TWINSPAN Analysis

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1. Import the Raw Data

Use the function read.csv to read in a species matrix stored as a .csv file.

Options:
header=TRUE treats the first row of data as a header row.
row.names = 1 specifies which column to use for row names (e.g. 1st column).

CulbinBar_Saltmarsh<- read.csv (file = 'CulbinBar_Saltmarsh.csv', header=TRUE, row.names = 1)

2. TWINSPAN

The function ‘twinspan’ carries out TWINSPAN (Two-Way Indicator Species Analysis) and assigns the results to the variable ‘tw’.

library(twinspan)
tw <- twinspan(CulbinBar_Saltmarsh)

The function ‘twinsform’ transforms TWINSPAN results for correspondence analysis and generates pseudospecies data.

colnames(twinsform(CulbinBar_Saltmarsh))

##  [1] "Glaux.maritima1"           "Agrostis.stolonifera1"    
##  [3] "Plantago.maritima1"        "Juncus.gerardii1"         
##  [5] "Atriplex.littoralis1"      "Armeria.maritima1"        
##  [7] "Suaeda.maritima1"          "Aster.tripolium1"         
##  [9] "Triglochin.maritimum1"     "Atriplex.prostrata1"      
## [11] "Carex.extensa1"            "Festuca.rubra1"           
## [13] "Centaurium.littorale1"     "Trifolium.repens1"        
## [15] "Lotus.corniculatus1"       "Carex.flacca1"            
## [17] "Cochlearia.sp.1"           "Puccinellia.maritima1"    
## [19] "Salicornia.europaea.agg.1" "Spergularia.media1"       
## [21] "Algal.mat1"                "Pelvetia.canescens1"      
## [23] "Glaux.maritima2"           "Agrostis.stolonifera2"    
## [25] "Plantago.maritima2"        "Juncus.gerardii2"         
## [27] "Armeria.maritima2"         "Suaeda.maritima2"         
## [29] "Aster.tripolium2"          "Triglochin.maritimum2"    
## [31] "Festuca.rubra2"            "Trifolium.repens2"        
## [33] "Carex.flacca2"             "Puccinellia.maritima2"    
## [35] "Salicornia.europaea.agg.2" "Spergularia.media2"       
## [37] "Algal.mat2"                "Glaux.maritima3"          
## [39] "Agrostis.stolonifera3"     "Plantago.maritima3"       
## [41] "Juncus.gerardii3"          "Armeria.maritima3"        
## [43] "Suaeda.maritima3"          "Aster.tripolium3"         
## [45] "Triglochin.maritimum3"     "Festuca.rubra3"           
## [47] "Trifolium.repens3"         "Carex.flacca3"            
## [49] "Puccinellia.maritima3"     "Salicornia.europaea.agg.3"
## [51] "Spergularia.media3"        "Algal.mat3"               
## [53] "Glaux.maritima4"           "Agrostis.stolonifera4"    
## [55] "Plantago.maritima4"        "Juncus.gerardii4"         
## [57] "Armeria.maritima4"         "Suaeda.maritima4"         
## [59] "Aster.tripolium4"          "Festuca.rubra4"           
## [61] "Trifolium.repens4"         "Carex.flacca4"            
## [63] "Puccinellia.maritima4"     "Salicornia.europaea.agg.4"
## [65] "Spergularia.media4"        "Algal.mat4"               
## [67] "Glaux.maritima5"           "Agrostis.stolonifera5"    
## [69] "Plantago.maritima5"        "Juncus.gerardii5"         
## [71] "Armeria.maritima5"         "Suaeda.maritima5"         
## [73] "Aster.tripolium5"          "Festuca.rubra5"           
## [75] "Carex.flacca5"             "Puccinellia.maritima5"    
## [77] "Salicornia.europaea.agg.5" "Spergularia.media5"

3. Plot Dendrogram of TWINSPAN Results

plot(tw, main = "Numeric Label")

plot(tw, binname = TRUE, main = "Binary Label")

4. Heat-map Summary

The ‘image’ function creates a heat-map summary of the classification.

image(tw, height="chi", leadingspecies=TRUE, reorder=TRUE)

5. DCA (Detrended Correspondence Analysis)

Function ‘decorana’ (Vegan package) carries out a DCA which is visualized as an ordination using the ‘plot’ function.

library(vegan)

## Loading required package: permute

## Loading required package: lattice

CulbinBar_Saltmarsh.dca <- decorana(CulbinBar_Saltmarsh)
CulbinBar_Saltmarsh.dca

## 
## Call:
## decorana(veg = CulbinBar_Saltmarsh) 
## 
## Detrended correspondence analysis with 26 segments.
## Rescaling of axes with 4 iterations.
## Total inertia (scaled Chi-square): 2.9466 
## 
##                        DCA1   DCA2   DCA3    DCA4
## Eigenvalues          0.8178 0.4083 0.3752 0.32853
## Additive Eigenvalues 0.8178 0.3400 0.1553 0.19463
## Decorana values      0.8542 0.2492 0.1200 0.09555
## Axis lengths         4.1151 2.0385 2.1555 1.96464

plot(CulbinBar_Saltmarsh.dca)