A quick introduction to Zonation........... - C
Contents
1. The ranking of sites is visualized by using different colors to indicate the priority rank of the site Me 5 E H Q RH oe Quick introduction to Zonation 21 Red The top 2 of the priority ranking landscape Dark Red The top 2 5 Magenta The top 5 10 Yellow The top 10 25 Light Blue Middle ranks 25 50 Dark Blue Below average 50 80 Black The lowest ranked 20 The color tabs can be adjusted to show a different percentage of the landscape and a custom color gradient can be designed and saved with the GUI The color scales can be tuned for powerful effect For example it is possible to visualize existing protected areas with one color an ideal network expansion with another and the rest of the landscape with a sliding color scale And you can save load you own color schemes Please see the full user manual for more details or find out simply by experimenting with the color sliders Note that if the map is very large 100 1000 million element range it may take some seconds or a minute to recolor it after the color scale is changed Text output Information about settings and input files used during a Zonation analysis are documented in a memo file which is also shown during run time in the Text tab of the Visual output window Some error messages and warnings are also printed in this window If in doubt we recommend searching for words such as error warning and unable to locate possible problem2. ranking starts from the full landscape and removes cells stepwise minimizing loss until there are none remaining Least valuable cells e g a few common species occurring are removed first while the most important cells for biodiversity e g high species richness and species occurrence are kept till the end These 5 Automated post processing functions 6 Leave run open in GUI for further exploration calculations are illustrated in the table on the next page Models of conservation value While the Zonation algorithm is the same under all analyses there are conceptually different models of aggregating conservation value All these models give highest priority for locations with high occurrences for many rare and or highly weighted species Low priorities go to areas where there is a small number of common widespread features parking lots Between these similarities there are differences in how much emphasis is given to many features versus rare features Quick introduction to Zonation 9 1 Input three 5x5 species distributions Spp A presence absence data B probabilities of occurrence C abundance weight 2 0 weight 1 0 weight 3 0 1 1 1 0 0 0 9 0 98 01 01 0 1 1 2 8 9 1 1 0
3. are too many of you to list here See also acknowledgements in the user manual Cover pictures of this manual by Enrico Di Minin layout Aija Kukkala Other special thanks go to Evgeniy Meyke for cover images of Zv2 and Zv3 manuals and to Brendan Wintle for allowing the use of Hunter Valley data in the Zonation tutorial Quick introduction to Zonation 29 For the latest version of Zonation please visit our website http cbig it helsinki fi Zonation implements methods and software for spatial conservation prioritization it is a decision support tool for conservation resource allocation Zonation identifies areas important for retaining habitat quality and connectivity for multiple species habitats ecosystems ecosystem services etc indirectly aiming at long term persistence of biodiversity When including costs Zonation produces cost efficient solutions Typical uses of Zonation include design of reserve networks and their expansions identification of areas for ecological impact avoidance and evaluation of proposed conservation solutions developed elsewhere Zonation also implements traditional target based planning commonly used within systematic conservation planning The operation of Zv4 is explained in this quick introduction guide See also Zv4 user manual scientific publications and our web site for further information Contact information C BIG Conservation Biology Informatics Group Finnish Centre of Excelle
4. extent for you In order to make sure that all rasters are correct in dimensions and extent pre processing in a GIS software or R is needed Compared to other planning tools Zonation can use spatial distribution models that take into account the predicted occurrence level of species in addition to presence absence distribution models Notably the outputs of statistical species distribution modeling tools such as MaxEnt which project where a species is likely to occur based on a set of environmental variables can be directly used in Zonation without needing to be converted to polygons or thresholded such as in some other conservation planning tools Note also that Zonation is capable of doing planning units based prioritization 8 How to do a simple Zonation run After you have installed Zonation and decided about the concept of conservation value which is implemented via the cell removal rule you need to define a set of basic parameters including the list of features to include the weights and targets if used for different features and additional options to enable and parameterize multiple analysis capabilities such as connectivity etc Starting with Zonation v4 simple setups can be generated from scratch using the Project Maker of the GUI See the video online Basic usage quick start with the project maker Z4 This is an easy way to start a Zonation project Alternatively you can create a new analysis setup as a set of
5. input files some of which are compulsory and some optional There are three types of files which are compulsory in all analyses and these are 10 http www gdal org l http www gdal org formats_list html Quick introduction to Zonation 13 i A project file specifying two main input files and the output files ii A list of biodiversity features There are parameters given to each feature including a weight and possibly feature specific connectivity responses iii A settings file that defines the analytical features that will be used in the Zonation priority ranking The project file bat can be created in any text editor e g Notepad and saved with the extension bat It calls Zonation and specifies the paths and names of the species and settings files used in the analysis as well as an output path where a number of outputs with the same name will be created Here is an example of a project file see the tutorial files for more File Edit Format View Help call zig4 exe r input settings dat input biodiversityfeatures spp output output txt 0 0 01 0 0 The feature list file spp includes a list of all biodiversity features species ecosystems etc included in the analysis This file is a text file that can be created in Notepad The file name extension spp is not compulsory but we often use it to indicate that the file is a Zonation species list file Each row in the file corresponds to a biodiversity featu
6. studies that use replacement cost analysis to evaluate existing or proposed conservation area networks Impact avoidance or biodiversity offsetting can be expected to become more prominent topics in the future The majority of studies using Zonation have been conducted in terrestrial systems This is largely a coincidence though as there is nothing that prevents analysis of freshwater or marine environments The freshwater studies are complicated by the need to describe catchments and river networks so that connectivity up and down river can be accounted for Of the major environments marine studies are the least common but a small number of them do exist as well The lack of Zonation use in marine environments may be because many marine studies have taken the path of target based planning using some other software Zonation has also been applied in urban environments Zonation studies have been done on all continents but most studies are in countries that have a tradition of using ecological information in conservation decision making Analysis can be equally done with high resolution like 1 ha data or at coarse resolution like 100 km grid cells Connectivity considerations become more relevant at high resolutions because then individual grid cells are population dynamically highly linked to neighboring and nearby cells and areas Species are the most commonly used biodiversity feature in Zonation analyses Habitat types or ecosystems are al
7. the Zonation software package These can be used as templates for your own analyses e The user manual nice but it is comprehensive and therefore slow to read e Individual Zonation methodological references or applications although usually these cover only a small bit about what can be done using Zonation e One day Zonation courses arranged in the context of major international conservation biology meetings You can also ask us for a special teaching session and consultation e The core references listed in the previous section e Contact the authors for scientific collaboration and advice e Also check youtube and or vimeo for any videos about the use of Zonation Zv4 onwards Quick introduction to Zonation 28 14 Credits amp brief history Implementation of the first version of Zonation was initiated in 2003 after a realization that metapopulation type connectivity measures could be computed for relatively large grids This opened up possibilities for development of reserve selection software with more advanced capabilities than before The basic method was described and published in 2005 and the v1 software developed at the University of Helsinki UH came available near the same time Development of new methods and analyses continued at UH with Zv2 released in 2008 and Zv3 in 2012 Zv4 is in the process of being released around the middle of 2014 Funding Zonation has been developed with funding from multiple sou
8. 00 0 9 0 98 01 0 0 1 1 2 7 12 1 1 0 00 0 5 0 4 0 01 0 O 0 0 2 5 7 1 0 0 00 0 5 0 1 0 01 0 O 0 0 0 5 5 0 0 0 0 0 0 5 0 1 0 1 0 0 0 0 0 2 2 Sp A sum of elements 8 Sp B sum of elements 6 18 Sp B sum of elements 72 2 Convert normalize to fraction of distribution in cell 0 125 0 125 0 125 0 O 0 146 0 159 0 016 0 O 0 014 0 014 0 028 0 111 0 125 0 125 0 125 0 0 0 0 146 0 159 0 016 0 O 0 014 0 014 0 028 0 097 0 167 0 125 0 125 0 0 0 0 081 0 065 0 002 0 O 0 0 0 028 0 069 0 097 0 125 0 0 0 0 0 081 0 016 0 002 0 O 0 0 0 0 069 0 069 0 0 0 07 0 0 081 0 016 0 016 0 O 0 0 0 0 028 0 028 3 Multiply by feature weights to get weighted fraction of distribution in cell Lowest amp highest scoring cell shaded 0 25 0 25 0 25 01 0 0 146 0 159 0 016 0 O 0 042 0 042 0 083 0 333 0 375 0 25 0 25 IW 0 146 0 159 0 016 0 O 0 042 0 042 0 083 0 292 0 500 0 25 0 25 0 0 0 0 081 0 065 0 002 0 O 0 0 0 083 0 208 0 292 0 25 0 0 0 0 0 081 0 016 0 002 0 O 0 0 0 0 208 0 208 0 0 0 0 0 0 081 0 016 0 016 0 0 0 0 0 0 083 0 083 4 Hypothetical distributions after several iterations when several cells have been removed marked in dark grey 1 1 IW 0 9 0 98 00 1 1 8 9 1 1 0 0 0 9 0 98 Di 1 1 7 12 1 0 0 5 0 0 7 Sp A remaining sum 5 Sp B remaining sum 4 26 Sp C remaining sum 47 5 Weighted fraction of remaining distribution in cells has now changed 0 4 0 4 0 0 0 211 0 230 Di 0 064 0 064 0 511 0 574 0 4 0 4 0 0 0 2
9. 1 4 E 0 8 4 0 8 vc sch E 4 2 j 4 2 0 6 4 50 6 4 E S j T S 3 d Boos j 04 got d ZS D 4 i e 4 5 4 e S EG a WER 0 25 ot BW o Oa meen EEN tery 1 0 8 0 6 0 4 0 2 D 1 0 8 0 6 0 4 0 2 0 proportion of landscape protected proportion of landscape protected 1 es 0 8 4 0 8 4 E S S g J 4 2 gv D 0 6 4 p o 4 3 4 A 5 Z ee F B 044 3 0 4 1 wo E g 0 24 50 2 Re o lA 0 maa Te e Se E E E nae SAES 0 20 000 40 000 60 000 80 000 100 000 120 000 1 0 8 0 6 0 4 0 2 0 cost needed to achieve given conservation value proportion of landscape protected Merged Map The Merged map can be used to visualize the overlap between different maps including both input maps and maps of analysis output The first map added to the merged map is an exact copy of the original Each time a new map is added the per pixel average color is calculated and the merged map is updated to reflect the new color values Except for limited functionality with the merged map histogram next page the merged map is meant for visual Quick introduction to Zonation 23 use it cannot be used for quantitative map Text output analysis as all numerical data associated with cells is lost when a map is added to the merged map window Please see the full user Map Peek Ctrl K manual for more information about the e P id Ctri 1 merged map function EJ Zoom to extent Ctri E a Zoomin Ciel Maps can be added to the merged m
10. 11 0 230 Di 0 064 0 064 0 447 0 766 0 4 0 0 117 0 0 0 447 6 At this stage Additive Benefit Function ABF would remove from the right side cluster cells with 0 447 and Core Area Zonation CAZ from the left At the left either connectivity or 2nd highest species occurrence would point to the shaded cell With ABF at the right connectivity would break the tie between the two cells with 0 447 7 Calculations such as illustrated above are used together with connectivity considerations and costs to determine the next cell to remove Remaining area is then updated and the process returns to step 4 Iteration recurs until no cells or planning units remain See next section for the Core Area Zonation CAZ and Additive Benefit Function ABF models for aggregating conservation value This example is simplified in that it is not shown how the benefit functions enter the ABF calculations In fact ABF does not do the range size renormalization but increasing marginal losses when representation goes down amount to a similar effect The additive benefit function ABF has the heuristic interpretation of minimization of expected extinction rates via feature specific species area curves It sums the loss across features converted via feature specific benefit functions Because it sums it implicitly ends up giving high importance to cells with many features in them that is high species richness of course tuned by l
11. 406 onsole View Error View showing only errors Quick introduction to Zonation 24 Interactive Plot The Interactive plots function can be opened by right clicking either on an instance in the project view or on a completed analysis and selecting Open interactive plot window The interactive plots window is a versatile tool that allows visualization of individual species feature performance There are four tabs available at the top of the interactive plots window General plots Remaining proportions Histogram of area qualities and Distribution x protection groups nn zemaan KN general plots remaining proportion tab Lee e TE Zensen GU terete plots vatori output oup n curves ot Aar zeen Renaneg prep rees oaites Dr x protecion groups Gores Seeugp Hsmgamot aes ege Onte x promcten yami beten ms raes 2 B sse z motaaon Sen SIE mmm hedini histogram of area qualities distribution x protection tab 25 000 The General plots tab allows plotting results relative to individual features groups of features administrative units and groups of features within administrative units The remaining proportion tab shows the total protection remaining for every feature species for a given top fraction of the landscape The Histogram of area qualities tab shows a histogram of cell qualities for a given t
12. Version 1 for Zv4 Victoria Veach as Joona Lehtomaki Sate Federico Montesino Pouzols gt Sy OA Atte Moilanen oe e PEAR H P a ef S Va a wb Quick introduction to Zonation 2 Table of Contents A Quick Introduction to Zonation le Whatis Z natron EE 5 2 Scope and alms OF Chis document seten ea a E E AE 5 3 What is Zonation ee 5 4 Whotan use Zonat on aaiae ii p EnEn a ee Seege 6 5 Why is Zonation different from other tools sssssssesesseseesereseereeseesrerrresresseseresee 7 What can Zonation be confused with seeeeseeessesesseseresressereresressessrerreeseeseeseesses 7 What about other software intended for approximately the same purpose 7 6 How does Zonation work essssseseesessesessseesseserssresseenrestessesstestesseesreseeeseeseeseresre 9 REENEN 12 8 How to do a simple Zonation TUM accics wiescegsncsacds decaskeansusg tags eeeacntdnowasdedennstanesevsanete 13 Theproject tile Hat eege enee ee a r a 14 The feature list file CS pp casscandinds enee engt EEN EA eg Sean 14 Re ern Sete es file CAL cle ae de dea see Nace Da odd ole ceva botnets te eae 15 9 How to interpret Zonation main output cece eenteceeeeceeeeeceeeeeceeeeeceeeeeeeeeees 17 EECHELEN 18 The priority rank Map orescence einai i a E E ia edia aiaa 18 10 The Zonation Graphical User Interface GUI eeseseeeeseseereesrrerrerersereresreeseese 19 portant EE e 19 Re 21 Vis al QUU oiana i aa des
13. a E E a E PEERI 21 Text 5 11 56 Spee are ee en een EE AR ANS a Ee TS 22 R ntime Oe 23 Een BE 23 Interactive Plot s cicascadeecheceacstyscoidess geed AEN 25 11 What Zonation has been used for eseeeeeesesseeesseseresressessresressersresreesessresreeseese 26 E Some COLE references oiii EE 27 13 Where to get more information sssessseeeesseesssssseesseeesssetsstesseesseeeseeesseeessrese 28 14 EE EE 29 Quick introduction to Zonation 3 This guide is a product of C BIG the Conservation Biology Informatics Group at the University of Helsinki Version 1 2014 ISBN 978 952 10 9921 2 paperback ISBN 978 952 10 9922 9 PDF Unigrafia OY Helsinki Quick introduction to Zonation 4 1 What is Zonation Zonation is a publically available decision support system for spatial conservation planning It is special purpose software built for solving various problems around spatial conservation resource allocation and it is capable of data rich large scale high resolution spatial conservation prioritization Zonation is a set of methods and analyses implemented in one package and compared to many other software programs with similar purpose has the broadest analysis options available for spatial conservation planning 2 Scope and aims of this document This manual was written to provide a quick and relatively simple explanation about what Zonation is what it is not who can use it and what it can be use
14. ap tab p Zoom out Ctri Down from the map tab right as well as from the project and process views To add a map from the map tab right click on the map and Ee select Add to merged map as in the Z Save Map as image Add to merged map photo below To add from the project or process views right click on the desired file and select Add to merged map Right clicking on a map in merged map window gives the option to open the Merged map histogram This window shows a table with all the colors in the map as well as the total number of cells of each color and the corresponding percentage of map cover see image below In order to simplify visual analysis of the merged map the number of colors applied to each map should be minimized The merged map histogram allows for example an easy way to investigate the extent to which two solutions overlap You can use a binary color scale like black amp light grey below Then overlap has three colors representing overlapping and non overlapping areas Project View ax Map Text output J Runtime plot Merged map Project C aZ64 Zv4 Tutorial do_abf b Project C aZ64 Zv4 Tutorial do_bip b Merged map histogram Je Process View ax done tutorial_output output_abf b Gone tutorial_output output_bip txt Color cells map Miss 249913 ni 9034 8 192 Ei 31842 28 87 69
15. d for We also summarize the basics of getting started with using Zonation We make reference to further literature where relevant 3 What is Zonation useful for There are many potential uses for Zonation and many examples of its use already exist in scientific literature All the following analyses are possible with suitable inputs and interpretation of outputs Please see the user manual and scientific literature for description of how Zonation analyses are typically set up and the associated case studies Standard usages possible with simple setups e Reserve selection Identification of the best part of the landscape reserve network that produces high return on investment and balanced outcome across all biodiversity features e Reserve network expansion Identify the optimal balanced expansion of an existing reserve network Can account for connectivity if desired e Evaluation of an existing or proposed conservation area network Comparison between how good it is and how good it could have been e Impact avoidance Identify areas where economic development leads to limited ecological losses e Balancing of alternative land uses Balance between many biodiversity features and the needs of several alternative land uses opportunity costs e Target based planning Solution of the minimum set coverage problem i e how to satisfy your targets with minimum cost Quick introduction to Zonation 5 Advanced usages with higher
16. data requirements or more complex analysis setup e Biodiversity offsetting Find areas that best compensate for ecological damage how to expand the existing reserve network in a balanced manner to compensate for specific losses e Planning under climate change Use present distributions and future distributions of biodiversity features as well as connectivity between the present and future distributions to identify current and future areas of relevance e Targeting of habitat restoration or habitat management Modeling of difference made by management restoration is accounted for in a complicated and data demanding analysis 4 Who can use Zonation Zonation is available for free and can be used by anyone Those working in conservation management research teaching consulting universities NGOs etc may be interested in this software There are no restrictions on the use of the software except that the appropriate scientific references describing the methods used should be made in documents and presentations While the Zonation software itself does not come with a license fee there nevertheless is a price associated with using it The time needed to understand and use the methods can in fact be quite long Additionally collating the input data is frequently a very time consuming phase Thus Zonation is not a free lunch do it all in a day solution into spatial conservation planning The structure of a Zonation project resourc
17. during strength of preference for corridors can be tuned ranking All of these connectivity methods have their uses see user manual but connectivity does not need to be used always use of it is optional Frequently an analysis without connectivity is informative already and simple application of the BLP distribution smoothing and interaction connectivity could go a long way in including realistic connectivity effects 7 About data Zonation is applicable to analysis of data about distributions of biodiversity features such as species ecosystems environment types or habitats accounting for current occurrence and possibly their future expected state dependent on conservation intervention In addition Zonation can account for data about the spatial distribution of socio economic factors relevant for finding conservation opportunities The numbers inside the data layers can be any non negative numbers presence absence probability of occurrence density abundance amount etc Here is a list of data that are commonly used in spatial conservation planning and may be included in Zonation Biodiversity features Socio economic features Threats Species Land cost Land use change Habitat types Opportunity costs Climate change Ecosystems Management costs Invasive plant species Ecosystem services Willingness to sell Pollution Note a simple Zonation analysis can use only one type of data such as species distributions While
18. e clicking on the file name Raster maps not included in the project files can also be opened from the Raster menu by selecting Open Raster Map This option opens a new window to browse for the desired raster file Running queuing an analysis Each command line in a batch file corresponds to a different variant of a Zonation run In the GUI each command line is listed as an Instance and referred to by the output name specified in the command line To begin a Zonation analysis right click either on Project to execute all instances at once or Instance to execute each command individually in the Project View and select Queue A project may include only one or multiple Zonation analysis instance The selected runs should now immediately appear in the Process View window middle left in main window Zonation will begin the analysis straight away when the instance has been added to the Process View Double click on a running or completed analysis in the Process View window in order to observe its progress it in the Visual Output window Each analysis has a row in the process view When the run still is in progress it 4 Project C Users veach zonation 3 4 Instance tutorial_output outpu Sutor DEE EEN Ate Open Project tutol R tutol 4 ni tutol tutoi tutorial_input species asc tutorial_input set dat ok 4 Output files Run info tutorial_output Output Curves tutoria
19. e species that only occur in the north CAZ pays relatively higher attention to core locations of the northern species with the unavoidable price of reduced priorities in the south The difference between ABF and CAZ is case specific and depends on how feature distributions are nested In target based planning Zonation calculates the traditional minimum set coverage solution as part of the priority ranking The minimum set solution can be extracted from the priority ranking right before the first target is about to fail with the removal of the next grid cell from the landscape In Zonation target based planning uses a special benefit function designed for the purpose We refer to the Zonation user manual for a full explanation on the other two cell removal rules generalized benefit function and random cell removal Here we provide a short video about how different types of cell removal work in Zonation Connectivity Zonation can presently account for connectivity in eight ways which are summarized in the table below Compared to many other conservation planning tools Zonation can uniquely account for feature specific connectivity at large extents using very fine resolution data For example with distribution smoothing the widths of the kernels can describe either the dispersal capability or scale of landscape use of the species related to home range size Connectivity method Type Brief characterization edge remova
20. eractions txt use mask 1 mask file Data 4_RegionalPlans Conservation SYKE_Al IlConsAreas_100m tif comunity analysis settings a load similarity matrix 1 connectivity similarity matrix file UML_O8_mMSP_mcki_ESS_L_abf_HM2_in UML_conn_matr ix txt apply to connectivity 1 4 While a detailed explanation of the run settings file is provided in the main Zonation manual we below provide a summary of some features that are commonly encountered in Zonation analyses In total there are over 70 different key words that can be used in the settings file here we only show a few Setting Explanation almost always used parameters removal rule CAZ 1 ABF 2 TBF 3 selects the model of conservation value edge removal Only allows removal from edge of remaining area warp factor Acceleration factor count of cells removed in one go some examples of frequently used and useful parameters use groups Specifies use of a group file which allows automated production of output for groups of features Also needed for linking condition transforms etc file name needs to be provided on another row BLP Value for the boundary length penalty simplest form of connectivity mask missing areas Mask some areas in input files into missing data thereby defining the study area use condition layer Takes into use condition layers that modify habitat quality layers use interactions Takes into u
21. ertainty land use restrictions multiple costs etc All and all there are great conceptual and practical differences between Zonation and the other software intended for similar purposes Please make a comparison for yourself Marxan with Zones differs from the methods cited above in that it seeks options over multiple different allocations for each planning unit polygon Allocation of different land uses has different costs and consequences for different features This is not a feature directly supported in Zonation See also the RobOff software for development of portfolios of conservation action across environments Integer programming IP methods are often too focused on globally optimal solution of specific problems while forgetting the realism of the problem formulation Limitations of IP formulations have included and these may not apply to all problem variants and solution methods requirement of binary presence absence input data applicability of limited 8 Zonation applies to efficient target based planning including the combined targets and benefits planning outlined in Laitila and Moilanen 2013 http cbig it helsinki fi software roboff Quick introduction to Zonation 8 connectivity methods only and applicability limited to small medium sized data In any case IP formulations are about target based planning and the comments about lowered return on investment apply as well 6 How does Zonation work Sectio
22. ervation investment see Laitila and Moilanen 2012 While Zonation can do target based planning perfectly well it also includes what can be called higher level models of conservation value These models apply more generic principles about how conservation value is aggregated across features space and possibly time Application of these generic principles leads to a balanced priority ranking which arises as an emergent property of the principles and input data As such the mode of operation is very different from target based planning in which the solution is in a sense defined a priori via the targets Another major difference between Zonation and Marxan are the outputs Marxan produces a solution for the minimum set coverage problem i e which areas satisfy your goals with minimum cost Zonation produces a balanced priority ranking in which top and bottom fractions of the landscape can be seen at the same time Also a range of conservation investments can be investigated rather than having a result for one target set There are also other major differences Zonation is deterministic and can operate on very large rasters v4 up to the order of 100 million elements Marxan operates on polygon vector data and is stochastic giving a different result each run Marxan has required input data to be classified into presence absence 1 0 while Zonation does not There also are differences in how well the approaches can account for connectivity unc
23. es needed risks and opportunities perceived by stakeholders are discussed in the open access article by Lehtom ki and Moilanen 2013 Zonation can be used by anyone working in systematic conservation planning spatial conservation prioritization reserve selection site selection reserve network design or spatial conservation planning and related fields in general Zonation can also be applied in the context of other land use planning where the focus is not on biodiversity conservation While different methods and software implementations may have different strengths we encourage you to compare alternatives in terms of the analytical options offered size of data that can be analyzed ease of use etc Zonation is also useful for teaching about spatial conservation prioritization The Zonation v4 graphical user interface GUI is easy to use and can also be used for investigating and visualizing input data Quick introduction to Zonation 6 5 Why is Zonation different from other tools There are two topics to cover here software intended for completely different purposes and software intended for approximately the same purpose What can Zonation be confused with Zonation is not software for statistical species distribution modeling SDM like e g MaxEnt or BIOMOD In SDM information about environmental variables is statistically related to conditions at locations where a species has been observed to occur The outcome is a s
24. harismatic megafauna with well surveyed taxonomic groups and habitat types Journal of Applied Ecology 51 281 288 Extensive review about the concepts of spatial prioritization open online Quick introduction to Zonation 27 Kukkala A and A Moilanen 2013 Core concepts of spatial prioritisation in systematic conservation planning Biological Reviews 88 443 464 For further reading please see the full literature list in the manual or the website Finally for prioritization of actions instead of space see the following publication and the RobOff software Pouzols F M Burgman M A and A Moilanen 2012 Methods for allocation of habitat management maintenance restoration and offsetting when conservation actions have uncertain consequences Biological Conservation 153 41 50 13 Where to get more information You can master Zonation step by step With the help of documents videos and learning material all available online you can quickly start using Zonation for basic analysis variants We encourage users to post any general questions and comments on our user forum At least the following sources of information are available e Frequently asked questions see C BIG website http cbig it helsinki fi software zonation e The Zonation user forum at the C BIG website e The Zonation teaching power points available from the C BIG website Please pick your slides freely e The tutorial examples distributed with
25. has direct correspondence with the performance curves top priority areas selected from the priority rank map include feature representation summarized by the respective performance curves For example if we select the top 10 of the priority rank map the corresponding representation for each biodiversity feature or for broader groups can be evaluated via the performance curves In addition Zonation outputs can also be visualized by using e g parallel boxplots below to display the median quartiles and minimum and maximum of original total occurrences remaining across a set of features or groups calculated for a specific priority top fraction of the landscape e g 10 Proportion of distribution 0 2 0 4 0 6 0 8 0 0 Birds Mammals Plants Ecosystems Quick introduction to Zonation 18 10 The Zonation Graphical User Interface GUI Project C aZ64 Zv4 Tutorial do_abt b Project C gZ64 Zv4 Tutorial do_blp b open map tab text output runtime plot merged map projects goen ZS d A Keep map settings Project View ax p me langa o p Megdma project view Process View l Ta See color bar 40 90 tutorial_output output_abf txt done tutorI_output output_blp tt analysis runs visual output process view Console View Error View showing only errors console view Figure A snip of the Zonation GUI with main components marked in red Project Managemen
26. ion to Zonation 14 decimal number parameter for a declining by distance dispersal kernel If distance units in the distribution layer files are in meters as is common the value 0 002 above corresponds to a one kilometre mean dispersal distance Please see the user manual for an explanation on how to calculate this value The fifth column has a couple of different uses depending on which cell removal rule is used If using the ABF this parameter controls how sensitive a biodiversity feature is to habitat loss This parameter is closely related to empirically observed species area curves and in the absence of further information a generic value of 0 25 can be used as has been done above If target based planning is enabled the parameter in column five used for setting targets 0 0 to 1 0 required for the representation proportional coverage of each biodiversity feature Below we show how targets could have been set in the fifth column of the species list file Edit Format View Help 4 0 0 002 1 1 S 1 1 1 1 1 1 1 1 1 1 tiger img kokapo img chinesegiantsalamander img kingcobra img tropical_forest img grassland img EE Hi vn Ohn ch wi The run settings file dat is used to activate a number of important features in Zonation It is a text file that can be edited with a text editor Make sure that the features activated from the settings file are written in separate rows and that the names are wri
27. l structural Usually used retains some continuity speeds computations BLP Boundary structural Most common connectivity method in reserve selection length penalty Reduces the edge to area ratio of remaining areas Quick introduction to Zonation 11 distribution feature specific Metapopulation type declining by distance connectivity smoothing measure Can be tuned according to the needs of each feature Identifies areas with a high density of high quality habitats BOP feature specific More highly parametric feature specific response Boundary Updated iteratively during ranking Slows computations quality penalty NOQP Directed feature specific Extension of the BQP for a tree like river system with connectivity connectivity responses both up and down the river Requires specification of linkages between planning units catchments interaction between pairs of Like distribution smoothing but computed between connectivity features either as positive or negative between two distributions Can be e g between predator and prey or between present and future matrix amongst many Recognizes that partially similar habitats that share connectivity partially similar many species help each other s connectivity For habitats example different forest types could help each other s connectivity corridor tries to retain Maintains corridors during the ranking Width and connectivity corridors
28. l_ou Rank layers Ctrl O Add to merged map IZ Zonation GUI 4 0 0b19_compact Project Raster Tools Window Help Project View a x 4 Project G Users v Ge aT taal Open Project A Reload Edits Close Project Ctrl O 4 tutorial_inpi 3 tutorial_ tutorial 3 tutorial_ tutorial amp Edit tutorial_input species5 asc tutorial_input species6 asc tutorial_input species7 asc tutorial_input set dat ok 4 Output files Run info tutorial_output Output Curves tutorial_ou Rank layers Queue Proportional loss layers S Process View HI Stop Queue Process View Il Stop Queue shows the percentage completed in the beginning of the line 16 96 in the image on the right When the run is completed is says done in front Quick introduction to Zonation 20 Console view The console view window is usually visible at the bottom but it can also be hidden to leave more space for visual output The console view has one primary functionality it shows error messages and warnings that occur when the project is loaded The types of messages that are shown can be selected from Tools gt Preferences from the top level menu Common errors include typos in file names or paths When a project is loaded a limited number of error checks are done for input file formats and content Anything found suspicious is reported here Visual Output Gx Map Text
29. le costs The latter is a description about what goes into the running of a Zonation project Moilanen A B J Anderson F Eigenbrod A Heinemeyer D B Roy S Gillings P R Armsworth K J Gaston and C D Thomas 2011 Balancing alternative land uses in conservation prioritization Ecological Applications 21 1419 1426 Lehtom ki J and A Moilanen 2013 Methods and workflow for spatial conservation prioritization using Zonation Environmental Modelling amp Software 47 128 137 For those wanting to delve deeper here is some additional material Why you can expect higher return on investment from Zonation compared to traditional target based planning Laitila J and A Moilanen 2012 Use of many low level conservation targets reduces high level conservation performance Ecological Modelling 247 40 47 Balancing of conservation across multiple administrative regions such as countries Moilanen A and Arponen A 2011 Administrative regions in conservation balancing local priorities with regional to global preferences in spatial planning Biological Conservation 144 1719 1725 The role of connectivity in conservation Hodgson J C D Thomas B A Wintle and A Moilanen 2009 Climate change connectivity and conservation decision making back to basics Journal of Applied Ecology 46 964 969 Surrogacy analysis using Zonation Di Minin E and Moilanen A 2014 Improving the surrogacy effectiveness of c
30. many types of data can be used it is not compulsory to do so Quick introduction to Zonation 12 Zonation requires that a raster layer for each biodiversity feature species ecosystems ecosystem services etc is included in the analysis Hence if you have a vegetation map that includes all vegetation types together this would need to be pre processed so that each habitat type is included separately Zonation can directly load raster maps and also point data but there are a fewer analytical options for point distribution data Polygon or vector data are not directly supported However they can be included after rasterizing the data by using commonly available GIS software or R Please bear in mind that Zonation cannot be used to pre process your data Virtually all standard raster formats are supported such as GeoTIFF tif or Erdas Imagine img Zonation uses the Geospatial Data Abstraction Library GDAL for this For an exhaustive list of formats supported see GDAL formats Det Regardless of the raster format used it is essential that all input rasters have the same cell size and extent In other words the number of columns and rows as well as the cell size in each raster should be the same and the geographical extent covered by the raster should be exactly the same Notice that Zonation will report an error while reading in the data if the rasters have a differing number of rows and columns but it will not check or correct the
31. nce in Metapopulation Biology Department of Biosciences P O Box 65 Viikinkaari 1 Fl 00014 University of Helsinki FINLAND atte moilanen helsinki fi ISBN 978 952 10 9921 2 paperback ISBN 978 952 10 9922 9 PDF The following partners have contributed significantly to the development of Zonation EN 2 X European A M Research Le METS HALLITUS EI ven Ri pol ese S ZA apos K wf Council ACADEMY OF FINLAND e D
32. ns 6 8 here include somewhat more detailed information about Zonation If you simply want to try it out you can skip to Section 10 about the Zonation graphical user interface It may also be useful to then look at Section 9 about interpretation of outputs Compared to other conservation planning tools Zonation produces a complementarity based and balanced ranking of conservation priority over the entire landscape Moilanen et al 2005 rather than satisfying specific targets at minimum cost On the right there is a summary of the flow of computational operations in Zonation The priority ranking is produced by iteratively removing the grid cell or planning unit that leads to smallest 1 Load amp verify data layers aggregate loss of conservation value while accounting 2 Pre processing transforms e distribution discounting e kernel type connectivity e condition for total and remaining distributions of features weights given to features and feature specific connectivity Here end cell means a pixel on a map Zonation uses a raster for each biodiversity feature where each cell 3 Iterative ranking range size renormalization some connectivity updates pixel contains a number for the occurrence level of that feature The way loss of conservation value is aggregated across features occurring in a cell depends on the so called cell removal rule Iterative priority 4 Output main results
33. ocal occurrence levels and weights of features With the ABF gains in Quick introduction to Zonation 10 conservation value level off when coverage for a feature increases which introduces a balance complementarity that it is preferable to have representation of all features in the solution Core area Zonation CAZ Instead of a sum CAZ bases ranking on the most important occurrence of a feature in the cell Therefore it is able to identify as high priority areas that have a high occurrence level for a single rare and or highly weighted feature Even generally feature poor cells can thus be identified as priorities Difference between ABF and CAZ The difference between ABF and CAZ is effectively the same as between a mean and a maximum taken from a set of numbers which here are the feature specific scores that are basis for deciding which cell to remove next Compared to CAZ ABF tends to produce a higher average proportion of feature distributions retained but smaller minimum This is because relatively feature rich areas may be favoured at the expense of some features occurring in generally feature poor areas Note that the choice between ABF and CAZ is not a binary black and white choice between richness and rarity it is more about a tendency between emphasis on richness and the need to cater for all features For example countries like UK or Canada would have highest species richness in the south but there nevertheless are som
34. onation offers ready made color schemes and you can create your own Quick introduction to Zonation 17 Performance curves are automatically produced and exported for each feature during a Zonation analysis This curve quantifies the proportion of the original occurrences retained for each biodiversity feature at each top fraction of the landscape chosen for conservation Performance curves start from 1 0 because the full landscape includes the full distribution of the biodiversity features At the other end no areas are chosen and correspondingly the protection level for the feature is zero Because the number of these curves can be high it is common to average and visualize curves across feature groups such as taxonomic groups Average curves usually are concave because the initial aggregate losses for biodiversity are low low priority areas such as densely populated urban areas contain relatively little biodiversity but aggregate losses unavoidably accelerate when moving to high priority areas with high feature richness rarity and occurrence levels The priority rank map is the other main output of a Zonation analysis run The priorities are derived from the order of iterative cell ranking removal Each grid cell in this map has a value between 0 and 1 meaning that values close to 0 were removed first low conservation value and priority while high values close to 1 were retained till the end high priority The priority rank map
35. op fraction of the landscape for a particular feature species The Distribution x protection groups tab displays a scatter plot of features for a given top fraction The axes are the proportion of cells remaining and the input distribution size distribution sum of the feature In this plot one expects that narrow range species would have a higher fraction covered than broad range species Quick introduction to Zonation 25 11 What Zonation has been used for Zonation can be used in many different environments anywhere in the world and for many different purposes using a range of data The challenge is to develop the analysis set up so that it is maximally informative given the planning need and available data Below is just a brief summary of the possible use of Zonation Please see the user manual Web Of Science Google Scholar or other such sources for additional information and references The most common use of Zonation is for the identification of conservation areas or expansions of protected area networks The latter of these involves the use of a hierarchic analysis There are also analyses that have spatially allocated habitat restoration or management instead of protection These analyses are less common because they involve additional effort as estimates of the difference made by restoration or management may be needed There also are a few studies of conservation prioritization under climate change using Zonation Less numerous are
36. output Runtime plot Merged map whfh The GUI produces three types of visual output that can be viewed in the Visual output window either during prioritization or after it has finished These are the map from the cell ranking in the Map tab a memo describing the analysis in the Text output tab and performance curves quantifying representativeness of the solution in the Runtime plot The Merged map can also be viewed in the Visual output window even though it is not an automatic output of a Zonation analysis but rather it requires you to specify what maps to merge there The Map amp color schemes The output map can be viewed in the Map tab of Visual output window In this tab the output map can be viewed to best suit the needs of the analysis You can use the mouse for dragging the map around and the mouse wheel zooms in and out Selecting keep map settings in the upper right corner will maintain the colors and the zoom when switching between analyses which is helpful when comparing different runs Right clicking on the map allows you to save it in different formats fm Keep map settings Color The default map has a white to black gradient with black representing the scheme highest priorities but additional including user defined color schemes K are also available in the Color scheme drop down list at the right of the window K The Classic Zonation color scheme shows below the nested ranking on a T map
37. pecies distribution model that extrapolates the expected occurrence level of the species across the landscape Zonation does not do SDMs However Zonation can use many SDM generated rasters as input layers Neither is Zonation a software for stochastic spatial population viability analysis SPVA such as RAMAS Like outputs from species distribution models the output of a SPVA e g predictions species extinction risks could be used as input for Zonation Zonation is about synthesizing information across many potentially very many species and other biodiversity features While Zonation does include many connectivity features it is not software primarily intended for analysis of connectivity it accounts for connectivity in prioritization Zonation integrates habitat quality habitat area and connectivity for many biodiversity features simultaneously It can also account for many costs and opportunity costs and other considerations See Hodgson et al 2009 about the role of connectivity in conservation While Zonation v4 graphical user interface has much improved capabilities in visualizing the spatial input and output data e g rasters it is not a GIS software You can easily view input raster data and do simple overlay analysis for the resulting spatial data e g the priority rank rasters but Zonation is not truly spatially aware i e there is no support for projections and coordinate systems and you cannot import additional
38. rces Zv1 and Zv2 were funded via a Research Fellow grant from the Academy of Finland to Atte Moilanen Development of Zv3 was further supported by the Academy of Finland s Finnish Centre of Excellence in Metapopulation Biology and by the EU FP7 project SCALES Development of Zv3 1 and Zv4 has been primarily supported by the ERC StG project GEDA Global Environmental Decision Analysis to A M Additional significant indirect support has been provided by the Finnish Ministry of Environment via the Natural Heritage Services Mets hallitus by the University of Helsinki and by the Academy of Finland center of Excellence in Metapopulation Biology Contributions to the software and documentation The Zonation project has been originated and funding for it secured by Atte Moilanen The computational software itself A M implemented Zv1 and Zv2 Jarno Lepp nen worked on a new Z GUI and Zv3 0 Federico Montesino Pouzols has developed Zv3 1 and Zv4 Scientific collaborations around Zonation are too numerous to be listed here thanks to everyone you know who you are Many people have contributed to the documentation of Zonation Major effort across entire manual versions has been expended by Heini Kujala Zv1 amp Zv2 Laura Meller Zv3 F M P Zv3 1 and Zv4 and Victoria Veach Zv4 A M has been involved through the entire project We thank all who have contributed to specific manual sections or who have reported ideas for improvement there
39. re For each biodiversity feature there are six columns of information which require values to be entered Frequently dummy values are used in columns that are not relevant for the particular case Below is a typical example of a species list file with some well known species and habitat types as biodiversity features The file name containing the distribution map for the feature is the last thing on each row a valid file name must always be entered Column one is feature weight It is used always except when in target based planning mode Weights can be assigned for example according to conservation status as illustrated below File Edit Format View Help 1 1 0 tiger img 1 1 0 kokapo img 1 1 0 chinesegiantsalamander img 1 1 0 kingcobra img 1 1 0 tropical_forest img 1 1 0 grassland img Typically weights have positive values but can also be set to 0 0 in surrogacy analyses Di Minin amp Moilanen 2014 or even have negative values for example when multiple opportunity costs are included in the analysis Moilanen et al 2011 A detailed strategy for weight setting is described in Lehtom ki amp Moilanen 2013 The second to fourth columns concern connectivity settings Columns 3 and 4 are integer parameters to selecting so called BQP connectivity responses often these options are not used in which case a dummy value of 1 is fine The second column is used more frequently it is a Quick introduct
40. s with the analysis Project View ax Map Text output Runtime plot I Merged map Project G aZ64 Zv4 Tutorial do_abfb Find Be Percentage of globally effective occurrencies 100 relative to total E effective cells 30 6173 relative to total cells Memory required for biodiversity features 9 058 MB of which base memory 4 641 MB and occurrencies require 4 417 MB Time now 1398631354 11 42 34 PM 2014 4 27 Finished preload counting effective occurrencies Elapsed 1 seconds Allocating memory for input layers finished successfully bed eee Loading feature e g species data layers Loaded biodiversity feature file 1 tutorial_input speciesl asc non missing cells 110282 their sum 35280 8 Loaded biodiversity feature file tutorial _input species2 non missing cells 110282 their sum 29142 7 Loaded biodiversity feature file 3 tutorial_input species3 asc non missing cells 110282 their sum 35307 7 Loaded biodiversity feature file tutorial _input species4 non missing cells 110282 their sum 35116 9 done tutorial_output output_abf txt Loaded biodiversity feature file tutorial_input species5 non missing cells 110282 their sum 22852 8 Loaded biodiversity feature file tutorial _input species non missing cells 110282 their sum 36691 1 Loaded biodiversity feature file tutorial input species7 non missing cells 110282 their sum 34740 3 Calculating richne
41. se connectivity interactions specified in another file use mask Specifies use of hierarchical mask file which is needed e g in the context of protected area network expansion use planning unit Specifies use of a planning unit layer which describes groups of cells layer that belong to the same planning unit Then ranking proceeds by planning units not by cells Quick introduction to Zonation 16 9 How to interpret Zonation main output Zonation automatically produces a number of different output files for each run Here we discuss the most relevant ones In the project file a filename is specified for all output files all output files of a project will have the same name but different suffixes and extensions 06 Global priorities present time Globe priorities 2040 Global priorities 2040 pessimistic 17 230 40 50 PO 80 0 Protected area of terrestrial world Species range protected on average oo 100 Figure The two Zonation main outputs visualized Top Priority rank map Bottom Performance curves here shown as averages across many here 26 000 features These curves are from a hierarchical analysis for reserve network expansion which explains the funny steps in the curves around the top 10 in this analysis ranks 0 10 includes only protected areas shown by their own color The map can be freely colored according to the needs of analysis and visualization Z
42. so commonly used With these it makes sense to account for pairwise similarity of habitats in connectivity computations Another significant feature used are ecosystem services Other types of features uncommonly used in analysis include environmental classes and distributions of alleles Whatever the type of the study factors such as costs threats and connectivity have been variably included Quick introduction to Zonation 26 12 Some core references There are many publications about Zonation both methodological and applied Most of these can be identified by checking the Web of Science or Google Scholar for publications that cite the original Zonation publication Moilanen A Franco A M A Early R Fox R Wintle B and C D Thomas 2005 Prioritising multiple use landscapes for conservation methods for large multi species planning problems Proc R Soc Lond B Biol Sci 272 1885 1891 Also the Zonation manual and the website include more extensive lists with descriptions of Zonation references However while there are many publications most of them concern a computational technique or a case study and are not good starting points for a general introduction In addition to this document and the Zonation manual the following two methodological references are easily accessible open access online and of more general utility The first of these explains the Zonation algorithm and how to balance multiple benefits and multip
43. spatial data Zonation does not deal with vector data at all What about other software intended for approximately the same purpose The most direct comparison is to software intended for systematic conservation planning or spatial prioritization including programs such as Marxan Marxan with zones ConsNet C Plan etc Also relevant is comparison to integer programming IP implementations meant http www gbif org resources 2596 https r forge r project org R group_id 302 http www ramas com ramas htm http www uq edu au marxan http www ugq edu au marxan latest r d http uts cc utexas edu consbio Cons consnet_home html 7 http www edg org au free tools cplan html Quick introduction to Zonation 7 for solving target based reserve selection problems Comparing software with different conceptual underpinnings and only partly overlapping objectives is far from trivial Thus the reader should consider the following as just a few general pointers and not as an exhaustive review Do an up to date comparison and see what fits the purpose of your work best There are major differences between Zonation Marxan with and without zones and ConsNet Marxan variants and ConsNet are intended for target based planning in which the typical aim is to achieve feature specific targets with minimum cost This aim implies that feature specific targets first need to be set a process that in itself leads to lowered return on cons
44. ss across biodiversity features Done in 0 seconds Time now 11 42 35 PM 2014 4 27 Saving raster map of weighted range size corrected richness Saving raster tutorial _output output_abf wrscr asc AAIGrid format DE Preparing to start the ranking process Note using edge removal Loaded data and initialized in 4 seconds Current time 11 42 36 PM 2014 4 27 Quick introduction to Zonation 22 Runtime plot The Runtime plot window below shows four plots 1 the average proportion of biodiversity feature distributions remaining as landscape is removed 2 cost needed to achieve a given conservation value 3 average extinction risk calculated from the canonical species area curve and 4 proportions of point distribution species occurrences SSI spp remaining The fourth curve is drawn only if point distribution features are included in the analysis The lowest fraction remaining across all biodiversity features worst off species is plotted with a red line the blue line represents the average across all species features in general and black is a weighted average across features If no cost layer is used the cost curve shows the number of cells needed for the respective top fractions otherwise it shows the cost of the respective top fraction of the landscape See the full user manual for more detailed information about interpreting the curves Map Text output Runtime plot Merged map
45. t Loading and editing a project A project can amp 8 a proj proj Sage SAAR enge be loaded in the GUI through either the ject Raster Toots on Window nttalp process view window or the File menu TO project yew amp x M load a project from the project view right click on the white area see right in the Project o M See eee ee View window and select Open Project to browse and select the appropriate batch file for the analysis To load a new project from the menu select Project and then Open Project After the desired project is selected the batch file Zonation run file as well as all the input files referred to in the batch file will appear in the Project View window next page The project is hierarchically organized To see its contents expand sections by clicking on the small triangular icons at the left in the Project View Quick introduction to Zonation 19 Plain text format input files can also be opened Zonation GUI4 0 0b19_compact and edited in the GUI To open and edit an input Project Raster Tools Window Help Project View ax file right click on the file and choose Edit from the popup menu Note that any changes will be saved in the files not the GUI and the project must be refreshed so that it will contain the edits To do this right click on the project and select Reload Edits see image below Input raster files can also be viewed in the GUI by doubl
46. tten exactly in the same way as in the user manual Note also that all optional layers taken into use must have the same cell size as well as number of columns and rows as the feature rasters The best way of avoiding mistakes is to mimic samples of settings files from the Zonation tutorials see Zonation development site download Below is an example of a simple settings file which can be generated by the project maker or manually using notepad or some other text editor File Edit Format View Help settings removal rule ar p factor 2000 edge removal 1 BLP 0 1 mask missing areas 1 area mask file Data 0O_Masks landmask_100m tif A list of all parameters available for the settings file is available from GitHub Next is an example of a relatively complicated settings file with many options visible Typically an option is switched on and off by setting it 1 or 0 respectively 7 https en wikipedia org wiki Species area_curve Quick introduction to Zonation 15 File Edit Format View settings removal rule 2 warp factor 2000 edge removal 1 BLP 0 5 mask missing areas 1 area mask file Data O_Masks landmask_100m tif use groups 1 groups file UML_O8_mMSP_mcki_ESS_L_abf_HM2_in UML_groups_v2 txt use condition layer 1 condition file UML_O8_mMSP_mcki_ESS_L_abf_HM2_in cond_list txt use interactions 2 interaction file UML_O8_MSP_mcki_ESS_L_abf_HM2_in Int
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