elevatr - Access Elevation Data from Various APIs

Several web services are available that provide access to elevation data. This package provides access to many of those services and returns elevation data either as an 'sf' simple features object from point elevation services or as a 'raster' object from raster elevation services. In future versions, 'elevatr' will drop support for 'raster' and will instead return 'terra' objects. Currently, the package supports access to the Amazon Web Services Terrain Tiles <https://registry.opendata.aws/terrain-tiles/>, the Open Topography Global Datasets API <https://opentopography.org/developers/>, and the USGS Elevation Point Query Service <https://apps.nationalmap.gov/epqs/>.

Last updated 4 months ago

digital-elevation-modelelevation-dataelevatrepamapzen-elevation-servicer-language

11.25 score 204 stars 3 dependents 1.2k scripts 3.9k downloads

httk - High-Throughput Toxicokinetics

Pre-made models that can be rapidly tailored to various chemicals and species using chemical-specific in vitro data and physiological information. These tools allow incorporation of chemical toxicokinetics ("TK") and in vitro-in vivo extrapolation ("IVIVE") into bioinformatics, as described by Pearce et al. (2017) (<doi:10.18637/jss.v079.i04>). Chemical-specific in vitro data characterizing toxicokinetics have been obtained from relatively high-throughput experiments. The chemical-independent ("generic") physiologically-based ("PBTK") and empirical (for example, one compartment) "TK" models included here can be parameterized with in vitro data or in silico predictions which are provided for thousands of chemicals, multiple exposure routes, and various species. High throughput toxicokinetics ("HTTK") is the combination of in vitro data and generic models. We establish the expected accuracy of HTTK for chemicals without in vivo data through statistical evaluation of HTTK predictions for chemicals where in vivo data do exist. The models are systems of ordinary differential equations that are developed in MCSim and solved using compiled (C-based) code for speed. A Monte Carlo sampler is included for simulating human biological variability (Ring et al., 2017 <doi:10.1016/j.envint.2017.06.004>) and propagating parameter uncertainty (Wambaugh et al., 2019 <doi:10.1093/toxsci/kfz205>). Empirically calibrated methods are included for predicting tissue:plasma partition coefficients and volume of distribution (Pearce et al., 2017 <doi:10.1007/s10928-017-9548-7>). These functions and data provide a set of tools for using IVIVE to convert concentrations from high-throughput screening experiments (for example, Tox21, ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK") (Wetmore et al., 2015 <doi:10.1093/toxsci/kfv171>).

Last updated 4 months ago

comptoxord

10.04 score 26 stars 1 dependents 266 scripts 654 downloads

tcpl - ToxCast Data Analysis Pipeline

The ToxCast Data Analysis Pipeline ('tcpl') is an R package that manages, curve-fits, plots, and stores ToxCast data to populate its linked MySQL database, 'invitrodb'. The package was developed for the chemical screening data curated by the US EPA's Toxicity Forecaster (ToxCast) program, but 'tcpl' can be used to support diverse chemical screening efforts.

Last updated 20 days ago

cctecomptoxord

9.36 score 32 stars 90 scripts 962 downloads

spsurvey - Spatial Sampling Design and Analysis

A design-based approach to statistical inference, with a focus on spatial data. Spatially balanced samples are selected using the Generalized Random Tessellation Stratified (GRTS) algorithm. The GRTS algorithm can be applied to finite resources (point geometries) and infinite resources (linear / linestring and areal / polygon geometries) and flexibly accommodates a diverse set of sampling design features, including stratification, unequal inclusion probabilities, proportional (to size) inclusion probabilities, legacy (historical) sites, a minimum distance between sites, and two options for replacement sites (reverse hierarchical order and nearest neighbor). Data are analyzed using a wide range of analysis functions that perform categorical variable analysis, continuous variable analysis, attributable risk analysis, risk difference analysis, relative risk analysis, change analysis, and trend analysis. spsurvey can also be used to summarize objects, visualize objects, select samples that are not spatially balanced, select panel samples, measure the amount of spatial balance in a sample, adjust design weights, and more. For additional details, see Dumelle et al. (2023) <doi:10.18637/jss.v105.i03>.

Last updated 5 months ago

ord

9.21 score 15 stars 1 dependents 223 scripts 764 downloads

ctxR - Utilities for Interacting with the 'CTX' APIs

Access chemical, hazard, bioactivity, and exposure data from the Computational Toxicology and Exposure ('CTX') APIs <https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis>. 'ctxR' was developed to streamline the process of accessing the information available through the 'CTX' APIs without requiring prior knowledge of how to use APIs. Most data is also available on the CompTox Chemical Dashboard ('CCD') <https://comptox.epa.gov/dashboard/> and other resources found at the EPA Computational Toxicology and Exposure Online Resources <https://www.epa.gov/comptox-tools>.

Last updated 7 days ago

comptox

8.00 score 9 stars 1 dependents 12 scripts 749 downloads

spmodel - Spatial Statistical Modeling and Prediction

Fit, summarize, and predict for a variety of spatial statistical models applied to point-referenced and areal (lattice) data. Parameters are estimated using various methods. Additional modeling features include anisotropy, non-spatial random effects, partition factors, big data approaches, and more. Model-fit statistics are used to summarize, visualize, and compare models. Predictions at unobserved locations are readily obtainable. For additional details, see Dumelle et al. (2023) <doi:10.1371/journal.pone.0282524>.

Last updated 2 months ago

7.66 score 15 stars 3 dependents 112 scripts 783 downloads

tcplfit2 - A Concentration-Response Modeling Utility

The tcplfit2 R package performs basic concentration-response curve fitting. The original tcplFit() function in the tcpl R package performed basic concentration-response curvefitting to 3 models. With tcplfit2, the core tcpl concentration-response functionality has been expanded to process diverse high-throughput screen (HTS) data generated at the US Environmental Protection Agency, including targeted ToxCast, high-throughput transcriptomics (HTTr) and high-throughput phenotypic profiling (HTPP). tcplfit2 can be used independently to support analysis for diverse chemical screening efforts.

Last updated 1 months ago

comptoxord

7.06 score 4 stars 1 dependents 24 scripts 406 downloads

SSN2 - Spatial Modeling on Stream Networks

Spatial statistical modeling and prediction for data on stream networks, including models based on in-stream distance (Ver Hoef, J.M. and Peterson, E.E., (2010) <DOI:10.1198/jasa.2009.ap08248>.) Models are created using moving average constructions. Spatial linear models, including explanatory variables, can be fit with (restricted) maximum likelihood. Mapping and other graphical functions are included.

Last updated 5 months ago

6.70 score 16 stars 2 dependents 35 scripts 518 downloads

RAQSAPI - A Simple Interface to the US EPA Air Quality System Data Mart API

Retrieve air monitoring data and associated metadata from the US Environmental Protection Agency's Air Quality System service using functions. See <https://aqs.epa.gov/aqsweb/documents/data_api.html> for details about the US EPA Data Mart API.

Last updated 7 months ago

united state environmental protection agencyenvironmental-data-retrievalair-quality-systemaqs-datamartair-monitoringenvironmental-monitoringairmonitoringaqsdatamartr03rprogrammingusepa

6.64 score 21 stars 32 scripts 739 downloads

ccdR - Utilities for Interacting with the 'CTX' APIs

Access chemical, hazard, bioactivity, and exposure data from the Computational Toxicology and Exposure ('CTX') APIs <https://api-ccte.epa.gov/docs/>. 'ccdR' was developed to streamline the process of accessing the information available through the 'CTX' APIs without requiring prior knowledge of how to use APIs. Most data is also available on the CompTox Chemical Dashboard ('CCD') <https://comptox.epa.gov/dashboard/> and other resources found at the EPA Computational Toxicology and Exposure Online Resources <https://www.epa.gov/comptox-tools>.

Last updated 6 months ago

6.60 score 2 stars 7 scripts 635 downloads

micromap - Linked Micromap Plots

This group of functions simplifies the creation of linked micromap plots. Please see <https://www.jstatsoft.org/v63/i02/> for additional details.

Last updated 3 months ago

ord

6.38 score 10 stars 53 scripts 765 downloads

pTITAN2 - Permutations of Treatment Labels and TITAN2 Analysis

Permute treatment labels for taxa and environmental gradients to generate an empirical distribution of change points. This is an extension for the 'TITAN2' package <https://cran.r-project.org/package=TITAN2>.

Last updated 3 years ago

epa-unknown

3.70 score 1 stars 7 scripts 208 downloads