From 8a558f01c5dc5b7b6d9cd17abf27369e1536116a Mon Sep 17 00:00:00 2001 From: ranjanan Date: Thu, 22 Nov 2018 21:14:27 -0500 Subject: [PATCH] Modify config for minimal headers, rename linkage mapper teams --- _config.yml | 4 +- about-the-linkage-mapper-team.md | 31 +++++++ about-the-authors.md => authors.md | 2 +- gnarly-landscape-utilities.md | 41 ++++++++++ linkage-mapper-tools.md | 85 ++++++++++++++++++++ linkage-mapper/index.md => linkage-mapper.md | 9 ++- linkage-mapper/linkage-mapper-tools.md | 5 -- 7 files changed, 168 insertions(+), 9 deletions(-) create mode 100644 about-the-linkage-mapper-team.md rename about-the-authors.md => authors.md (97%) create mode 100644 gnarly-landscape-utilities.md create mode 100644 linkage-mapper-tools.md rename linkage-mapper/index.md => linkage-mapper.md (92%) delete mode 100644 linkage-mapper/linkage-mapper-tools.md diff --git a/_config.yml b/_config.yml index 2f41367..e199cd0 100644 --- a/_config.yml +++ b/_config.yml @@ -36,9 +36,9 @@ header_pages: - docs.md - downloads.md - about.md - - linkage-mapper + - linkage-mapper.md - pubs.md - - about-the-authors.md + - authors.md # Exclude from processing. # The following items will not be processed, by default. Create a custom list diff --git a/about-the-linkage-mapper-team.md b/about-the-linkage-mapper-team.md new file mode 100644 index 0000000..91caa27 --- /dev/null +++ b/about-the-linkage-mapper-team.md @@ -0,0 +1,31 @@ +--- +layout: page +title: About the LinkageMapper Team +--- + +Our “Founding Father” is Brad McRae. He was a Senior Landscape Ecologist with The Nature Conservancy, but was struck down by cancer in 2017. He was an amazing man. His supervisor, Joe Fargione, wrote a wonderful eulogy: “...Everyone who knew Brad was impressed with his intelligence, thoughtfulness, integrity, honesty, and his steadfast commitment to what he cared about: his family, friends and conserving the natural world...” + + + +“...Brad leaves an impressive legacy. He pioneered the use of circuit theory to model connectivity and gene flow across fragmented landscapes, and how to combine this with least-cost corridor theory. The software tools he developed, Circuitscape and Linkage Mapper, are now used in conservation planning around the world. He was passionate about supporting others' efforts to use these software packages to make real changes on the ground…” Rest his soul. + +Brad was the leader for Linkage Mapper Version 1.x, which includes five tools. He was joined by many gifted programmers and scientists in the endeavor. Darren Kavanagh joined the team early on to improve the code base and be the lead developer for Climate Linkage Mapper. Darren has also been very active and helpful in the release of Version 2.0. Tristan Nunez developed the climate corridor model, which became the basis for Climate Linkage Mapper. Viral Shah helped develop Circuitscape, which is the engine behind Pinchpoint Mapper and Centrality Mapper. Other noted contributors to Linkage Mapper Version 1.x were Brian Cosentino, Jeff Jenness, Andrew Gilmer, Theresa Nogeire, and Jenny McGuire. + +In 2009, John Gallo developed a python script to not only map the linkages, but also prioritize among them. In 2013-14 Brad and John, who had met a decade earlier at a corridor workshop, found out about each other’s algorithms and met up again. They decided John should merge his algorithm into Linkage Mapper. John hired Randal Greene to be the lead developer for this project which became the Linkage Priority Tool of Version 2.0. In 2017 Brad asked John to take over as the leader for the entire Linkage Mapper project, and with Conservation Biology Institute committing to provide baseline support, John accepted. + +Annie Prisbrey and Nik Stevenson-Molnar from CBI join John and Darren to help with week to week tasks, with additional involvement from Tim Sheehan, Mike Gough, Gwynne Corrigan, and Ann Van Zee. + +Linkage Mapper Version 2.0 was assessed and improved by many great beta-testers and supporters, including Morgan Gray, Waverley Birch, Randal Greene, Mark Duttweiler, Indranil Mondal, Gretchen Fowles, Jesus Alarcon, Alejandro Gonzalez Bernal, Tania Urquiza, Diana Ramirez, Oscar Godinez, Wolke Tobon, Zaire Yaneth, Megan Jennings, Claudia Moreno, Angela Cuervo, Sylvia Ruiz, and Patricia Koleff. + +The Washington Wildlife Habitat Connectivity Working Group’s (WHCWG) initiated all this with their [2010 statewide connectivity analysis](http://www.waconnected.org/statewide-analysis/), and they continue to develop the project via action research with [several other analyses](http://waconnected.org/habitat-connectivity-analyses/), past and present. Conservation Biology Institute helped develop Version 2.0 through action research in the [Mojave Desert](https://databasin.org/galleries/5552d3a0c7ea48e3a07f225339d9ff7a), [Sacramento Valley](https://databasin.org/galleries/a3869718cda049ab8df821f1f0698196), [Modoc Plateau](https://databasin.org/galleries/833f3aef966240b6b4828362baa58cc5), and [Santa Barbara County](https://databasin.org/maps/9ee809b252f64d8ab4f843354692a724). + + + +Linkage Mapper was bolstered by the direct financial support from from several other institutions. Linkage Pathways was developed with support from the Great Northern Landscape Conservation Cooperative, the Wildlife Conservation Society's Wildlife Action Opportunities Fund, and the Nature Conservancy. The new modules of Version 1.x were supported by the North Pacific Landscape Conservation Cooperative and The Nature Conservancy. + +Linkage Priority Tool was supported by South African National Research Foundation, Nelson Mandela Metropolitan University, Sonoma County Agricultural Preservation and Open Space District, the Islands Trust, the Wilderness Society, and Conservation Biology Institute. + +Finally, the involvement and enthusiasm from the Linkage Mapper community has been the fuel for the project. Please continue that forth with additional discussion on [the community group](https://groups.google.com/forum/#!forum/linkage-mapper), and please chime in with answers to questions, even if only a partial answer. You can contribute and/or vote for code development on our [Github site](https://github.com/linkagescape/linkage-mapper), and also post your projects result on our new and [interactive shared maps Gallery](https://databasin.org/galleries/027492e42545494cae53ca1f61b46c17). + +One of Brad’s early decisions was to make Linkage Mapper an open source project. As a result, it is now a project for all us. Continuation of this project is now in dedication to both Brad, and his mission: conservation of the natural world! + diff --git a/about-the-authors.md b/authors.md similarity index 97% rename from about-the-authors.md rename to authors.md index 13f2a55..efd3495 100644 --- a/about-the-authors.md +++ b/authors.md @@ -1,6 +1,6 @@ --- layout: page -title: About the Authors +title: Authors --- diff --git a/gnarly-landscape-utilities.md b/gnarly-landscape-utilities.md new file mode 100644 index 0000000..65d60f1 --- /dev/null +++ b/gnarly-landscape-utilities.md @@ -0,0 +1,41 @@ +--- +layout: page +title: Gnarly Landscape Utilities +permalink: /gnarly-landscape-utilities/ +--- + +Gnarly Landscape Utilities is an ArcGIS toolbox designed to support some of the less-glamorous tasks involved with connectivity modeling. It includes tools for **creating resistance and habitat layers** and **core area mapping.** The core area mapping functionality was formerly packaged as the HCA Toolkit. + +We created the tools to support connectivity analyses by the [Washington Wildlife Habitat Connectivity Working Group](https://waconnected.org/habitat-connectivity-analyses/) as well as work by the Western Governors' Association and the [Nature Conservancy](http://www.nature.org/). They can be used to create resistance, habitat, and core area maps used by Linkage Mapper, Circuitscape, and other connectivity software packages. + +[**Download Gnarly Landscape Utilities** here.](/downloads/) + +Version 0.1.9, released Aug 2, 2016. + +*You can also see our project on [Github](https://github.com/thenatureconservancy/gnarly-landscape-utilities).* + +**If you use these tools, please cite them so others can find them!** + +**Citation for Core Mapper:** + +Shirk, A.J., and B.H. McRae. 2013. Gnarly Landscape Utilities: Core Mapper User Guide. The Nature Conservancy, Fort Collins, CO. Available at: https://www.circuitscape.org/gnarly-landscape-utilities. + +**Citation for Resistance and Habitat Calculator:** + +McRae, B.H., A.J. Shirk, and J.T. Platt. 2013. Gnarly Landscape Utilities: Resistance and Habitat Calculator User Guide. The Nature Conservancy, Fort Collins, CO. Available at: https://www.circuitscape.org/gnarly-landscape-utilities. + +**Authors** + +Andrew Shirk, Climate Impacts Group, University of Washington + +Brad McRae, The Nature Conservancy + +Jim Platt, The Nature Conservancy + +**Acknowledgements** + +These tools were developed for projects supported by the [Great Northern Landscape Conservation Cooperative](https://www.nrmsc.usgs.gov/gnlcc), the [North Pacific Landscape Conservation Cooperative](http://www.fws.gov/pacific/Climatechange/nplcc/), and the [Doris Duke Charitable Foundation](http://www.ddcf.org/Programs/Environment/). + +**Support** + +Please send bug reports to [Brad McRae](mailto:mcrae@circuitscape.org). \ No newline at end of file diff --git a/linkage-mapper-tools.md b/linkage-mapper-tools.md new file mode 100644 index 0000000..f6fe9c5 --- /dev/null +++ b/linkage-mapper-tools.md @@ -0,0 +1,85 @@ +--- +layout: page +title: Linkage Mapper Tools +permalink: /linkage-mapper/linkage-mapper-tools/ +--- + +### **Linkage Pathways Tool** + +The primary and original tool in the Linkage Mapper toolbox is Linkage Pathways. (Originally, the Linkage Pathways tool was informally called “Linkage Mapper”, and formally called the “Build Network and Map Linkages” tool. Linkage Pathways uses GIS maps of core habitat areas and resistances to identify and map linkages between core areas. Each cell in a resistance map is attributed with a value reflecting the energetic “cost”, (i.e. difficulty and mortality risk) of moving across that cell. Resistance values are typically determined by cell characteristics, such as land cover or housing density, combined with species-specific landscape resistance models. As animals move away from specific core areas, cost-weighted distance analyses produce maps of total movement resistance accumulated. The Linkage Pathways tool uses ArcGIS and Python scripts to identify adjacent (neighboring) core areas and creates maps of least-cost corridors between them. It then mosaics the individual corridors to create a single composite corridor map. The result shows the relative value of each grid cell in providing connectivity between core areas, allowing users to identify which routes encounter more or fewer features that facilitate or impede movement between core areas. Linkage Pathways also produces vector layers that can be queried for corridor statistics [(McRae & Kavanagh 2011)](https://paperpile.com/c/f97yev/9jQPB). ![img](https://circuitscape.org/img/lm1.png)Linkage Pathways output and Habitat Concentration Areas (HCAs) for white-tailed jackrabbit (Lepus townsendii). (Mount hood, Oregon, is in the top left corner) [Link here for the Interactive Map.](https://databasin.org/maps/342bc86a67984c2892e56fdf6a8befd4/active) + +### **Climate Linkage Mapper** + +This tool can be thought of as the “Climate-Traversing Linkage Pathways Tool.” It fine tunes the routes of mapped linkages between core areas such that they minimize the range of micro-climates (e.g. temperatures, or climatic water difference) that are encountered along the linkage. Consider the example of two mountain ridges on the east and west of a hot valley, and joined together at the north end, to make a U-shape. Climate linkage mapper will suggest that the linkage from a core on one ridge to a core on the other is traversing along the ridgelines, connecting at the north, rather than the traditional least cost corridor that ignores climate ranges and goes down into the hot valley and then back up the other side [(Kavanagh et al. 2012)](https://paperpile.com/c/f97yev/Ktrz). This increases the likelihood that the mapped linkage is the one actually used by wildlife, especially by climate sensitive wildlife. Also, the only linkages mapped are those that meet a user-defined climatic difference threshold between the two cores. (This feature is also included now in the Linkage Priority tool, where you also have the option of including linkages connecting similar climates, and just giving them a lower conservation priority value.) See Littlefield et al. [(2017)](https://paperpile.com/c/f97yev/ApMA/?noauthor=1) and Nuñez et al. [(Nuñez et al. 2013)](https://paperpile.com/c/f97yev/SM3q) for more details on the use of the Climate Linkage mapper tool in connectivity modelling. ![img](https://circuitscape.org/img/lm2.png)Climate Linkage Mapper output for whitebark pine, in the transboundary region between Washington and British Columbia. Note, Linkage Mapper can model connectivity for plants as well as animals. [Link here to the Interactive Map.](https://nplcc.databasin.org/maps/859e97aa40034b868f0de21de0d519a0/active) + +### **Pinchpoint Mapper** + +Once corridors have been mapped using Linkage Pathways, or Climate Linkage Mapper, Pinchpoint Mapper utilizes circuit theory to run Circuitscape [(McRae & Shah 2009)](https://paperpile.com/c/f97yev/hP2QF) within the resulting corridors. This produces current-maps that identify and map pinch points (i.e., constrictions or bottlenecks) within the linkages [(McRae 2012a)](https://paperpile.com/c/f97yev/3RNsw). [(McRae 2012a)](https://paperpile.com/c/f97yev/3RNsw). More details on circuit theory and on Circuitscape software can be found in McRae et al. [(2008)](https://paperpile.com/c/f97yev/MgVqV/?noauthor=1) and McRae and Shah [(2009)](https://paperpile.com/c/f97yev/hP2QF/?noauthor=1). Pinch points represent areas where movement would be funneled and thus may be particularly important to keeping intact. Even a small loss of area in these pinch points would disproportionately compromise connectivity [(Castilho et al. 2015)](https://paperpile.com/c/f97yev/DscGZ). ![img](https://circuitscape.org/img/lm3.png)Pinchpoint mapper output and Habitat Concentration Areas (HCAs) for white-tailed jackrabbit (Lepus townsendii). [Link here for the Interactive Map.](https://databasin.org/maps/2147e6fa4419481f803ff916b5cd7b9f/active) **Barrier Mapper** + +Once linkages are created using the Linkage Pathways tool, or Climate Linkage Mapper, Barrier Mapper quantifies the importance of “barriers” that affect the quality and/or location of the corridors [(McRae 2012c)](https://paperpile.com/c/f97yev/t3cy). The term “barriers” is used in a general way and includes portions of a landscape that are difficult to pass through for wildlife, but are not barriers in the formal sense of the term. In essence, they identify areas for restoration and mitigation. Much more detail is provided in a publication by McRae et al. [(2012)](https://paperpile.com/c/f97yev/nTRR/?noauthor=1). ![img](https://circuitscape.org/img/lm4.png)Barrier mapper output and Habitat Concentration Areas (HCAs) for white-tailed jackrabbit (Lepus townsendii). [Link here for the Interactive Map.](https://databasin.org/maps/07b161cf59c14039b79d81d4ffd9038b/active) + +### **Centrality Mapper** + +Once corridors have been mapped using Linkage Pathways or Climate Linkage Mapper, Centrality Mapper analyzes the resulting linkage networks, calculating “current flow centrality” across the networks [(McRae 2012b)](https://paperpile.com/c/f97yev/N31oa). Current flow centrality is a measure of how important a linkage is for keeping the overall network connected. It utilizes Circuitscape to implement this circuit theory approach. According to Dutta et al. [(2015)](https://paperpile.com/c/f97yev/4kf3/?noauthor=1) Centrality Mapper treats each core as a “node”, each linkage as a single resistor, and assigns a resistance equal to the cost-weighted distance of the corresponding least-cost corridor. It then iterates through all core area pairs, injecting 1 amp of current into one core area and setting the other to ground. It then adds up current flow for each core and linkage to generate a map of cumulative current flow, indicating the importance of each linkage in maintaining connectivity across the entire network of cores, and can be considered as a measure of linkage and core centrality. ![img](https://circuitscape.org/img/lm5.png) + +Centrality of Linkages and Habitat Concentration Areas (HCAs) for white-tailed jackrabbit (Lepus townsendii). [Link here for the Interactive Map.](https://databasin.org/maps/fbf173ac249e4f689d095b2696b3c923/active) + +### + +### **Linkage Priority Tool** (New in v2.0) + +The Linkage Priority Tool was implemented to help quantify the relative conservation priority of each linkage in a landscape. Linkage Priority Tool is based on weighted combinations of many factors (Diagram 1). The lower set of factors in the diagram estimate the relative value of the two cores at either end of a linkage. Core priority is is evaluated on the shape, mean resistance value, size, and expert opinion. Users can also include climate by giving a higher value to cores with higher potential to serve as climate refugia. The Tool calculates relative value for every core, and the average value of the two cores associated with each linkage. This then becomes one of the factors determining linkage priority. Hence, a linkage which connects two really important core areas is a higher conservation priority than one that connects two marginal core areas. The average core area value of the two cores of a linkage is then combined with the other higher level factors ([Figure 2](https://docs.google.com/document/d/1-mC_aDD_eX2CW1h2x8oD9dDaWdkOZzP4T27k4Sq4TjI/edit#fig_ConceptualDiagram) top row) that relate directly to linkage priority, including the permeability of each linkage (i.e., the mean resistance values along the least cost path), the proximity of the two cores, the centrality, and expert opinion if available. Users can also include climate signature difference between two cores, giving higher priority to linkages that span a climate gradient, facilitating species range shifts. The tool provides the option of using the difference between the current climate signature of the cooler core, and the future climate signature of the hotter core, to simulate the climate gradient that slow moving species will encounter. A detailed user guide is provided online [(Gallo & Greene 2018)](https://paperpile.com/c/f97yev/fPPHe). Additional details will be presented at the North American Congress of Conservation Biology (2018). Reports are in revision. Prototype applications of various beta versions of the Linkage Priority Tool have been performed in six regions in California -Sierra Nevada mountains, Sonoma County, Santa Barbara County, West Mojave, Sacramento Valley, and Modoc Plateau - with reports and publications in preparation. In the last three of these studies, climate was considered in three ways in determining priority: (1) quantifying which linkages best facilitated long-term species range shifts, (2) which core areas provided more projected climate stability, and (3) which core areas contained more climate micro-refugia for withstanding climate change.![img](https://circuitscape.org/img/lm6.png)Diagram 1: Conceptual diagram of the Linkage Priority Tool. Optional climate wise features have a dashed line. ![img](https://circuitscape.org/img/lm7.png)Linkage Priority output combined with Linkage Pathways and Pinchpoint Mapper outputs. This provides an estimate of connectivity conservation priorities for American badger (Taxidea taxus), in the Sacramento Valley. Core areas are in grey, with relative core area value mapped. [Link here for the Interactive Map.](https://databasin.org/maps/a79bb15434a24871ba70bdf68e5c7249/active) [![American badger on the move](https://circuitscape.org/img/lm8.jpg)](https://circuitscape.org/img/lm8.jpg?attredirects=0)An American badger on the move (photo by James Maughn) + +### + +### **References** + + + +[Castilho CS, Hackbart VCS, Pivello VR, dos Santos RF. 2015. Evaluating Landscape Connectivity for Puma concolor and Panthera onca Among Atlantic Forest Protected Areas. Environmental management 55:1377–1389. Available from ](http://paperpile.com/b/f97yev/DscGZ)[.](http://paperpile.com/b/f97yev/DscGZ) + + + +[Dutta T, Sharma S, McRae BH, Roy PS, DeFries R. 2015. Connecting the dots: mapping habitat connectivity for tigers in central India. Regional Environmental Change 16:53–67. Springer Berlin Heidelberg. Available from ](http://paperpile.com/b/f97yev/4kf3)[ (accessed August 5, 2016).](http://paperpile.com/b/f97yev/4kf3) + + + +[Gallo JA, Greene R. 2018. Connectivity Analysis Software for Estimating Linkage Priority. Conservation Biology Institute, Corvallis, OR. Available from ](http://paperpile.com/b/f97yev/fPPHe)[ (accessed March 26, 2018).](http://paperpile.com/b/f97yev/fPPHe) + + + +[Kavanagh DM, Nuñez TA, McRae BH. 2012. Climate linkage mapper connectivity analysis software. The Nature Conservancy, Seattle WA. Available from ](http://paperpile.com/b/f97yev/Ktrz)[www.circuitscape.org/linkagemapper](http://www.circuitscape.org/linkagemapper)[.](http://paperpile.com/b/f97yev/Ktrz) + + + +[Littlefield CE, McRae BH, Michalak JL, Lawler JJ, Carroll C. 2017. Connecting today’s climates to future climate analogs to facilitate movement of species under climate change. Conservation biology: the journal of the Society for Conservation Biology 31:1397–1408. Available from ](http://paperpile.com/b/f97yev/ApMA)[.](http://paperpile.com/b/f97yev/ApMA) + + + +[McRae BH. 2012a. Pinchpoint Mapper Connectivity Analysis Software. The Nature Conservancy, Seattle, WA. Available from ](http://paperpile.com/b/f97yev/3RNsw)[.](http://paperpile.com/b/f97yev/3RNsw) + + + +[McRae BH. 2012b. Centrality Mapper Connectivity Analysis Software. The Nature Conservancy, Seattle WA. Available from ](http://paperpile.com/b/f97yev/N31oa)[.](http://paperpile.com/b/f97yev/N31oa) + + + +[McRae BH. 2012c. Barrier Mapper Connectivity Analysis Software. The Nature Conservancy, Seattle, WA.](http://paperpile.com/b/f97yev/t3cy) + + + +[McRae BH, Dickson BG, Keitt TH, Shah VB. 2008. Using circuit theory to model connectivity in ecology, evolution, and conservation. Ecology 89:2712–2724. Available from ](http://paperpile.com/b/f97yev/MgVqV)[.](http://paperpile.com/b/f97yev/MgVqV) + + + +[McRae BH, Hall SA, Beier P, Theobald DM. 2012. Where to restore ecological connectivity? Detecting barriers and quantifying restoration benefits. PloS one 7:e52604. journals.plos.org. Available from ](http://paperpile.com/b/f97yev/nTRR)[.](http://paperpile.com/b/f97yev/nTRR) + +[McRae BH, Kavanagh DM. 2011. Linkage Mapper Connectivity Analysis Software. The Nature Conservancy, Seattle, WA. Available from ](http://paperpile.com/b/f97yev/9jQPB) + +[McRae B, Shah V. 2009. Circuitscape User Guide. University of California, Santa Barbara. Available from ](http://paperpile.com/b/f97yev/hP2QF)[http://www.circuitscape.org](http://www.circuitscape.org/)[.](http://paperpile.com/b/f97yev/hP2QF) + +[Nuñez TA, Lawler JJ, McRae BH, Pierce DJ, Krosby MB, Kavanagh DM, Singleton PH, Tewksbury JJ. 2013. Connectivity planning to address climate change. Conservation biology: the journal of the Society for Conservation Biology 27:407–416. Wiley Online Library. Available from ](http://paperpile.com/b/f97yev/SM3q)[.](http://paperpile.com/b/f97yev/SM3q) + + + +. \ No newline at end of file diff --git a/linkage-mapper/index.md b/linkage-mapper.md similarity index 92% rename from linkage-mapper/index.md rename to linkage-mapper.md index 5801134..ac8903d 100644 --- a/linkage-mapper/index.md +++ b/linkage-mapper.md @@ -1,6 +1,7 @@ --- layout: page title: Linkage Mapper +permalink: /linkage-mapper/ --- @@ -30,4 +31,10 @@ Linkage Mapper is an open access project in active development by a [**dynamic t Linkage Mapper User Group for support and updates on new releases. You can contribute and comment on development by joining our [**Github Site and Group**](https://github.com/linkagescape/linkage-mapper), and you can post your final maps, or work in progress, at our shared [**Data Basin Gallery**](https://databasin.org/galleries/027492e42545494cae53ca1f61b46c17). -Please see the **Linkage Mapper Tools** **page for further details and maps** of each output. \ No newline at end of file +Please see the [**Linkage Mapper Tools** ](/linkage-mapper-tools/) page for further details and maps of each output. + +## More information + +* [Linkage Mapper Tools](/linkage-mapper-tools/) + +* [About the Linkage Mapper Team](/about-the-linkage-mapper-team/) diff --git a/linkage-mapper/linkage-mapper-tools.md b/linkage-mapper/linkage-mapper-tools.md deleted file mode 100644 index f9c7218..0000000 --- a/linkage-mapper/linkage-mapper-tools.md +++ /dev/null @@ -1,5 +0,0 @@ ---- -layout: page -title: Linkage Mapper Tools -permalink: /linkage-mapper/linkage-mapper-tools/ ----