disttransform: Community Matrix Transformation

Description Usage Arguments Details Value Author(s) References Examples

Description

Transforms a community matrix. Some transformation methods are described by distances for the original community matrix that result in the same distance matrix as calculated with the euclidean distance from the transformed community matrix. In several cases (methods of "hellinger", "chord", "profiles" and "chi.square), the method makes use of function decostand. In several other cases ("Braun.Blanquet", "Domin", "Hult", "Hill", "fix" and "coverscale.log"), the method makes use of function coverscale. For method "dispweight" a call is made to function dispweight.

Usage

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disttransform(x, method="hellinger")

Arguments

x

Community data frame with sites as rows, species as columns and species abundance as cell values.

method

Distance measure for the original community matrix that the euclidean distance will calculate for the transformed community matrix: partial match to "hellinger", "chord", "profiles", "chi.square", "log", "square", "pa", "Braun.Blanquet", "Domin", "Hult", "Hill", "fix", "coverscale.log" and "dispweight".

Details

This functions transforms a community matrix.

Some transformation methods ("hellinger", "chord", "profiles" and "chi.square") have the behaviour that the euclidean distance from the transformed matrix will equal a distance of choice for the original matrix. For example, using method "hellinger" and calculating the euclidean distance will result in the same distance matrix as by calculating the Hellinger distance from the original community matrix.

Transformation methods ("Braun.Blanquet", "Domin", "Hult", "Hill", "fix" and "coverscale.log") call function coverscale.

Method "dispweight" uses function dispweight without specifying a grouping structure.

Value

The function returns a transformed community matrix.

Author(s)

Roeland Kindt (World Agroforestry Centre)

References

Legendre, P. & Gallagher, E.D. (2001). Ecologically meaningful transformations for ordination of species data. Oecologia 129: 271-280.

Kindt, R. & Coe, R. (2005) Tree diversity analysis: A manual and software for common statistical methods for ecological and biodiversity studies.

https://www.worldagroforestry.org/output/tree-diversity-analysis

Examples

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library(vegan)
data(dune)
Community.1 <- disttransform(dune, method='hellinger')
Distmatrix.1 <- vegdist(Community.1,method='euclidean')
Distmatrix.1

Example output

Loading required package: tcltk
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-7
Loading required package: vegan3d
Loading required package: rgl
Registered S3 methods overwritten by 'lme4':
  method                          from
  cooks.distance.influence.merMod car 
  influence.merMod                car 
  dfbeta.influence.merMod         car 
  dfbetas.influence.merMod        car 
BiodiversityR 2.12-2: Use command BiodiversityRGUI() to launch the Graphical User Interface; 
to see changes use BiodiversityRGUI(changeLog=TRUE, backward.compatibility.messages=TRUE)

Warning messages:
1: no DISPLAY variable so Tk is not available 
2: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
3: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'. 
           1         2         3         4         5         6         7
2  0.7678545                                                            
3  0.7920098 0.6264258                                                  
4  0.8943463 0.7192846 0.5400578                                        
5  0.9430999 0.7280506 0.8892324 0.9098505                              
6  1.0171844 0.9282652 0.9547253 1.0354086 0.5091523                    
7  0.9368566 0.8050230 0.9381138 0.9621067 0.4911255 0.3939843          
8  1.0472028 0.9114901 0.6842637 0.7406581 1.0739565 0.9981598 0.9906787
9  0.9222294 0.8320346 0.6317466 0.6840087 0.9005191 0.9497139 0.8931083
10 0.9483916 0.6311564 0.8835514 0.8964769 0.6028827 0.6588449 0.5458461
11 1.0408330 0.9874070 0.9570237 0.9506235 0.9713722 0.8059636 0.8282823
12 1.3321507 1.0716015 0.8575013 0.8555550 1.0890511 1.0431866 1.0323713
13 1.1915289 0.9549890 0.7933204 0.8193681 1.1257986 1.1372754 1.0465416
14 1.4142136 1.2065498 1.1785987 1.1768379 1.2774333 1.2381090 1.2721161
15 1.4142136 1.2855435 1.1509215 1.1340170 1.2547531 1.1929286 1.2484927
16 1.3549458 1.2833725 1.0349070 1.0741993 1.2907012 1.2695209 1.2923709
17 1.2587435 1.1804575 1.2861285 1.3007997 0.9870182 1.0224256 0.9921000
18 1.1602932 0.9880296 0.9522491 1.0216116 0.9198088 0.8375777 0.8800135
19 1.4142136 1.2333429 1.2452061 1.1833092 1.1422506 1.1029492 1.1600329
20 1.4142136 1.3508231 1.2131626 1.1843904 1.3080063 1.2723992 1.3039304
           8         9        10        11        12        13        14
2                                                                       
3                                                                       
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5                                                                       
6                                                                       
7                                                                       
8                                                                       
9  0.6790951                                                            
10 0.9847745 1.0144881                                                  
11 0.9258698 0.9889721 0.7790085                                        
12 0.8185886 0.6793924 1.1414737 1.1061903                              
13 0.7262631 0.7341519 1.1033129 1.1650968 0.6159341                    
14 0.9862972 1.1783602 1.2140666 1.2106180 1.1371854 1.0731862          
15 0.7998785 1.0639632 1.2282368 1.1594401 1.0830508 1.1323853 0.7480211
16 0.7341262 1.0294627 1.3037099 1.3243176 0.9766546 0.9960268 0.9130265
17 1.2793360 1.2966389 0.9586281 1.0595139 1.3510832 1.3011860 1.3376029
18 1.0241152 1.0660445 0.7792063 0.6075805 1.1472449 1.2206524 1.2162987
19 1.1692726 1.1835064 1.1065868 0.9593408 1.1046611 1.2268492 1.2214743
20 0.9117132 1.1384173 1.3080063 1.2430587 1.1679710 1.1770400 0.8779266
          15        16        17        18        19
2                                                   
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11                                                  
12                                                  
13                                                  
14                                                  
15                                                  
16 0.7094850                                        
17 1.3359069 1.4142136                              
18 1.1133395 1.2929640 1.1270162                    
19 1.1726671 1.3354355 0.8872667 0.9911680          
20 0.6398055 0.6671950 1.3470354 1.0839671 1.1415556

BiodiversityR documentation built on April 20, 2021, 5:07 p.m.