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Site Map for CADDIS

On this page:

  • CADDIS
    Home
  • CADDIS
    Volume 1
  • CADDIS
    Volume 2
  • CADDIS
    Volume 3
  • CADDIS
    Volume 4
  • CADDIS
    Volume 5
Search CADDIS
 
CADDIS Home
  • Basic Information
  • Recent Additions
  • Frequently Asked Questions
  • Glossary
  • Publications
  • Related Links
  • Authors & Contributors

Volume 1- Stressor Identification

  • Basic Information
  • About Causal Assessment
  • Guide Overview
  • Casual Concepts
  • Casual History

Stressor Identification Guidebook

  • Getting Started
    • Using the Step-by-Step Guide
    • Guide Overview
    • Fundamentals of Causal Analysis
  • Step 1. Define the Case
    • Overview
    • In-depth Look
    • Results and Next Steps
  • Step 2. Candidate Causes
    • Overview
    • In-depth Look
    • Results and Next Steps
  • Step 3. Data from the Case
    • Overview
    • In-depth Look
    • Results and Next Steps
  • Step 4. Data from Elsewhere
    • Overview
    • In-depth Look
    • Results and Next Steps
  • Step 5. Identify Probable Causes
    • Overview
    • Weigh Evidence for Each Cause
    • Compare Evidence Among Causes
    • Complete Causal Analysis
  • About Causal Assessment
    • Our Causal Approach
    • Weigh Evidence for Each Cause
    • Compare Evidence Among Causes
    • Complete Causal Analysis
  • Quantifying Uncertainty
  • Summary Tables of Types of Evidence
  • Summary Tables of Scores
    • Scoring the Evidence
  • Tips for Listing Candidate Causes
  • Listing Multiple Stressors as Candidate Causes

Volume 2 - Sources, Stressors and Responses

  • Basic Information
  • Learn About Sources
  • Learn About Stressors
  • Learn About Responses
  • Learn About Conceptual Diagrams

Source / Stressor Module

  • Ammonia
  • Dissolved Oxygen
  • Flow Alteration
  • Herbicides
  • Insecticides
  • Ionic Strength
  • Metals
  • Nutrients
  • pH
  • Physical Habitat
  • Sediment
  • Temperature
  • Unspecified Toxic Chemicals
  • Urbanization
    • What is Urbanization?
    • Riparian/Channel Alteration
    • What Are Wastewater Inputs?
    • Stormwater Runoff and Impervious Surfaces
    • Water and Sediment Quality in Urban Streams
    • Urbanization and Stream Temperature
    • Hydrology: Flow Alteration in Urban Streams
    • Physical Habitat in Urban Streams
    • Urbanization and Basal Energy Sources
    • References for the Urbanization Module

Volume 3 - Examples and Applications

  • Basic Information
  • Analytical Examples
    • Spatial Co-occurrence
    • Verified Prediction (PECBO)
    • Stressor-Response from the Field
    • Stressor-Response from the Lab
    • Verified Prediction (Traits)
  • Worksheet Examples (Little Scioto River, OH)
    • Overview
    • Define the Case
    • List Candidate Causes
    • Assemble Data from the Case
    • Spatial/Temporal Co-occurrence
    • Evidence of Exposure or Mechanism
    • Causal Pathway
    • Stressor-Response from the Field
      • Sediment
      • Riffle/Pool
      • Dissolved Oxygen
      • Ammonia
      • Metals
    • Summary of Scores from the Case
      • Increased % DELT
      • Increased Relative Weight
      • Decreased % Mayflies and Increased % Tolerant Macroinvertebrates
    • Assemble Data from Elsewhere
    • Stressor-Response from Laboratory Studies
    • Mechanistically Plausible Cause
    • Summary of Scores from Elsewhere
      • Increased % DELT
      • Increased Relative weight
      • Decreased % Mayflies and Increased % Tolerant Macroinvertebrates
    • Evaluating Multiple Lines of Evidence
      • Increased % DELT
      • Increased Relative weight
      • Decreased % Mayflies and Increased % Tolerant Macroinvertebrates
    • Identify Probable Cause
  • State Examples
  • Case Studies
  • Galleries
    • Chronic Concentration-Response
    • SSDs
    • Field Stressor-Response
    • References

Volume 4 - Data Analysis

  • Basic Information
  • Selecting an Analysis Approach
    • How Can I Use My Data?
    • Establishing Differences from Expectations
    • Estimating Stressor-Response Relationships
  • Getting Started
    • Assembling Data
    • Matching Data
    • Organizing Data Along Causal Pathways
    • Data Quality
  • Basic Principles and Issues
    • Interpreting Statistics
    • Autocorrelation
    • Confounding
  • Exploratory Data Analysis
    • Exploratory Data Analysis (EDA)
    • Variable Distributions
    • Scatterplots
    • Correlation Analysis
    • Conditional Probability Analysis
    • Multivariate Approaches for Exploring Associations Among Stressor Variables
    • Mapping Data: Spatial Analysis and GIS

Analysis and Tools

  • Basic Analyses
    • Tests of Significant Difference
    • Regression Analysis
    • Quantile Regression
    • Classification and Regression Tree (CART) Analysis
  • Advanced Analyses
    • Controlling for Natural Variability
    • Predicting Environmental Conditions from Biological Observations (PECBO)
    • Analyzing Trait Data
    • Propensity Score Analysis
    • Species Sensitivity Distributions (SSDs)
  • Download Software
    • Overview
    • CADStat
    • Species Sensitivity Distribution (SSD) Generator
    • R Command Line Tutorial

Data Analysis Topics

  • Autocorrelation
  • Classification and Regression Trees
  • Conditional Probability
  • Confidence Intervals
  • Confounding
  • Controlling for Natural Variability
  • Correlation Analysis
  • Interpreting Statistics
  • Multivariate Data Exploration
  • PECBO
  • Propensity Scores
  • Quantile Regression
  • Regression Analysis
  • Scatterplots
  • Spatial Analysis and GIS
  • SSDs
  • Tests of Significant Difference
  • Traits

Volume 4 - Predicting Environmental Conditions from Biological Observations (PECBO)
Appendix: Technical Details and Programs

Introduction

  • Overview
  • Module Organization
  • Theory
  • Definitions

Using Existing Taxon-Environment Relationships

  • Overview
  • Download Files & Set Up R
  • Standardize Taxonomy
  • Assign Operational Taxonomic Units (OTUs)
  • Compute Biological Inferences

Estimating Taxon-Environment Relationships

  • Overview
  • Central Tendencies
  • Environmental Limits
  • Parametric Regressions
  • Non-parametric Regression
  • Assessing Model Fit
  • Measurement Error
  • Survey Weighting
  • Placing Taxa into Tolerance Categories

Computing Inferences

  • Overview
  • Weighted Average Inferences
  • Maximum Likelihood Inferences

R Scripts

  • Overview
  • Loading Data
  • Central Tendencies
  • Environmental Limits
  • Parametric Regressions
  • Non-Parametric Regressions
  • Significance Tests
  • Area Under the ROC Curve
  • Curve Shape
  • Weighted Average Inference
  • Estimate Taxon-Environment Relationships Using taxon.env()
  • Download Scripts and Sample Data

Volume 5 - Casual Databases

  • Basic Information
  • Learn about CADLink
  • Learn about Interactive Conceptual Diagrams (ICDs)

Causal Analysis/Diagnosis Decision Information System (CADDIS)

  • CADDIS Home
    • About CADDIS
    • Frequent Questions
    • Publications
    • Recent Additions
    • Related Links
    • CADDIS Glossary
  • Volume 1: Stressor Identification
    • About Causal Assessment
    • Getting Started
    • Step 1. Define the Case
    • Step 2. List Candidate Causes
    • Step 3. Evaluate Data from the Case
    • Step 4. Evaluate Data from Elsewhere
    • Step 5. Identify Probable Causes
  • Volume 2: Sources, Stressors and Responses
    • About Sources
      • Urbanization
    • About Stressors
  • Volume 3: Examples and Applications
    • Analytical Examples
    • Worksheet Examples
    • State Examples
    • Case Studies
    • Galleries
  • Volume 4: Data Analysis
    • Selecting an Analysis Approach
    • Getting Started
    • Basic Principles & Issues
    • Exploratory Data Analysis
    • Basic Analyses
    • Advanced Analyses
    • PECBO Appendix
    • Download Software
    • Data Analysis Topics (A -Z)
  • Volume 5: Causal Databases
    • Learn about CADLink
Contact Us about CADDIS
Contact Us about CADDIS to ask a question, provide feedback, or report a problem.
Last updated on February 4, 2025
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