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Coding conventions and principles for a National Land-Change Modeling Framework

This report establishes specific rules for writing computer source code for use with the National Land-Change Modeling Framework (NLCMF). These specific rules consist of conventions and principles for writing code primarily in the C and C++ programming languages. Collectively, these coding conventions and coding principles create an NLCMF programming style. In addition to detailed naming conventions, this report provides general coding conventions and principles intended to facilitate the development of high-performance software implemented with code that is extensible, flexible, and interoperable. Conventions for developing modular code are explained in general terms and also enabled and demonstrated through the appended templates for C++ base source-code and header files. The NLCMF limited-extern approach to module structure, code inclusion, and cross-module access to data is both explained in the text and then illustrated through the module templates. Advice on the use of global variables is provided.

Techniques and Methods↗

The basin characterization model—A regional water balance software package

This report documents the computer software package, Basin Characterization Model, version 8 (BCMv8)—a monthly, gridded, regional water-balance model—and provides detailed operational instructions and example applications. After several years of many applications and uses of a previous version, CA-BCM, published in 2014, the BCMv8 was refined to improve the accuracy of the water-balance components, particularly the recharge estimate, which is the most difficult to accurately assess. The improvement of the various water-balance components targeted the actual evapotranspiration component, which, in turn, reduced the uncertainty of the recharge estimate. The improvement of this component was enabled by the availability of a national, gridded actual-evapotranspiration product from the U.S. Geological Survey that was unique in its scope to combine remotely sensed spatial variability and ground-based long-term water-balance constraints. This dataset provided the ability to assess monthly actual evapotranspiration for 62 vegetation types and to perform regional calibration in watersheds throughout California with the objective of closing the water balance using improved estimates for each component. The refinements, including vegetation-specific evapotranspiration, enabled the development of applications that could explore various aspects of landscape disturbance, such as wildfire, forest management, or urbanization. The improvements to BCMv8 also provided the ability to assess long-term sustainability of water resources under a variety of management applications or future climate projections.

California↗

Fast, Inclusive Searches for Geographic Names Using Digraphs

An algorithm specifies how to quickly identify names that approximately match any specified name when searching a list or database of geographic names. Based on comparisons of the digraphs (ordered letter pairs) contained in geographic names, this algorithmic technique identifies approximately matching names by applying an artificial but useful measure of name similarity. A digraph index enables computer name searches that are carried out using this technique to be fast enough for deployment in a Web application. This technique, which is a member of the class of n-gram algorithms, is related to, but distinct from, the soundex, PHONIX, and metaphone phonetic algorithms. Despite this technique's tendency to return some counterintuitive approximate matches, it is an effective aid for fast, inclusive searches for geographic names when the exact name sought, or its correct spelling, is unknown.

Techniques and Methods↗

GenEst statistical models—A generalized estimator of mortality

Introduction GenEst (a generalized estimator of mortality) is a suite of statistical models and software tools for generalized mortality estimation. It was specifically designed for estimating the number of bird and bat fatalities at solar and wind power facilities, but both the software (Dalthorp and others, 2018) and the underlying statistical models are general enough to be useful in various situations to estimate the size of open populations when detection probabilities and search coverages are less than 1. In this report, we outline the statistical models and data structures underlying the estimator. The models are numerous, complex, and intricately interwoven. Discussion begins with broad, high-level overviews of the general models. The lower-level technical details are then gradually added. Broader and less technical discussions on the general context and applications of the models and the use of the software are available in the software user guide (Simonis and others, 2018), vignettes bundled with the software, and the help files within the software itself.

Techniques and Methods↗

Accounting for the fraction of carcasses outside the searched area in the estimation of bird and bat fatalities at wind energy facilities

Accurate estimation of bird and bat mortality at wind energy facilities requires accounting for carcasses that lie outside the search plots because they lie beyond the search radius or in areas within the search radius that remain unsearched due to sub-optimal search conditions such as thick vegetation, rough or dangerous ground, water, or restricted access to the land. However, carcass density is not constant around a turbine and the fraction of carcasses within the unsearched area can vary greatly depending on where the area lies relative to the turbine. The density-weighted proportion approach takes into account the changing density of carcasses around turbines to estimate the fraction of carcasses lying in unsearched areas (dwp). It involves tallying the carcasses found in concentric rings centered at the turbine, fitting a curve to the carcass densities in the rings, and dividing the integral of the curve over the area searched by the integral over the total area. Accounting for unsearched area presents special difficulties such as extrapolation beyond the search radius, spatial prediction, and model selection, which are frequently ignored or under-appreciated, potentially resulting in substantial estimation errors. A powerful new R software package (dwp) is available to perform the calculations, given the distances at which carcasses were found from turbines and a map of the searched area used to discern the fraction of the ground searched at each distance. If all ground within a given search radius has been searched, the map is simply the search radius. For more complicated search plots, other kinds of maps may be used: R polygons for plots that can be readily delineated into searched and not-searched areas (for example, searches restricted to access roads and turbine pads), GIS shape files for complicated search patterns (for example, non-uniform vegetation or ground texture resulting in spatially varying search conditions), or raster files for complicated search patterns coupled with carcass spatial distribution that depends on both distance and direction from turbines. This study discusses estimation and interpretation of dwp in the context of several realistic examples; provides guidance for use of the dwp software for doing the analyses; and addresses questions of extrapolation, spatial prediction, and model selection.

Techniques and Methods↗

Best practices for distributing and deploying U.S. Geological Survey Shiny applications

A goal of U.S. Geological Survey (USGS) research is to create actionable science for U.S. Department of the Interior managers and partners. Properly managed and released software tools can quickly, accurately, and easily translate scientific results to aid managers’ decision-making. The USGS policies on software development and distribution affect how authors of USGS software products must navigate the review and approval process. Understanding these rules and procedures will save time and effort in making science useful and visible through software development. This document outlines USGS policies on software development as they pertain to Shiny applications, which use R code to create interactive web-based applications. The requirements and procedures described here will also be relevant for other USGS software applications. This document is not intended to be a step-by-step guide on building a Shiny application or to go into detail about any of the referenced software programs. An understanding of the referenced software programs, including R, Git, and hypertext markup language/cascading style sheets (HTML/CSS) is needed to use this document efficiently, though links for more thorough guidance are included throughout.

Techniques and Methods↗

fatalityCMR: capture-recapture software to correct raw counts of wildlife fatalities using trial experiments for carcass detection probability and persistence time

Many industrial and agricultural activities involve wildlife fatalities by collision, poisoning or other involuntary harvest: wind turbines, highway network, utility network, tall structures, pesticides, etc. Impacted wildlife may benefit from official protection, including the requirement to monitor the impact. Carcass counts can often be conducted to quantify the number of fatalities, but they need to be corrected for carcass persistence time (removal by scavengers and decay) and detection probability (searcher efficiency). In this article we introduce a new piece of software that fits a superpopulation capture-recapture model to raw count data. It uses trial data to estimate detection and daily persistence probabilities. A recurrent issue is that fatalities of rare, protected species are infrequent, in which case the software offers the option to switch to an ‘evidence of absence’ mode, i.e., estimate the number of carcasses that may have been missed by field crews. The software allows distinguishing between different turbine types (e.g. different vegetation cover under turbines, or different technical properties), as well between two carcass age-classes or states, with transition between those classes (e.g, fresh and dry). There is a data simulation capacity that may be used at the planning stage to optimize sampling design. Resulting mortality estimates can be used 1) to quantify the required amount of compensation, 2) inform mortality projections for proposed development sites, and 3) inform decisions about management of existing sites.

Techniques and Methods↗

Approaches in highly parameterized inversion—PEST++ Version 3, a Parameter ESTimation and uncertainty analysis software suite optimized for large environmental models

The PEST++ Version 1 object-oriented parameter estimation code is here extended to Version 3 to incorporate additional algorithms and tools to further improve support for large and complex environmental modeling problems. PEST++ Version 3 includes the Gauss-Marquardt-Levenberg (GML) algorithm for nonlinear parameter estimation, Tikhonov regularization, integrated linear-based uncertainty quantification, options of integrated TCP/IP based parallel run management or external independent run management by use of a Version 2 update of the GENIE Version 1 software code, and utilities for global sensitivity analyses. The Version 3 code design is consistent with PEST++ Version 1 and continues to be designed to lower the barriers of entry for users as well as developers while providing efficient and optimized algorithms capable of accommodating large, highly parameterized inverse problems. As such, this effort continues the original focus of (1) implementing the most popular and powerful features of the PEST software suite in a fashion that is easy for novice or experienced modelers to use and (2) developing a software framework that is easy to extend. The PEST++ Version 3 software suite can be compiled for Microsoft Windows®4 and Linux®5 operating systems; the source code is available in a Microsoft Visual Studio®6 2013 solution; Linux Makefiles are also provided. PEST++ Version 3 continues to build a foundation for an open-source framework capable of producing robust and efficient parameter estimation tools for large environmental models.

Techniques and Methods↗

User’s guide for GcClust—An R package for clustering of regional geochemical data

GcClust is a software package developed by the U.S. Geological Survey for statistical clustering of regional geochemical data, and similar data such as regional mineralogical data. Functions within the software package are written in the R statistical programming language. These functions, their documentation, and a copy of the user’s guide are bundled together in R’s unit of sharable code, which is called a “package.” The user’s guide includes step-by-step instructions showing how the functions are used to cluster data and to evaluate the clustering results. These functions are demonstrated in this report using test data, which are included in the package.

Techniques and Methods↗

User’s guide for MapMark4—An R package for the probability calculations in three-part mineral resource assessments

MapMark4 is a software package that implements the probability calculations in three-part mineral resource assessments. Functions within the software package are written in the R statistical programming language. These functions, their documentation, and a copy of this user’s guide are bundled together in R’s unit of shareable code, which is called a “package.” This user’s guide includes step-by-step instructions showing how the functions are used to carry out the probability calculations. The calculations are demonstrated using test data, which are included in the package.

Techniques and Methods↗

Probability calculations for three-part mineral resource assessments

Three-part mineral resource assessment is a methodology for predicting, in a specified geographic region, both the number of undiscovered mineral deposits and the amount of mineral resources in those deposits. These predictions are based on probability calculations that are performed with computer software that is newly implemented. Compared to the previous implementation, the new implementation includes new features for the probability calculations themselves and for checks of those calculations. The development of the new implementation lead to a new understanding of the probability calculations, namely the assumptions inherent in the probability calculations. Several assumptions strongly affect the mineral resource predictions, so it is crucial that they are checked during an assessment. The evaluation of the new implementation leads to new findings about the probability calculations,namely findings regarding the precision of the computations,the computation time, and the sensitivity of the calculation results to the input.

Techniques and Methods↗

Overview of a compre­hensive resource database for the assessment of recoverable hydrocarbons produced by carbon dioxide enhanced oil recovery

A database called the “Comprehensive Resource Database” (CRD) was prepared to support U.S. Geological Survey (USGS) assessments of technically recoverable hydrocarbons that might result from the injection of miscible or immiscible carbon dioxide (CO 2 ) for enhanced oil recovery (EOR). The CRD was designed by INTEK Inc., a consulting company under contract to the USGS. The CRD contains data on the location, key petrophysical properties, production, and well counts (number of wells) for the major oil and gas reservoirs in onshore areas and State waters of the conterminous United States and Alaska. The CRD includes proprietary data on petrophysical properties of fields and reservoirs from the “Significant Oil and Gas Fields of the United States Database,” prepared by Nehring Associates in 2012, and proprietary production and drilling data from the “Petroleum Information Data Model Relational U.S. Well Data,” prepared by IHS Inc. in 2012. This report describes the CRD and the computer algorithms used to (1) estimate missing reservoir property values in the Nehring Associates (2012) database, and to (2) generate values of additional properties used to characterize reservoirs suitable for miscible or immiscible CO 2 flooding for EOR. Because of the proprietary nature of the data and contractual obligations, the CRD and actual data from Nehring Associates (2012) and IHS Inc. (2012) cannot be presented in this report.

Techniques and Methods↗

User’s guide for MapMark4GUI—A graphical user interface for the MapMark4 R package

MapMark4GUI is an R graphical user interface (GUI) developed by the U.S. Geological Survey to support user implementation of the MapMark4 R statistical software package. MapMark4 was developed by the U.S. Geological Survey to implement probability calculations for simulating undiscovered mineral resources in quantitative mineral resource assessments. The GUI provides an easy-to-use tool to input data, run simulations, and format output results for the MapMark4 package. The GUI is written and accessed in the R statistical programming language. This user’s guide includes instructions on installing and running MapMark4GUI and descriptions of the statistical output processes, output files, and test data files.

Techniques and Methods↗

GenEst user guide—Software for a generalized estimator of mortality

GenEst (Generalized Estimator) is a software tool for estimating the total number of individuals arriving in an area during a specific time period when their detection probability is unknown but estimable. Its development was motivated by the need to accurately estimate the total number of bird and bat fatalities occurring at wind and solar energy facilities, but it is applicable in a variety of other contexts as well. Simple counts of carcasses are not an accurate measure of the true number of fatalities because some carcasses are inevitably missed in carcass searches. Furthermore, simple carcass counts do not allow comparison among locations or years because carcasses may be detected at different rates. This software uses data collected during carcass searches and estimates of detection rates to accurately estimate the number of fatalities and to provide a measure of precision associated with the estimate. These estimates are fundamental to understanding acute and cumulative effects of renewable energy development on wildlife populations. The software package is available with a user-friendly graphic interface as well as a flexible and powerful command-line implementation. GenEst includes tools for estimating searcher efficiency, carcass persistence, and other detection probability parameters from experimental field trials. Included in the software are example datasets for analyses, standard R package help files, this user guide, and vignettes detailing use at the command-line.

Techniques and Methods↗

User guide to the bayesian modeling of non-stationary, univariate, spatial data using R language package BMNUS

Bayesian modeling of non-stationary, univariate, spatial data is performed using the R-language package BMNUS. A unique advantage of this package is that it can map the mean, standard deviation, quantiles, and probability of exceeding a specified value. The package includes several R-language classes that prepare the data for the modeling, help select suitable model parameters, and help analyze the results. This user guide describes the BMNUS package and presents step-by-step instructions to model data that accompany the package.

Techniques and Methods↗

Approaches to highly parameterized inversion: PEST++ Version 5, a software suite for parameter estimation, uncertainty analysis, management optimization and sensitivity analysis

PEST++ Version 5 extends and enhances the functionality of the PEST++ Version 3 software suite, providing environmental modeling practitioners access to updated Version 3 tools as well as new tools to support decision making with environmental models. Version 5 of PEST++ includes tools for global sensitivity analysis (PESTPP-SEN); least-squares parameter estimation with integrated first-order, second-moment parameter and forecast uncertainty estimation (PESTPP-GLM); an iterative, localized ensemble smoother (PESTPP-IES); and a tool for management optimization under uncertainty (PESTPP-OPT). Additionally, all PEST++ Version 5 tools have a built-in fault-tolerant, multithreaded parallel run manager and are model independent, using the same protocol as the widely used PEST software suite. PEST++ Version 5 is consistent with PEST++ Version 3 conventions and design philosophy. The software’s emphasis continues to target efficient and optimized algorithms that have proven beneficial in decision-support settings and can accommodate large, highly parameterized problems. Expanded and new capabilities are now available to express uncertainty using Monte Carlo and analytical uncertainty approaches and allow evaluation of thousands to millions of parameters. New management optimization capabilities in Version 5 also allow environmental models to be used to answer management questions using multiple societal constraints in a risk-based framework. The PEST++ Version 5 software suite can be compiled for Microsoft Windows® and Unix-based operating systems such as Apple and Linux®; the source code is available with a Microsoft Visual Studio® 2019 solution; and CMake support for all three operating system is also provided. PEST++ Version 5 continues to build a foundation for an open-source framework capable of producing model-independent, robust, and efficient decision-support tools for large environmental models. The functionality of each of the PEST++ tools are demonstrated on a simple example problem. Implications of decisions used when using the PEST++ suite tools are also discussed.

Techniques and Methods↗

An apparent dip calculator for spreadsheets

This report and spreadsheet calculator contain Microsoft Excel-based equations that are useful in structural geology to calculate plunge or apparent dip when measuring lineations on a plane. The spreadsheet allows users to measure the trend or the plunge of a lineation and calculate the corresponding unknown value of trend or plunge. The spreadsheet provides the user with two options: Option 1: Calculates the plunge of a lineation from the measured strike and dip of a plane and the measured trend of a lineation. Option 2: Calculates two potential trends of a lineation from the measured strike and dip of a plane and a measured plunge of a lineation. The user can decide which trend is appropriate for their data.

Techniques and Methods↗

Bayesian mapping of regionally grouped, sparse, univariate earth science data

Some earth science data are naturally grouped by region, and it is often desirable to map these data by region. However, if there are only a few samples within each region, then the map should be smoothed in an appropriate way to mitigate the problems that arise from having only a few samples. A smoothing algorithm based on a Bayesian hierarchical model is developed and presented in this report. This algorithm has several features that make it especially suitable for mapping earth science data: it can account for measurements that are censored, it can process multiple datasets with different measurement errors and different censoring thresholds, and it can calculate the uncertainty in any statistic that is mapped. The algorithm is demonstrated by mapping gold concentrations that are measured in streambed sediments in the Taylor Mountains quadrangle in southwestern Alaska.

Alaska↗