Latex: Typesetting Tables in LaTeX

In vegsoup: Classes and Methods for Phytosociology

Description

Creates meaningful table structures to be compiled by LaTeX.

Usage

## S4 method for signature 'VegsoupPartitionFidelity'
Latex(obj, choice = "species", recursive = FALSE, file,
	mode = 1,
	p.max = .05,
	stat.min,
	constancy.min = 95,
	taxa.width = "60mm",
	col.width = "10mm",
	footer.width = "150mm",
	footer.threshold,
	molticols.footer,
	use.letters = FALSE,
	caption.text = NULL,
	quantile.select,
	coverscale = FALSE,
	sep = "/",
	sites.columns,
	newpage = TRUE,
	template = FASLE,
	verbose, ...)

Arguments

obj	'VegsoupPartition' object.
choice	character. Either "species" or "sites", partial matches allowed.
recursive	logical. If TRUE, loop over partitions and create a standalone tables for each partition. If FALSE, the default, summarize information in single table.
file	character. Output filename. If missing a default filename is choosen depending on arguments choice and recursive, otherwise file is tested for validity.
mode	integer. With defaults values for choice and species (‘Details’), mode determines the type of ouput created. mode = 1 will typeset a species by cluster fidelity table. mode = 2 will typeset a summary table for each cluster. See ‘Details’.
p.max	numeric. Threshold value for Fisher test.
stat.min	numeric. Threshold value of fidelity statistic.
constancy.min	numeric. Threshold value of the constancy of species(-layer replicate).
taxa.width	LaTeX tag to set column width for taxon column. See ‘Details’.
col.width	LaTeX tag to set column width of all other columns. Recycled as necessary. See ‘Details’.
footer.threshold	integer. Minimum number of occurences of a species to become excluded from the table, defaults to 2.
molticols.footer	integer. Number of columns to typeset species meeting conditions implied by footer.threshold
footer.width	LaTeX tag to set column width for footer columns.
quantile.select	a character vector selecting dimensions returned by quantile to become pasted to the constancy value. Only applicable if mode == 2. See ‘Details’.
caption.text	character. Additional user supplied text pasted into automatically generated table caption. See ‘Details’.
sites.columns	character. Selceting columns from sites data frame.
use.letters	logical. Use additional letters. Only applicable if getK(object <= 26).
verbose	logical. Print messages on screen.
sep	character. Optional character string to separate the summary statistics of Fivenum, defaults to "/".
coverscale	logical. Recode result returend from Fivenum to ordinal scale if applicable, defaults to FALSE.
newpage	logical. Insert LaTex newpage command.
template	logical. Enclose in Latex template.
...	arguments passed to fidelity if object is not of class 'VegsoupPartitionFidelity'.

Details

Typical usages are

Latex(obj)

Latex(obj, choice = "species", recursive = FALSE, file = "foo.tex", mode = 1)

Latex(obj, "species", FALSE, mode = 1, ...)

Latex(obj, "species", FALSE, mode = 2, ...)

Latex(obj, "species", TRUE,  ...)

Latex(obj, "sites",   FALSE, ...)

Latex(obj, "sites",   TRUE,  ...)

If arguments choice and recursive are missing the default for both arguments apply (see ‘Usage’).

Latex is a complex function to create input files for LaTeX to typeset vegetation tables and related community summaries. It comes in four (five) flavours (see above). Some usages have many arguments, most of which have some sensible default values.

The method accepts both a 'VegsoupPartition' as well as a 'VegsoupPartitionFidelity' object. The first class is promoted to the latter class by internally calling fidelity with it's default arguments.

The choice = "species" and recursive = FALSE usage currently provides two different types of output. With mode = 1 an ordered vegetation table based on a fidelity (indicator species) statistic is created. With mode = 2 descriptive summaries for each partition (cluster) are returned. It embeds it's ouput using LaTeX package subfloat.

Set template = TRUE to wrap output in LaTex template preamble.

Value

A "list" containing the lines written to the file:

table	The main table. For mode = 2 a list of subtables for each partition (cluster).
footer.sites	Additional lines for table footer.
footer.species	Additional lines for table footer, giving species excluded from the table.

Note

To prevent the LaTeX file from being displayed on screen store the result of Latex in an object.

Author(s)

Roland Kaiser

See Also

write.verbatim

Examples

require(vegsoup)

data(windsfeld)
x <- VegsoupPartition(windsfeld, k = 2, method = "flexible")

## Not run: 
tex <- Latex(x, file = tempfile())

fid <- fidelity(x)
class(fid)

tex <- Latex(fid, file = tempfile())

head(tex$table)

## End(Not run)

vegsoup documentation built on Feb. 24, 2021, 3 a.m.