CADDIS Volume 4: Data Analysis
Predicting Environmental Conditions from Biological Observations (PECBO) Appendix
- Using Existing Taxon-Environment
- Estimating Taxon-Environment
- Computing Inferences
- R Scripts
Topics in R Scripts
Data of various formats can be loaded into R. The sample data supplied in this module 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
Download the sample data and place the files into your working directory. 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:
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")