In this course, you will learn to work within the free and open-source R environment with a specific focus on working with and analyzing geospatial data. We will cover a wide variety of data and spatial data analytics topics, and you will learn how to code in R along the way. The Introduction module provides more background info about the course and course set up. This course is designed for someone with some prior GIS knowledge. For example, you should know the basics of working with maps, map projections, and vector and raster data. You should be able to perform common spatial analysis tasks and make map layouts. If you do not have a GIS background, we would recommend checking out the West Virginia View GIScience class. We do not assume that you have any prior experience with R or with coding. So, don't worry if you haven't developed these skill sets yet. That is a major goal in this course. Background material will be provided using code examples, videos, and presentations. We have provided assignments to offer hands-on learning opportunities. Data links for the lecture modules are provided within each module while data for the assignments are linked to the assignment buttons below. Please see the sequencing document for our suggested order in which to work through the material. After completing this course you will be able to: prepare, manipulate, query, and generally work with data in R. perform data summarization, comparisons, and statistical tests. create quality graphs, map layouts, and interactive web maps to visualize data and findings. present your research, methods, results, and code as web pages to foster reproducible research. work with spatial data in R. analyze vector and raster geospatial data to answer a question with a spatial component. make spatial models and predictions using regression and machine learning. code in the R language at an intermediate level.

This data repository hosts datasets that are used for students to practice spatial operations introduced in R-as-GIS lectures and workshops.

This dataset was created to be used in my Capstone Project for the Google Data Analytics Professional Certificate. Data was web scraped from the state websites to combine the GIS information like FIPS, latitude, longitude, and County Codes by both number and Mailing Number.

RStudio was used for this web scrape and join. For details on how it was done you can go to the following link for my Github repository.

Feel free to follow my Github or LinkedIn profile to see what I end up doing with this Dataset.

Data files for the examples in the book Geographic Data Science in R: Visualizing and Analyzing Environmental Change by Michael C. Wimberly.

The Digital Geomorphic-GIS Map of Gulf Islands National Seashore (5-meter accuracy and 1-foot resolution 2006-2007 mapping), Mississippi and Florida is composed of GIS data layers and GIS tables, and is available in the following GRI-supported GIS data formats: 1.) a 10.1 file geodatabase (guis_geomorphology.gdb), a 2.) Open Geospatial Consortium (OGC) geopackage, and 3.) 2.2 KMZ/KML file for use in Google Earth, however, this format version of the map is limited in data layers presented and in access to GRI ancillary table information. The file geodatabase format is supported with a 1.) ArcGIS Pro map file (.mapx) file (guis_geomorphology.mapx) and individual Pro layer (.lyrx) files (for each GIS data layer), as well as with a 2.) 10.1 ArcMap (.mxd) map document (guis_geomorphology.mxd) and individual 10.1 layer (.lyr) files (for each GIS data layer). The OGC geopackage is supported with a QGIS project (.qgz) file. Upon request, the GIS data is also available in ESRI 10.1 shapefile format. Contact Stephanie O'Meara (see contact information below) to acquire the GIS data in these GIS data formats. In addition to the GIS data and supporting GIS files, three additional files comprise a GRI digital geologic-GIS dataset or map: 1.) A GIS readme file (guis_geology_gis_readme.pdf), 2.) the GRI ancillary map information document (.pdf) file (guis_geomorphology.pdf) which contains geologic unit descriptions, as well as other ancillary map information and graphics from the source map(s) used by the GRI in the production of the GRI digital geologic-GIS data for the park, and 3.) a user-friendly FAQ PDF version of the metadata (guis_geomorphology_metadata_faq.pdf). Please read the guis_geology_gis_readme.pdf for information pertaining to the proper extraction of the GIS data and other map files. Google Earth software is available for free at: https://www.google.com/earth/versions/. QGIS software is available for free at: https://www.qgis.org/en/site/. Users are encouraged to only use the Google Earth data for basic visualization, and to use the GIS data for any type of data analysis or investigation. The data were completed as a component of the Geologic Resources Inventory (GRI) program, a National Park Service (NPS) Inventory and Monitoring (I&M) Division funded program that is administered by the NPS Geologic Resources Division (GRD). For a complete listing of GRI products visit the GRI publications webpage: For a complete listing of GRI products visit the GRI publications webpage: https://www.nps.gov/subjects/geology/geologic-resources-inventory-products.htm. For more information about the Geologic Resources Inventory Program visit the GRI webpage: https://www.nps.gov/subjects/geology/gri,htm. At the bottom of that webpage is a "Contact Us" link if you need additional information. You may also directly contact the program coordinator, Jason Kenworthy (jason_kenworthy@nps.gov). Source geologic maps and data used to complete this GRI digital dataset were provided by the following: U.S. Geological Survey. Detailed information concerning the sources used and their contribution the GRI product are listed in the Source Citation section(s) of this metadata record (guis_geomorphology_metadata.txt or guis_geomorphology_metadata_faq.pdf). Users of this data are cautioned about the locational accuracy of features within this dataset. Based on the source map scale of 1:26,000 and United States National Map Accuracy Standards features are within (horizontally) 13.2 meters or 43.3 feet of their actual location as presented by this dataset. Users of this data should thus not assume the location of features is exactly where they are portrayed in Google Earth, ArcGIS, QGIS or other software used to display this dataset. All GIS and ancillary tables were produced as per the NPS GRI Geology-GIS Geodatabase Data Model v. 2.3. (available at: https://www.nps.gov/articles/gri-geodatabase-model.htm).

This is a collection of all GPS- and computer-generated geospatial data specific to the Alpine Treeline Warming Experiment (ATWE), located on Niwot Ridge, Colorado, USA. The experiment ran between 2008 and 2016, and consisted of three sites spread across an elevation gradient. Geospatial data for all three experimental sites and cone/seed collection locations are included in this package. ––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– Geospatial files include cone collection, experimental site, seed trap, and other GPS location/terrain data. File types include ESRI shapefiles, ESRI grid files or Arc/Info binary grids, TIFFs (.tif), and keyhole markup language (.kml) files. Trimble-imported data include plain text files (.txt), Trimble COR (CorelDRAW) files, and Trimble SSF (Standard Storage Format) files. Microsoft Excel (.xlsx) and comma-separated values (.csv) files corresponding to the attribute tables of many files within this package are also included. A complete list of files can be found in this document in the “Data File Organization” section in the included Data User's Guide. Maps are also included in this data package for reference and use. These maps are separated into two categories, 2021 maps and legacy maps, which were made in 2010. Each 2021 map has one copy in portable network graphics (.png) format, and the other in .pdf format. All legacy maps are in .pdf format. .png image files can be opened with any compatible programs, such as Preview (Mac OS) and Photos (Windows). All GIS files were imported into geopackages (.gpkg) using QGIS, and double-checked for compatibility and data/attribute integrity using ESRI ArcGIS Pro. Note that files packaged within geopackages will open in ArcGIS Pro with “main.” preceding each file name, and an extra column named “geom” defining geometry type in the attribute table. The contents of each geospatial file remain intact, unless otherwise stated in “niwot_geospatial_data_list_07012021.pdf/.xlsx”. This list of files can be found as an .xlsx and a .pdf in this archive. As an open-source file format, files within gpkgs (TIFF, shapefiles, ESRI grid or “Arc/Info Binary”) can be read using both QGIS and ArcGIS Pro, and any other geospatial softwares. Text and .csv files can be read using TextEdit/Notepad/any simple text-editing software; .csv’s can also be opened using Microsoft Excel and R. .kml files can be opened using Google Maps or Google Earth, and Trimble files are most compatible with Trimble’s GPS Pathfinder Office software. .xlsx files can be opened using Microsoft Excel. PDFs can be opened using Adobe Acrobat Reader, and any other compatible programs. A selection of original shapefiles within this archive were generated using ArcMap with associated FGDC-standardized metadata (xml file format). We are including these original files because they contain metadata only accessible using ESRI programs at this time, and so that the relationship between shapefiles and xml files is maintained. Individual xml files can be opened (without a GIS-specific program) using TextEdit or Notepad. Since ESRI’s compatibility with FGDC metadata has changed since the generation of these files, many shapefiles will require upgrading to be compatible with ESRI’s latest versions of geospatial software. These details are also noted in the “niwot_geospatial_data_list_07012021” file.

**THIS NEWER 2016 DIGITAL MAP REPLACES THE OLDER 2014 VERSION OF THE GRI GATE Geomorphological-GIS data. The Unpublished Digital Pre-Hurricane Sandy Geomorphological-GIS Map of the Gateway National Recreation Area: Sandy Hook, Jamaica Bay and Staten Island Units, New Jersey and New York is composed of GIS data layers and GIS tables in a 10.1 file geodatabase (gate_geomorphology.gdb), a 10.1 ArcMap (.MXD) map document (gate_geomorphology.mxd), individual 10.1 layer (.LYR) files for each GIS data layer, an ancillary map information (.PDF) document (gate_geomorphology.pdf) which contains source map unit descriptions, as well as other source map text, figures and tables, metadata in FGDC text (.TXT) and FAQ (.HTML) formats, and a GIS readme file (gate_gis_readme.pdf). Please read the gate_gis_readme.pdf for information pertaining to the proper extraction of the file geodatabase and other map files. To request GIS data in ESRI 10.1 shapefile format contact Stephanie O’Meara (stephanie.omeara@colostate.edu; see contact information below). The data is also available as a 2.2 KMZ/KML file for use in Google Earth, however, this format version of the map is limited in data layers presented and in access to GRI ancillary table information. Google Earth software is available for free at: http://www.google.com/earth/index.html. Users are encouraged to only use the Google Earth data for basic visualization, and to use the GIS data for any type of data analysis or investigation. The data were completed as a component of the Geologic Resources Inventory (GRI) program, a National Park Service (NPS) Inventory and Monitoring (I&M) Division funded program that is administered by the NPS Geologic Resources Division (GRD). Source geologic maps and data used to complete this GRI digital dataset were provided by the following: Rutgers University Institute of Marine and Coastal Sciences. Detailed information concerning the sources used and their contribution the GRI product are listed in the Source Citation section(s) of this metadata record (gate_metadata_faq.html; available at http://nrdata.nps.gov/geology/gri_data/gis/gate/gate_pre-sandy_metadata_faq.html). Users of this data are cautioned about the locational accuracy of features within this dataset. Based on the source map scale of 1:6,000 and United States National Map Accuracy Standards features are within (horizontally) 5.08 meters or 16.67 feet of their actual location as presented by this dataset. Users of this data should thus not assume the location of features is exactly where they are portrayed in Google Earth, ArcGIS or other software used to display this dataset. All GIS and ancillary tables were produced as per the NPS GRI Geology-GIS Geodatabase Data Model v. 2.3. (available at: http://science.nature.nps.gov/im/inventory/geology/GeologyGISDataModel.cfm). The GIS data projection is NAD83, UTM Zone 18N, however, for the KML/KMZ format the data is projected upon export to WGS84 Geographic, the native coordinate system used by Google Earth. The data is within the area of interest of Gateway National Recreation Area.

In the last decade, a plethora of algorithms have been developed for spatial ecology studies. In our case, we use some of these codes for underwater research work in applied ecology analysis of threatened endemic fishes and their natural habitat. For this, we developed codes in Rstudio® script environment to run spatial and statistical analyses for ecological response and spatial distribution models (e.g., Hijmans & Elith, 2017; Den Burg et al., 2020). The employed R packages are as follows: caret (Kuhn et al., 2020), corrplot (Wei & Simko, 2017), devtools (Wickham, 2015), dismo (Hijmans & Elith, 2017), gbm (Freund & Schapire, 1997; Friedman, 2002), ggplot2 (Wickham et al., 2019), lattice (Sarkar, 2008), lattice (Musa & Mansor, 2021), maptools (Hijmans & Elith, 2017), modelmetrics (Hvitfeldt & Silge, 2021), pander (Wickham, 2015), plyr (Wickham & Wickham, 2015), pROC (Robin et al., 2011), raster (Hijmans & Elith, 2017), RColorBrewer (Neuwirth, 2014), Rcpp (Eddelbeuttel & Balamura, 2018), rgdal (Verzani, 2011), sdm (Naimi & Araujo, 2016), sf (e.g., Zainuddin, 2023), sp (Pebesma, 2020) and usethis (Gladstone, 2022).

It is important to follow all the codes in order to obtain results from the ecological response and spatial distribution models. In particular, for the ecological scenario, we selected the Generalized Linear Model (GLM) and for the geographic scenario we selected DOMAIN, also known as Gower's metric (Carpenter et al., 1993). We selected this regression method and this distance similarity metric because of its adequacy and robustness for studies with endemic or threatened species (e.g., Naoki et al., 2006). Next, we explain the statistical parameterization for the codes immersed in the GLM and DOMAIN running:

In the first instance, we generated the background points and extracted the values of the variables (Code2_Extract_values_DWp_SC.R). Barbet-Massin et al. (2012) recommend the use of 10,000 background points when using regression methods (e.g., Generalized Linear Model) or distance-based models (e.g., DOMAIN). However, we considered important some factors such as the extent of the area and the type of study species for the correct selection of the number of points (Pers. Obs.). Then, we extracted the values of predictor variables (e.g., bioclimatic, topographic, demographic, habitat) in function of presence and background points (e.g., Hijmans and Elith, 2017).

Subsequently, we subdivide both the presence and background point groups into 75% training data and 25% test data, each group, following the method of Soberón & Nakamura (2009) and Hijmans & Elith (2017). For a training control, the 10-fold (cross-validation) method is selected, where the response variable presence is assigned as a factor. In case that some other variable would be important for the study species, it should also be assigned as a factor (Kim, 2009).

After that, we ran the code for the GBM method (Gradient Boost Machine; Code3_GBM_Relative_contribution.R and Code4_Relative_contribution.R), where we obtained the relative contribution of the variables used in the model. We parameterized the code with a Gaussian distribution and cross iteration of 5,000 repetitions (e.g., Friedman, 2002; kim, 2009; Hijmans and Elith, 2017). In addition, we considered selecting a validation interval of 4 random training points (Personal test). The obtained plots were the partial dependence blocks, in function of each predictor variable.

Subsequently, the correlation of the variables is run by Pearson's method (Code5_Pearson_Correlation.R) to evaluate multicollinearity between variables (Guisan & Hofer, 2003). It is recommended to consider a bivariate correlation ± 0.70 to discard highly correlated variables (e.g., Awan et al., 2021).

Once the above codes were run, we uploaded the same subgroups (i.e., presence and background groups with 75% training and 25% testing) (Code6_Presence&backgrounds.R) for the GLM method code (Code7_GLM_model.R). Here, we first ran the GLM models per variable to obtain the p-significance value of each variable (alpha ≤ 0.05); we selected the value one (i.e., presence) as the likelihood factor. The generated models are of polynomial degree to obtain linear and quadratic response (e.g., Fielding and Bell, 1997; Allouche et al., 2006). From these results, we ran ecological response curve models, where the resulting plots included the probability of occurrence and values for continuous variables or categories for discrete variables. The points of the presence and background training group are also included.

On the other hand, a global GLM was also run, from which the generalized model is evaluated by means of a 2 x 2 contingency matrix, including both observed and predicted records. A representation of this is shown in Table 1 (adapted from Allouche et al., 2006). In this process we select an arbitrary boundary of 0.5 to obtain better modeling performance and avoid high percentage of bias in type I (omission) or II (commission) errors (e.g., Carpenter et al., 1993; Fielding and Bell, 1997; Allouche et al., 2006; Kim, 2009; Hijmans and Elith, 2017).

Table 1. Example of 2 x 2 contingency matrix for calculating performance metrics for GLM models. A represents true presence records (true positives), B represents false presence records (false positives - error of commission), C represents true background points (true negatives) and D represents false backgrounds (false negatives - errors of omission).

Validation set

Model

True

False

Presence

A

B

Background

C

D

We then calculated the Overall and True Skill Statistics (TSS) metrics. The first is used to assess the proportion of correctly predicted cases, while the second metric assesses the prevalence of correctly predicted cases (Olden and Jackson, 2002). This metric also gives equal importance to the prevalence of presence prediction as to the random performance correction (Fielding and Bell, 1997; Allouche et al., 2006).

The last code (i.e., Code8_DOMAIN_SuitHab_model.R) is for species distribution modelling using the DOMAIN algorithm (Carpenter et al., 1993). Here, we loaded the variable stack and the presence and background group subdivided into 75% training and 25% test, each. We only included the presence training subset and the predictor variables stack in the calculation of the DOMAIN metric, as well as in the evaluation and validation of the model.

Regarding the model evaluation and estimation, we selected the following estimators:

1) partial ROC, which evaluates the approach between the curves of positive (i.e., correctly predicted presence) and negative (i.e., correctly predicted absence) cases. As farther apart these curves are, the model has a better prediction performance for the correct spatial distribution of the species (Manzanilla-Quiñones, 2020).

2) ROC/AUC curve for model validation, where an optimal performance threshold is estimated to have an expected confidence of 75% to 99% probability (De Long et al., 1988).

Existing methods for calculating directional relations in polygons (i.e. the directional similarity model, the cone-based model, and the modified cone-based model) were compared to human perceptions of change through an online survey. The results from this survey provide the first empirical validation of computational approaches to calculating directional relations in polygonal spatial data. We have found that while the evaluated methods generally agreed with each other, they varied in their alignment with human perceptions of directional relations. Specifically, translation transformations of the target and reference polygons showed greatest discrepancy to human perceptions and across methods. The online survey was developed using Qualtrics Survey Software, and participants were recruited via online messaging on social media (i.e., Twitter) with hashtags related to geographic information science. In total sixty-one individuals responded to the survey. This survey consisted of nine questions. For the first question, participants indicated how many years they have worked with GIS and/or spatial data. For the remaining eight questions, participants ranked pictorial database scenes according to degrees of their match to query scenes. Each of these questions represented a test case that Goyal and Egenhofer (2001) used to empirically evaluate the directional similarity model; participants were randomly presented with four of these questions. The query scenes were created using ArcMap and contained a pair of reference and target polygons. The database scenes were generated by gradually changing the geometry of the target polygon within each query scene. The relations between the target and reference polygon varied by the type of movement, the scaling change of the polygon, and changes in rotation. The scenarios were varied in order to capture a representative range of variability in polygon movements and changes in real world data. The R statistical computing environment was used to determine the similarity value that corresponds with each database scene based on the directional similarity model, the cone-based model, and the modified cone-based model. Using the survey responses, the frequency of first, second, third, etc. ranks were calculated for each database scene. Weight variables were multiplied by the frequencies to create an overall rank based on participant responses. A rank of one was weighted as a five, a rank of two was weighted as a four, and so on. Spearman’s rank-order correlation was used to measure the strength and direction of association between the rank determined using the three models and the rank determined using participant responses.

This seminar is an applied study of deep learning methods for extracting information from geospatial data, such as aerial imagery, multispectral imagery, digital terrain data, and other digital cartographic representations. We first provide an introduction and conceptualization of artificial neural networks (ANNs). Next, we explore appropriate loss and assessment metrics for different use cases followed by the tensor data model, which is central to applying deep learning methods. Convolutional neural networks (CNNs) are then conceptualized with scene classification use cases. Lastly, we explore semantic segmentation, object detection, and instance segmentation. The primary focus of this course is semantic segmenation for pixel-level classification. The associated GitHub repo provides a series of applied examples. We hope to continue to add examples as methods and technologies further develop. These examples make use of a vareity of datasets (e.g., SAT-6, topoDL, Inria, LandCover.ai, vfillDL, and wvlcDL). Please see the repo for links to the data and associated papers. All examples have associated videos that walk through the process, which are also linked to the repo. A variety of deep learning architectures are explored including UNet, UNet++, DeepLabv3+, and Mask R-CNN. Currenlty, two examples use ArcGIS Pro and require no coding. The remaining five examples require coding and make use of PyTorch, Python, and R within the RStudio IDE. It is assumed that you have prior knowledge of coding in the Python and R enviroinments. If you do not have experience coding, please take a look at our Open-Source GIScience and Open-Source Spatial Analytics (R) courses, which explore coding in Python and R, respectively. After completing this seminar you will be able to: explain how ANNs work including weights, bias, activation, and optimization. describe and explain different loss and assessment metrics and determine appropriate use cases. use the tensor data model to represent data as input for deep learning. explain how CNNs work including convolutional operations/layers, kernel size, stride, padding, max pooling, activation, and batch normalization. use PyTorch, Python, and R to prepare data, produce and assess scene classification models, and infer to new data. explain common semantic segmentation architectures and how these methods allow for pixel-level classification and how they are different from traditional CNNs. use PyTorch, Python, and R (or ArcGIS Pro) to prepare data, produce and assess semantic segmentation models, and infer to new data.

This dataset reflects reported incidents of crime (with the exception of murders where data exists for each victim) that occurred in the City of Chicago from 2001 to present, minus the most recent seven days. Data is extracted from the Chicago Police Department's CLEAR (Citizen Law Enforcement Analysis and Reporting) system. In order to protect the privacy of crime victims, addresses are shown at the block level only and specific locations are not identified. Should you have questions about this dataset, you may contact the Research & Development Division of the Chicago Police Department at 312.745.6071 or RandD@chicagopolice.org. Disclaimer: These crimes may be based upon preliminary information supplied to the Police Department by the reporting parties that have not been verified. The preliminary crime classifications may be changed at a later date based upon additional investigation and there is always the possibility of mechanical or human error. Therefore, the Chicago Police Department does not guarantee (either expressed or implied) the accuracy, completeness, timeliness, or correct sequencing of the information and the information should not be used for comparison purposes over time. The Chicago Police Department will not be responsible for any error or omission, or for the use of, or the results obtained from the use of this information. All data visualizations on maps should be considered approximate and attempts to derive specific addresses are strictly prohibited. The Chicago Police Department is not responsible for the content of any off-site pages that are referenced by or that reference this web page other than an official City of Chicago or Chicago Police Department web page. The user specifically acknowledges that the Chicago Police Department is not responsible for any defamatory, offensive, misleading, or illegal conduct of other users, links, or third parties and that the risk of injury from the foregoing rests entirely with the user. The unauthorized use of the words "Chicago Police Department," "Chicago Police," or any colorable imitation of these words or the unauthorized use of the Chicago Police Department logo is unlawful. This web page does not, in any way, authorize such use. Data is updated daily Tuesday through Sunday. The dataset contains more than 65,000 records/rows of data and cannot be viewed in full in Microsoft Excel. Therefore, when downloading the file, select CSV from the Export menu. Open the file in an ASCII text editor, such as Wordpad, to view and search. To access a list of Chicago Police Department - Illinois Uniform Crime Reporting (IUCR) codes, go to http://data.cityofchicago.org/Public-Safety/Chicago-Police-Department-Illinois-Uniform-Crime-R/c7ck-438e

This fileset contains example data and R scripts for a student workshop at the 2013 USIALE annual Meeting held in Austin TX. More information about this workshop is available at https://sites.google.com/site/ialestudentworkshop/

Input data for openSTARS.

This archive contains a geology map of the general Roosevelt Hot Springs region, both in PDF and ArcGIS geodatabase formats, that was created as part of the Utah FORGE project.

Note: This LCMS CONUS Cause of Change image service has been deprecated. It has been replaced by the LCMS CONUS Annual Change image service, which provides updated and consolidated change data.Please refer to the new service here: https://usfs.maps.arcgis.com/home/item.html?id=085626ec50324e5e9ad6323c050ac84dThis product is part of the Landscape Change Monitoring System (LCMS) data suite. It shows LCMS change attribution classes for each year. See additional information about change in the Entity_and_Attribute_Information or Fields section below.LCMS is a remote sensing-based system for mapping and monitoring landscape change across the United States. Its objective is to develop a consistent approach using the latest technology and advancements in change detection to produce a "best available" map of landscape change. Because no algorithm performs best in all situations, LCMS uses an ensemble of models as predictors, which improves map accuracy across a range of ecosystems and change processes (Healey et al., 2018). The resulting suite of LCMS change, land cover, and land use maps offer a holistic depiction of landscape change across the United States over the past four decades.Predictor layers for the LCMS model include outputs from the LandTrendr and CCDC change detection algorithms and terrain information. These components are all accessed and processed using Google Earth Engine (Gorelick et al., 2017). To produce annual composites, the cFmask (Zhu and Woodcock, 2012), cloudScore, and TDOM (Chastain et al., 2019) cloud and cloud shadow masking methods are applied to Landsat Tier 1 and Sentinel 2a and 2b Level-1C top of atmosphere reflectance data. The annual medoid is then computed to summarize each year into a single composite. The composite time series is temporally segmented using LandTrendr (Kennedy et al., 2010; Kennedy et al., 2018; Cohen et al., 2018). All cloud and cloud shadow free values are also temporally segmented using the CCDC algorithm (Zhu and Woodcock, 2014). LandTrendr, CCDC and terrain predictors can be used as independent predictor variables in a Random Forest (Breiman, 2001) model. LandTrendr predictor variables include fitted values, pair-wise differences, segment duration, change magnitude, and slope. CCDC predictor variables include CCDC sine and cosine coefficients (first 3 harmonics), fitted values, and pairwise differences from the Julian Day of each pixel used in the annual composites and LandTrendr. Terrain predictor variables include elevation, slope, sine of aspect, cosine of aspect, and topographic position indices (Weiss, 2001) from the USGS 3D Elevation Program (3DEP) (U.S. Geological Survey, 2019). Reference data are collected using TimeSync, a web-based tool that helps analysts visualize and interpret the Landsat data record from 1984-present (Cohen et al., 2010).Outputs fall into three categories: change, land cover, and land use. Change relates specifically to vegetation cover and includes slow loss (not included for PRUSVI), fast loss (which also includes hydrologic changes such as inundation or desiccation), and gain. These values are predicted for each year of the time series and serve as the foundational products for LCMS. References: Breiman, L. (2001). Random Forests. In Machine Learning (Vol. 45, pp. 5-32). https://doi.org/10.1023/A:1010933404324Chastain, R., Housman, I., Goldstein, J., Finco, M., and Tenneson, K. (2019). Empirical cross sensor comparison of Sentinel-2A and 2B MSI, Landsat-8 OLI, and Landsat-7 ETM top of atmosphere spectral characteristics over the conterminous United States. In Remote Sensing of Environment (Vol. 221, pp. 274-285). https://doi.org/10.1016/j.rse.2018.11.012Cohen, W. B., Yang, Z., and Kennedy, R. (2010). Detecting trends in forest disturbance and recovery using yearly Landsat time series: 2. TimeSync - Tools for calibration and validation. In Remote Sensing of Environment (Vol. 114, Issue 12, pp. 2911-2924). https://doi.org/10.1016/j.rse.2010.07.010Cohen, W. B., Yang, Z., Healey, S. P., Kennedy, R. E., and Gorelick, N. (2018). A LandTrendr multispectral ensemble for forest disturbance detection. In Remote Sensing of Environment (Vol. 205, pp. 131-140). https://doi.org/10.1016/j.rse.2017.11.015Foga, S., Scaramuzza, P.L., Guo, S., Zhu, Z., Dilley, R.D., Beckmann, T., Schmidt, G.L., Dwyer, J.L., Hughes, M.J., Laue, B. (2017). Cloud detection algorithm comparison and validation for operational Landsat data products. Remote Sensing of Environment, 194, 379-390. https://doi.org/10.1016/j.rse.2017.03.026Gorelick, N., Hancher, M., Dixon, M., Ilyushchenko, S., Thau, D., and Moore, R. (2017). Google Earth Engine: Planetary-scale geospatial analysis for everyone. In Remote Sensing of Environment (Vol. 202, pp. 18-27). https://doi.org/10.1016/j.rse.2017.06.031Healey, S. P., Cohen, W. B., Yang, Z., Kenneth Brewer, C., Brooks, E. B., Gorelick, N., Hernandez, A. J., Huang, C., Joseph Hughes, M., Kennedy, R. E., Loveland, T. R., Moisen, G. G., Schroeder, T. A., Stehman, S. V., Vogelmann, J. E., Woodcock, C. E., Yang, L., and Zhu, Z. (2018). Mapping forest change using stacked generalization: An ensemble approach. In Remote Sensing of Environment (Vol. 204, pp. 717-728). https://doi.org/10.1016/j.rse.2017.09.029Kennedy, R. E., Yang, Z., and Cohen, W. B. (2010). Detecting trends in forest disturbance and recovery using yearly Landsat time series: 1. LandTrendr - Temporal segmentation algorithms. 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In Remote Sensing of Environment (Vol. 144, pp. 152-171). https://doi.org/10.1016/j.rse.2014.01.011This record was taken from the USDA Enterprise Data Inventory that feeds into the https://data.gov catalog. Data for this record includes the following resources: ISO-19139 metadata ArcGIS Hub Dataset ArcGIS GeoService For complete information, please visit https://data.gov.

A major objective of plant ecology research is to determine the underlying processes responsible for the observed spatial distribution patterns of plant species. Plants can be approximated as points in space for this purpose, and thus, spatial point pattern analysis has become increasingly popular in ecological research. The basic piece of data for point pattern analysis is a point location of an ecological object in some study region. Therefore, point pattern analysis can only be performed if data can be collected. However, due to the lack of a convenient sampling method, a few previous studies have used point pattern analysis to examine the spatial patterns of grassland species. This is unfortunate because being able to explore point patterns in grassland systems has widespread implications for population dynamics, community-level patterns and ecological processes. In this study, we develop a new method to measure individual coordinates of species in grassland communities. This method records plant growing positions via digital picture samples that have been sub-blocked within a geographical information system (GIS). Here, we tested out the new method by measuring the individual coordinates of Stipa grandis in grazed and ungrazed S. grandis communities in a temperate steppe ecosystem in China. Furthermore, we analyzed the pattern of S. grandis by using the pair correlation function g(r) with both a homogeneous Poisson process and a heterogeneous Poisson process. Our results showed that individuals of S. grandis were overdispersed according to the homogeneous Poisson process at 0-0.16 m in the ungrazed community, while they were clustered at 0.19 m according to the homogeneous and heterogeneous Poisson processes in the grazed community. These results suggest that competitive interactions dominated the ungrazed community, while facilitative interactions dominated the grazed community. In sum, we successfully executed a new sampling method, using digital photography and a Geographical Information System, to collect experimental data on the spatial point patterns for the populations in this grassland community.

Methods 1. Data collection using digital photographs and GIS

A flat 5 m x 5 m sampling block was chosen in a study grassland community and divided with bamboo chopsticks into 100 sub-blocks of 50 cm x 50 cm (Fig. 1). A digital camera was then mounted to a telescoping stake and positioned in the center of each sub-block to photograph vegetation within a 0.25 m2 area. Pictures were taken 1.75 m above the ground at an approximate downward angle of 90° (Fig. 2). Automatic camera settings were used for focus, lighting and shutter speed. After photographing the plot as a whole, photographs were taken of each individual plant in each sub-block. In order to identify each individual plant from the digital images, each plant was uniquely marked before the pictures were taken (Fig. 2 B).

Digital images were imported into a computer as JPEG files, and the position of each plant in the pictures was determined using GIS. This involved four steps: 1) A reference frame (Fig. 3) was established using R2V software to designate control points, or the four vertexes of each sub-block (Appendix S1), so that all plants in each sub-block were within the same reference frame. The parallax and optical distortion in the raster images was then geometrically corrected based on these selected control points; 2) Maps, or layers in GIS terminology, were set up for each species as PROJECT files (Appendix S2), and all individuals in each sub-block were digitized using R2V software (Appendix S3). For accuracy, the digitization of plant individual locations was performed manually; 3) Each plant species layer was exported from a PROJECT file to a SHAPE file in R2V software (Appendix S4); 4) Finally each species layer was opened in Arc GIS software in the SHAPE file format, and attribute data from each species layer was exported into Arc GIS to obtain the precise coordinates for each species. This last phase involved four steps of its own, from adding the data (Appendix S5), to opening the attribute table (Appendix S6), to adding new x and y coordinate fields (Appendix S7) and to obtaining the x and y coordinates and filling in the new fields (Appendix S8).

1. Data reliability assessment

To determine the accuracy of our new method, we measured the individual locations of Leymus chinensis, a perennial rhizome grass, in representative community blocks 5 m x 5 m in size in typical steppe habitat in the Inner Mongolia Autonomous Region of China in July 2010 (Fig. 4 A). As our standard for comparison, we used a ruler to measure the individual coordinates of L. chinensis. We tested for significant differences between (1) the coordinates of L. chinensis, as measured with our new method and with the ruler, and (2) the pair correlation function g of L. chinensis, as measured with our new method and with the ruler (see section 3.2 Data Analysis). If (1) the coordinates of L. chinensis, as measured with our new method and with the ruler, and (2) the pair correlation function g of L. chinensis, as measured with our new method and with the ruler, did not differ significantly, then we could conclude that our new method of measuring the coordinates of L. chinensis was reliable.

We compared the results using a t-test (Table 1). We found no significant differences in either (1) the coordinates of L. chinensis or (2) the pair correlation function g of L. chinensis. Further, we compared the pattern characteristics of L. chinensis when measured by our new method against the ruler measurements using a null model. We found that the two pattern characteristics of L. chinensis did not differ significantly based on the homogenous Poisson process or complete spatial randomness (Fig. 4 B). Thus, we concluded that the data obtained using our new method was reliable enough to perform point pattern analysis with a null model in grassland communities.

SR41-42 Northern Prince Charles Mountains - 1:1 Million Topographic GIS Dataset is part of the International Map of the World 1:1000000 map series.\r \r The dataset contains all natural features. Attributes are held for line point and polygon features.\r \r The dataset was originally produced as a base to supply data for the second edition hard copy map series.\r \r This dataset was updated in 2001/02 with the integration of data from the AAT Coastline 2001 dataset.

Environmental Sensitivity Index (ESI) maps are an integral component in oil-spill contingency planning and assessment. They serve as a source of information in the event of an oil spill incident. ESI maps are a product of the Hazardous Materials Response Division of the Office of Response and Restoration (OR&R).ESI maps contain three types of information: shoreline habitats (classified accordin...

Example computer code (R script) and associated data to run the Greater Glider simulation example in the manuscript.

Open Access# Data and R code used in: Plant geographic distribution influences chemical defenses in native and introduced Plantago lanceolata populations ## Description of the data and file structure * 00_ReadMe_DescriptonVariables.csv: A list with the description of variables from each file used. * 00_Metadata_Coordinates.csv : A dataset that includes the coordinates of each Plantago lanceolata population used. * 00_Metadata_Climate.csv : A dataset that includes coordinates, bioclimatic parameters, and the results of PCA. The dataset was created based on the script '1_Environmental variables.qmd' * 00_Metadata_Individuals.csv: A dataset that includes general information about each plant individual. Information about root traits and chemistry is missing in four samples since we lost the samples. * 01_Datset_PlantTraits.csv: Size-related and resource allocation traits measured of Plantago lanceolata and herbivore damage. * 02_Dataset_TargetedCompounds.csv: Phytohormones, Iridoid glycosides, Verbascoside and Flavonoids quantification of the leaves and roots of Plantago lanceolata. Data generated from HPLC * 03_Dataset_Volatiles_Area.csv: Area of identified volatile compounds. Data generated from GC-FID * 03_Dataset_Volatiles_Compounds.csv: Information on identified volatile compounds. Data generated from GC-MS. * 04_Dataset_Metabolome_Negative_Metadata.txt: Metadata for files in negative mode * 04_Dataset_Metabolome_Negative_Intensity.xlsx : File with the intensity of the metabolite features in negative mode. The file was generated from Metaboscape and adapted as required for the Notame package. * 04_Dataset_Metabolome_Negative_Intensity_filtered.xlsx: File generated after preprocessing of features in negative mode. During the notadame pacakged preprossesing 0 were converted to na * 04_Dataset_Metabolome_Negative.msmsonly.csv: File with a intensity of the the metabolite features in negative mode with ms/ms data. File generated from Metaboscape. * 04_Results_Metabolome_Negative_canopus_compound_summary.tsv: Feature classification. Results generated from Sirius software. * 04_Results_Metabolome_Negative_compound_identifications.tsv: Feature identification. Results generated from Sirius software. * 05_Dataset_Metabolome_Positive_Metadata.txt: Metadata for files in positive mode * 05_DatasetMetabolome_Positive_Intensity.xlsx : File with a intensity of the the metabolite features in positive mode. File generated from Metaboscape and adapted as required for the Notame package. * 05_Dataset_Metabolome_Positive_Intensity_filtered: File generated after preprocessing of features in positive mode.During the notadame pacakged preprossesing 0 were converted to na ## ## Code/Software * 1_Environmental vairables.qmd: Rscript to Retrieve bioclimatic variables from based on the coordinates of each population and then perform a principal components analysis to reduce the axes variation and included the first principal component as an explanatory variable in our model to estimate trait differences between native and introduced populations. Figure 1b and 1d * 2_PlantTraits_and_Herbivory: Rscript for statistical anaylsis of size-related traits, resource allocation traits and herbivore damage. Figure 2. It needs to source: Model_1_Fucntion.R, Model_2_Fucntion.R, Plot_Function.R * 3_Metabolome: Rscript for statistical anaylsis of Plantago lanceolata metabolome. Figure 3. It needs to source: Metabolome_preprocessing_R, Model_1_Fucntion.R, Model_2_Fucntion.R, Plot_Function.R. * 4_TargetedCompounds: Rscript for statistical anaylsis of Plantago lanceolata targeted compounds. Figure 4. It needs to source: Model_1_Fucntion.R, Model_2_Fucntion.R, Plot_Function.R * 5_Volatilome: Rscript for statistical anaylsis of Plantago lanceolata metabolome. Figure 5. It needs to source: Model_1_Fucntion.R, Model_2_Fucntion.R, Plot_Function.R * Model_1_Function.R : Function to run statistical models * Model_2_Function.R : Function to run statistical models * Plots_Function.R : Function to run plot graphs * Metabolome_prepocessing.R: Script to preprocess features