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  2. Causal Analysis/Diagnosis Decision Information System (CADDIS)

Loading Data into R

  • Introduction
  • Using Taxon-Environment Relationships
  • Estimating Taxon-Environment Relationships
  • Computing Inferences
  • R Scripts

How to Load Data into R

Helpful Links
Topics In R Scripts
  • Overview
  • Download R Scripts and Sample Data
  • 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()

PECBO Appendix Site Map 

Data of various formats can be loaded into R. The sample data supplied in this module (see the Download Scripts and Sample Data page) is formatted as tab-delimited text and can be loaded using the following command:

data.set <- read.delim(filename)  # Loads a tab-delimited data file

Then, load these data files into R as follows:

site.species <- read.delim("site.species.txt")
site.species.or <- read.delim("site.species.or.txt")
env.data <- read.delim("env.data.txt")
env.data.or <- read.delim("env.data.or.txt")

Examine the data files you loaded and review how they are formatted:

fix(site.species)
fix(env.data)

The site-species data has a column with a site identifier and then a column for each taxon and a row for each site. Each numerical entry indicates the number of individuals for a given taxon and a given site.

The environmental data has a column with a site identifier and a column for each environmental variable (stream temperature, "temp"; and log-transformed percent sand and fines, "sed").

Next, merge data files so that each set of environmental data is matched with the appropriate biological data.

dfmerge <- merge(site.species, env.data, by = "SITE.ID")
dfmerge.or <- merge(site.species.or, env.data.or, by = "SITE.ID")

Causal Analysis/Diagnosis Decision Information System (CADDIS)

  • CADDIS Home
    • About CADDIS
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    • 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 to ask a question, provide feedback, or report a problem.
Last updated on February 7, 2025
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