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Species functional role in the general recruitment network

Source: R/funtopol_rec.R
funtopol_rec.Rd

provides summary information of the frequency of species of each functional role and the classification of species in each role.

Usage

funtopol_rec(int_data, cover_data)

Arguments

int_data

data frame containing interaction data.

cover_data

data frame with the abundance of each canopy species in each plot.

Value

A list with two elements, one with descriptors of the networks and another with the role of each species.

The first element of the list provides the following information:

  • Num. nodes: Total number of nodes in the network.

  • Num. edges: Total number of links in the network.

  • Connectance: Proportion of links observed relative to all the possible links (C). In the case of recruitment networks, we use the formula $C = L /(N^2 - N)$ since the node "Open" does not act as a recruit (i.e. Open is represented by a row of zeroes in the adjacency matrix).

  • Num. non-trivial SCCs: Number of SCCs formed by more than one node in the network.

  • Num. core species: Number of species in the core SCC.

  • Prop. core species: Proportion of species in the core relative to the total number of species in the network.

  • Num. satellite species: Number of satellite species in the network.

  • Prop. satellite species: Proportion of satellite species relative to the total number of species in the network.

  • Num. disturbance-dependent transients: Number of disturbance-dependent transient species in the network.

  • Prop. disturbance-dependent transients: Proportion of disturbance-dependent transient species relative to the total number of species in the network.

  • Num. strict transients: Number of strict transient species in the network.

  • Prop. strict transients: Proportion of strict transient species relative to the total number of species in the network.

  • Qualitative Persistence: The sum of the proportion of core and satellite species. The second element of the list, provides the role for each plant species in the network, whose interpretations differ in each plant-plant interaction type. Each node (i.e. species) can be:

  • Part of the core core. In the case of general recruitment networks, the direction of the links represents that the space occupied by canopy species (predecessor node) will be replaced by the species recruiting under its canopy (successor node). In this case, all species in the core must recruit, at least, under the canopy of another core species, and allow the recruitment of at least another core species.

  • A satellite species: these are non-core species that can be reached from some core species, following the direction of the arrows. In general recruitment networks, these are species that recruit under the canopy of some core species but that do not show recruitment of any core species under their canopy.

  • A disturbance-dependent transient species: these are species that can be reached from the "Open" node but not from core or satellite species (i.e. for example, pioneer species that only recruit away from established plants).

  • A strict transient species: a species that cannot be reached from any other node. In the case of general recruitment networks strict transients are those species that do not recruit in the studied local assemblage (e.g., a pioneer species in a mature forest patch or a relict species at it distribution limit).

Examples

funtopol_rec(Amoladeras_int,Amoladeras_cover)
#> $Descriptors
#>                                               Value
#> Num. nodes                              24.00000000
#> Num. edges                             221.00000000
#> Connectance                              0.40036232
#> Num. non-trivial SCCs                    1.00000000
#> Num. core species                       19.00000000
#> Prop. core species                       0.82608696
#> Num. satellite species                   2.00000000
#> Prop. satellite species                  0.08695652
#> Num. disturbance-dependent transients    2.00000000
#> Prop. disturbance-dependent transients   0.08695652
#> Num. strict transients                   0.00000000
#> Prop. strict transients                  0.00000000
#> Qualitative Persistence                  0.91304348
#> 
#> $Functional_classification
#>                       id                            group
#> 3   Artemisia_barrelieri                             Core
#> 1   Artemisia_campestris                        Satellite
#> 4        Asparagus_albus                             Core
#> 5     Asparagus_horridus                             Core
#> 6        Ballota_hirsuta                             Core
#> 7   Helichrysum_stoechas                             Core
#> 8      Hyparrhenia_hirta                             Core
#> 9    Launaea_arborescens                             Core
#> 2       Launaea_lanifera                        Satellite
#> 10    Lycium_intrincatum                             Core
#> 11        Lygeum_spartum                             Core
#> 12 Maytenus_senegalensis                             Core
#> 13         Ononis_natrix                             Core
#> 14    Phagnalon_saxatile                             Core
#> 15 Piptatherum_miliaceum                             Core
#> 16 Salsola_oppositifolia                             Core
#> 23     Stipa_tenacissima Disturbance_dependent_transients
#> 17  Teucrium_lusitanicum                             Core
#> 18       Teucrium_polium                             Core
#> 19     Thymelaea_hirsuta                             Core
#> 20       Thymus_hyemalis                             Core
#> 21   Whitania_frutescens                             Core
#> 22        Ziziphus_lotus Disturbance_dependent_transients
#>