Substrate composition was estimated by summarizing the size distribution of particles at five locations on 21 transects. Stream temperature was measured at the time of sampling. A reach 40 times the wetted width of the stream was delineated for sampling. Both organizations used a similar sampling protocol. Environmental Protection Agency's Environmental Management and Assessment Program-Western Pilot Project (EMAP-West) from 2000 to 2002, and the second data set was collected in western Oregon by the Oregon Department of Environmental Quality (DEQ) from 1999 to 2000 (Figures 22 and 23). Two sample data sets are provided here to illustrate the analysis methods described in this module. The library can be installed by typing at the R prompt: The library also contains the script that computes maximum likelihood inference and other tools. To estimate multivariate taxon-environment relationships, or to format any taxon-environment relationship correctly for maximum likelihood inferences, you will need to use the scripts provided in the R library bio.infer. Compare Taxa Names in Tolerance Value and Assessment Data.Chi-Square Tests for Parametric and Non-parametric Models.Calculate Weighted Average Tolerance Values.Before running any of the other analysis programs, the first script listed (Set Up Variables) should be run to set up R data files. The scripts listed below assume that data have been downloaded and stored in the working directory. Each script can be then run by executing the following command in R: ![]() R scripts from this section can be saved directly on your hard drive as an ".R" file. For novice R users, please note that the web pages in the Helpful Links box have additional information that will help you successfully run the script. This section is provided for users who are very comfortable with R and who wish to download scripts directly. Estimate Taxon-Environment Relationships Using taxon.env().
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