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CADDIS Volume 4: Data Analysis

Predicting Environmental Conditions from Biological Observations (PECBO) Appendix

Topics in Using Existing Taxon-Environment Relationships

Compute Biological Inferences

Biological inferences are computed using a maximum likelihood approach.

Instructions for computing inferences:

  1. Check that you have loaded the biological inference library and a taxon-environment coefficient file.

    • To load the biological inference library, type at the R prompt:

      library(bio.infer)

    • A file starting with coef (e.g., coef.west.wt) should have been loaded when you set up your workspace (see Step 6 on the Download Files page).

    • You should also have run get.otu and saved the results in a data frame (e.g., bcnt.otu).

  2. Run the R script that generates a site-OTU matrix.

    • Type at the R prompt:

      ss <- makess(bcnt.otu)

      This command runs the R script makess and stores the resulting site-OTU matrix in the data frame ss. The only input to the script is bcnt.otu, a benthic count file with OTUs assigned (i.e., the output from get.otu).

  3. Run the R script that computes inferences.

    • Type at the R prompt:

      inferences <- mlsolve(ss, coef.west.wt)

      The script mlsolve solves the maximum likelihood inference that provides the most probable environmental conditions at the site, given biological assemblage composition at the site and given taxon-environment relationships. Two inputs to the script are required: the site-OTU matrix generated by the previous step (e.g., ss) and the taxon-environment data file (e.g., coef.west.wt).

    • Inferences for each sample in the data set are stored in the data frame inferences.

  4. Interpret inference results.

    • The inference data frame will have a column with the site identifier, columns for each of the inferred environmental variables, and a column labeled "Inconsistent". Sites at which Inconsistent is TRUE are sites in which the solution algorithm did not converge to a single solution. These sites typically do not have enough taxa to confidently infer environmental conditions, so inferences at these sites should be used with caution.

    • Inferences provide an estimate of the environmental conditions at a site. This estimate is comparable to a direct environmental measurement and can be analyzed in a similar way to help inform a causal analysis. In particular, environmental inferences must be compared with inferences at reference sites to establish whether or not the conditions at the site have departed from natural expectations.

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