bipartite-package: Analysis of bipartite ecological webs

Description Details versionlog Author(s) References Examples

Description

Bipartite provides functions to visualise webs and calculate a series of indices commonly used to describe pattern in (ecological) networks, a.k.a. webs. It focusses on webs consisting of only two levels, e.g. pollinator-visitation or predator-prey webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the webs topology.

Details

Input for most analyses is an interaction matrix of m species from one group (“higher”) with n species from another group (“lower”), i.e. a n x m matrix, where higher level species are in columns, lower level species in rows. Column and row names can be provided. This is fundamentally different from “one-mode” webs, which are organised as k x k matrix, i.e. one group of species only, in which each species can interact with each other. Such a format is incompatible with the functions we provide here. (Note, however, that functions as.one.mode and web2edges are convenience functions to morph bipartite networks into one-mode webs. Furthermore, some indices build on one-mode networks and are called from bipartite.)

Before you start with the network, you have to get the data into the right shape. The function frame2webs aims to facilitate this process. Arranging a web, e.g. by size, is supported by sortweb.

The typical first step is to visualise the network. Two functions are on offer here: one (visweb) simply plots the matrix in colours depicting the strength of an interaction and options for re-arranging columns and rows (e.g. to identify compartments or nesting). The other function (plotweb) plots the actual web with participants (as two rows of rectangles) connected by lines (proportional to interaction strength). Both can be customised by many options.

The second step is to calculate indices describing network topography. There are three different levels this can be achieved at: the entire web (using function networklevel), at the level of each group (also using function networklevel) or the individual species (using function specieslevel). Most other functions in the package are helpers, although some can be called on their own and return the respective result (dfun, H2fun and second.extinct with slope.bipartite).

The third step is to compare results to null models. Many interaction matrices are very incomplete snapshots of the true underlying network (e.g. a one-week sampling of a pollination network on a patch of 4 x 4 meters). As a consequence, many species were rarely observed, many are singletons (only one recording). To make analyses comparable across networks with different sampling intensity and number of species per group, we need a common yardstick. We suggest that users should use a null model, i.e. an algorithm that randomises entries while constraining some web properties (such as dimensions, marginal totals or connectance). The function nullmodel provides a few such null models, but this is a wide field of research and we make no recommendations (actually, we do: see Dormann et al. 2009 and Dormann 2011, both shipping in the doc-folder of this package). You can also simulate networks using genweb or null.distr.

Finally, bipartite comes with 23 quantitative pollination network data sets taken from the NCEAS interaction webs data base (use data(package="bipartite") to show their names) and it has a few miscellaneous functions looking at some special features of bipartite networks (such as modularity: computeModules or apparent competition: PAC).

Speed: The code of bipartite is almost exclusively written in R. You can increase the speed a bit (by 30 to 50 %, depending on the functions you use) by compiling functions on-the-fly. To do so, you need to load the compiler package and type: enableJIT(3). The first time you call a function, it will be compiled to bytecode (just-in-time: jit), which takes a few seconds, but the second call will be substantially faster than without compilation. In the few tests we have run, this improvement was NOT substantial (i.e. a few tens of percent), indicating, I guess, that our R code wasn't too bad. See compiler-help files or http://www.r-statistics.com/2012/04/speed-up-your-r-code-using-a-just-in-time-jit-compiler/ for details.

See help pages for details and examples.

For an overview of other computing resources, data, books, journals etc. check out this page: https://github.com/briatte/awesome-network-analysis.

Package: bipartite
Type: Package
Version: 2.08
Date: 2017-03-30
License: GPL

versionlog

Please see help page versionlog for all changes and updates prior to version 2.00. This page will only list most recent changes.

Author(s)

Carsten F. Dormann, Jochen Fründ and Bernd Gruber, with additional code from many others (referred to in the respective help file), noticeably from Tore Opsahl's tnet package.

Maintainer: Carsten Dormann [email protected]

References

Alarcon, R., Waser, N.M. and Ollerton, J. 2008. Year-to-year variation in the topology of a plant-pollinator interaction network. Oikos 117, 1796–1807

Almeida-Neto, M. and Ulrich, W. (2011) A straightforward computational approach for measuring nestedness using quantitative matrices. Environmental Modelling & Software, 26, 173–178

Bascompte, J., Jordano, P. and Olesen, J. M. (2006) Asymmetric coevolutionary networks facilitate biodiversity maintenance. Science 312, 431–433

Beckett, S.J. 2016. Improved community detection in weighted bipartite networks. Royal Society open science 3, 140536

Bersier, L. F., Banasek-Richter, C. and Cattin, M. F. (2002) Quantitative descriptors of food-web matrices. Ecology 83, 2394–2407

Blüthgen, N., Menzel, F. and Blüthgen, N. (2006) Measuring specialization in species interaction networks. BMC Ecology 6, 12

Blüthgen, N., Menzel, F., Hovestadt, T., Fiala, B. and Blüthgen, N. (2007) Specialization, constraints, and conflicting interests in mutualistic networks. Current Biology 17, 1–6

Corso G., de Araújo A.I.L. and de Almeida A.M. (2008) A new nestedness estimator in community networks. arXiv, 0803.0007v1 [physics.bio-ph]

Dalsgaard, B., A. M. Martín González, J. M. Olesen, A. Timmermann, L. H. Andersen, and J. Ollerton. (2008) Pollination networks and functional specialization: a test using Lesser Antillean plant-hummingbird assemblages. Oikos 117, 789–793

Devoto M., Bailey S., Craze P. & Memmott J. (2012) Understanding and planning ecological restoration of plant-pollinator networks. Ecology Letters 15, 319–328

Dormann, C.F., Fründ, J., Blüthgen, N., and Gruber, B. (2009) Indices, graphs and null models: analysing bipartite ecological networks. The Open Ecology Journal 2, 7–24

Dormann, C.F. (2011) How to be a specialist? Quantifying specialisation in pollination networks. Network Biology 1, 1–20

Galeano J., Pastor J.M. and Iriondo J.M. (2008) Weighted-Interaction Nestedness Estimator (WINE): A new estimator to calculate over frequency matrices. arXiv 0808.3397v1 [physics.bio-ph]

Martín Gonzáles, A.M., Dalsgaard, B. and Olesen, J.M. (2009) Centrality measures and the importance of generalist species in pollination networks. Ecological Complexity, 7, 36–43

Memmott, J., Waser, N. M. and Price, M. V. (2004) Tolerance of pollination networks to species extinctions. Proceedings of the Royal Society B 271, 2605–2611

Morris, R. J., Lewis, O. T. and Godfray, H. C. J. (2004) Experimental evidence for apparent competition in a tropical forest food web. Nature 428, 310–313

Morris, R. J., Lewis, O. T. and Godfray, H. C. J. (2005) Apparent competition and insect community structure: towards a spatial perspective. Annales Zoologica Fennici 42, 449–462.

Müller, C. B., Adriaanse, I. C. T., Belshaw, R. and Godfray, H. C. J. (1999) The structure of an aphid-parasitoid community. Journal of Animal Ecology 68, 346–370

Poisot, T., Lepennetier, G., Martinez, E., Ramsayer, J., and Hochberg, M.E. (2011a) Resource availability affects the structure of a natural bacteria-bacteriophage community. Biology Letters 7, 201–204

Poisot, T., Bever, J.D., Nemri, A., Thrall, P.H., and Hochberg, M.E. (2011b) A conceptual framework for the evolution of ecological specialisation. Ecology Letters 14, 841–851

Tylianakis, J. M., Tscharntke, T. and Lewis, O. T. (2007) Habitat modification alters the structure of tropical host-parasitoid food webs. Nature 445, 202–205

Vázquez, D. P. and Aizen, M. A. (2004) Asymmetric specialization: A pervasive feature of plant-pollinator interactions. Ecology 85, 1251–1257

Vázquez, D.P., Chacoff, N.,P. and Cagnolo, L. (2009) Evaluating multiple determinants of the structure of plant-animal mutualistic networks. Ecology 90, 2039–2046.

Examples

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Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-3
Loading required package: sna
Loading required package: statnet.common
Loading required package: network
network: Classes for Relational Data
Version 1.13.0 created on 2015-08-31.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.

sna: Tools for Social Network Analysis
Version 2.4 created on 2016-07-23.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
 For citation information, type citation("sna").
 Type help(package="sna") to get started.

 This is bipartite 2.08
 For latest changes see versionlog in  ?"bipartite-package".
 For citation see: citation("bipartite").
 Have a nice time plotting and analysing two-mode networks.


Attaching package: 'bipartite'

The following object is masked from 'package:vegan':

    nullmodel

                      connectance                     web asymmetry 
                       0.16049383                        0.50000000 
                links per species            number of compartments 
                       1.08333333                        2.00000000 
            compartment diversity               cluster coefficient 
                       1.49621915                        0.11111111 
                       nestedness               weighted nestedness 
                      19.88853204                        0.38901213 
                    weighted NODF    interaction strength asymmetry 
                      11.60637382                        0.39072657 
         specialisation asymmetry                   linkage density 
                      -0.16331384                        1.60253736 
             weighted connectance                      Fisher alpha 
                       0.04451493                        7.83379039 
                Shannon diversity              interaction evenness 
                       1.58249027                        0.28808894 
     Alatalo interaction evenness                                H2 
                       0.40981947                        0.85373072 
             number.of.species.HL              number.of.species.LL 
                      27.00000000                        9.00000000 
mean.number.of.shared.partners.HL mean.number.of.shared.partners.LL 
                       0.47293447                        0.44444444 
           cluster.coefficient.HL            cluster.coefficient.LL 
                       0.15309735                        0.28167814 
  weighted.cluster.coefficient.HL   weighted.cluster.coefficient.LL 
                       0.38109672                        0.06065982 
                 niche.overlap.HL                  niche.overlap.LL 
                       0.32776461                        0.04794504 
                  togetherness.HL                   togetherness.LL 
                       0.16068376                        0.03529412 
                       C.score.HL                        C.score.LL 
                       0.56160969                        0.77042484 
                       V.ratio.HL                        V.ratio.LL 
                       0.58064516                        6.49285714 
                   discrepancy.HL                    discrepancy.LL 
                      21.00000000                       16.00000000 
              extinction.slope.HL               extinction.slope.LL 
                       2.62186579                        1.33478953 
                    robustness.HL                     robustness.LL 
                       0.71584997                        0.57436742 
    functional.complementarity.HL     functional.complementarity.LL 
                    1683.80420725                     1627.11857340 
             partner.diversity.HL              partner.diversity.LL 
                       0.17686749                        0.60896198 
                    generality.HL                  vulnerability.LL 
                       1.24808506                        1.95698966 
$`higher level`
                        degree normalised.degree species.strength
Policana albopilosa          1         0.1111111      0.851898734
Bombus dahlbomii             2         0.2222222      1.670940171
Ruizantheda mutabilis        2         0.2222222      0.539240506
Trichophthalma amoena        1         0.1111111      0.400000000
Syrphus octomaculatus        3         0.3333333      0.360149573
Manuelia gayi                1         0.1111111      0.033653846
Allograpta.Toxomerus         4         0.4444444      0.988141026
Trichophthalma jaffueli      1         0.1111111      0.014423077
Phthiria                     2         0.2222222      1.038461538
Platycheirus1                2         0.2222222      0.009870983
Sapromyza.Minettia           1         0.1111111      0.004807692
Formicidae3                  1         0.1111111      0.400000000
Nitidulidae                  1         0.1111111      0.050000000
Staphilinidae                2         0.2222222      0.219230769
Ichneumonidae4               2         0.2222222      1.001265823
Braconidae3                  1         0.1111111      0.100000000
Chalepogenus caeruleus       1         0.1111111      0.750000000
Vespula germanica            1         0.1111111      0.019230769
Torymidae2                   1         0.1111111      0.450000000
Phthiria1                    1         0.1111111      0.004807692
Svastrides melanura          1         0.1111111      0.028846154
Sphecidae                    1         0.1111111      0.004807692
Thomisidae                   1         0.1111111      0.004807692
Corynura prothysteres        2         0.2222222      0.015688900
Ichneumonidae2               1         0.1111111      0.019230769
Ruizantheda proxima          1         0.1111111      0.019230769
Braconidae2                  1         0.1111111      0.001265823
                        interaction.push.pull nestedrank       PDI
Policana albopilosa             -0.1481012658 0.34615385 1.0000000
Bombus dahlbomii                 0.3354700855 0.07692308 0.9456169
Ruizantheda mutabilis           -0.2303797468 0.11538462 0.9931818
Trichophthalma amoena           -0.6000000000 0.73076923 1.0000000
Syrphus octomaculatus           -0.2132834758 0.03846154 0.7750000
Manuelia gayi                   -0.9663461538 0.46153846 1.0000000
Allograpta.Toxomerus            -0.0029647436 0.00000000 0.8333333
Trichophthalma jaffueli         -0.9855769231 0.65384615 1.0000000
Phthiria                         0.0192307692 0.19230769 0.9843750
Platycheirus1                   -0.4950645083 0.26923077 0.9687500
Sapromyza.Minettia              -0.9951923077 0.80769231 1.0000000
Formicidae3                     -0.6000000000 0.42307692 1.0000000
Nitidulidae                     -0.9500000000 0.84615385 1.0000000
Staphilinidae                   -0.3903846154 0.23076923 0.9062500
Ichneumonidae4                   0.0006329114 0.15384615 0.9916667
Braconidae3                     -0.9000000000 0.76923077 1.0000000
Chalepogenus caeruleus          -0.2500000000 0.69230769 1.0000000
Vespula germanica               -0.9807692308 0.53846154 1.0000000
Torymidae2                      -0.5500000000 0.38461538 1.0000000
Phthiria1                       -0.9951923077 0.88461538 1.0000000
Svastrides melanura             -0.9711538462 0.50000000 1.0000000
Sphecidae                       -0.9951923077 0.92307692 1.0000000
Thomisidae                      -0.9951923077 0.96153846 1.0000000
Corynura prothysteres           -0.4921555501 0.30769231 0.9583333
Ichneumonidae2                  -0.9807692308 0.57692308 1.0000000
Ruizantheda proxima             -0.9807692308 0.61538462 1.0000000
Braconidae2                     -0.9987341772 1.00000000 1.0000000
                        resource.range species.specificity.index         PSI
Policana albopilosa              1.000                 1.0000000 0.851898734
Bombus dahlbomii                 0.875                 0.7243424 0.798038249
Ruizantheda mutabilis            0.875                 0.9432075 0.152728066
Trichophthalma amoena            1.000                 1.0000000 0.400000000
Syrphus octomaculatus            0.750                 0.5038120 0.109577228
Manuelia gayi                    1.000                 1.0000000 0.033653846
Allograpta.Toxomerus             0.625                 0.4683885 0.331639194
Trichophthalma jaffueli          1.000                 1.0000000 0.014423077
Phthiria                         0.875                 0.8819171 0.145299145
Platycheirus1                    0.875                 0.8000000 0.005012171
Sapromyza.Minettia               1.000                 1.0000000 0.004807692
Formicidae3                      1.000                 1.0000000 0.400000000
Nitidulidae                      1.000                 1.0000000 0.050000000
Staphilinidae                    0.875                 0.6700594 0.096703297
Ichneumonidae4                   0.875                 0.9317532 0.937579114
Braconidae3                      1.000                 1.0000000 0.100000000
Chalepogenus caeruleus           1.000                 1.0000000 0.750000000
Vespula germanica                1.000                 1.0000000 0.019230769
Torymidae2                       1.000                 1.0000000 0.450000000
Phthiria1                        1.000                 1.0000000 0.004807692
Svastrides melanura              1.000                 1.0000000 0.028846154
Sphecidae                        1.000                 1.0000000 0.004807692
Thomisidae                       1.000                 1.0000000 0.004807692
Corynura prothysteres            0.875                 0.7603453 0.011133763
Ichneumonidae2                   1.000                 1.0000000 0.019230769
Ruizantheda proxima              1.000                 1.0000000 0.019230769
Braconidae2                      1.000                 1.0000000 0.001265823
                        node.specialisation.index.NSI betweenness
Policana albopilosa                          1.863636  0.00000000
Bombus dahlbomii                             1.272727  0.00000000
Ruizantheda mutabilis                        1.636364  0.04807692
Trichophthalma amoena                        2.090909  0.00000000
Syrphus octomaculatus                        1.227273  0.02307692
Manuelia gayi                                1.272727  0.00000000
Allograpta.Toxomerus                         1.136364  0.41730769
Trichophthalma jaffueli                      1.272727  0.00000000
Phthiria                                     1.272727  0.00000000
Platycheirus1                                1.090909  0.24423077
Sapromyza.Minettia                           1.272727  0.00000000
Formicidae3                                  1.000000  0.00000000
Nitidulidae                                  1.000000  0.00000000
Staphilinidae                                1.227273  0.02307692
Ichneumonidae4                               1.863636  0.00000000
Braconidae3                                  1.000000  0.00000000
Chalepogenus caeruleus                       2.090909  0.00000000
Vespula germanica                            1.272727  0.00000000
Torymidae2                                   1.000000  0.00000000
Phthiria1                                    1.272727  0.00000000
Svastrides melanura                          1.272727  0.00000000
Sphecidae                                    1.272727  0.00000000
Thomisidae                                   1.272727  0.00000000
Corynura prothysteres                        1.090909  0.24423077
Ichneumonidae2                               1.272727  0.00000000
Ruizantheda proxima                          1.272727  0.00000000
Braconidae2                                  1.863636  0.00000000
                        weighted.betweenness   closeness weighted.closeness
Policana albopilosa               0.00000000 0.031499203        0.007653246
Bombus dahlbomii                  0.27133479 0.045454545        0.016935668
Ruizantheda mutabilis             0.18161926 0.035885167        0.007635430
Trichophthalma amoena             0.00000000 0.026315789        0.002008598
Syrphus octomaculatus             0.26805252 0.046650718        0.009803161
Manuelia gayi                     0.00000000 0.045454545        0.007645691
Allograpta.Toxomerus              0.17943107 0.049043062        0.004113559
Trichophthalma jaffueli           0.00000000 0.045454545        0.004331303
Phthiria                          0.00000000 0.045454545        0.008236576
Platycheirus1                     0.09956236 0.050239234        0.003845416
Sapromyza.Minettia                0.00000000 0.045454545        0.001720655
Formicidae3                       0.00000000 0.007177033                 NA
Nitidulidae                       0.00000000 0.007177033                 NA
Staphilinidae                     0.00000000 0.046650718        0.006203052
Ichneumonidae4                    0.00000000 0.031499203        0.001525954
Braconidae3                       0.00000000 0.007177033                 NA
Chalepogenus caeruleus            0.00000000 0.026315789        0.002535735
Vespula germanica                 0.00000000 0.045454545        0.005345012
Torymidae2                        0.00000000 0.007177033                 NA
Phthiria1                         0.00000000 0.045454545        0.001720655
Svastrides melanura               0.00000000 0.045454545        0.006978210
Sphecidae                         0.00000000 0.045454545        0.001720655
Thomisidae                        0.00000000 0.045454545        0.001720655
Corynura prothysteres             0.00000000 0.050239234        0.004526406
Ichneumonidae2                    0.00000000 0.045454545        0.005345012
Ruizantheda proxima               0.00000000 0.045454545        0.005345012
Braconidae2                       0.00000000 0.031499203        0.001525954
                        Fisher.alpha partner.diversity effective.partners
Policana albopilosa     1.153134e-01         0.0000000           1.000000
Bombus dahlbomii        3.033554e-01         0.6135242           1.846929
Ruizantheda mutabilis   3.433080e-01         0.2035609           1.225760
Trichophthalma amoena   7.959266e-01         0.0000000           1.000000
Syrphus octomaculatus   1.171275e+00         1.0933747           2.984328
Manuelia gayi           3.192569e-01         0.0000000           1.000000
Allograpta.Toxomerus    3.878375e+00         1.2770343           3.585989
Trichophthalma jaffueli 5.252615e-01         0.0000000           1.000000
Phthiria                7.972188e-01         0.3488321           1.417411
Platycheirus1           1.235493e+00         0.5004024           1.649385
Sapromyza.Minettia      1.677721e+09         0.0000000           1.000000
Formicidae3             3.016702e-01         0.0000000           1.000000
Nitidulidae             1.677721e+09         0.0000000           1.000000
Staphilinidae           9.354130e-01         0.6829081           1.979626
Ichneumonidae4          6.033405e-01         0.2337917           1.263381
Braconidae3             7.959266e-01         0.0000000           1.000000
Chalepogenus caeruleus  5.252615e-01         0.0000000           1.000000
Vespula germanica       4.279460e-01         0.0000000           1.000000
Torymidae2              2.878510e-01         0.0000000           1.000000
Phthiria1               1.677721e+09         0.0000000           1.000000
Svastrides melanura     3.426574e-01         0.0000000           1.000000
Sphecidae               1.677721e+09         0.0000000           1.000000
Thomisidae              1.677721e+09         0.0000000           1.000000
Corynura prothysteres   1.591816e+00         0.5623351           1.754765
Ichneumonidae2          4.279460e-01         0.0000000           1.000000
Ruizantheda proxima     4.279460e-01         0.0000000           1.000000
Braconidae2             1.677721e+09         0.0000000           1.000000
                        proportional.generality proportional.similarity
Policana albopilosa                   0.3777479             0.699115044
Bombus dahlbomii                      0.6976735             0.247787611
Ruizantheda mutabilis                 0.4630282             0.712389381
Trichophthalma amoena                 0.3777479             0.004424779
Syrphus octomaculatus                 1.1273237             0.261061947
Manuelia gayi                         0.3777479             0.184070796
Allograpta.Toxomerus                  1.3545997             0.164096081
Trichophthalma jaffueli               0.3777479             0.184070796
Phthiria                              0.5354241             0.184955752
Platycheirus1                         0.6230516             0.883185841
Sapromyza.Minettia                    0.3777479             0.184070796
Formicidae3                           0.3777479             0.017699115
Nitidulidae                           0.3777479             0.017699115
Staphilinidae                         0.7477997             0.197345133
Ichneumonidae4                        0.4772396             0.075774336
Braconidae3                           0.3777479             0.017699115
Chalepogenus caeruleus                0.3777479             0.003539823
Vespula germanica                     0.3777479             0.184070796
Torymidae2                            0.3777479             0.017699115
Phthiria1                             0.3777479             0.184070796
Svastrides melanura                   0.3777479             0.184070796
Sphecidae                             0.3777479             0.184070796
Thomisidae                            0.3777479             0.184070796
Corynura prothysteres                 0.6628589             0.434070796
Ichneumonidae2                        0.3777479             0.184070796
Ruizantheda proxima                   0.3777479             0.184070796
Braconidae2                           0.3777479             0.699115044
                                d
Policana albopilosa     0.6905693
Bombus dahlbomii        0.8581794
Ruizantheda mutabilis   0.1554289
Trichophthalma amoena   0.8474066
Syrphus octomaculatus   0.3859789
Manuelia gayi           0.3202602
Allograpta.Toxomerus    0.6482363
Trichophthalma jaffueli 0.2647268
Phthiria                0.3916793
Platycheirus1           0.0000000
Sapromyza.Minettia      0.2000132
Formicidae3             0.8115396
Nitidulidae             0.5510016
Staphilinidae           0.4092484
Ichneumonidae4          0.9007713
Braconidae3             0.6165417
Chalepogenus caeruleus  0.9500994
Vespula germanica       0.2834746
Torymidae2              0.8322740
Phthiria1               0.2000132
Svastrides melanura     0.3083018
Sphecidae               0.2000132
Thomisidae              0.2000132
Corynura prothysteres   0.1209998
Ichneumonidae2          0.2834746
Ruizantheda proxima     0.2834746
Braconidae2             0.0000000

$`lower level`
                         degree normalised.degree species.strength
Aristotelia chilensis         6        0.22222222        4.0607759
Alstroemeria aurea           17        0.62962963       13.6071500
Schinus patagonicus           1        0.03703704        0.9375000
Berberis darwinii             2        0.07407407        0.6603103
Rosa eglanteria               4        0.14814815        1.0517241
Cynanchum diemii              4        0.14814815        4.0000000
Ribes magellanicum            2        0.07407407        1.4285714
Mutisia decurrens             1        0.03703704        0.1111111
Calceolaria crenatiflora      2        0.07407407        1.1428571
                         interaction.push.pull nestedrank       PDI
Aristotelia chilensis               0.51012931      0.125 0.9933135
Alstroemeria aurea                  0.74159706      0.000 0.9865135
Schinus patagonicus                -0.06250000      0.875 1.0000000
Berberis darwinii                  -0.16984486      0.500 0.9971297
Rosa eglanteria                     0.01293103      0.375 0.9423077
Cynanchum diemii                    0.75000000      0.250 0.9529915
Ribes magellanicum                  0.21428571      0.625 0.9743590
Mutisia decurrens                  -0.88888889      1.000 1.0000000
Calceolaria crenatiflora            0.07142857      0.750 0.9871795
                         species.specificity.index resource.range PSI
Aristotelia chilensis                    0.8575243      0.8076923   1
Alstroemeria aurea                       0.7328574      0.3846154   1
Schinus patagonicus                      1.0000000      1.0000000   1
Berberis darwinii                        0.9304758      0.9615385   1
Rosa eglanteria                          0.5114083      0.8846154   1
Cynanchum diemii                         0.5924201      0.8846154   1
Ribes magellanicum                       0.7081938      0.9615385   1
Mutisia decurrens                        1.0000000      1.0000000   1
Calceolaria crenatiflora                 0.7813942      0.9615385   1
                         node.specialisation.index.NSI betweenness
Aristotelia chilensis                         1.571429         0.3
Alstroemeria aurea                            1.142857         0.5
Schinus patagonicus                           2.428571         0.0
Berberis darwinii                             1.857143         0.0
Rosa eglanteria                               1.285714         0.2
Cynanchum diemii                                   NaN         0.0
Ribes magellanicum                            1.714286         0.0
Mutisia decurrens                             2.000000         0.0
Calceolaria crenatiflora                      1.714286         0.0
                         weighted.betweenness  closeness weighted.closeness
Aristotelia chilensis               0.2222222 0.12931034        0.022311369
Alstroemeria aurea                  0.4074074 0.16810345        0.019174528
Schinus patagonicus                 0.0000000 0.08620690        0.028303507
Berberis darwinii                   0.0000000 0.11206897        0.018597603
Rosa eglanteria                     0.3703704 0.15517241        0.020088268
Cynanchum diemii                    0.0000000 0.00000000                 NA
Ribes magellanicum                  0.0000000 0.12500000        0.014799036
Mutisia decurrens                   0.0000000 0.09913793        0.005731637
Calceolaria crenatiflora            0.0000000 0.12500000        0.006640118
                         Fisher.alpha partner.diversity effective.partners
Aristotelia chilensis    8.826098e-01         0.4631689           1.589102
Alstroemeria aurea       4.379926e+00         1.2340874           3.435242
Schinus patagonicus      2.411918e-01         0.0000000           1.000000
Berberis darwinii        3.812192e-01         0.2521995           1.286853
Rosa eglanteria          1.784783e+00         1.3095258           3.704417
Cynanchum diemii         1.503506e+00         1.1058899           3.021912
Ribes magellanicum       1.235493e+00         0.6730117           1.960132
Mutisia decurrens        1.677721e+09         0.0000000           1.000000
Calceolaria crenatiflora 1.591816e+00         0.5623351           1.754765
                         proportional.similarity proportional.generality
Aristotelia chilensis                0.706071469               0.3896704
Alstroemeria aurea                   0.263214772               0.8423705
Schinus patagonicus                  0.014159292               0.2452143
Berberis darwinii                    0.207964602               0.3155547
Rosa eglanteria                      0.127433628               0.9083760
Cynanchum diemii                     0.017699115               0.7410161
Ribes magellanicum                   0.007964602               0.4806523
Mutisia decurrens                    0.007964602               0.2452143
Calceolaria crenatiflora             0.008849558               0.4302935
                                 d
Aristotelia chilensis    0.9613968
Alstroemeria aurea       0.8043229
Schinus patagonicus      0.9846607
Berberis darwinii        0.5619798
Rosa eglanteria          0.5590405
Cynanchum diemii         1.0000000
Ribes magellanicum       0.9036839
Mutisia decurrens        0.6625752
Calceolaria crenatiflora 0.9106928

bipartite documentation built on May 30, 2017, 1:25 a.m.