Dataset Information

The geodiv r package: Tools for calculating gradient surface metrics.

ABSTRACT: The geodiv r package calculates gradient surface metrics from imagery and other gridded datasets to provide continuous measures of landscape heterogeneity for landscape pattern analysis. geodiv is the first open-source, command line toolbox for calculating many gradient surface metrics and easily integrates parallel computing for applications with large images or rasters (e.g. remotely sensed data). All functions may be applied either globally to derive a single metric for an entire image or locally to create a texture image over moving windows of a user-defined extent.We present a comprehensive description of the functions available through geodiv. A supplemental vignette provides an example application of geodiv to the fields of landscape ecology and biogeography. geodiv allows users to easily retrieve estimates of spatial heterogeneity for a variety of purposes, enhancing our understanding of how environmental structure influences ecosystem processes. The package works with any continuous imagery and may be widely applied in many fields where estimates of surface complexity are useful.

SUBMITTER: Smith AC

PROVIDER: S-EPMC9292368 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature

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The geodiv r package: Tools for calculating gradient surface metrics.

Smith Annie C AC Dahlin Kyla M KM Record Sydne S Costanza Jennifer K JK Wilson Adam M AM Zarnetske Phoebe L PL

Methods in ecology and evolution 20210802 11

The geodiv r package calculates gradient surface metrics from imagery and other gridded datasets to provide continuous measures of landscape heterogeneity for landscape pattern analysis. geodiv is the first open-source, command line toolbox for calculating many gradient surface metrics and easily integrates parallel computing for applications with large images or rasters (e.g. remotely sensed data). All functions may be applied either globally to derive a single metric for an entire image or loc ...[more]

PMID: 35874973

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Project description:IntroductionIn smoking cessation clinical trials, timeline followback (TLFB) interviews are widely used to track daily cigarette consumption. However, there are no standard tools for calculating abstinence based on TLFB data. Individual research groups have to develop their own calculation tools, which is not only time- and resource-consuming but might also lead to variability in the data processing and calculation procedures.Aims and methodsTo address these issues, we developed a novel open-source Python package named abstcal to calculate abstinence using TLFB data. This package provides data verification, duplicate and outlier detection, missing-data imputation, integration of biochemical verification data, and calculation of a variety of definitions of abstinence, including continuous, point-prevalence, and prolonged abstinence.ResultsWe verified the accuracy of the calculator using data derived from a clinical smoking cessation study. To improve the package's accessibility, we have made it available as a free web app.ConclusionsThe abstcal package is a reliable abstinence calculator with open-source access, providing a shared validated online tool to the addiction research field. We expect that this open-source abstinence calculation tool will improve the rigor and reproducibility of smoking and addiction research by standardizing TLFB-based abstinence calculation.ImplicationsAbstinence calculation is an essential task in any smoking intervention study. However, there have not been standard open-source tools available to the researchers. This commentary describes a Python-based package called abstcal that can calculate abstinence from TLFB data, a common methodology to collect smoking consumption data in research settings. The package supports the calculation of point-prevalence, prolonged, and continuous abstinence. Importantly, the package has a web app interface that allows researchers to use the tool without any coding experience. This tool will facilitate smoking research by providing a standardized and easy-to-use abstinence calculation tool.

Dataset Information

The geodiv r package: Tools for calculating gradient surface metrics.

Publications

The geodiv r package: Tools for calculating gradient surface metrics.

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