vegemite: Display Compact Ordered Community Tables

In vegan: Community Ecology Package

Description

Functions vegemite and tabasco display compact community tables. Function vegemite prints text tables where species are rows, and each site takes only one column without spaces. Function tabasco provides interface for heatmap for a colour 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

vegemite(x, use, scale, sp.ind, site.ind, zero=".", select ,...)
tabasco(x, use, sp.ind = NULL, site.ind = NULL, select,
    Rowv = TRUE, Colv = TRUE, ...) 
coverscale(x, scale=c("Braun.Blanquet", "Domin", "Hult", "Hill", "fix","log"),
           maxabund)

Arguments

x	Community data.
use	Either a vector, or an object from cca, decorana etc. or hclust or a dendrogram for ordering sites and species.
sp.ind, site.ind	Species and site indices. In tabasco, these can also be hclust tree, agnes clusterings or dendrograms.
zero	Character used for zeros.
select	Select a subset of sites. This can be a logical vector (TRUE for selected sites), or a vector of indices of selected sites. The order of indices does not influence results, but you must specify use or site.ind to reorder sites.
Rowv, Colv	Re-order dendrograms for the rows (sites) or columns (species) of x. If the Rowv = TRUE, row dendrograms are ordered by the first axis of correspondence analysis, and when Colv = TRUE column dendrograms by the weighted average (wascores) of the row order. Alternatively, the arguments can be vectors that are used to reorder the dendrogram.
scale	Cover scale used (can be abbreviated).
maxabund	Maximum abundance used with scale = "log". Data maximum in the selected subset will be used if this is missing.
...	Arguments passed to coverscale (i.e., maxabund) in vegemite and to heatmap in tabasco.

Details

The function vegemite prints a traditional community table. 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 tabasco produces a similar table as vegemite using 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 (use for sites, sp.ind for species).

The parameter use will be used to re-order output. The use can be a vector or an object from hclust or agnes, a dendrogram or any ordination result recognized by scores (all ordination methods in vegan and some of those not in vegan). The hclust, agnes and dendrogram must be for sites. The dendrogram is displayed above the sites in tabasco, but is not shown in vegemite. No dendrogram for species is displayed, except when given in sp.ind.

If use is a vector, it is used for ordering sites. If 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 use is an object from hclust, agnes or a dendrogram, the sites are ordered similarly as in the cluster dendrogram. Function tabasco re-orders the dendrogram if Rowv = TRUE or Rowv is a vector. Such re-ordering is not available for vegemite, but it can be done by hand using reorder.dendrogram or reorder.hclust. Please note that dendrogram and hclust reordering can differ: unweighted means of merged branches are used in dendrogram, but weighted means (= means of leaves of the cluster) are used in reorder.hclust. In all cases where species scores are missing, species are ordered by their weighted averages (wascores) on site order.

Species and sites can be ordered explicitly giving their indices or names in parameters sp.ind and site.ind. If these are given, they take precedence over use. A subset of sites can be displayed using argument select, but this cannot be used to order sites, but you still must give use or site.ind. However, tabasco makes two exceptions: site.ind and select cannot be used when use is a dendrogram (clustering result). In addition, the sp.ind can be an hclust tree, agnes clustering or a dendrogram, and in that case the dendrogram is plotted on the left side of the heatmap. Phylogenetic trees cannot be directly used, as.hclust.phylo (package ape) can transform these to hclust trees.

If scale is given, vegemite calls coverscale to transform percent cover scale or some other scales into traditional class scales used in vegetation science (coverscale can be called directly, too). Braun-Blanquet and Domin scales are actually not strict cover scales, and the limits used for codes r and + are arbitrary. Scale Hill may be inappropriately named, since Mark O. Hill probably never intended this as a cover scale. However, it is used as default 'cut levels' in his TWINSPAN, and surprisingly many users stick to this default, and this is a de facto standard in publications. All traditional scales assume that values are cover percentages with maximum 100. However, non-traditional alternative log can be used with any scale range. Its class limits are integer powers of 1/2 of the maximum (argument maxabund), with + used for non-zero entries less than 1/512 of the maximum (log stands alternatively for logarithmic or logical). Scale fix is intended for ‘fixing’ 10-point scales: it truncates scale values to integers, and replaces 10 with X and positive values below 1 with +.

Value

The functions are used mainly to display a table, but they return (invisibly) a list with items:

species	Ordered species indices
sites	Ordered site indices

These items can be used as arguments sp.ind and site.ind to reproduce the table. In addition to the proper table, vegemite prints the numbers of species and sites and the name of the used cover scale at the end.

Note

The name vegemite was chosen because the output is so compact, and the tabasco because it is just as compact, but uses heat colours.

Author(s)

Jari Oksanen

References

The cover scales are presented in many textbooks of vegetation science; I used:

Shimwell, D.W. (1971) The Description and Classification of Vegetation. Sidgwick & Jackson.

See Also

cut and approx for making your own ‘cover scales’ for vegemite. Function tabasco is based on heatmap which in turn is based on image. Both functions order species with weighted averages using wascores.

Examples

data(varespec)
## Print only more common species 
freq <- apply(varespec > 0, 2, sum)
vegemite(varespec, scale="Hult", sp.ind = freq > 10)
## Order by correspondence analysis, use Hill scaling and layout:
dca <- decorana(varespec)
vegemite(varespec, dca, "Hill", zero="-")
## Show one class from cluster analysis, but retain the ordering above
clus <- hclust(vegdist(varespec))
cl <- cutree(clus, 3)
sel <- vegemite(varespec, use=dca, select = cl == 3, scale="Br")
## 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"), 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)

Example output

Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
                                  
          1122212121122       1112
          854739268340575634292011
 Callvulg 111...11.311...1111.111.
 Empenigr 211332121112211111212213
 Vaccviti 323332212113221211233234
 Pinusylv 111.111111111.11.1111111
 Dicrfusc 12.111441121211111111111
 Dicrpoly .11.11.11..1.11....1.111
 Pleuschr 144533435123411111111131
 Polyjuni 111.11.111112111.111.111
 Pohlnuta 111111111111.1..11.11111
 Ptilcili 1111111111..1..11.11..12
 Cladarbu 321122121332143423111121
 Cladrang 321221131312145443313241
 Cladstel 11111311.211.11254555542
 Cladunci 112111111131111111111111
 Cladcocc 11..11111111111111.1.11.
 Cladcorn 111111111111111111111111
 Cladgrac 111111111111111111111.11
 Cladfimb 11.1111111111111111111.1
 Cladcris 111111111111111111111111
 Cladchlo ..1.111..1...1.11.11.1.1
 Cetreric 111...11.111111111.1.1..
 Cetrisla .11....1111.1....1.11111
 Stersp   111.11.1111.112111...11.
 Claddefo 1111111111111111111111.1
  sites species 
     24      24 
scale:  Hult 
                                  
           1   1  1 11122211122222
          203942561738913046572458
 Flavniva -1114-11-1-11-1---------
 Cladstel 5555551451425411111211--
 Cladphyl -1-1----1-------1-------
 Cladcerv 1---1-----------------1-
 Cladsp   ---11--1--11---1-1-11-1-
 Cladamau --1---1----1------------
 Cladchlo 1111---1-11-111-----11--
 Cladrang 535254555555223414332321
 Diphcomp --11-----112----------1-
 Stersp   -11-1-4111111-1-111--111
 Pinusylv 11-111111-111111111-1111
 Polypili ------111--11-11--1-----
 Cetrisla -1-111--1-1--1--111--111
 Cladcocc -1111-1111111-11111-1-11
 Cladarbu 113142453555313343413231
 Vacculig --1-1----3-1---1---12-11
 Pohlnuta -11111--11111111111111-1
 Cladfimb 11111111-111111111111-11
 Callvulg 111-21-12-51---1221-21--
 Icmaeric ------1--1------11------
 Empenigr 342214131314344333143131
 Vaccviti 342514244334455432444443
 Cladgrac 1-1111111111111111111111
 Cetreric -1111-11-111---1111-111-
 Cladcorn 111111111111111111111111
 Cladcris 111111111111111111111111
 Peltapht --------1-11--1----1--1-
 Ptilcili 1-11---11-11141--1111111
 Barbhatc ----------1-121----1----
 Claddefo 11111111-111111111111111
 Cladbotr ----------1-1111---1-1-1
 Betupube -------------1------1-1-
 Dicrpoly -1-1--1-11--1211-11--1-1
 Cladunci 111111122111111251212311
 Polycomm ------------11--1--1--1-
 Polyjuni 11-11-1111111121111--131
 Rhodtome ----------1--2-----21--1
 Dicrfusc 111111111121112145425-41
 Pleuschr 111213114132524434555555
 Vaccmyrt ---1------1-24--12133--4
 Descflex ----1----1--11-----21-11
 Nepharct --1------1-1---1------2-
 Dicrsp   -----1----1--1-1-11-1541
 Hylosple ---------------1---3--13
  sites species 
     24      44 
scale:  Hill 
               
           1 12
          20921
 Flavniva .++..
 Cladstel 55542
 Cladphyl .++..
 Cladcerv r....
 Cladsp   ..+..
 Cladchlo r++.+
 Cladrang 22121
 Diphcomp ..+..
 Stersp   .+...
 Pinusylv r++1+
 Cetrisla .++++
 Cladcocc .++..
 Cladarbu +1+1+
 Pohlnuta .++++
 Cladfimb r++++
 Callvulg r+.+.
 Empenigr 22122
 Vaccviti 22223
 Cladgrac r.+++
 Cetreric .++..
 Cladcorn r+++r
 Cladcris r++++
 Ptilcili r.+.2
 Barbhatc ....1
 Claddefo r++++
 Cladbotr ....+
 Betupube ....+
 Dicrpoly .++.1
 Cladunci +++1+
 Polycomm ....+
 Polyjuni r++.+
 Rhodtome ....1
 Dicrfusc r++++
 Pleuschr ++121
 Vaccmyrt ..+.2
 Descflex ....+
 Dicrsp   ...++
  sites species 
      5      37 
scale:  Braun.Blanquet 
               
           1 12
          20921
 Flavniva .11..
 Cladstel 55552
 Cladphyl .11..
 Cladcerv 1....
 Cladsp   ..1..
 Cladchlo 111.1
 Cladrang 32131
 Diphcomp ..1..
 Stersp   .1...
 Pinusylv 11111
 Cetrisla .1111
 Cladcocc .11..
 Cladarbu 11111
 Pohlnuta .1111
 Cladfimb 11111
 Callvulg 11.1.
 Empenigr 22123
 Vaccviti 22334
 Cladgrac 1.111
 Cetreric .11..
 Cladcorn 11111
 Cladcris 11111
 Ptilcili 1.1.2
 Barbhatc ....1
 Claddefo 11111
 Cladbotr ....1
 Betupube ....1
 Dicrpoly .11.1
 Cladunci 11111
 Polycomm ....1
 Polyjuni 111.1
 Rhodtome ....1
 Dicrfusc 11111
 Pleuschr 11111
 Vaccmyrt ..1.3
 Descflex ....1
 Dicrsp   ...11
  sites species 
      5      37 
scale:  Hult 
                                  
            1   111  1211221212222
          431567380922149306254578
 Flavniva 21.111.111....11........
 Cladamau .1.1...1................
 Stersp   111211111....111.1.111.1
 Polypili ..111..1......111..1....
 Diphcomp .1...111.1...........1..
 Cladphyl ..1.....11...1..........
 Cladrang 344544332133111223121121
 Cladcerv 1.........1..........1..
 Cladstel 454121215555213111111.1.
 Cladarbu 322344331111132222121111
 Vacculig 11...2.1........1.1..111
 Callvulg 111.1.311.11.1..11111...
 Icmaeric ...1.1.......1...1......
 Cladsp   1...1.11.1......111..11.
 Cladcocc 1111111111...1111111.1.1
 Pinusylv 1.111.1111111111111111.1
 Cladchlo .1..111.111.1.11..1.1...
 Cetrisla 1.1...1.11.111...1.111.1
 Cladfimb 11.11111111111111111.111
 Peltapht ..1...11.......1.....11.
 Cetreric 11.1111111...1..111111..
 Cladgrac 11111111.111111111111111
 Pohlnuta 111..11111.1111111111.11
 Ptilcili .11.1.11.11.2.11.1111111
 Barbhatc ......1.....1.11......1.
 Cladcorn 111111111111111111111111
 Vaccviti 113122132323412331223232
 Cladcris 111111111111111111111111
 Empenigr 111111122122312322111231
 Cladbotr ......1.....1.111...1.11
 Betupube ............1.....1..1..
 Cladunci 111111111111131111112111
 Claddefo 11.111111111111111111111
 Dicrpoly ..11.1..11..1.1111.11..1
 Polycomm ............111......11.
 Rhodtome ......1.....1.....1...11
 Polyjuni 1.111111111.111111.112.1
 Dicrfusc 11111111111112111442.211
 Pleuschr 113111111111123333444455
 Vaccmyrt ......1..1..311..111..13
 Nepharct .1...1.1........1....1..
 Dicrsp   ......1....11...111133.1
 Descflex 1....1......1.1...1..111
 Hylosple ................1....122
  sites species 
     24      44 
scale:  Hult 
Warning message:
non-integer data: divided by smallest positive value 

vegan documentation built on May 2, 2019, 5:51 p.m.