option does not apply to the Link change analysis it only affects the Link removal and Link improvement modalities 15 Precision of the calculations high or standard The precision in the calculation of the values that Conefor will produce as an output can be set to either High or Standard In version 2 2 the standard precision was used no choice was possible in that version and that was fine for the applications for which that version was intended to be used However when the three fractions intra flux connector of IIC and PC are to be computed separately as provided in this new version a higher precision is advisable to provide more accurate results for these three fractions especially in large graphs habitat networks Therefore the high precision is the default in this new version The high precision will consume more RAM and require a slightly higher processing time than the standard precision depending on the size of the network and on the computer characteristics but this should not make a significant difference for most of the users unless your network is so large and or your RAM memory so small that you are forced to use the standard precision to make
20. g the importance only for the added NoOdeS cccseessssececececesseseaececeesseesesnsaeeeeeesseeees 11 14 Calculating link importance values for different modalities removal improvement change 12 15 Precision of the calculations high or Standard ccccccccccssssccecsscececssssececssssececsssseeessssaeesesssaeess 17 16 Other comments related to ConefOr 2 6 00 eecceesceceeececeeeeeesaeeeeaaeceeeeeesaeeeeaaeseeaeeseeeeesaeeneaaeseeeeeees 17 17 GIS EXtensiOns s soos ck ad Slt aaah Ma eae kA Bae tee oe wees 17 CI APPllCAti ONS srexesccie caves eaa chee aa a a oe tadendet incu a a a aaa 18 19 Empinical SUPPO neoan sanie re ene EAEE E TAA EE EAEE A EE E A E EE EEE AREO Aa 18 P E EE E A EEEE E E E 18 1 What is Conefor Conefor is a software package that allows quantifying the importance of habitat areas and links for the maintenance or improvement of landscape connectivity as well as evaluating the impact of habitat and land use changes on connectivity It is conceived as a tool for decision making support in conservation and landscape planning through the identification and prioritization of critical sites for ecological connectivity Conefor includes new functional connectivity indices integral index of connectivity IIC probability of connectivity PC that have been shown to present an improved performance compared to other existing indices and to be particularly suited for landscape conservation planning and chan
21. ge monitoring applications Pascual Hortal and Saura 2006 Saura and Pascual Hortal 2007 Saura and Rubio 2010 Saura et al 2011a These indices are based on spatial graphs and on the concept of measuring habitat availability reachability at the landscape scale This concept consists in Conefor 2 6 user manual considering a habitat patch itself as a space where connectivity occurs integrating the connected resources existing within the patches intrapatch connectivity with the resources made available by reachable through the connections with other habitat patches in the landscape interpatch connectivity In this way connectivity is conceived and measured as that property of the landscape that determines the amount of reachable habitat in the landscape no matter if such reachable habitat comes from big and or high quality habitat patches themselves intrapatch connectivity from strong connections between different patches interpatch connectivity or more frequently from a combination of both 2 Authors Conefor 2 6 has been developed by Santiago Saura and Josep Torn at Universidad Polit cnica de Madrid as an evolution of the previous 2 2 version Saura and Torn 2009 See www conefor org for further details and section 20 for appropriate references Conefor Sensinode 2 2 released in June 2007 was developed by the same authors at University of Lleida Funding for developing Conefor has been provided by the Spanish Ministry of
22. h Download 1 short version as published on paper Download 2 expanded version as available only online at http www revistamontes net For the generalized Betweenness Centrality metrics BC IIC and BC PC Bodin O amp Saura S 2010 Ranking individual habitat patches as connectivity providers integrating network analysis and patch removal experiments Ecological Modelling 221 2393 2405 Download For the complete non redundant and multifaceted view provided by the C or PC related fractions or metrics Baranyi G Saura S Podani J amp Jordan F 2011 Contribution of habitat patches to network connectivity redundancy and uniqueness of topological indices Ecological Indicators 11 1301 1310 Download For the software Saura S amp Torn J 2009 Conefor Sensinode 2 2 a software package for quantifying the importance of habitat patches for landscape connectivity Environmental Modelling amp Software 24 135 139 Download We prefer any of the references above for citing the Conefor software package or the metrics and methods implemented in it If however for some reason you need to cite this manual for any content that is not available in the previous papers please use the following reference Saura S amp Torn J 2012 Conefor 2 6 user manual April 2012 Universidad Polit cnica de Madrid Available at www conefor org 19
23. he software you can even run the software directly from a USB stick As for version 2 2 Conefor only runs in computers with a Windows operating system any Windows version is fine including Windows XP Vista 7 and others It runs both in 32 bit and 64 bit architectures although the current Conefor compilation is only using 32 bits i e it cannot make use of more than 4 GB RAM in your computer In the future we plan to produce Conefor compilations for 64 bits and also for other operating systems different from Windows check the Conefor website for updates and or for subscribing to the Conefor email list if you want to be automatically notified of future versions or other relevant news Note that in the input files for Conefor node file and connection file the point and not the comma should be set as the decimal symbol and that no symbol should be used as a thousand separator e g a correct number format is 1235 45 while 1 234 45 or 1235 45 or 1 235 45 or 1 234 45 are incorrect Conefor will expect all the numerical values in the input files in accordance with these specifications and will write the results in the same format If any numerical value in the input files is not written according to this format an error will occur when trying to run Conefor using those input files This means that the regional configuration settings of your computer should be set accordingly before generating the input files for Conefor through any of the GIS e
24. hese variables The changes evaluated through this option might correspond to an increased effective distance or resistance due to the intensification of a certain part of the landscape matrix e g the development of a highway or other type of barrier to an increase in the permeability or hospitability of the landscape matrix or to many other types and intensities of change that may be of interest in particular case studies and regions in accordance with the objectives of a given connectivity analysis Note that in fact the Link removal and Link improvement options are just particular cases of the Link change modality but with the former two not requiring to include a fourth column in the connection file since they assume that all the evaluated links change exactly to the same state which is the disappearance of a link or the unlimited improvement of the quality of a link respectively If you use the Link change option and your connection file is for example a distance file then if you set the fourth column all to zero values the Link change result will be the same as that for Link improvement If in the same case you set all the values in the fourth column to arbitrarily large infinite values then the Link change result will be the same as for Link removal If your connection file is either a probabilities file or a link file then setting all the values in the fourth column to zero will provid
25. higher than zero For the same reason as above in the probabilistic connection model the one that applies for PC those pairs of patches that have no direct connection between them p 0 will surely have dM 0 and varM 0 For the rest of the cases pairs of patches with p gt 0 Conefor will change the p value for each pair of patches from its initial value in the intact landscape to p 0 and recalculate the value of M after that change Master which will result in a dM and varM that might be higher than zero In the binary connection model all the link losses are comparable in the magnitude of change they represent a link that existed in the initial landscape is removed completely to evaluate the impact of its loss However in the probabilistic model the initial value of p for each link in the initial landscape might be very different among the different links This introduces some complication when trying to 13 Conefor 2 6 user manual directly compare the dM or varM values resulting from this analysis for the different links in the probabilistic model since the actual magnitude of change in the strength or probability of use of each link as characterized by p might be quite different for each link For example it is not the same obtaining dW 10 for a link which had p 0 01 in the initial landscape than obtaining the same dM 10 for another link that had a p 0 9 in the initial landscape This has to be taken into account when try
26. icular node A node will be highly central as quantified through these metrics when it is involved in the shortest optimal movement routes between many other pairs of patches by serving as an intermediate stepping stone patch These Betweenness Centrality metrics differ from all the other metrics implemented in Conefor in that they can only be calculated at the level of individual nodes i e these BC metrics do not provide an overall value characterizing the connectivity of the entire landscape There is no M landscape level value see equations in section 9 for these metrics Therefore when you select these centrality metrics for calculation their values will only appear in the node importance file and not in the results for the overall index values Conefor 2 6 user manual The values of the centrality metrics for individual nodes as shown in the node importance file are calculated differently from the rest of the metrics The centrality values for an individual node are obtained taking into account the topological position of that node in the intact initial landscape without performing any node removal procedure the formula for dM or varM in section 9 above does not apply for these metrics See Bodin and Saura 2010 for further details Therefore even if the values of BC BC IIC and BC PC are shown in the node importance file together with the dM or varM values for the rest of the metrics it should be kept in mind that they are calcul
27. ifferent than the value in the third column a smaller distance or a larger probability in the fourth than in the third column will correspond to the case in which the quality or strength of the link 15 Conefor 2 6 user manual between two patches increases in a given change scenario and a higher distance or smaller probability in the fourth than in the third column will mean that the connection between those two patches gets weaker All types of combinations and different types of changes are possible for each of the links in a given landscape and Link change analysis For example some connections may be improved some others may decrease its quality or even disappear completely and some other links may suffer no change at all in the same analysis depending on the particular values for each link that are specified in the third and fourth columns of the connection file Obviously for those links with the same values in the third and fourth column of the connection file the result will necessarily be dM 0 and varM 0 since that would mean that no change is foreseen evaluated for that particular link It is also possible to use a link file as the connection file for the Link change option although in this case only binary metrics such as IIC can be calculated with the only possible changes for individual links being the complete disappearance of an existing link or the addition of a link direct connection between patches that did not e
28. individual nodes The link importance analysis can be performed under the following three different modalities that can be selected in the Link importance box in the Conefor interface link removal link improvement and link change 14 2 Link removal the impact of losing an existing link When the Link removal option is selected Conefor will remove one by one each of the links existing in the landscape network individual link removal only one link removed at the same time and calculate the impact of that link loss on landscape connectivity according to dM or varM where M can be any of the metrics implemented in Conefor except the Betweenness Centrality metrics although IC and PC are the ones recommended for this and other types of analyses This will produce a dM or varM value for all the pairs of patches nodes in the landscape each link being represented by the IDs of the nodes it connects In the binary connection model the one that applies for C those patches that are not linked in the initial intact landscape will surely have dM 0 and varM 0 there is obviously no impact in the potential loss of a link between two patches if such link does not actually exist in the initial landscape For those pairs of patches that do have a link in the initial landscape Conefor will recalculate the index value after removing that link Master see section 9 which will result in a dM and varM that might be although not necessarily
29. ing to interpret and summarize the results of this link removal analysis for the probabilistic connection model If the Link removal option is selected there is the possibility to use the Reduce calculations option see the box for the link importance options in the Conefor interface Such Reduce calculations option allows specifying a maximum distance if the connection file is a distance file or a minimum probability if the connection file is a probability file so that the calculations are performed only for the pairs of patches links with a distance not larger than the specified maximum or with a probability p not smaller than the specified minimum Note that in this case the rest of the links those weak links with large distances or small probabilities will get dM 0 and varM 0 because they have not been evaluated in the analysis this does not mean that the results would be necessarily zero if the Reduce calculations option would not have been selected 14 3 Link improvement the potential benefits of strengthening connections between habitat patches When the option Link improvement is selected Conefor will perform quite the opposite analysis to that of the Link removal option In the binary connection model the one that applies for IIC Conefor will add one link only one at a time to each of those pairs of patches that are not directly linked in the initial landscape and will recalculate the M v
30. lometers no matter how much increase in the permeability or hospitability of the landscape matrix you may be able to achieve However the link improvement option will evaluate such hypothetical and unrealistic improvement in the strength or feasibility of use of that link as characterized by py in the same way as for all the other pairs of patches The resultant dM or varM values may be therefore only feasible to obtain in reality for a small subset of the total number of links direct connections in your graph To overcome this issue and perform a more fine tuned and detailed analysis related to the potential changes in the links in your landscape you might consider instead the Link change modality that is described in the next subsection Finally in the same way as described above for the Link removal analysis if the Link improvement option is selected there is also the possibility to use the Reduce calculations option see the box for the link importance options in the Conefor interface Such Reduce calculations option allows specifying a maximum distance if the connection file is a distance file or a minimum probability if the connection file is a probability file so that the calculations are performed only for the pairs of patches links with a distance not larger than the specified maximum or with a probability p not smaller than the specified minimum Note that in this case the rest of the links those we
31. lues of the Betweenness Centrality metrics BC BC IIC BC PC these metrics are calculated in a different way see section 10 below and not according to the formulas shown above for dM or varM The Betweenness Centrality metrics included in Conefor 2 6 are calculated for each node just according to their position in the intact initial landscape and not following a node patch removal procedure as for the rest of the metrics Conefor 2 6 user manual Finally it should be noted that the CCP index Class Coincidence Probability is no longer included in Conefor 2 6 This is because CCP does not present good prioritization abilities compared to other metrics see Pascual Hortal and Saura 2006 and we intend to avoid an excessive number of metrics being calculated by Conefor if this is not necessary On the other hand CCP it is quite similar analytically to LCP Since LCP is included in Conefor 2 6 it is very easy to get the CCP values from the LCP ones calculated by Conefor 2 6 if you wish to do so see the formulas in Pascual Hortal and Saura 2006 to understand how to make this simple calculation In the rare case that you still want to get the CCP values directly you can use the older version Conefor Sensinode 2 2 for that particular purpose this older version will be still available for download in the Conefor website 10 Generalized Betweenness Centrality metrics 10 1 Which network centrality metrics are calculated by Conefor C
32. on 2 2 Several sensilink functionalities are included in version 2 6 as described in section 14 link removal link improvement link change Given that Conefor is now not just performing analyses related to the nodes sensinode but also to the links sensilink in the network the name of the software package has been shortened and simplified from Conefor Sensinode to Conefor in this version 2 6 and future ones e The values of the Equivalent Connectivity EC corresponding to the C and PC metrics Saura et al 2011a 2011b are also presented in the results for the overall indices see section 12 Conefor 2 6 user manual e The values of Betweenness Centrality BC metrics can now be calculated and presented as part of the results in the node importance file This includes the classical BC metric as defined by Freeman and more importantly the generalized and improved versions BC IIC and BC PC which provide more ecological realism to this metric and allow it to match with the requirements and desirable properties of C and PC see section 10 All these metrics are integrated in a single analytical framework with the same units of measurement as described in detail by Bodin and Saura 2010 5 Installation operating system and computer configuration This new version 2 6 has no particular installation requirements Simply copy the executable file Conefor26 exe anywhere in your computer and double click the file to run t
33. onefor 2 6 calculates for each node BC the classical Betweenness Centrality metric as originally defined by Freeman 1977 Sociometry 40 35 41 BC IIC and BC PC the improved versions of the BC metric that were proposed by Bodin and Saura 2010 in order to incorporate some considerations that are important to increase the ecological realism of this metric and to make it match with the characteristics and desirable properties of IIC and PC In this way BC IIC and BC PC are placed integrated within the same analytical framework as the IC and PC metrics All these metrics are expressed in the same units of measurement and can be directly compared In particular the normalized BC IIC and BC PC values for each node are equal or higher than the connector fraction of the IIC and PC metrics respectively see section 10 5 below as shown by Bodin and Saura 2010 The values of BC BC IIC and BC PC are calculated only for the nodes that exist in the landscape standard node importance analysis and not for the links or the nodes to add 10 2 What do the Betweenness Centrality metrics measure and how are they calculated The baseline concept for all these centrality metrics BC BC IIC BC PC is the same they measure how much a specific node sits between all other pairs of nodes in a network i e these metrics capture the degree to which the shortest or optimal paths for movement between other habitat patches pass through a part
34. option Alternative calculation mode has been added This is however an implementation in progress that should be handled with much care We recommend users not to perform any calculations of the PC metric with this option activated 17 GIS extensions Several GIS extensions have been developed specifically for Conefor These extensions allow generating from a spatial layer in either vector or raster format the files required as an input to perform the connectivity analyses in Conefor These extensions generate these input files node file and connection file directly in the exact format required by Conefor therefore these files can be 17 Conefor 2 6 user manual used as they result from the GIS extensions with no other changes or intermediate processing steps The extensions allow for batch processing of multiple files layers You can find more details about these extensions including the web pages from where they can be downloaded at http www conefor org gisextensions html 18 Applications Conefor and the new IIC and PC metrics have been used in a wide variety of conservation and management plans scientific studies and official reports on biodiversity indicators by the European Commission and the European Environmental Agency among other connectivity related applications Such applications have been reported in numerous studies comprising different types of species and ecosystems and a large number of countries from China to
35. pond to negative dM and varM values In the binary connection model all the link gains are comparable in the magnitude of change they represent a link that did not exist in the initial landscape is added to evaluate the potential benefits of its creation or restoration However in the probabilistic model the initial value of p for each link in the initial landscape might be very variable among the different links This introduces some complication when trying to directly compare the dM or varM values resulting from this analysis for 14 Conefor 2 6 user manual the different links in the probabilistic model since the actual magnitude of change in the strength or probability of use of each link as characterized by p might be quite different for each link For example it is not the same obtaining dM 10 for a link which had p 0 01 in the initial landscape than obtaining the same dM 10 for another link that had a p 0 9 in the initial landscape This has to be taken into account when trying to interpret and summarize the results of this link improvement analysis for the probabilistic connection model Note that not all the link changes that are set by the Link improvement option can be considered realistic For example if the dispersal abilities of your analyzed species are in the range of a few hundred meters it would be certainly unrealistic to consider that p can improve up to 1 for two patches that are separated by hundreds of ki
36. r BC IIC and BC IIC being shown in different columns in the node importance file The three metrics BC IIC and BC IIC will be calculated even if you are interested only in BC IIC but this is not of much concern because BC IIC is the most computationally intensive metric among these three Calculating BC IIC will consume most 8 Conefor 2 6 user manual of the total processing time On the other hand some of the calculations performed to get the BC and IC values are also needed to obtain the results for BC IIC If you wish to calculate BC and IIC but not BC IIC then you should run Conefor two times one with only BC selected and the other with only IIC selected If you wish to calculate the BC PC metric then you should select both BC in the box for the binary indices and PC in the box for the probabilistic indices Conefor will understand that you want to calculate not only BC and PC but also BC PC This will result in the values for BC PC and BC PC being shown in different columns in the node importance file The three metrics BC PC and BC PC will be calculated even if you are interested only in BC PC but this is not of much concern because BC PC is the most computationally intensive metric among these three Calculating BC PC will consume most of the total processing time On the other hand some of the calculations performed to get the BC and PC values are also needed to obtain the results for BC PC Note that if your input
37. r PC and go for the Results gt Overall index values you will notice that in this new version in addition to the IIC or PC or ICjym Or PCrum Values already provided by version 2 2 the results also include the EC Equivalent Connectivity values for these two indices EC IIC and EC PC This corresponds to the Equivalent Connected Area ECA index as described in Saura et al 2011a 2011b where the patch habitat area was used as the node attribute ECA IIC and ECA PC are defined as the size of a single habitat patch maximally connected that would provide the same value of the IIC and PC metric respectively as the actual habitat pattern in the landscape In a more general case in which the attributes of the nodes might correspond to some other characteristic different from just habitat area e g habitat quality population size etc this index is better renamed as EC Equivalent Connectivity Therefore this more general name EC is the one used in Conefor 2 6 EC or ECA is just computed as the square root of the numerator of the IIC and PC indices C and PCrum yielding EC IIC and EC PC respectively Although Saura et al 2011a 2011b only used EC ECA for the PC index EC PC the same approach and advantages see below apply for IIC EC IIC Both EC PC and EC IIC are calculated by this new version You just need to select IIC or PC for analysis and the results for the overall index values will also show the EC I
38. ric value caused by the removal of that individual node from the landscape see manual for version 2 2 and related papers for further details This includes the intra flux and connector fractions for IIC or PC as described by Saura and Rubio 2010 these fractions will be automatically calculated if any of these two metrics is selected for the analysis The importance of a node or link see section 14 according to a given connectivity index metric M can be expressed in relative terms deltas in Conefor 2 6 dM or in absolute terms vars in Conefor 2 6 varM M Mafter dM 100 varM M Mafter Where M is the overall connectivity index metric value when all the nodes are present in the landscape i e the metric value for the initial intact undisturbed landscape and M after is the overall index value after the removal of that individual node from the landscape Therefore dM and varM quantify respectively the relative and absolute variation in the overall connectivity metric value for the whole landscape M after the loss of a particular node patch The same equations apply for other changes related to the links between patches as will be described later in section 14 You should select at least Show deltas or Show vars before running the software unless the option Only overall index is activated see below in section 11 If you select the option Show deltas this is the default
39. rovided by k as a connecting element or stepping stone has been largely or fully compensated by other patches and alternative paths available for movement in the landscape If however k is the only element sustaining the connectivity between other habitat areas and there are no other alternative patches or paths available to compensate for its loss the removal of k will have a large impact in the connectivity of the remnant network d Cconnector will be in this case as high as ABC IIC Therefore these metrics capture how much of the current stepping stone connecting role played by a particular patch in the intact landscape dBC IIC is lost when that patch is removed from the landscape d iCconnector See Bodin and Saura 2010 for further details on these metrics and their ecological interpretation BC IIC or BC PC can be considered as a fourth fraction of the IIC or PC metrics being measured with the same units and within the same analytical framework than the intra flux and connector fractions a common currency for connectivity These four metrics fractions provide a multifaceted complete and non redundant view of the different ways in which habitat patches can be important as connectivity providers as supported both in analytical grounds Saura and Rubio 2010 Bodin and Saura 2010 and by statistical assessments on their practical outcomes as compared to a wider set of connectivity metrics as shown by figure 5 and the rest of th
40. s Pascual Hortal L amp Saura S 2006 Comparison and development of new graph based landscape connectivity indices towards the priorization of habitat patches and corridors for conservation Landscape Ecology 21 7 959 967 Download Saura S amp Pascual Hortal L 2007 A new habitat availability index to integrate connectivity in landscape conservation planning comparison with existing indices and application to a case study Landscape and Urban Planning 83 2 3 91 103 Download For the three fractions of the PC or IIC metrics intra flux connector Saura S amp Rubio L 2010 A common currency for the different ways in which patches and links can contribute to habitat availability and connectivity in the landscape Ecography 33 523 537 Download 18 Conefor 2 6 user manual For the Equivalent Connectivity EC or Equivalent Connected Area ECA index and its use for monitoring changes in landscape connectivity Saura S Estreguil C Mouton C amp Rodriguez Freire M 2011a Network analysis to assess landscape connectivity trends application to European forests 1990 2000 Ecological Indicators 11 407 416 Download Saura S Gonzdlez Avila S amp Elena Rosselld R 2011b Evaluaci n de los cambios en la conectividad de los bosques el indice del rea conexa equivalente y su aplicaci n a los bosques de Castilla y Le n Montes Revista de mbito Forestal 106 15 21 only available in Spanis
41. se two metrics in large landscapes with many nodes It might be unfeasible to compute BC I C or BC PC in very large networks due to the excessive computational time that would be required The standard BC metric can however be calculated much faster 10 4 How to select the BC BC IIC and BC PC metrics for calculation in the Conefor interface If you wish to calculate the classical BC metric then you should select BC in the box for the binary connectivity indices in the Conefor interface The resultant values for each node will be shown in one of the columns of the node importance file The BC value calculated by Conefor for a particular node k correspond to the sum of all separate shortest paths between all pairs of patches different from k that go through k divided by the total number of shortest paths between all pairs of patches equation 5 in Bodin and Saura 2010 No matter if you select Show deltas or Show vars the same result for BC will appear in the node importance file even if you select both Show deltas and Show vars only one column will be produced for BC in the node importance file with the values calculated as described above If you wish to calculate the BC I C metric then you should select both BC and IIC in the box for the binary connectivity indices in the Conefor interface Conefor will understand that you want to calculate not only BC and IIC but also BC I C This will result in the values fo
42. ted Conefor will just calculate b i e it will only evaluate how much each of the new potential habitat areas nodes to add would contribute to improve connectivity if they were added in the landscape Since in general the number of candidate nodes to be added in the landscape b is much smaller than all the nodes patches that exist in it a this option can save a lot of processing time by just calculating the dM or varM values for the nodes to add and not for the existing nodes Note that BC BC IIC and BC PC metrics are not calculated for the nodes to add the values for these metrics will be equal to zero in the node importance file but this just means that they have not been calculated 14 Calculating link importance values for different modalities removal improvement change 14 1 What does link importance mean and which results are obtained through this analysis Conefor 2 6 includes the possibility of calculating the contribution of individual links to maintain or improve overall landscape connectivity This goes beyond the capabilities of previous Conefor versions in which such type of analysis was possible only for nodes and not for links Some recent studies have benefited from this new functionality in Conefor see the section on applications at the Conefor website for the full references Gurrutxaga et al 2011 Landscape and Urban Planning 101 310 320 Saura et al 2011 Forest Ecology and Management 262 150 160
43. ult selected in the Conefor interface the user should be aware that for links these values correspond in fact 12 Conefor 2 6 user manual exclusively to the connector fraction that is they correspond to d iCconnector varllCconnector dPCconnector and varPCconnector respectively even if this is not written explicitly in the link importance result files Note also that the link importance analysis can be much more time consuming than the node importance analysis While a node importance analysis will require n 1 calculations of the metric value M in a graph with n nodes a link importance analysis in the same graph will require n n 1 2 1 calculations of the metric value since n n 1 2 is the number of links in an undirected complete graph with n nodes This can be considerably slow and even unfeasible in large networks especially for computationally intensive metrics like PC Users should keep this in mind when trying to analyze large datasets through this new functionality in Conefor 2 6 Some options that might allow users to reduce the number of calculations and the required processing time are being evaluated and might be included in a future version of this software package check www conefor org for updates or subscribe there to the Conefor email list if desired The link importance analysis in Conefor 2 6 does not include the calculation of any of the Betweenness Centrality metrics see section 10 which are only calculated for
44. xist in the initial landscape Therefore in this case both the third and the fourth column of the connection file can only contain either O or 1 for each pair of patches indicating if a link exists 1 or not 0 between those patches in the initial landscape third column and if it will be lost gained or will remain unchanged in a given scenario as specified in the forth column of the connection file In the Link change analysis Conefor will replace the value for a particular pair of patches in the third column of the connection file by the value in the fourth column of that file which in general might either make a link appear or disappear binary connection model or change the p value that is associated to that link probabilistic connection model Conefor will recalculate the network connectivity as evaluated by the value of Mater for the entire landscape after that change and will report the resultant dM or varM value This change will be done only for individual links one at a time so that dM or varM values correspond to the connectivity change either gain or loss that would result from implementing that change in a given link while all the others remain unchanged As said above for the other modalities of link importance analysis the connectivity losses as measured by IIC or PC will correspond to positive dM and varM values while connectivity gains will correspond to negative dM or varM values see formulas in section 9 for t
45. xtensions that have been developed specifically for this purpose see section 17 Otherwise the GIS extensions will write the Conefor input files with the wrong numerical format and these files will not be usable for subsequent processing in Conefor 6 Conditions of use Conefor is freeware and has the same conditions of use as version 2 2 This means that it can be used with no restrictions for non commercial purposes with the only condition of citing the software its website and the appropriate references see www conefor org and section 20 below 7 Questions or further information For any question or further information please visit www conefor org where you can find the most recent versions of the Conefor software package the user manuals GIS extensions related papers an overview of the applications in which Conefor has been applied around the world empirical support studies and other relevant information You can also contact us at conefor gmail com The authors would appreciate hearing about the applications in which Conefor is used as well as help in reporting bugs and suggestions for improvement However very limited user support will be provided and only for specific questions regarding this software and the methods implemented in it 3 Conefor 2 6 user manual that cannot be solved by other means e g by carefully reading the manuals and the different related papers 8 An overview of the new features in the graphical
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