[Vegan-commits] r2442 - in pkg/vegan: man tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Feb 17 08:05:38 CET 2013
Author: jarioksa
Date: 2013-02-17 08:05:38 +0100 (Sun, 17 Feb 2013)
New Revision: 2442
Modified:
pkg/vegan/man/vegemite.Rd
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
upgdate vegemite.Rd for tabasco
Modified: pkg/vegan/man/vegemite.Rd
===================================================================
--- pkg/vegan/man/vegemite.Rd 2013-02-15 10:23:18 UTC (rev 2441)
+++ pkg/vegan/man/vegemite.Rd 2013-02-17 07:05:38 UTC (rev 2442)
@@ -5,12 +5,13 @@
\title{Display Compact Ordered Community Tables }
\description{
- The functions display compact community tables. Function
- \code{vegemite} prints text tables where species are rows, and each
- site takes only one column without spaces. Function \code{tabasco}
- provides interface for \code{\link{heatmap}} for a colour map of
- the data. The community table can be ordered by explicit indexing,
- by environmental variables or results from an ordination or cluster
+ Functions \code{vegemite} and \code{tabasco} display compact
+ community tables. Function \code{vegemite} prints text tables where
+ species are rows, and each site takes only one column without
+ spaces. Function \code{tabasco} provides interface for
+ \code{\link{heatmap}} for a colour \code{\link{image}} of the
+ data. The community table can be ordered by explicit indexing, by
+ environmental variables or results from an ordination or cluster
analysis.
}
\usage{
@@ -22,78 +23,85 @@
}
\arguments{
- \item{x}{Vegetation data. }
+ \item{x}{Community data. }
\item{use}{Either a vector, or an object from \code{cca},
\code{decorana} \emph{etc.} or \code{hclust} or a
\code{\link{dendrogram}} for ordering sites and species.}
- \item{sp.ind}{Species indices. In \code{tabasco}, this can also be an
- \code{\link{hclust}} tree or a \code{\link{dendrogram}}. }
- \item{site.ind}{Site indices. }
+ \item{sp.ind, site.ind}{Species and site indices. In \code{tabasco},
+ these can also be \code{\link{hclust}} tree,
+ \code{\link[cluster]{agnes}} clusterings or
+ \code{\link{dendrogram}}s. }
\item{zero}{Character used for zeros. }
\item{select}{Select a subset of sites. This can be a logical vector
(\code{TRUE} for selected sites), or a vector of indices of selected
sites. The order of indices does not influence results, but you
must specify \code{use} or \code{site.ind} to reorder sites.
}
- \item{Rowv, Colv}{Reorder dendrograms for the rows (sites) or columns
- (species) of \code{x}. If the arguments are \code{TRUE}, row
+ \item{Rowv, Colv}{Re-order dendrograms for the rows (sites) or
+ columns (species) of \code{x}. If the \code{Rowv = TRUE}, row
dendrograms are ordered by the first axis of correspondence
- analysis, and column dendrograms by the weighted average
- (\code{\link{wascores}}) of the order in the row. Alternatively
- these can be vectors that are used to reorder the dendrogram. }
+ analysis, and when \code{Colv = TRUE} column dendrograms by the
+ weighted average (\code{\link{wascores}}) of the row order.
+ Alternatively, the arguments can be vectors that are used to
+ reorder the dendrogram. }
\item{scale}{Cover scale used (can be abbreviated).}
\item{maxabund}{Maximum abundance used with \code{scale = "log"}.
Data maximum in the \code{select}ed subset will be used if this is
missing.}
- \item{...}{Arguments passed to \code{coverscale} (i.e., \code{maxabund}) in
+ \item{\dots}{Arguments passed to \code{coverscale} (i.e., \code{maxabund}) in
\code{vegemite} and to \code{\link{heatmap}} in \code{tabasco}.}
}
\details{
The function \code{vegemite} prints a traditional community table.
- Unlike in ordinary data matrices, species are used as rows and sites
- as columns. The table is printed in compact form: only one character
+ The display is transposed, so that species are in rows and sites in
+ columns. The table is printed in compact form: only one character
can be used for abundance, and there are no spaces between
columns. Species with no occurrences are dropped from the table.
Function \code{tabasco} produces a similar table as \code{vegemite}
- using \code{\link{heatmap}}, where abundances are coded by heatmap
- colours.
+ using \code{\link{heatmap}}, where abundances are coded by
+ colours. The function can also display dendrograms for sites
+ (columns) or species if these are given as an argument (\code{use}
+ for sites, \code{sp.ind} for species).
- The parameter \code{use} can be a vector or an object from
- \code{\link{hclust}}, a \code{\link{dendrogram}} or any ordination
- result recognized by \code{\link{scores}} (all ordination methods in
- \pkg{vegan} and some of those not in \pkg{vegan}). The
- \code{\link{hclust}} and \code{\link{dendrogram}} must be for
- sites. The dendrogram is displayed above the sites in
- \code{tabasco}. No dendrogram for species is displayed, except when
- given in \code{sp.ind}.
+ The parameter \code{use} will be used to re-order output. The
+ \code{use} can be a vector or an object from \code{\link{hclust}} or
+ \code{\link[cluster]{agnes}}, a \code{\link{dendrogram}} or any
+ ordination result recognized by \code{\link{scores}} (all ordination
+ methods in \pkg{vegan} and some of those not in \pkg{vegan}). The
+ \code{\link{hclust}}, \code{\link[cluster]{agnes}} and
+ \code{\link{dendrogram}} must be for sites. The dendrogram is
+ displayed above the sites in \code{tabasco}, but is not shown in
+ \code{vegemite}. No dendrogram for species is displayed, except
+ when given in \code{sp.ind}.
- If \code{use} is a vector, it is used
- for ordering sites. If \code{use} is an object from ordination, both
- sites and species are arranged by the first axis.
- When \code{use} is an
- object from \code{\link{hclust}} or a \code{\link{dendrogram}}, the
- sites are ordered similarly
- as in the cluster dendrogram.
- If ordination methods provide species scores, these are used for
- ordering species. In all cases where species scores are missing,
- species are ordered by their weighted averages (\code{\link{wascores}})
- on site scores. There is no natural, unique ordering in hierarchic
- clustering, but in some cases species are still nicely ordered (please
- note that you can \code{\link{reorder.dendrogram}} to have such a
- natural order).
+ If \code{use} is a vector, it is used for ordering sites. If
+ \code{use} is an object from ordination, both sites and species are
+ arranged by the first axis (provided that results are available both
+ also for species). When \code{use} is an object from
+ \code{\link{hclust}}, \code{\link[cluster]{agnes}} or a
+ \code{\link{dendrogram}}, the sites are ordered similarly as in the
+ cluster dendrogram. Function \code{tabasco} re-orders the
+ dendrogram if \code{Rowv = TRUE} or \code{Rowv} is a vector. Such
+ re-ordering is not available for \code{vegemite}, but it can be done
+ by hand using \code{\link{reorder.dendrogram}}. In all cases where
+ species scores are missing, species are ordered by their weighted
+ averages (\code{\link{wascores}}) on site order.
Species and sites can be ordered explicitly giving their indices or
names in parameters \code{sp.ind} and \code{site.ind}. If these are
- given, they take precedence over \code{use}. A subset of sites can be
- displayed using argument \code{select}, but this cannot be used to
- order sites, but you still must give \code{use} or \code{site.ind}.
- However, \code{tabasco} makes two exceptions: \code{site.ind} and
- \code{select} cannot be used when \code{use} is an
- \code{\link{hclust}} tree or a \code{\link{dendrogram}}. In addition,
- the \code{sp.ind} can also be an \code{\link{hclust}} tree or a
- \code{\link{dendrogram}}, and in that case the dendrogram is plotted
- on the left side of the \code{\link{heatmap}}.
+ given, they take precedence over \code{use}. A subset of sites can
+ be displayed using argument \code{select}, but this cannot be used
+ to order sites, but you still must give \code{use} or
+ \code{site.ind}. However, \code{tabasco} makes two exceptions:
+ \code{site.ind} and \code{select} cannot be used when \code{use} is
+ a dendrogram (clustering result). In addition, the \code{sp.ind} can
+ be an \code{\link{hclust}} tree, \code{\link[cluster]{agnes}}
+ clustering or a \code{\link{dendrogram}}, and in that case the
+ dendrogram is plotted on the left side of the
+ \code{\link{heatmap}}. Phylogenetic trees cannot be directly used,
+ \code{\link[ape]{as.hclust.phylo}} (package \pkg{ape}) can transform
+ these to \code{\link{hclust}} trees.
If \code{scale} is given, \code{vegemite} calls
\code{coverscale} to transform percent cover
@@ -117,11 +125,12 @@
10 with \code{X} and positive values below 1 with \code{+}.
}
\value{
- The functions are used mainly to display a table, but it returns
+ The functions are used mainly to display a table, but they return
(invisibly) a list
with items:
\item{species}{Ordered species indices}
\item{sites}{Ordered site indices}
+
These items can be used as arguments \code{sp.ind} and \code{site.ind}
to reproduce the table. In addition to the proper table, \code{vegemite}
prints the numbers of species and sites and the name of the used cover
@@ -137,9 +146,9 @@
\seealso{\code{\link{cut}} and \code{\link{approx}} for making your
own \sQuote{cover scales} for \code{vegemite}. Function
- \code{tabasco} is based on \code{\link{heatmap}}. Both functions
- order species with weighted averages using \code{\link{wascores}}.
- }
+ \code{tabasco} is based on \code{\link{heatmap}} which in turn is
+ based on \code{\link{image}}. Both functions order species with
+ weighted averages using \code{\link{wascores}}. }
\note{
@@ -160,18 +169,31 @@
clus <- hclust(vegdist(varespec))
cl <- cutree(clus, 3)
sel <- vegemite(varespec, use=dca, select = cl == 3, scale="Br")
-# Re-create previous
+## Re-create previous
vegemite(varespec, sp=sel$sp, site=sel$site, scale="Hult")
+## Re-order clusters by ordination
+clus <- as.dendrogram(clus)
+clus <- reorder(clus, scores(dca, choices=1, display="sites"), agglo.FUN = mean)
+vegemite(varespec, clus, scale = "Hult")
## Abundance values have such a wide range that they must be rescaled
## or all abundances will not be shown in tabasco
-tabasco(decostand(varespec, "log"), clus)
-## reorder dendrogram by the first DCA axis
-clus <- as.dendrogram(clus)
-clus <- reorder(clus, scores(dca, choices=1, display="sites"))
-tabasco(decostand(varespec, "log"), clus)
+tabasco(decostand(varespec, "log"), dca)
+## Classification trees for species
+data(dune, dune.taxon)
+taxontree <- hclust(taxa2dist(dune.taxon))
+plotree <- hclust(vegdist(dune), "average")
+## Automatic reordering of clusters
+tabasco(dune, plotree, sp.ind = taxontree)
+## No reordering of taxonomy
+tabasco(dune, plotree, sp.ind = taxontree, Colv = FALSE)
+## Species cluster: most dissimilarity indices do a bad job when
+## comparing rare and common species, but Raup-Crick makes sense
+sptree <- hclust(vegdist(t(dune), "raup"), "average")
+tabasco(dune, plotree, sptree)
}
-\keyword{ print }
-\keyword{ manip }
+\keyword{print}
+\keyword{manip}
+\keyword{hplot}
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2013-02-15 10:23:18 UTC (rev 2441)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2013-02-17 07:05:38 UTC (rev 2442)
@@ -161,7 +161,7 @@
Formula:
y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x10245b5b8>
+<environment: 0x10245a8e8>
Total model degrees of freedom 3
GCV score: 0.04278782
@@ -4908,7 +4908,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10ac51d18>
+<environment: 0x10a9cc178>
Estimated degrees of freedom:
6.45 total = 7.45
@@ -4924,7 +4924,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x109d00ed8>
+<environment: 0x10ac80208>
Estimated degrees of freedom:
6.12 total = 7.12
@@ -5092,7 +5092,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x109cb80e8>
+<environment: 0x107e94708>
Estimated degrees of freedom:
8.93 total = 9.93
@@ -5105,7 +5105,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10adbb588>
+<environment: 0x10851f590>
Estimated degrees of freedom:
7.75 total = 8.75
@@ -5118,7 +5118,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x108d98b90>
+<environment: 0x109432720>
Estimated degrees of freedom:
8.9 total = 9.9
@@ -7692,7 +7692,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10b44d008>
+<environment: 0x10a8a53c8>
Estimated degrees of freedom:
2 total = 3
@@ -7941,7 +7941,7 @@
sites species
5 37
scale: Braun.Blanquet
-> # Re-create previous
+> ## Re-create previous
> vegemite(varespec, sp=sel$sp, site=sel$site, scale="Hult")
1 12
@@ -7986,17 +7986,78 @@
sites species
5 37
scale: Hult
+> ## Re-order clusters by ordination
+> clus <- as.dendrogram(clus)
+> clus <- reorder(clus, scores(dca, choices=1, display="sites"), agglo.FUN = mean)
+> vegemite(varespec, clus, scale = "Hult")
+
+ 1 111 1211221212222
+ 431567380922149306254578
+ Cet.niv 21.111.111....11........
+ Cla.ama .1.1...1................
+ Ste.sp 111211111....111.1.111.1
+ Pol.pil ..111..1......111..1....
+ Dip.mon .1...111.1...........1..
+ Cla.phy ..1.....11...1..........
+ Cla.ran 344544332133111223121121
+ Cla.cer 1.........1..........1..
+ Cla.ste 454121215555213111111.1.
+ Cla.arb 322344331111132222121111
+ Vac.uli 11...2.1........1.1..111
+ Cal.vul 111.1.311.11.1..11111...
+ Ich.eri ...1.1.......1...1......
+ Cla.sp 1...1.11.1......111..11.
+ Cla.coc 1111111111...1111111.1.1
+ Pin.syl 1.111.1111111111111111.1
+ Cla.chl .1..111.111.1.11..1.1...
+ Cet.isl 1.1...1.11.111...1.111.1
+ Cla.fim 11.11111111111111111.111
+ Pel.aph ..1...11.......1.....11.
+ Cet.eri 11.1111111...1..111111..
+ Cla.gra 11111111.111111111111111
+ Poh.nut 111..11111.1111111111.11
+ Pti.cil .11.1.11.11.2.11.1111111
+ Bar.lyc ......1.....1.11......1.
+ Cla.cor 111111111111111111111111
+ Vac.vit 113122132323412331223232
+ Cla.cri 111111111111111111111111
+ Emp.nig 111111122122312322111231
+ Cla.bot ......1.....1.111...1.11
+ Bet.pub ............1.....1..1..
+ Cla.unc 111111111111131111112111
+ Cla.def 11.111111111111111111111
+ Dic.pol ..11.1..11..1.1111.11..1
+ Pol.com ............111......11.
+ Led.pal ......1.....1.....1...11
+ Pol.jun 1.111111111.111111.112.1
+ Dic.fus 11111111111112111442.211
+ Ple.sch 113111111111123333444455
+ Vac.myr ......1..1..311..111..13
+ Nep.arc .1...1.1........1....1..
+ Dic.sp ......1....11...111133.1
+ Des.fle 1....1......1.1...1..111
+ Hyl.spl ................1....122
+ sites species
+ 24 44
+scale: Hult
>
> ## Abundance values have such a wide range that they must be rescaled
> ## or all abundances will not be shown in tabasco
-> tabasco(decostand(varespec, "log"), clus)
+> tabasco(decostand(varespec, "log"), dca)
Warning: non-integer data: divided by smallest positive value
-> ## reorder dendrogram by the first DCA axis
-> clus <- as.dendrogram(clus)
-> clus <- reorder(clus, scores(dca, choices=1, display="sites"))
-> tabasco(decostand(varespec, "log"), clus)
-Warning: non-integer data: divided by smallest positive value
>
+> ## Classification trees for species
+> data(dune, dune.taxon)
+> taxontree <- hclust(taxa2dist(dune.taxon))
+> plotree <- hclust(vegdist(dune), "average")
+> ## Automatic reordering of clusters
+> tabasco(dune, plotree, sp.ind = taxontree)
+> ## No reordering of taxonomy
+> tabasco(dune, plotree, sp.ind = taxontree, Colv = FALSE)
+> ## Species cluster: most dissimilarity indices do a bad job when
+> ## comparing rare and common species, but Raup-Crick makes sense
+> sptree <- hclust(vegdist(t(dune), "raup"), "average")
+> tabasco(dune, plotree, sptree)
>
>
>
@@ -8183,7 +8244,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 104.54 1.972 107.111 0 0
+Time elapsed: 82.333 1.542 86.731 0 0
> grDevices::dev.off()
null device
1
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