taxon.env {bio.infer}  R Documentation 
Estimate taxonenvironment relationships
Description
taxon.env
estimates taxonenvironment relationships using
logistic regression.
Usage
taxon.env(form, bcnt, envdata, bcnt.siteid, bcnt.abndid,
env.siteid,tlevs = "all", dumpdata = FALSE)
Arguments
form 
Regression
formula for model.
Format is identical to that used for 
bcnt 
A benthic count file with a full taxonomic hierarchy that
results from running 
envdata 
Environmental data file 
bcnt.siteid 
Field name for 
bcnt.abndid 
Field name for 
env.siteid 
Field name for 
tlevs 
Taxonomic levels to compute taxonenvironment relationships. 
dumpdata 
Logical field specifying whether data used to estimate taxonenvironment relationships should be included in the output. 
Details
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 taxonenvironment relationships are computed using the
parameter tlevs
. The default value for tlevs
computes
relationships at all levels.
Value
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

Author(s)
Lester L. Yuan
See Also
Examples
data(envdata.OR)
data(bcnt.tax.OR)
coef < taxon.env(~sed + sed^2, bcnt.tax.OR, envdata.OR, "SVN",
"CountValue", "STRM.ID")