References

Installing RAQSAPI | Option 1: Installing the stable version from CRAN (preferred method) | Option 2: Installing the development version of RAQSAPI (unstable)

Data Mart aggregate functions | See the RAQSAPI vignette for more details

About the timeliness of AQS Data

Acknowledgements

EPA Disclaimer

Introduction

The Air Quality System (AQS) | About AQS Data Mart | Benefits of using RAQSAPI | References

RAQSAPI functions | Variable descriptions and usage. | RAQSAPI functional families | Sign up and credentials | Data Mart API metadata functions | Data Mart API list functions | Data Mart aggregate functions | Data Mart aggregate functions _by_site | Data Mart aggregate functions _by_county | Data Mart aggregate functions _by_state | Data Mart aggregate functions by Monitoring agency (MA) | Data Mart aggregate functions by Core Based Statistical Area (cbsa) | Data Mart aggregate functions by Primary Quality Assurance Organization (pqao) | Data Mart aggregate functions by latitude/longitude bounding box (_by_box) | RAQSAPI Miscellaneous functions

Troubleshooting

Usage tips and precautions

Using The RAQSAPI library | Load RAQSAPI | Sign up and setting up user credentials with the RAQSAPI library | (suggested) Use the keyring package to manage credentials

Introduction | Suggested packages for use with this vignette | Load Data | Level 1 processing | Level 2 processing | Level 3 processing | Best Practices: Food for thought | References

Introduction | Suggested packages for use with this vignette | Load Data | Level 1 processing | Level 2 processing | Level 3 processing | Level 4 processing | Best Practices: Food for thought | Appendix | L4 Bayesian Modeling Information | Measurement Model | Estimation of Blanks | Estimation of Calibration Curve | Clearance Model | Estimation of Metabolic Clearance | Estimation of Abiotic Clearance | Post-MCMC Estimates | JAGS to L4 Equation Notation Tables | References

Introduction | Suggested packages for use with this vignette | Load Data | Level 1 processing | Level 2 processing | Level 3 processing | Level 4 processing | Best Practices: Food for thought | Appendix | L4 Bayesian Modeling Information | Measurement Model | Estimation for Blanks with No Plasma | Estimation for Blanks with Plasma | Estimation for Initial Time (T0) | Estimation for the Calibration Curve | Estimation for the RED Plasma Protein Binding Assay | Concentrations for Replicates | Estimation for PBS | Estimation for Plasma | Post-MCMC Estimates | Fraction of Chemical Unbound in Plasma (Bayesian Estimates) | Fraction Unbound in Plasma (Empirical Point Estimate) | JAGS to L4 Equation Notation Tables | References

Introduction | Suggested packages for use with this vignette | Load Data | Level 1 processing | Level 2 processing | Level 3 processing | Level 4 processing | Best Practices: Food for thought | Appendix | L4 Bayesian Modeling Information | Measurement Model | Estimation of Response Observations | Binding Model | Post-MCMC Estimates | Fraction of Chemical Stability | Fraction of Chemical Unbound in Plasma (Bayesian Estimates) | Fraction Unbound in Plasma (Empirical Point Estimate) | JAGS to L4 Equation Notation Tables | References

Introduction | The Data | Spatial Linear Models | Model Summaries | Prediction (Kriging) | An Additional Example | Spatial Generalized Linear Models | Function Glossary | Support for Additional R Packages | References

Background | Input Data | SSN Objects in SSN2 | The Middle Fork Data | Spatial Stream Network (SSN) Models | Linear SSN Models | Model Summaries | Prediction (Kriging) | Advanced Features | Generalized Linear SSN Models | Simulating Spatial Stream Network Data | Advanced Modeling Features in SSN2 | Function Glossary | From SSN to SSN2 | The Future of SSN2 | Additional Spatial Stream Network Tools | R Code Appendix | References

Installing and loading StreamCatTools | Background | Vignettes in StreamCatTools | Citation information

Introduction | Suggested packages for use with this vignette | Overview | ToxCast Publications | Connection Configuration | Database Structure | Level 0 | SC Data-containing Tables | - Level 1 (sc1) | - Level 2 (sc1) | - Aggregated IDs (sc2_agg) | - Representative Samples (sc2_chid) | MC Data-containing Tables | - Level 1 (mc1) | - Level 2 (mc2) | - Level 3 (mc3) | - Aggregated IDs (mc4_agg) | - Level 4 (mc4) | - Level 4 Parameters (mc4_param) | - Level 5 (mc5) | - Level 5 Parameters (mc5_param) | - Representative Samples (mc5_chid) | - Level 6 (mc6) | - Level 7 (mc7) | Assay and Auxiliary Annotation Tables | - Assay_Source | - Assay | - Assay_Component | - Assay_Component_Endpoint | - Assay_Component_Map | - Assay_Descriptions | - Chemical | - Chemical_Lists | - Sample | Assay Registration | Assay Nomenclature | Minimum Required Fields | Assay Source | Assay | Assay Component | Assay Component Endpoint | Naming Revision | Chemical Registration | Chemicals | Samples | Chemical Lists | Level 0 Pre-Processing | Required Fields | Well Types | Writing New Data | Data Processing | Level IDs | Methods | Data Normalization | SC Data Processing | > Level 1 | - Methods Assignment | > Level 2 | - Overwrite Bidirectionality | MC Data Processing | > Level 3 | > Level 4 | - Pre-Modeling Processes | - Concentration-Response Modeling Details | - Curve Fitting | > Level 5 | -- Overwrite Bidirectionality Methods | -- LOEC Methods | - Winning Model Selection | - Level 6 | - Level 7 | Compiled Processing Examples | - SC Data | - MC Data | Data Interpretation | Hit Calls | Cutoff | Potency Estimates | Activity Concentrations at Specified Response | Benchmark Dose | LOEC | Fit Categories | Flags (Level 6) | Example of Flags | Representative Samples | MC Representative Samples | SC Representative Samples | Variable Matrices | Cytotoxicity Burst Distribution | Burst Endpoints | Implementation | Assay Description Documents | Administered Equivalent Doses | Options Applied | Analytical QC and Applicability Domain | Descriptions of Fields and Possible Options | Data Retrieval in invitrodb | Retrieving Assay Element IDs | Retrieving Assay Annotations | Retrieving Chemical Information | Retrieving Methods | Retrieving Data | Retrieving Level 0 Data | - Load SC0 Data | - Load MC0 Data | - Review MC assay quality | Retrieving SC Data and Methods | - Load SC2 Data | - Load SC Methods | Retrieving MC Data and Methods | - Load MC5 Data | - Load MC Methods | Data Retrieval via API | Assay Elements | Data | Assay Annotations | Retrieving Processed MC Data and Annotations | - By ID | - By level | Load aeid | Load acid | Load aid | Load asid | Load unit | Sample and Chemical information | Load concentration unit | Load chemical info | Plotting | Individual Plotting | - Output PDF of Verbose, Multiple Plots per Page, by aeid and/or spid | - Output Image File (JPG) of Single Verbose Plot, by aeid and spid | - Output to Console, by m4id or by aeid and spid | - Output PDF of Single Concentration Plots, Multiple Plots per Page, by aeid | Comparison Plotting | - Output PDF of Multiple Comparison Plots per Page, by aeid and Compared by spid | - Output PDF of Multiple Single Concentration Comparison Plots per Page, by aeid and Compared by spid | - Output PDF of Multiple Comparison Plots per Page, By aeid and Compared by Chemical | - Output Image File (JPG) of Single Expanded Comparison Plot by aeid | Advanced Comparison Plotting | API Configuration | - Output Image File (JPG) of Single Verbose Plot, by M4ID | - Output PDF of Multiple Comparison Plots per Page, By AEID and Compared by Chemical | Additional Examples | - Load Data for a Specific Chemical | - Plot Sample Subset | - Plot LOEC (Lowest Observed Effective Concentration) | Example Integrations with Other Computational Toxicology Tools | Evaluate ToxCast AEDs for a single chemical and target | Consider ToxRefDB in vivo toxicity benchmarks as POD-Traditional | Consider ToxCast in vitro bioactivity data as POD-NAM | Compare POD-Traditional with POD-NAM | Apply ToxCast to examine EcoTox hazard for a single chemical | Consider POD-NAM and POD-Traditional | Consider SeqAPASS | Consider EcoTox | Compare

Introduction | Bioactivity Assay Resource | Get annotation by aeid | Get all assay annotations | Bioactivity Data Resource | Get summary data | Get data | Conclusion

Introduction to the CCD | Searching one chemical at a time (single-substance search) | Batch search | Challenges of web-based dashboard search | Introduction to the CTX APIs | Authentication | Request Construction | Introduction to ctxR | Package Settings | API Key Storage | Quick Start Examples | Chemical API | Chemical Details Resource | Chemical Property Resource | Hazard API | Hazard Resource | Bioactivity API | Bioactivity Resource | Conclusion

Introduction | Chemical Details Resource | Get chemical data | By DTXSID | By DTXCID | By Batch Search | Pubchem Link to GHS classification | GHS classification | Chemical Property Resource | Chemical Fate Resource | Chemical Search Resource | By starting value | By exact value | By substring value | Subset for MS-Ready Structures | By Mass Range | By Chemical Formula | List Resource | Get all list types | All lists by type | List by name | Lists containing a specific chemical | DTXSIDs for chemical list and starting value | DTXSIDs for chemical list and exact value | DTXSIDs for chemical list and containing value | Chemicals in a specific list | Chemical File Resource | Get mrv by DTXSID or DTXCID | Get mol by DTXSID or DTXCID | Get structure image by DTXSID, DTXCID, or SMILES | Chemical Synonym Resource | Conclusion

Introduction | Hazard Resource | Get Hazard Data by DTXSID | Skin Eye Resource | Cancer Resource | Genetox Resource | Example Use Case: Comparing Hazard Data Across Chemical Lists | Obtain Lists of Chemicals | Review Genotoxicity Data for a Single Chemical | Review Genotoxicity Data for Chemical Lists | Conclusion

Introduction | Functional Use Resource | Functional Use | Functional Use Probability | Functional Use Probability Batch | Functional Use Categories | Product Data Resource | Product Data | Product Use Category Data | httk Data Resource | httk Data | List Presence Resource | List Presence Tags | List Presence Tag Data | Exposure Predictions | General Exposure Predictions | Demographic Exposure Predictions | Comptox Chemicals Dashboard (CCD) | Biomonitoring data | Chemical use and weight fractions | Multimedia Database (MMDB) | Medium Categories | Single Sample records | Aggregate Records | Batch Search | Conclusion

Installing and loading spsurvey | Citation information | spsurvey terminology | Vignettes in spsurvey | Installing a previous version of spsurvey | sf objects | Coordinate reference systems | References

Object-Oriented Design | Model Specification | Creating a Model object | Using a Model object | Translating and compiling MCSim model specification text without creating a Model object

A Mathematical Model for Exponential Growth or Decay | MCSim Model Specification | Element 1: States | Element 2: Outputs | Element 3: Inputs | Element 4: Parameters | Element 5: Initialize Section | Element 6: Dynamics Section | Element 7: End Keyword | Building the Model | Solving an Initial Value Problem (i.e., Performing a Model Simulation) | Examining the Results

Model Description | MCSim Model Specification | Building the Model | Predicting the Temperature of a Cup of Tea | Examining the Results

Model Description | MCSim Model Specification | Building the Model | Predicting the Numbers of Rabbits and Foxes | Examining the Results

Model Description | MCSim Model Specification | Building the Model | Predicting the Blood Concentration of a Substance Following an Oral Dose | Examining the Results | Predicting the Blood Concentration of a Substance Following an IV Dose | Comparing AUC Values for Oral and IV Dosing Scenarios

Input Variables | A Classical Pharmacokinetic Model | MCSim Model Specification | Building the Model | Predicting the Blood Concentration of a Substance Following Oral Dosing | Examining the Results

Events | A Classical Pharmacokinetic Model | MCSim Model Specification | Building the Model | Predicting the Blood Concentration of a Substance During Repeated Oral Dosing using Events | Examining the Results

Model Description | MCSim Model Specification | Building the Model | Verifying Conservation of Mass | Verifying Conservation of Flow | Examining the Simulation Results

Introduction | Data Notation | Function Notation

Overview | Suggested packages for use with this vignette | Raw Data File Exploration | Data Catalog | Chemical ID Map | Level-0 (L0) Data Compilation | Best Practices for Data Processing | References

Introduction | Set Up | plot_clint.R | plot_fup_uc.R | References

Introduction | Suggested packages for use with this vignette | Concentration-Response Modeling | Concentration-Response Modeling for a Single Series with concRespCore | Concentration-Response Modeling for Multiple Series with tcplfit2_core and tcplhit2_core | Concentration-Response Modeling for tcpl-like data without a database connection | - Source Data Formatting | - Adjustments | - Normalization | - Dose-Response Curve Fitting | Hitcalling | - $p_1$: AIC Weight | - $p_2$: Responses Outside Cutoff | - $p_3$: Top Likelihood Ratio | Visual Representation of Proportional Weights | Consideration: Continuous Hitcalls to Activity Calls | Bounding the Benchmark Dose (BMD) | Imposing Lower BMD Bounds | Imposing Upper BMD Bounds | Bounding BMDs with tcplhit2_core | Impacts if BMD is between the BMD Lower Bound and Lowest Dose Tested | Plotting | Plotting All Models with concRespCore and concRespPlot | Plotting All Models with tcplfit2_core Output | Plotting the Winning Model with concRespPlot2 | Customizing concRespPlot2 Plots | - Adding a Plot Title, Shade Cutoff Band, and Potency Estimates | - Label All Potency Estimates | - Add Additional Curves | Area Under the Curve (AUC) | Area Under the Curve (AUC) with concRespCore | Area Under the Curve (AUC) with tcplfit2_core and tcplhit2_core | - Positive Responses | - Negative Responses | - Bi-phasic Responses | Model Details | Polynomial 1 (poly1) | Polynomial 2 (poly2) | Power (pow) | Hill | Gain-Loss (gnls) | Exponential 2 (Exp2) | Exponential 3 (Exp3) | Exponential 4 (Exp4) | Exponential 5 (Exp5) | Table of All Model Details | Glossary

Key information about version 0.99.0 and upcoming versions of elevatr | Get Point Elevation Data | USGS Elevation Point Query Service | Using get_elev_point() to Access The USGS Elevation Point Query Service | Point elevation from Amazon Web Service Terrain Tiles | Get Raster Elevation Data | Using get_elev_raster() to access the Terrain Tiles on AWS. | Access OpenTopography API with get_elev_raster()

Introduction | Functions | Chemical Details Resource | Get chemical data | By DTXSID | By DTXCID | Chemical Property Resource | Chemical Fate Resource | Chemical Search Resource | By starting value | By exact value | By substring value | Subset for MS-Ready Structures | Mass Range | Chemical Formula | DTXCID | List Resource | All lists by type | List by name | Lists containing a specific chemical | Chemicals in a specific list | Chemical File Resource | Get mrv by DTXSID or DTXCID | Get mol by DTXSID or DTXCID | Get structure image by DTXSID or DTXCID | Chemical Synonym Resource | Example Use Case: Comparing Physico-chemical Properties Across Chemical Lists | Obtain Lists of Chemicals | Access Physico-chemical Property Data for Chemical Lists | Review Physico-Chemical Properties Across Chemical Lists | Vapor Pressure | Henry's Law constant | Boling Point | Conclusion

Introduction to the CompTox Chemicals Dashboard (CCD) | Searching one chemical at a time (single-substance search) | Batch search | Challenges of web-based dashboard search | Application Programming Interfaces (APIs) for Automated Batch Search of the CCD | Authentication | Request Construction | Introduction to ccdR | Package Settings | API Key Storage | Quick Start Examples | Chemical API | Chemical Details Resource | Chemical Property Resource | Hazard API | Hazard Resource | Bioactivity API | Bioactivity Resource | Conclusion

Introduction | Functions | Bioactivity Assay Resource | Get annotation by aeid | Get all assay annotations | Bioactivity Data Resource | Get summary data | Get data | Conclusion

Introduction | Functions | Functional Use Resource | Exposure Functional Use | Exposure Functional Use Probability | Exposure Functional Use Categories | Product Data Resource | Exposure Product Data | Exposure Product Use Category Data | List Presence Resource | List Presence Tags | List Presence Tag Data | Batch Search | Functional use probability batch | Conclusion

Introduction | Functions | Hazard Resource | Get Hazard Data by DTXSID | Get Human Hazard Data by DTXSID | Get EcoTox Hazard Data by DTXSID | Skin Eye Resource | Cancer Resource | Genetox Resource | Example Use Case: Comparing Hazard Data Across Chemical Lists | Obtain Lists of Chemicals | Review Genotoxicity Data for a Single Chemical | Review Genotoxicity Data for Chemical Lists | Review Hazard Data for Chemical Lists | Conclusion

Introduction | Methods | Operation: | Implementation: | Example | Example data | Function occurrences | Function permute | Running TITAN2::titan | Analyzing the results | Conclusions | Data | Software availability | Author Contributions | Competing Interests | Grant Information | Acknowledgments | References