Package: manureshed 0.1.5

Olatunde D. Akanbi

manureshed: Spatiotemporal Nutrient Balance Analysis Across Agricultural and Municipal Systems

A comprehensive framework for analyzing agricultural nutrient balances across multiple spatial scales (county, 'HUC8', 'HUC2') with integration of wastewater treatment plant ('WWTP') effluent loads for both nitrogen and phosphorus. Supports classification of spatial units as nutrient sources, sinks, or balanced areas based on agricultural surplus and deficit calculations. Includes visualization tools, spatial transition probability analysis, and nutrient flow network mapping. Built-in datasets include agricultural nutrient balance data from the Nutrient Use Geographic Information System ('NuGIS'; The Fertilizer Institute and Plant Nutrition Canada, 1987-2016) <https://nugis.tfi.org/tabular_data/> and U.S. Environmental Protection Agency ('EPA') wastewater discharge data from the 'ECHO' Discharge Monitoring Report ('DMR') Loading Tool (2007-2016) <https://echo.epa.gov/trends/loading-tool/water-pollution-search>. Data are downloaded on demand from the Open Science Framework ('OSF') repository to minimize package size while maintaining full functionality. The integrated 'manureshed' framework methodology is described in Akanbi et al. (2025) <doi:10.1016/j.resconrec.2025.108697>. Designed for nutrient management planning, environmental analysis, and circular economy research at watershed/administrative to national scales. This material is based upon financial support by the National Science Foundation, EEC Division of Engineering Education and Centers, NSF Engineering Research Center for Advancing Sustainable and Distributed Fertilizer Production (CASFER), NSF 20-553 Gen-4 Engineering Research Centers award 2133576. We thank Dr. Robert D. Sabo (U.S. Environmental Protection Agency) for his valuable contributions to the conceptual development and review of this work. We acknowledge Dr. Sheri Spiegal (U.S. Department of Agriculture–Agricultural Research Service) for foundational contributions to the manureshed classification framework (Spiegal et al. 2020) <doi:10.1016/j.agsy.2020.102813>.

Authors:Olatunde D. Akanbi [aut, cre, cph], Vibha Mandayam [aut], Atharva Gupta [aut], K. Colton Flynn [aut], Jeffrey Yarus [aut], Erika I. Barcelos [aut, cph], Roger H. French [aut, cph]

manureshed_0.1.5.tar.gz
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manureshed_0.1.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html
DESCRIPTION |NEWS
card.svg |card.png
manureshed/json (API)

# Install 'manureshed' in R:
install.packages('manureshed', repos = c('https://cwru-sdle.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cwru-sdle/manureshed/issues

Pkgdown/docs site:https://exelegch.github.io

On CRAN:

Conda:

5.90 score 2 stars 25 scripts 568 downloads 80 exports 54 dependencies

Last updated from:8ba8ec237d. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE208
source / vignettesOK245
linux-release-x86_64NOTE197
macos-release-arm64NOTE124
macos-oldrel-arm64NOTE144
windows-develNOTE125
windows-releaseNOTE117
windows-oldrelNOTE118
wasm-releaseOK164

Exports:add_centroid_coordinatesadd_texas_huc8agri_classify_completeagri_classify_complete_customagri_classify_nitrogenagri_classify_nitrogen_customagri_classify_phosphorusagri_classify_phosphorus_customagri_process_nugisbatch_analysis_enhancedbatch_analysis_parallelbatch_analysis_yearsbenchmark_analysiscalculate_cropland_thresholdcalculate_transition_probabilitiescheck_builtin_datacitation_infoclean_category_namesclear_data_cachecompare_analysescompare_regionscompare_scenariosCONUS_STATESconvert_load_unitscreate_analysis_reportcreate_classification_summarycreate_network_plotdownload_all_datadownload_osf_dataexport_for_gisexport_for_policyexport_for_publicationfilter_by_stateformat_huc8get_cropland_thresholdget_nutrient_colorsget_region_definitionsget_state_boundariesget_state_fipshealth_checkintegrate_completeintegrate_wwtp_agriculturalKG_TO_TONSlaunch_dashboardLBS_TO_KGLBS_TO_TONSlist_available_yearslist_regionsload_builtin_boundariesload_builtin_nugisload_builtin_wwtpload_user_wwtpMANURESHED_CRSmap_agricultural_classificationmap_wwtp_columnsmap_wwtp_influencemap_wwtp_pointsP2O5_TO_Pplot_absolute_changesplot_before_after_comparisonplot_impact_ratiosquick_analysisquick_checkquick_state_analysisrun_builtin_analysisrun_state_analysissave_analysis_summarysave_centroid_datasave_plotsave_spatial_datasave_transition_matrixsummarize_resultstest_osf_connectionview_cheatsheetwwtp_aggregate_by_boundarieswwtp_classify_sourceswwtp_clean_datawwtp_filter_positive_loadswwtp_process_completewwtp_to_spatial

Dependencies:askpassclassclassIntclicpp11curlDBIdplyre1071farvergenericsggplot2gluegtablehttrigraphisobandjsonliteKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmimeopensslpillarpkgconfigproxypurrrR6rappdirsRColorBrewerRcpprlangs2S7scalessfstringistringrsystibbletidyrtidyselecttigrisunitsutf8uuidvctrsviridisLitewithrwk

Hub Site Selection for Nutrient Recovery Operations
Overview | What the module does | The 3 × 3 scoring framework | Installation of optional dependencies | Step 1 — Run run_builtin_analysis() | Step 2 — Download the CAFO data | Step 3 — Score hub sites | Default usage | Compute a single score | With CDL raster (optional) | Step 4 — Inspect results | Step 5 — Map results | Step 6 — Export results | Multi-year analysis | Varying the catchment radius | Understanding the scoring dimensions | Performance notes | See also

Last update: 2026-05-11
Started: 2026-05-11

Getting Started with manureshed
What is manureshed? | View cheatsheet | Quick Start - Complete Analysis | Step-by-Step Analysis | 1. Check Available Data | 2. Basic Agricultural Analysis | 3. Add WWTP Data | Understanding the Results | Classifications | Accessing Results | Creating Maps | Classification Maps | WWTP Maps | Working with Different Years | Single Years | Multiple Years | Using Custom WWTP Data | State-Specific Analysis | Loading Individual Datasets | Tips for Success | Memory Management | Quality Checks | Next Steps | Getting Help

Last update: 2026-01-28
Started: 2026-01-02

Scenario Comparison Analysis
Overview | Basic Usage | Simple Comparison: Agricultural vs. WWTP | Understanding the Results | 1. Comparison Data | 2. Summary Statistics | 3. Visualization Plots | Advanced Examples | Multiple Scenarios | Year-over-Year Comparison | Scale Comparison | Saving Results | Save Plots | Save Data | Auto-save During Comparison | Interpreting Results | Understanding Deltas | Key Metrics to Watch | Use Cases | Management Analysis | Sensitivity Analysis | Regional Comparison | Tips and Best Practices | 1. Keep Comparisons Meaningful | 2. Name Scenarios Clearly | 3. Document Your Analysis | 4. Consider Statistical Significance | Troubleshooting | Different Scales | Missing Data | Related Functions | See Also

Last update: 2026-01-24
Started: 2026-01-24

Using the Interactive Dashboard
Overview | Installation Requirements | Launching the Dashboard | Dashboard Interface | Main Components | Sidebar Controls | Analysis Parameters | Action Buttons | Using the Map Tab | Interactive Map Features | Map Navigation Tips | Using the Statistics Tab | Value Boxes | Classification Distribution | Surplus/Deficit Distribution | Summary Statistics | Using the Data Table Tab | Interactive Table Features | Useful Filters | Help Tab | Workflow Examples | Example 1: Basic State Analysis | Example 2: Compare Agricultural vs. Integrated | Example 3: Year-over-Year Exploration | Example 4: Threshold Sensitivity | Example 5: Create Presentation Materials | Downloading Results | Data Download | Using Downloaded Data | Performance Tips | For Faster Analysis | Browser Performance | Troubleshooting | Dashboard Won't Launch | Analysis Fails | Map Not Displaying | Value Boxes Show Zero | Comparison with Programmatic Interface | When to Use Dashboard | When to Use R Code | Hybrid Approach | Sharing Results | For Colleagues Without R | For R Users | For Presentations | Accessibility Features | Privacy and Security | Advanced: Deploying for Teams | Option 1: Shinyapps.io | Option 2: RStudio Connect | Option 3: Shiny Server | Getting Help | Related Vignettes | Summary

Last update: 2026-01-24
Started: 2026-01-24

Advanced Features
Overview | Custom Thresholds | Understanding Thresholds | Automatic Threshold Calculation | State-Specific Analysis | Single State Analysis | Multi-State Comparison | Batch Processing | Multiple Years | Parallel Processing | Enhanced Batch Analysis | Performance Optimization | Benchmarking | Memory Management | Advanced Spatial Analysis | Transition Probabilities | Spatial Statistics | Custom Analysis Workflows | Research-Specific Analysis | Time Series Analysis | Data Export and Integration | Export for Other Software | Integration with Other Packages | Quality Control | Advanced Validation | Tips for Advanced Users | Performance Tips | Reproducibility

Last update: 2026-01-02
Started: 2026-01-02

Creating Maps and Plots
Overview | Quick Maps with quick_analysis() | Step-by-Step Map Creation | 1. Get Analysis Results First | 2. Agricultural Classification Maps | 3. Combined Maps (Agricultural + WWTP) | 4. WWTP Facility Maps | 5. WWTP Influence Maps | Comparison Plots | Before/After WWTP Integration | Network Plots | Spatial Transition Networks | Customizing Maps | Save Options | Custom Colors | Working with Different Scales | County Level | HUC8 Watersheds | HUC2 Regions | State-Specific Maps | Multi-Panel Figures | Tips for Good Maps | Map Quality | Color Choices | File Management | Troubleshooting | Common Issues

Last update: 2026-01-02
Started: 2026-01-02

Sensitivity Analysis with Custom Efficiency Factors
Overview | Standard vs. Custom Efficiency Factors | Basic Sensitivity Analysis | Load Required Data | Compare Different Nitrogen Efficiencies | Visualize Sensitivity Results | Phosphorus Sensitivity Analysis | Combined Sensitivity Analysis | Mapping Results Across Scenarios | Interpreting Results | Recommended Practice | Example: Complete Sensitivity Workflow | Summary | References

Last update: 2026-01-02
Started: 2026-01-02

Using Your Own Data
Overview | Using Custom WWTP Data | For Years Outside 2007-2016 | Advanced Custom Data Integration | Adding Other Nutrient Sources | Working with Different Time Periods | Custom Agricultural Data | Data Validation and Quality Control | Exporting Results | Troubleshooting Common Issues | WWTP Data Issues | Agricultural Data Issues | Getting Help | Common Questions | Function Help | Getting More Help | Handling Different Data Formats | Standard EPA Format | Different Units | Different File Format | Custom Column Names | Manual WWTP Processing | Unit Conversions | Common Conversions | Handling P2O5 vs P | Working with Different Spatial Scales | County Data (FIPS Codes) | HUC8 Watersheds | HUC2 Regions | State-Specific Analysis | Single State | Multiple States | Quality Control | Validate Your Data | Common Data Issues | Working with Multiple Years | Time Series Analysis | Data Management Tips | File Organization | Memory Management | Example: Complete Custom Workflow | Integration Issues | Best Practices for Custom Data | Data Documentation | Quality Assurance Workflow | Reporting Issues

Last update: 2026-01-02
Started: 2026-01-02

Readme and manuals

Help Manual

Help pageTopics
Add Centroid Coordinates to Spatial Dataadd_centroid_coordinates
Add Texas HUC8 Data (Updated for OSF)add_texas_huc8
Complete Agricultural Classification Pipelineagri_classify_complete
Complete Agricultural Classification Pipeline with Custom Efficiency Factorsagri_classify_complete_custom
Classify Agricultural Nitrogen Statusagri_classify_nitrogen
Classify Agricultural Nitrogen Status with Custom Efficiency Factoragri_classify_nitrogen_custom
Classify Agricultural Phosphorus Statusagri_classify_phosphorus
Classify Agricultural Phosphorus Status with Custom Efficiency Factoragri_classify_phosphorus_custom
Process NuGIS Data for Manureshed Analysisagri_process_nugis
Enhanced Batch Analysis with Full Visualizationsbatch_analysis_enhanced
Batch Analysis with Parallel Processingbatch_analysis_parallel
Batch Analysis Across Multiple Yearsbatch_analysis_years
Benchmark Analysis Performancebenchmark_analysis
Calculate Cropland Threshold for Exclusioncalculate_cropland_threshold
Calculate Spatial Transition Probabilitiescalculate_transition_probabilities
Check Data Availability from OSFcheck_builtin_data
Display Package Citation Informationcitation_info
Clean Category Names for Displayclean_category_names
Clean Text Dataclean_text
Clear Data Cacheclear_data_cache
Compare Two Analysis Resultscompare_analyses
Compare Multiple Regionscompare_regions
Compare Multiple Analysis Scenarioscompare_scenarios
CONUS StatesCONUS_STATES
Convert Load Units to Tonsconvert_load_units
Create Analysis Reportcreate_analysis_report
Create Classification Summary Tablecreate_classification_summary
Create Network Plot from Transition Probabilitiescreate_network_plot
NuGIS and EPA WWTP Data Sourcesdata_sources
Download All Datasets from OSFdownload_all_data
Download and Cache Data from OSFdownload_osf_data
Export Results for GIS Applicationsexport_for_gis
Export for Policy Briefsexport_for_policy
Export for Publicationexport_for_publication
Filter Data by Statefilter_by_state
Format HUC8 Codesformat_huc8
Get Cropland Threshold by Scaleget_cropland_threshold
Default Color Schemes for Nutrient Classificationsget_nutrient_colors
Get Built-in Region Definitionsget_region_definitions
Get State Boundaries for Mappingget_state_boundaries
Get State FIPS Codeget_state_fips
Check Package Health and Dependencieshealth_check
Complete Integration Pipeline (Updated)integrate_complete
Integrate WWTP Data with Agricultural Classifications (Updated)integrate_wwtp_agricultural
Conversion Factor: Kilograms to US TonsKG_TO_TONS
Launch Interactive Manureshed Dashboardlaunch_dashboard
Conversion Factor: Pounds to KilogramsLBS_TO_KG
Conversion Factor: Pounds to US TonsLBS_TO_TONS
List Available Built-in Yearslist_available_years
List Available Regionslist_regions
Load Built-in Spatial Boundaries from OSFload_builtin_boundaries
Load Built-in NuGIS Data from OSFload_builtin_nugis
Load Built-in WWTP Data from OSFload_builtin_wwtp
Load User WWTP Dataload_user_wwtp
manureshed: Manureshed Analysis with WWTP Integrationmanureshed-package manureshed
Standard CRS for Manureshed AnalysisMANURESHED_CRS
Create Agricultural Classification Mapmap_agricultural_classification
Map WWTP Column Names to Standard Formatmap_wwtp_columns
Create WWTP Influence Mapmap_wwtp_influence
Create WWTP Point Mapmap_wwtp_points
Conversion Factor: P2O5 to PP2O5_TO_P
Create Absolute Change Plotplot_absolute_changes
Create Before/After Comparison Plotplot_before_after_comparison
Create Impact Ratio Plotplot_impact_ratios
Quick Analysis with Visualizationquick_analysis
Quick Data Checkquick_check
Quick State Analysis with Visualizationquick_state_analysis
Complete Manureshed Analysis Workflow (Built-in Data)run_builtin_analysis
Run State-Level Analysisrun_state_analysis
Save Analysis Summarysave_analysis_summary
Save Centroid Datasave_centroid_data
Save Plotsave_plot
Save Spatial Datasave_spatial_data
Save Transition Probability Matrixsave_transition_matrix
Print Summary of Analysis Resultssummarize_results
Test OSF Connectiontest_osf_connection
Validate Required Columnsvalidate_columns
View Package Cheat Sheetview_cheatsheet
Aggregate WWTP Data by Spatial Boundarieswwtp_aggregate_by_boundaries
Classify WWTP Sources by Load Sizewwtp_classify_sources
Clean WWTP Datawwtp_clean_data
Filter WWTP Data for Positive Loadswwtp_filter_positive_loads
Complete WWTP Processing Pipelinewwtp_process_complete
Convert WWTP Data to Spatial Formatwwtp_to_spatial