This webmap features the USGS GAP application of the vegetation cartography design based on NVCS mapping being done at the Alliance level by the California Native Plant Society (CNPS), the California Dept of Fish and Game (CDFG), and the US National Park Service, combined with Ecological Systems Level mapping being done by USGS GAP, Landfire and Natureserve. Although the latter are using 3 different approaches to mapping, this project adopted a common cartography and a common master crossover in order to allow them to be used intercheangably as complements to the detailed NVCS Alliance & Macrogroup Mapping being done in Calif by the California Native Plant Society (CNPS) and Calif Dept of Fish & Wildlife (CDFW). A primary goal of this project was to develop ecological layers to use as overlays on top of high-resolution imagery, in order to help interpret and better understand the natural landscape. You can see the source national GAP rasters by clicking on either of the "USGS GAP Landcover Source RASTER" layers at the bottom of the contents list.Using polygons has several advantages: Polygons are how most conservation plans and land decisions/managment are done so polygon-based outputs are more directly useable in management and planning. Unlike rasters, Polygons permit webmaps with clickable links to provide additional information about that ecological community. At the analysis level, polygons allow vegetation/ecological systems depicted to be enriched with additional ecological attributes for each polygon from multiple overlay sources be they raster or vector. In this map, the "Gap Mac base-mid scale" layers are enriched with links to USGS/USNVC macrogroup summary reports, and the "Gap Eco base scale" layers are enriched with links to the Naturserve Ecological Systems summary reports.Comparsion with finer scale ground ecological mapping is provided by the "Ecol Overlay" layers of Alliance and Macrogroup Mapping from CNPS/CDFW. The CNPS Vegetation Program has worked for over 15 years to provide standards and tools for identifying and representing vegetation, as an important feature of California's natural heritage and biodiversity. Many knowledgeable ecologists and botanists support the program as volunteers and paid staff. Through grants, contracts, and grass-roots efforts, CNPS collects field data and compiles information into reports, manuals, and maps on California's vegetation, ecology and rare plants in order to better protect and manage them. We provide these services to governmental, non-governmental and other organizations, and we collaborate on vegetation resource assessment projects around the state. CNPS is also the publisher of the authoritative Manual of California Vegetation, you can purchase a copy HERE. To support the work of the CNPS, please JOIN NOW and become a member!The CDFG Vegetation Classification and Mapping Program develops and maintains California's expression of the National Vegetation Classification System. We implement its use through assessment and mapping projects in high-priority conservation and management areas, through training programs, and through working continuously on best management practices for field assessment, classification of vegetation data, and fine-scale vegetation mapping.HOW THE OVERLAY LAYERS WERE CREATED:Nserve and GapLC Sources: Early shortcomings in the NVC standard led to Natureserve's development of a mid-scale mapping-friendly "Ecological Systems" standard roughly corresponding to the "Group" level of the NVC, which facilitated NVC-based mapping of entire continents. Current scientific work is leading to the incorporation of Ecological Systems into the NVC as group and macrogroup concepts are revised. Natureserve and Gap Ecological Systems layers differ slightly even though both were created from 30m landsat data and both follow the NVC-related Ecological Systems Classification curated by Natureserve. In either case, the vector overlay was created by first enforcing a .3ha minimum mapping unit, that required deleting any classes consisting of fewer than 4 contiguous landsat cells either side-side or cornerwise. This got around the statistical problem of numerous single-cell classes with types that seemed improbable given their matrix, and would have been inaccurate to use as an n=1 sample compared to the weak but useable n=4 sample. A primary goal in this elimination was to best preserve riparian and road features that might only be one pixel wide, hence the use of cornerwise contiguous groupings. Eliminated cell groups were absorbed into whatever neighboring class they shared the longest boundary with. The remaining raster groups were vectorized with light simplification to smooth out the stairstep patterns of raster data and hopefully improve the fidelity of the boundaries with the landscape. The resultant vectors show a range of fidelity with the landscape, where there is less apparent fidelity it must be remembered that ecosystems are normally classified with a mixture of visible and non-visible characteristics including soil, elevation and slope. Boundaries can be assigned based on the difference between 10% shrub cover and 20% shrub cover. Often large landscape areas would create "godzilla" polygons of more than 50,000 vertices, which can affect performance. These were eliminated using SIMPLIFY POLYGONS to reduce vertex spacing from 30m down to 50-60m where possible. Where not possible DICE was used, which bisects all large polygons with arbitrary internal divisions until no polygon has more than 50,000 vertices. To create midscale layers, ecological systems were dissolved into the macrogroups that they belonged to and resymbolized on macrogroup. This was another frequent source for godzillas as larger landscape units were delineate, so simplify and dice were then run again. Where the base ecol system tiles could only be served up by individual partition tile, macrogroups typically exhibited a 10-1 or 20-1 reduction in feature count allowing them to be assembled into single integrated map services by region, ie NW, SW. CNPS / CDFW / National Park Service Sources: (see also base service definition page) Unlike the Landsat-based raster modelling of the Natureserve and Gap national ecological systems, the CNPS/CDFW/NPS data date back to the origin of the National Vegetation Classification effort to map the US national parks in the mid 1990's.
These mapping efforts are a hybrid of photo-interpretation, satellite and corollary data to create draft ecological land units, which are then sampled by field crews and traditional vegetation plot surveys to quantify and analyze vegetation composition and distribution into the final vector boundaries of the formal NVC classes identified and classified. As such these are much more accurate maps, but the tradeoff is they are only done on one field project area at a time so there is not yet a national or even statewide coverage of these detailed maps.
However, with almost 2/3d's of California already mapped, that time is approaching. The challenge in creating standard map layers for this wide diversity of projects over the 2 decades since NVC began is the extensive evolution in the NVC standard itself as well as evolution in the field techniques and tools. To create a consistent set of map layers, a master crosswalk table was built using every different classification known at the time each map was created and then crosswalking each as best as could be done into a master list of the currently-accepted classifications. This field is called the "NVC_NAME" in each of these layers, and it contains a mixture of scientific names and common names at many levels of the classification from association to division, whatever the ecologists were able to determine at the time. For further precision, this field is split out into scientific name equivalents and common name equivalents.MAP LAYER NAMING: The data sublayers in this webmap are all based on the US National Vegetation Classification, a partnership of the USGS GAP program, US Forest Service, Ecological Society of America and Natureserve, with adoption and support from many federal & state agencies and nonprofit conservation groups. The USNVC grew out of the US National Park Service Vegetation Mapping Program, a mid-1990's effort led by The Nature Conservancy, Esri and the University of California. The classification standard is now an international standard, with associated ecological mapping occurring around the world. NVC is a hierarchical taxonomy of 8 levels, from top down: Class, Subclass, Formation, Division, Macrogroup, Group, Alliance, Association. The layers in this webmap represent 4 distinct programs: 1. The California Native Plant Society/Calif Dept of Fish & Wildlife Vegetation Classification and Mapping Program (Full Description of these layers is at the CNPS MS10 Service Registration Page and Cnps MS10B Service Registration Page . 2. USGS Gap Protected Areas Database, full description at the PADUS registration page . 3. USGS Gap Landcover, full description below 4. Natureserve Ecological Systems, full description belowLAYER NAMING: All Layer names follow this pattern: Source - Program - Level - Scale - RegionSource - Program = who created the data: Nserve = Natureserve, GapLC = USGS Gap Program Landcover Data PADUS = USGS Gap Protected Areas of the USA program Cnps/Cdfw = California Native Plant Society/Calif Dept of Fish & Wildlife, often followed by the project name such as: SFhill = Sierra Foothills, Marin Open Space, MMWD = Marin Municipal Water District etc. National Parks are included and may be named by their standard 4-letter code ie YOSE = Yosemite, PORE = Point Reyes.Level: The level in the NVC Hierarchy which this layer is based on: Base = Alliances and Associations Mac =

Geographic Information System (GIS) analyses are an essential part of natural resource management and research. Calculating and summarizing data within intersecting GIS layers is common practice for analysts and researchers. However, the various tools and steps required to complete this process are slow and tedious, requiring many tools iterating over hundreds, or even thousands of datasets. USGS scientists will combine a series of ArcGIS geoprocessing capabilities with custom scripts to create tools that will calculate, summarize, and organize large amounts of data that can span many temporal and spatial scales with minimal user input. The tools work with polygons, lines, points, and rasters to calculate relevant summary data and combine them into a single output table that can be easily incorporated into statistical analyses. These tools are useful for anyone interested in using an automated script to quickly compile summary information within all areas of interest in a GIS dataset.

Toolbox Use
License
Creative Commons-PDDC
Recommended Citation
Welty JL, Jeffries MI, Arkle RS, Pilliod DS, Kemp SK. 2021. GIS Clipping and Summarization Toolbox: U.S. Geological Survey Software Release. https://doi.org/10.5066/P99X8558

The files linked to this reference are the geospatial data created as part of the completion of the baseline vegetation inventory project for the NPS park unit. Current format is ArcGIS file geodatabase but older formats may exist as shapefiles. We converted the photointerpreted data into a format usable in a geographic information system (GIS) by employing three fundamental processes: (1) orthorectify, (2) digitize, and (3) develop the geodatabase. All digital map automation was projected in Universal Transverse Mercator (UTM), Zone 16, using the North American Datum of 1983 (NAD83). Orthorectify: We orthorectified the interpreted overlays by using OrthoMapper, a softcopy photogrammetric software for GIS. One function of OrthoMapper is to create orthorectified imagery from scanned and unrectified imagery (Image Processing Software, Inc., 2002). The software features a method of visual orientation involving a point-and-click operation that uses existing orthorectified horizontal and vertical base maps. Of primary importance to us, OrthoMapper also has the capability to orthorectify the photointerpreted overlays of each photograph based on the reference information provided. Digitize: To produce a polygon vector layer for use in ArcGIS (Environmental Systems Research Institute [ESRI], Redlands, California), we converted each raster-based image mosaic of orthorectified overlays containing the photointerpreted data into a grid format by using ArcGIS. In ArcGIS, we used the ArcScan extension to trace the raster data and produce ESRI shapefiles. We digitally assigned map-attribute codes (both map-class codes and physiognomic modifier codes) to the polygons and checked the digital data against the photointerpreted overlays for line and attribute consistency. Ultimately, we merged the individual layers into a seamless layer. Geodatabase: At this stage, the map layer has only map-attribute codes assigned to each polygon. To assign meaningful information to each polygon (e.g., map-class names, physiognomic definitions, links to NVCS types), we produced a feature-class table, along with other supportive tables and subsequently related them together via an ArcGIS Geodatabase. This geodatabase also links the map to other feature-class layers produced from this project, including vegetation sample plots, accuracy assessment (AA) sites, aerial photo locations, and project boundary extent. A geodatabase provides access to a variety of interlocking data sets, is expandable, and equips resource managers and researchers with a powerful GIS tool.

(Link to Metadata) Circa 2001 land use / land cover (LULC) for the Lake Champlain Basin. The goal in creating this layer was to generate an "improved" version of NLCD 2001 using ancillayr GIS data and Landsat satellite imagery. The Lake Champlain Basin Program (LCBP) is a joint federal-state initiative that helps to monitor and protect Lake Champlain and its contributing watersheds. One area of particular concern is nutrient loading to the Lake, particularly phosphorus (P), from terrestrial and non-lake sources. In order to quantify how much P is entering the lake, it is crucial to have an accurate representation of land use for the Basin. This layer represents an updated digital land use - land cover (LULC) map for the entire Lake Champlain Basin, termed LCB 2001. This updated LULC layer was generated by using an expert system that integrated the 2001 National Land Cover Database (NLCD) with ancillary GIS datasets and circa 2001 Landsat satellite imagery. A primary focus of this expert system was to improve the mapping accuracy of the agriculture LULC class by reducing the confusion with urban open space. An accuracy assessment was carried out by comparing the classification to temporally comparable high resolution imagery. The overall accuracy of LCB 2001 was 88%. The user's accuracy for the urban and agricultural classes, those considered to be the greatest sources of phosphorous, was 84% and 89% respectively. LCB 2001 was produced largely by improving NLCD 2001 using ancillary data. The process of generating LCB 2001 was comprised of three phases: 1) overlay of roads, 2) expert system classification, and 3) assessment and manual correction. Phase 1 was carried out using the aggregate 8-class version of NLCD 2001. The corrected road vector lines were converted to a raster layer with a cell size and alignment matching that of NLCD 2001. The road pixels were incorporated into the NLCD 2001 layer using standard raster overlay procedures in which any pixel in NLCD 2001 that corresponded with a road pixel was reassigned to the urban category. The expert system was employed largely to deal with the accuracy issues surrounding agriculture and urban open land. Edge effects and registration differences between NLCD 2001 and the improved CLU layer made simply overlaying the two an unacceptable solution. To overcome this limitation the expert system was developed and deployed using Definiens Professional software (Definiens AG, Munich, Germany). The expert system took advantage of Definiens Professional's ability to "segment" object polygons from image and thematic raster layers. Image object polygons are groups of pixels with similar spectral and spatial characteristics. Image object polygons allow for the inclusion of rules based on complex topological relationships. Image object polygons for this project were derived from both the spring and fall circa 2001 Landsat satellite scenes, but were constrained to the boundaries of the Improved CLU layer and NLCD 2001. Thus, each object polygon consisted of groups of pixels that were spectrally and spatially similar and share the same attributes with respect to the Improved CLU layer and the NLCD 2001 layer. The expert system first evaluated whether or not the object fell into the confirmed agriculture or urban-open categories based on the Improved CLU layer. If either of these tests proved true then the object was assigned to the corresponding class. If the test failed then the alternate scenarios were evaluated. For objects originally classified as agriculture in NLCD 2001 the object was assigned to the output agriculture class only if the object bordered an object already classified as agriculture (to deal with edge effects and layer alignment issues) or if the object was also in the improved CLU layer's possible agriculture category. This rule ran in an iterative loop to compensate for the fact that once objects were classified as agriculture they would influence other border objects. The rule only stopped executing once all objects were finished changing their class assignment. If the object was not assigned to the output agriculture class at this stage (those classified as agriculture in NLCD 2001, but not in LCB 2001) it was evaluated using a series of spectral and spatial rules to assign it to the output brush or urban-open classes. This set of spectral and spatial rules applied a fuzzy class assignment. The object was considered to be more likely to be brush the darker it was and the further it was from urban areas. The object was considered more likely to be urban if it was near urban areas and brighter. For all other classes the objects adopted the NLCD 2001 class. Following the running of the expert system the output classification was manually compared to the Landsat imagery and any objects that appeared to be misclassified were reassigned. As the goal of the project was to maintain as much consistency with NLCD 2001 as possible the layer was maintained in its original coordinate system - USA Albers Equal Area Conic, USGS Version, NAD83 datum (meters).

In order to use the QGIS plugin ‘Seilaplan’ for digital cable line planning, a digital terrain model (DTM) is required. In this tutorial video, we show how to merge multiple DTM raster tiles into one file, using the QGIS tool ‘Virtual Raster’. This simplifies the digital planning of a cable line using the QGIS plugin ‘Seilaplan’. Please note that the tutorial language is German! Link to Seilaplan website: https://seilaplan.wsl.ch

Für die Verwendung des QGIS Plugins Seilaplan zur digitalen Seillinienplanung ist ein digitales Höhenmodell (DHM) nötig. In diesem Tutorialvideo zeigen wir, wie man mit dem QGIS-Plugin Virtuelles Raster mehrere DHM-Kacheln zu einem einzigen Rasterfile zusammenfügen und abspeichern kann. Für die Seillinienplanung mit Seilaplan muss nun nur noch eine Datei, mein neues virtuelles Raster, ausgewählt werden. Link zur Seilaplan-Website: https://seilaplan.wsl.ch

Please visit the User Guide to learn about using the Conservation Opportunities Modeler.

CA Nature supports the California Natural Resources Agency’s goals for equitable access for all, the conservation of the state’s biodiversity, and expanding the use of nature-based solutions to address climate change.

The Conservation Opportunities Modeler uses a technique called a Weighted Raster Overlay (WRO) to evaluate multiple factors simultaneously. You can select layers from almost 50 layers in library, assign a weight to each selected layer, and then a scores to the available variables. These are then combined to show the range of combined values across the landscape, whether high or low based on your assigned weights.

Data libraries are available to explore opportunities for access for all, biodiversity, climate mitigation and adaptation, as well as opportunities that integrate across multiple challenges. After your model is complete, run it online and explore the results through interactive summaries and comparison against data from CA Nature or other sources.

Use the Conservation Opportunities Modeler to explore opportunities through building your own scenarios.

The files linked to this reference are the geospatial data created as part of the completion of the baseline vegetation inventory project for the NPS park unit. Current format is ArcGIS file geodatabase but older formats may exist as shapefiles. We converted the photointerpreted data into a GIS-usable format employing three fundamental processes; (1) orthorectify, (2) digitize, and (3) database enhancement. All digital map automation was projected in Universal Transverse Mercator (UTM) projection, Zone 12, using North American Datum of 1983 (NAD83). To produce a polygon vector coverage for use in GIS, we converted each raster-based image mosaic of orthorectified overlays containing the photointerpreted data into a grid format using ArcInfo (Version 8.0.2, Environmental Systems Research Institute, Redlands, California). In ArcTools, we used the ArcScan utility to trace the polygon data and produce ArcInfo vector-based coverages. We digitally assigned map attribute codes (both map class codes and physiognomic modifier codes) to the polygons, and checked the digital data against the photointerpreted overlays for line and attribute consistency. Ultimately, we merged the 78 individual coverages into a seamless map coverage of GNP and immediate environs. We synchronized polygons and attributes along the boundary between the GNP and WLNP map coverages. Although GNP and WLNP are two separate map coverages, they are seamless in the sense they edge tie perfectly in both polygon location and map attribute.

Summary: This repository contains spatial data files representing the density of vegetation cover within a 200 meter radius of points on a grid across the land area of New York City (NYC), New York, USA based on 2017 six-inch resolution land cover data, as well as SQL code used to carry out the analysis. The 200 meter radius was selected based on a study led by researchers at the NYC Department of Health and Mental Hygiene, which found that for a given point in the city, cooling benefits of vegetation only begin to accrue once the vegetation cover within a 200 meter radius is at least 32% (Johnson et al. 2020). The grid spacing of 100 feet in north/south and east/west directions was intended to provide granular enough detail to offer useful insights at a local scale (e.g., within a neighborhood) while keeping the amount of data needed to be processed for this manageable. The contained files were developed by the NY Cities Program of The Nature Conservancy and the NYC Environmental Justice Alliance through the Just Nature NYC Partnership. Additional context and interpretation of this work is available in a blog post.

References: Johnson, S., Z. Ross, I. Kheirbek, and K. Ito. 2020. Characterization of intra-urban spatial variation in observed summer ambient temperature from the New York City Community Air Survey. Urban Climate 31:100583. https://doi.org/10.1016/j.uclim.2020.100583

Files in this Repository: Spatial Data (all data are in the New York State Plane Coordinate System - Long Island Zone, North American Datum 1983, EPSG 2263): Points with unique identifiers (fid) and data on proportion tree canopy cover (prop_canopy), proportion grass/shrub cover (prop_grassshrub), and proportion total vegetation cover (prop_veg) within a 200 meter radius (same data made available in two commonly used formats, Esri File GeoDatabase and GeoPackage): nyc_propveg2017_200mbuffer_100ftgrid_nowater.gdb.zip nyc_propveg2017_200mbuffer_100ftgrid_nowater.gpkg Raster Data with the proportion total vegetation within a 200 meter radius of the center of each cell (pixel centers align with the spatial point data) nyc_propveg2017_200mbuffer_100ftgrid_nowater.tif Computer Code: Code for generating the point data in PostgreSQL/PostGIS, assuming the data sources listed below are already in a PostGIS database. nyc_point_buffer_vegetation_overlay.sql

Data Sources and Methods: We used two openly available datasets from the City of New York for this analysis: Borough Boundaries (Clipped to Shoreline) for NYC, from the NYC Department of City Planning, available at https://www.nyc.gov/site/planning/data-maps/open-data/districts-download-metadata.page Six-inch resolution land cover data for New York City as of 2017, available at https://data.cityofnewyork.us/Environment/Land-Cover-Raster-Data-2017-6in-Resolution/he6d-2qns All data were used in the New York State Plane Coordinate System, Long Island Zone (EPSG 2263). Land cover data were used in a polygonized form for these analyses. The general steps for developing the data available in this repository were as follows: Create a grid of points across the city, based on the full extent of the Borough Boundaries dataset, with points 100 feet from one another in east/west and north/south directions Delete any points that do not overlap the areas in the Borough Boundaries dataset. Create circles centered at each point, with a radius of 200 meters (656.168 feet) in line with the aforementioned paper (Johnson et al. 2020). Overlay the circles with the land cover data, and calculate the proportion of the land cover that was grass/shrub and tree canopy land cover types. Note, because the land cover data consistently ended at the boundaries of NYC, for points within 200 meters of Nassau and Westchester Counties, the area with land cover data was smaller than the area of the circles. Relate the results from the overlay analysis back to the associated points. Create a raster data layer from the point data, with 100 foot by 100 foot resolution, where the center of each pixel is at the location of the respective points. Areas between the Borough Boundary polygons (open water of NY Harbor) are coded as "no data." All steps except for the creation of the raster dataset were conducted in PostgreSQL/PostGIS, as documented in nyc_point_buffer_vegetation_overlay.sql. The conversion of the results to a raster dataset was done in QGIS (version 3.28), ultimately using the gdal_rasterize function.

Background: Malaria continues to pose a major public health challenge in tropical regions. Despite significant efforts to control malaria in Tanzania, there are still residual transmission cases. Unfortunately, little is known about where these residual malaria transmission cases occur and how they spread. In Tanzania, for example, the transmission is heterogeneously distributed. In order to effectively control and prevent the spread of malaria, it is essential to understand the spatial distribution and transmission patterns of the disease. This study seeks to predict areas that are at high risk of malaria transmission so that intervention measures can be developed to accelerate malaria elimination efforts.

Methods: This study employs a geospatial-based model to predict and map out malaria risk area in Kilombero Valley. Environmental factors related to malaria transmission were considered and assigned valuable weights in the Analytic Hierarchy Process (AHP), an online system using a pairwise comparison technique. The malaria hazard map was generated by a weighted overlay of the altitude, slope, curvature, aspect, rainfall distribution, and distance to streams in Geographic Information Systems (GIS). Finally, the risk map was created by overlaying components of malaria risk including hazards, elements at risk, and vulnerability. Results: The study demonstrates that the majority of the study area falls under the moderate-risk level (61%), followed by the low-risk level (31%), while the high-malaria risk area covers a small area, which occupies only 8% of the total area. Conclusion: The findings of this study are crucial for developing spatially targeted interventions against malaria transmission in residual transmission settings. Predicted areas prone to malaria risk provide information that will inform decision-makers and policymakers for proper planning, monitoring, and deployment of interventions. Methods Data acquisition and description The study employed both primary and secondary data, which were collected from numerous sources based on the input required for the implementation of the predictive model. Data collected includes the locations of all public and private health centers that were downloaded free from the health portal of the United Republic of Tanzania, Ministry of Health, Community Development, Gender, Elderly, and Children, through the universal resource locator (URL) (http://moh.go.tz/hfrportal/). Human population data was collected from the 2012 population housing census (PHC) for the United Republic of Tanzania report. Rainfall data were obtained from two local offices; Kilombero Agricultural Training and Research Institute (KATRIN) and Kilombero Valley Teak Company (KVTC). These offices collect meteorological data for agricultural purposes. Monthly data from 2012 to 2017 provided from thirteen (13) weather stations. Road and stream network shapefiles were downloaded free from the MapCruzin website via URL (https://mapcruzin.com/free-tanzania-arcgis-maps-shapefiles.htm). With respect to the size of the study area, five neighboring scenes of the Landsat 8 OLI/TIRS images (path/row: 167/65, 167/66, 167/67, 168/66 and 168/67) were downloaded freely from the United States Geological Survey (USGS) website via URL: http://earthexplorer.usgs.gov. From July to November 2017, the images were selected and downloaded from the USGS Earth Explorer archive based on the lowest amount of cloud cover coverage as viewed from the archive before downloading. Finally, the digital elevation data with a spatial resolution of three arc-seconds (90m by 90m) using WGS 84 datum and the Geographic Coordinate System were downloaded free from the Shuttle Radar Topography Mission (SRTM) via URL (https://dds.cr.usgs.gov/srtm/version2_1/SRTM3/Africa/). Only six tiles that fall in the study area were downloaded, coded tiles as S08E035, S09E035, S10E035, S08E036, S09E036, S10E036, S08E037, S09E037 and S10E037. Preparation and Creation of Model Factor Parameters Creation of Elevation Factor All six coded tiles were imported into the GIS environment for further analysis. Data management tools, with raster/raster data set/mosaic to new raster feature, were used to join the tiles and form an elevation map layer. Using the spatial analyst tool/reclassify feature, the generated elevation map was then classified into five classes as 109–358, 359–530, 531–747, 748–1017 and >1018 m.a.s.l. and new values were assigned for each class as 1, 2, 3, 4 and 5, respectively, with regards to the relationship with mosquito distribution and malaria risk. Finally, the elevation map based on malaria risk level is levelled as very high, high, moderate, low and very low respectively. Creation of Slope Factor A slope map was created from the generated elevation map layer, using a spatial analysis tool/surface/slope feature. Also, the slope raster layer was further reclassified into five subgroups based on predefined slope classes using standard classification schemes, namely quantiles as 0–0.58, 0.59–2.90, 2.91–6.40, 6.41–14.54 and >14.54. This classification scheme divides the range of attribute values into equal-sized sub-ranges, which allow specifying the number of the intervals while the system determines where the breaks should be. The reclassified slope raster layer subgroups were ranked 1, 2, 3, 4 and 5 according to the degree of suitability for malaria incidence in the locality. To elaborate, the steeper slope values are related to lesser malaria hazards, and the gentler slopes are highly susceptible to malaria incidences. Finally, the slope map based on malaria risk level is leveled as very high, high, moderate, low and very low respectively. Creation of Curvature Factor Curvature is another topographical factor that was created from the generated elevation map using the spatial analysis tool/surface/curvature feature. The curvature raster layer was further reclassified into five subgroups based on predefined curvature class. The reclassified curvature raster layer subgroups were ranked to 1, 2, 3, 4 and 5 according to their degree of suitability for malaria occurrence. To explain, this affects the acceleration and deceleration of flow across the surface. A negative value indicates that the surface is upwardly convex, and flow will be decelerated, which is related to being highly susceptible to malaria incidences. A positive profile indicates that the surface is upwardly concave and the flow will be accelerated which is related to a lesser malaria hazard, while a value of zero indicates that the surface is linear and related to a moderate malaria hazard. Lastly, the curvature map based on malaria risk level is leveled as very high, high, moderate, low, and very low respectively.
Creation of Aspect Factor As a topographic factor associated with mosquito larval habitat formation, aspect determines the amount of sunlight an area receives. The more sunlight received the stronger the influence on temperature, which may affect mosquito larval survival. The aspect of the study area also was generated from the elevation map using spatial analyst tools/ raster /surface /aspect feature. The aspect raster layer was further reclassified into five subgroups based on predefined aspect class. The reclassified aspect raster layer subgroups were ranked as 1, 2, 3, 4 and 5 according to the degree of suitability for malaria incidence, and new values were re-assigned in order of malaria hazard rating. Finally, the aspect map based on malaria risk level is leveled as very high, high, moderate, low, and very low, respectively. Creation of Human Population Distribution Factor Human population data was used to generate a population distribution map related to malaria occurrence. Kilombero Valley has a total of 42 wards, the data was organized in Ms excel 2016 and imported into the GIS environment for the analysis, Inverse Distance Weighted (IDW) interpolation in the spatial analyst tool was applied to interpolate the population distribution map. The population distribution map was further reclassified into five subgroups based on potential to malaria risk. The reclassified map layer subgroups were ranked according to the vulnerability to malaria incidence in the locality such as areas having high population having the highest vulnerability and the less population having less vulnerable, and the new value was assigned as 1, 2, 3, 4 and 5, and then leveled as very high, high, moderate, low and very low malaria risk level, respectively. Creation of Proximity to Health Facilities Factor The distribution of health facilities has a significant impact on the malaria vulnerability of the population dwellings in the Kilombero Valley. The health facility layer was created by computing distance analysis using proximity multiple ring buffer features in spatial analyst tool/multiple ring buffer. Then the map layer was reclassified into five sub-layers such as within (0–5) km, (5.1–10) km, (10.1–20) km, (20.1–50) km and >50km. According to a WHO report, it is indicated that the human population who live nearby or easily accessible to health facilities is less vulnerable to malaria incidence than the ones who are very far from the health facilities due to the distance limitation for the health services. Later on, the new values were assigned as 1, 2, 3, 4 and 5, and then reclassified as very high, high, moderate, low and very low malaria risk levels, respectively. Creation of Proximity to Road Network Factor The distance to the road network is also a significant factor, as it can be used as an estimation of the access to present healthcare facilities in the area. Buffer zones were calculated on the path of the road to determine the effect of the road on malaria prevalence. The road shapefile of the study area was inputted into GIS environment and spatial analyst tools / multiple ring buffer feature were used to generate five buffer zones with the

scripts.zip

arcgisTools.atbx: terrainDerivatives: make terrain derivatives from digital terrain model (Band 1 = TPI (50 m radius circle), Band 2 = square root of slope, Band 3 = TPI (annulus), Band 4 = hillshade, Band 5 = multidirectional hillshades, Band 6 = slopeshade). rasterizeFeatures: convert vector polygons to raster masks (1 = feature, 0 = background).

makeChips.R: R function to break terrain derivatives and chips into image chips of a defined size. makeTerrainDerivatives.R: R function to generated 6-band terrain derivatives from digital terrain data (same as ArcGIS Pro tool). merge_logs.R: R script to merge training logs into a single file. predictToExtents.ipynb: Python notebook to use trained model to predict to new data. trainExperiments.ipynb: Python notebook used to train semantic segmentation models using PyTorch and the Segmentation Models package. assessmentExperiments.ipynb: Python code to generate assessment metrics using PyTorch and the torchmetrics library. graphs_results.R: R code to make graphs with ggplot2 to summarize results. makeChipsList.R: R code to generate lists of chips in a directory. makeMasks.R: R function to make raster masks from vector data (same as rasterizeFeatures ArcGIS Pro tool).

terraceDL.zip

dems: LiDAR DTM data partitioned into training, testing, and validation datasets based on HUC8 watershed boundaries. Original DTM data were provided by the Iowa BMP mapping project: https://www.gis.iastate.edu/BMPs. extents: extents of the training, testing, and validation areas as defined by HUC 8 watershed boundaries. vectors: vector features representing agricultural terraces and partitioned into separate training, testing, and validation datasets. Original digitized features were provided by the Iowa BMP Mapping Project: https://www.gis.iastate.edu/BMPs.

Reason for SelectionThe Southeast United States is a global biodiversity hotspot that supports many rare and endemic reptile and amphibian species (Barrett et al. 2014, EPA 2014). These species are experiencing dramatic population declines driven by habitat loss, pollution, invasive species, and disease (Sutherland and deMaynadier 2012, EPA 2014, CI et al. 2004). Amphibians provide an early signal of environmental change because they rely on both terrestrial and aquatic habitats, are sensitive to pollutants, and are often narrowly adapted to specific geographic areas and climatic conditions. As a result, they serve as effective indicators of ecosystem health (CI et al. 2004, EPA 2014). Their association with particular microhabitats and microclimates makes amphibians vulnerable to climate change, and Southeast amphibians are predicted to lose significant amounts of climatically suitable habitat in the future (Barrett et al. 2014). PARCAs also represent the condition and arrangement of embedded isolated wetlands. Many amphibians breed in temporary (i.e., ephemeral) wetlands surrounded by upland habitat, which are not well-captured by existing indicators in the Blueprint (Erwin et al. 2016).Input DataSoutheast Blueprint 2024 extent2023 U.S. Census TIGER/Line state boundaries, accessed 4-5-2024: download the data Southeast Priority Amphibian and Reptile Conservation Areas (PARCAs) PARCAs for all Southeast states except for Mississippi, Virginia, and Kentucky, shared by José Garrido with the Amphibian and Reptile Conservancy (ARC) on 3-5-2024PARCAs for Mississippi, shared by Luis Tirado with ARC on 4-26-2024 (these PARCAs were identified more recently and were not yet captured in ARC’s Southeast PARCAs dataset)South Atlantic PARCAs: Neuse Tar River PARCA (this PARCA was identified through a project funded by the South Atlantic Landscape Conservation Cooperative and is not yet captured in ARC’s Southeast PARCAs dataset; we added this PARCA after consultation with ARC staff) To view a map depicting some of the PARCAs provided, scroll to the bottom of the work page of the ARC website under the heading “PARCAs Nationwide”; to access the data, email info@ARCProtects.org. PARCA is a nonregulatory designation established to raise public awareness and spark voluntary action by landowners and conservation partners to benefit amphibians and/or reptiles. Areas are nominated using scientific criteria and expert review, drawing on the concepts of species rarity, richness, regional responsibility, and landscape integrity. Modeled in part after the Important Bird Areas program developed by BirdLife International, PARCAs are intended to be nationally coordinated but locally implemented at state or regional scales. Importantly, PARCAs are not designed to compete with existing landscape biodiversity initiatives, but to complement them, providing an additional spatially explicit layer for conservation consideration.
PARCAs are intended to be established in areas: capable of supporting viable amphibian and reptile populations, occupied by rare, imperiled, or at-risk species, and rich in species diversity or endemism. For example, species used in identifying the PARCAs in the Southeast include: alligator snapping turtle, Barbour’s map turtle, one-toed amphiuma, Savannah slimy salamander, Mabee’s salamander, dwarf waterdog, Neuse river waterdog, chicken turtle, spotted turtle, tiger salamander, rainbow snake, lesser siren, gopher frog, Eastern diamondback rattlesnake, Southern hognose snake, pine snake, flatwoods salamander, gopher tortoise, striped newt, pine barrens tree frog, indigo snake, and others. There are four major implementation steps: Regional PARC task teams or state experts can use the criteria and modify them when appropriate to designate potential PARCAs in their area of interest. Following the identification of all potential PARCAs, the group then reduces these to a final set of exceptional sites that best represent the area of interest. Experts and stakeholders in the area of interest collaborate to produce a map that identifies these peer-reviewed PARCAs. Final PARCAs are shared with the community to encourage the implementation of voluntary habitat management and conservation efforts. PARCA boundaries can be updated as needed. Mapping Steps Merge the three PARCA polygon datasets and convert from vector to a 30 m pixel raster using the ArcPy Feature to Raster function. Give all PARCAs a value of 1.Add zero values to represent the extent of the source data and to make it perform better in online tools. Convert to raster the TIGER/Line state boundaries for all SEAFWA states except for Virginia and Kentucky and assign them a value of 0. We excluded Virginia and Kentucky because PARCAs have not yet been identified for these states. Use the Cell Statistics “MAX” function to combine the two above rasters.As a final step, clip to the spatial extent of Southeast Blueprint 2024. Note: For more details on the mapping steps, code used to create this layer is available in the Southeast Blueprint Data Download under > 6_Code.Final indicator valuesIndicator values are assigned as follows:1 = Priority Amphibian and Reptile Conservation Area (PARCA) 0 = Not a PARCA (excluding Kentucky and Virginia)Known IssuesThe mapping of this indicator is relatively coarse and doesn’t always capture differences in pixel-level quality in the outer edge of PARCAs. For example, some PARCAs include developed areas.This indicator is binary and doesn’t capture the full continuum of value across the Southeast.The methods of combining expert knowledge and data in this indicator may have caused some poorly known and/or under-surveyed areas to be scored too low.This indicator underprioritizes important reptile and amphibian habitat in Kentucky and Virginia because PARCAs have not yet been identified for these areas. ARC is working to expand PARCAs to more states in the future.Because of the state-by-state PARCA development and review process, sometimes PARCA boundaries stop at the state line, though suitable habitat for reptiles and amphibians does not always follow jurisdictional boundaries.This indicator excludes “protected” PARCAs maintained by ARC that are too small and spatially explicit to share publicly due to concerns about poaching. As a result, it underprioritizes some important reptile and amphibian habitat. However, these areas are, with a few exceptions in northwest Arkansas and Tennessee, generally well-represented in the Blueprint due to their value for other indicators.This indicator contains small gaps 1-2 pixels wide between some adjoining PARCAs that likely should be continuous, often on either side of a state line. These are represented in the source data as separate polygons with tiny gaps between them, and these translate into gaps in the resulting indicator raster. This results from the PARCA digitizing process and does not reflect meaningful differences in priority.Disclaimer: Comparing with Older Indicator VersionsThere are numerous problems with using Southeast Blueprint indicators for change analysis. Please consult Blueprint staff if you would like to do this (email hilary_morris@fws.gov).Literature CitedAmphibian and Reptile Conservancy. Priority Amphibian and Reptile Conservation Areas (PARCAs). Revised February 7, 2024. Apodaca, Joseph. 2013. Determining Priority Amphibian and Reptile Conservation Areas (PARCAs) in the South Atlantic landscape, and assessing their efficacy for cross-taxa conservation: Geographic Dataset. [https://www.sciencebase.gov/catalog/item/59e105a1e4b05fe04cd000df]. Barrett, Kyle, Nathan P. Nibbelink, John C. Maerz; Identifying Priority Species and Conservation Opportunities Under Future Climate Scenarios: Amphibians in a Biodiversity Hotspot. Journal of Fish and Wildlife Management 1 December 2014; 5 (2): 282–297. [https://doi.org/10.3996/022014-JFWM-015]. Conservation International, International Union for the Conservation of Nature, NatureServe. 2004. Global Amphibian Assessment Factsheet. [https://www.natureserve.org/sites/default/files/amphibian_fact_sheet.pdf]. Environmental Protection Agency. 2014. Mean Amphibian Species Richness: Southeast. EnviroAtlas Factsheet. [https://enviroatlas.epa.gov/enviroatlas/DataFactSheets/pdf/ESN/MeanAmphibianSpeciesRichness.pdf]. Erwin, K. J., Chandler, H. C., Palis, J. G., Gorman, T. A., & Haas, C. A. (2016). Herpetofaunal Communities in Ephemeral Wetlands Embedded within Longleaf Pine Flatwoods of the Gulf Coastal Plain. Southeastern Naturalist, 15(3), 431–447. [https://www.jstor.org/stable/26454722]. Sutherland and deMaynadier. 2012. Model Criteria and Implementation Guidance for a Priority Amphibian and Reptile Conservation Area (PARCA) System in the USA. Partners in Amphibian and Reptile Conservation, Technical Publication PARCA-1. 28 pp. [https://parcplace.org/wp-content/uploads/2017/08/PARCA_System_Criteria_and_Implementation_Guidance_FINAL.pdf]. U.S. Department of Commerce, U.S. Census Bureau, Geography Division, Spatial Data Collection and Products Branch. TIGER/Line Shapefile, 2023, U.S. Current State and Equivalent National. 2023. [https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-line-file.html].

Accurate coastal wave and hydrodynamic modelling relies on quality bathymetric input. Many national scale modelling studies, hindcast and forecast products, have, or are currently using a 2009 digital elevation model (DEM), which does not include recently available bathymetric surveys and is now out of date. There are immediate needs for an updated national product, preceding the delivery of the AusSeabed program’s Global Multi-Resolution Topography for Australian coastal and ocean models. There are also challenges in stitching coarse resolution DEMs, which are often too shallow where they meet high-resolution information (e.g. LiDAR surveys) and require supervised/manual modifications (e.g. NSW, Perth, and Portland VIC bathymetries). This report updates the 2009 topography and bathymetry with a selection of nearshore surveys and demonstrates where the 2009 dataset and nearshore bathymetries do not matchup. Lineage: All of the datasets listed in Table 1 (see supporting files) were used in previous CSIRO internal projects or download from online data portals and processed using QGIS and R’s ‘raster’ package. The Perth LiDAR surveys were provided as points and gridded in R using raster::rasterFromXYZ(). The Macquarie Harbour contour lines were regridded in QGIS using the TIN interpolator. Each dataset was mapped with an accompanying Type Identifier (TID) following the conventions of the GEBCO dataset. The mapping went through several iterations, at each iteration the blending was checked for inconstancy, i.e., where the GA250m DEM was too shallow when it met the high-resolution LiDAR surveys. QGIS v3.16.4 was used to draw masks over inconstant blending and GA250 values falling within the mask and between two depths were assigned NA (no-data). LiDAR datasets were projected to +proj=longlat +datum=WGS84 +no_defs using raster::projectRaster(), resampled to the GA250 grid using raster::resample() and then merged with raster::merge(). Nearest neighbour resampling was performed for all datasets except for GEBCO ~500m product, which used the bilinear method. The order of the mapping overlay is sequential from TID = 1 being the base, through to 107, where 0 is the gap filled values.

Permissions are required for all code and internal datasets (Contact Julian OGrady).