labdsv 1.3-1

This is a bug fix for 1.3-0.  dsvdis.R was missing a cast of the 
taxon data.frame to "as.double" and would fail on taxon matrices that
are strictly integers.  Taxon matrices with real numbers worked.

labdsv 1.3-0

A number of small changes, and a couple of larger ones were made in
the revision to 1.3-0.

1) A bug was fixed in the duleg FORTRAN code that compared a four-byte
floating point number to an eight-byte number.  This bug would only
appear in relatively few cases, and affected the calculated
probability of some observations, not the indicator value itself.  I
also improved the permutation code used in the probability estimates.

2) Subsequent to the discovery of duleg bug, all remaining four-byte
floating points (FORTRAN REAL) were converted to eight-byte floating
point (FORTRAN DOUBLE PRECISION) to achieve better correspondence with
R and avoid problems.  It does increase the storage requirement of
some programs, but this seems to rarely be a problem on modern
computers.

3) I discovered that I was using specialized FORTRAN code in several
places where the base package "dist()" function would work.  I
replaced all of those instances.  This resulted in dropping function
"vardist," and modifying internal function "orddist."

4) I modified function "ordcomp," changing the default
dimensionality to full dimensionality, rather than n=2.  It is still
possible to specify any desired dimensionality through the "dim="
argument; I only changed the default.

5) While updating function "ordcomp" I realized that it would be just
as easy to have function "ordcomp" avoid the call to internal function
"orddist" and do the calculations directly.  Consequently, function
"orddist" is now a stand-alone function useful for calculating the
pair-wise distances in an ordination for any purpose.  Function
"orddist" returns an object of class "dist."

6) I changed the surface fitting routine in all versions of the "surf"
functions (for pca, pco, and nmds) to use the "predict.gam" function
of package "mgcv" in place of the function "interp" from package
"akima."  This resulted in smoother, better fit surfaces, and allowed
me to no longer require package "akima" to load labdsv.  This change
was suggested and first implemented by Jari Oksanen for function
"ordisurf" in package "vegan."  Again, following the lead of vegan, I
made the default surface fitter a thin plate spline, rather then
additive independent smooth splines.  The original behavior is still
available by specifying thinplate=FALSE.  Finally, I added a
gamma argument to the surf function to allow users to control the 
smoothness of the surface by passing gamma tot he underlying gam 
function.

7) In response to a problem identified by P. Legendre, I inserted
checks to see that "taxa" is converted to a dataframe, rather than a
matrix, wherever necessary.

8) I added two new routines to simplify working with large sparse
data sets: "matrify" and "dematrify".  "matrify" takes data in three
column database format (sample_id, taxon, abundance) and converts it
into an expanded sparse matrix data.frame.  This routine allows users
to store their data in a compacted, three column form for exchange
with other programs.  "dematrify" takes a data.frame of taxa abundance
in sparse matrix form and writes it out three column database format
(sample_id, taxon, abundance).  

9) I added a new routine to nmds() and pco() called "density" which
calculates the fraction of plots within a convex hull that belong to 
the same type as the type that defines the convex hull.

10) Once again, I had to re-organize the web server that supports labdsv
and other activities.  The general site for all material is

http://ecology.msu.montana.edu/labdsv/

The material specifically relevant to this pacakage is at

http://ecology.msu.montana.edu/labdsv/R/labdsv


labdsv 1.2-2

fixed a bug in jsurf.nmds where the ordination was not called
correctly

deleted extraneous files in the man directory (don't know why 
they were there in the first place)

moved confus to package optpart

labdsv 1.2-1

function tabdev.R was deleted to temporarily solve inscrutable
problems with Windows server.  tabdev.R worked under linux
and Windows XP, so there may be no need to update on your system.

In addition, the URL in the decsription file was updated to 
point to the current location of the lab manual for LabDSV.

labdsv 1.2-0

A couple of general changes were made to many functions.

1) in several functions the dataframe "veg" was changed to "taxa"
   to better represent the full range of community ecology the code
   is suitable for

2) in functions that used classified types or community types the
   vector specifying that was changed from "class" to "clustering"
   to avoid conflict with a reserved word, and to integrate better
   with code from package "cluster".

3) the package was checked and built on both linux and Windows to
   help ensure better utility on windows

In addition, a number of small changes were made to several functions,
listed below:

abuocc.R
	changed veg to taxa in function and documentation
confus.R
	added a correction for plotting factors correctly
	example changed to "\dontrun" because it requires library tree
const.R
	changed veg to taxa in function and documentation
	changed class to clustering in function and documentation
	changed class test to inheritance
	generally improved documentation
dga.R
	added an invisible return
	improved the example in the documentation
disana.R
	eliminated null class test
	eliminated FORTRAN call by using apply with na.rm
	corrected point labels to "attr(x,'Labels')"
dissim.R
	removed function dissim
dsvdis.R
	changed an attribute label from "index" to "method" to
		match dist()
	changed the test of step from > to >= so that step=1.0 works
duarm.R
	changed veg to taxa in function and documentation
	changed class to clustering
	simplified the presentation of results
duleg.R
	changed veg to taxa in function and documentation
	changed class to clustering
	enforced better casting of variable types in FORTRAN call
	added numitr to FORTRAN call and return
	improved the labeling of row and column names in output
	fixed possible bugs from unitiated values in FORTRAN code
envrtest.R
	added an argument to function call to control plotting
	improved the default title on the plot
euclidify.R
	cast the input object to class "dist"
	improved the information in the attributes of the output object
hilight.R
	converted hilight to a generic function and wrote separate 
		methods for PCA. PCO, and NMDS
importance.R
	changed veg to taxa
	changed class to clustering
	changed class test to inheritance
metrify.R
	cast the input object as class "dist"
	changed the output attribute from "index" to "method" to
		match dist()
nmds.R
	deleted test for null class
	changed the name of the overlayed object in the 
		points.nmds function from "overlay" to "which"
	added "cex=0.8" as the default to function surf.nmds and jsurf.nmds
	corrected logical values from "T" to "TRUE"	
	improved the bestnmds function
	improved the hilight function by adding better control of colors
		and glyphs
	added a convex hull function called chullord.nmds()
npmmds.R
	dropped function npmmds()
ordcomp.R
	deleted the test of NULL class and the option to submit a matrix
		instead of a "dist" object
	added an invisible return
orddist.R
	cast the input object to double in FORTRAN call
ordpart.R
	added default axes to the plot, and renamed axes to ax and ay
	cast the values to double in FORTRAN call
        significantly improved the documentation
ordtest.R
	added an inheritance test for object of class "pco", "nmds" and 
		"metaMDS"
ordutils.R
	added hilight() and chullord() as generic functions
pca.R
	added an explicit "cex = 1" as the default in points.pca()
	corrected logicals from "T" to "TRUE"
	corrected the scaling on variance accounted for in varplot()
	added a jsurf.pca() function to jitter coordinates if necessary
	added hilight.pca() as a method
	added chullord.pca() as a method
	improved the documentation
pco.R
	eliminated NULL class test
	corrected logical "T" to "TRUE"
	added hilight.pco() as a method
	added chullord.pco() as a method
refine.R
	dropped function refine()
rndveg.R
	renamed rndveg() to rndtaxa()
	changed veg to taxa in function
simenv.R
	dropped function simenv(), replaced by envrtest()
spcdisc.R
	corrected logical "F" to "FALSE"
tabdev.R
	changed veg to taxa
	cast most variables as double in FORTRAN call
vardist.R
	cast arguments as double in FORTRAN call
vegtab.R
	changed veg to taxa
vegtrans.R
	eliminated FORTRAN call by conversion of algorithm to pure R
	eliminated function stdveg() to standardize by plot or
		species max
zzz.R
	no longer require stats (now included in base)
