taxon.env: Estimate taxon-environment relationships
In bio.infer: Predict Environmental Conditions from Biological Observations

Description Usage Arguments Details Value Author(s) See Also Examples

taxon.env estimates taxon-environment relationships using logistic regression.

1 2	taxon.env(form, bcnt, envdata, bcnt.siteid, bcnt.abndid, env.siteid,tlevs = "all", dumpdata = FALSE)

`form`	Regression formula for model. Format is identical to that used for `glm`.
`bcnt`	A benthic count file with a full taxonomic hierarchy that results from running `get.taxonomic`.
`envdata`	Environmental data file
`bcnt.siteid`	Field name for `bcnt` unique site identifier.
`bcnt.abndid`	Field name for `bcnt` taxon abundance.
`env.siteid`	Field name for `envdata` unique site identifier.
`tlevs`	Taxonomic levels to compute taxon-environment relationships.
`dumpdata`	Logical field specifying whether data used to estimate taxon-environment relationships should be included in the output.

This script generates logistic regression models for taxa at various levels of taxonomic resolution (as specified by the user). The script computes the degrees of freedom specified by the model ($df$) and selects taxa that occur in at least 10 times df and is absent from at least 10 times df sites. Then, logistic regression models based on the formula specified by the user are computed for each taxon using glm. The user can select the taxonomic levels (e.g., CLASS, ORDER, SPECIES, etc.) at which taxon-environment relationships are computed using the parameter tlevs. The default value for tlevs computes relationships at all levels.

Regression coefficient file that can be used with mlsolve to infer environmental conditions.

`tnames`	Taxon names for which models are calculated
`csave`	Matrix of regression coefficients
`xvar`	Character vector with names of explanatory variables
`xlims`	Range of each explanatory variable
`form`	Model formula
`roc`	Area under receiver operator curve for model for each taxon.
`raw.data`	Data used to estimate relationships. Only included if `dumpdata = T`.

Lester L. Yuan

get.taxonomic

data(envdata.OR)
data(bcnt.tax.OR)
coef <- taxon.env(~sed + sed^2, bcnt.tax.OR, envdata.OR, "SVN",
"CountValue", "STRM.ID")

Loading required package: tcltk
Warning message:
no DISPLAY variable so Tk is not available 
Model formula:  resp ~sed+I(sed^2) 
Minimum number of occurrences:  30 
Number of taxa modeled:
   TAXON.LEVEL NUM.MODS
1       PHYLUM        4
2    SUBPHYLUM        2
3        CLASS        5
4     SUBCLASS        3
5   INFRACLASS        0
6   SUPERORDER        0
7        ORDER        3
8     SUBORDER        3
9   INFRAORDER        6
10 SUPERFAMILY        4
11      FAMILY       26
12   SUBFAMILY       23
13       TRIBE       11
14       GENUS       50
15     SPECIES       26