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Calculate width of canopy service and recruitment niches

Source: R/node_degrees.R
node_degrees.Rd

Calculate width of canopy service and recruitment niches

Usage

node_degrees(int_data, cover_data, int_type = c("rec", "fac", "comp"))

Arguments

int_data

data frame containing interaction data.

cover_data

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

int_type

Indicates the type of plant-plant interaction that will be presented in the output matrix: general recruitment, recruitment enhancement (i.e. facilitation) or recruitment depression (i.e. competition). It may take three possible values:

  • rec: Estimates the node degree based on all plant-plant interaction that contribute to recruitment.

  • fac: Estimates the node degree based on only those pairwise interactions that enhance recruitment. Not every observed interaction in the field has to be present in the matrix. In this case non-detected interactions are not considered and "Open" is not included as a canopy species category.

  • comp: Estimates the node degree based on only those pairwise interactions that depress recruitment. Not every observed interaction in the field has to be present in the matrix. However, in this case non-detected interactions are considered (i.e. expanding with 0 all possible interactions in the study system). "Open" is not included as a canopy species category.

Value

The output depends on the type of interaction considered. For the recruitment networks it returns a single data frame with the following information:

  • Node: plant species (either as canopy or recruit)

  • Ac: Area of the canopy species (and "Open" interspaces), measured as the distance (m, in transects) or area (m^2^, in plots) used to estimate canopy cover in the study site.

  • canopy_service_width: the number of species that recruit under a given canopy species (i.e., the canopy species' out-degree); this can be interpreted as the width of its canopy service.

  • canopy_contribution: number of recruits of any species associated with the canopy species. When the degrees are weighted by the frequency of recruitment (Fcr), then it can be interpreted as the contribution of the canopy species to the multispecific sapling bank.

  • effective_canopy_service: The weighted degrees are transformed to the effective number of partners, accounting for the dominance of certain interactions in the recruit bank. The effective canopy service is estimated as e^H, where H is Shannon's index of diversity calculated for a canopy species from Fcr.

  • recruitment_niche_width: number of canopy species that allow its recruitment (the recruit species' in-degree); this can be interpreted as the width of its recruitment niche.

  • recruit_bank_abundance: number of recruits of a species in the study site. When the degrees are weighted by the frequency of recruitment (Fcr), then it can be interpreted as species abundance in the recruit bank.

  • effective_recruitment_niche: The weighted degrees are transformed to the effective number of partners, accounting for the dominance of certain interactions in the recruit bank. The effective recruitment niche width is estimated as $e^H$, where H is Shannon's index of diversity calculated for a recruit species from Fcr.

For facilitation or recruitment depressing interactions, the output consists in two data frames, one for the canopy species and another for the recruit species. The data frame with information for the canopy species provides the following information:

  • Nurse (or Canopy) sp: Canopy species.

  • Ac: Area of the canopy species (and "Open" interspaces), measured as the distance (m, in transects) or area (m^2^, in plots) used to estimate canopy cover in the study site.

  • N enhanced (or depressed) recruit sp: number of species whose recruitment is enhanced (or depressed) under its canopy, this can be interpreted as the width of its enhancing of (depressing) effect.

The data frame with information for the recruit species contains the following information:

  • Facilitated (or recruit) sp: Recruit species.

  • N_ind: number of recruits of the facilitated (or depressed) species in the study site.

  • N enhancing (or depressing) canopy sp: number of canopy species that enhance its recruitment (i.e. nurse species) or depress it (i.e. competing species). These can be interpreted as the width of its niche of nurses or competitors.

Examples

out <- node_degrees(Amoladeras_int, Amoladeras_cover, int_type="rec")
head(out)
#>                   Node      Ac canopy_service_width canopy_contribution
#> 1 Artemisia_barrelieri  1.0000                    5                  18
#> 2 Artemisia_campestris  0.1100                    0                   0
#> 3      Asparagus_albus 27.7250                    7                  14
#> 4   Asparagus_horridus  1.5725                    3                   6
#> 5      Ballota_hirsuta 38.4550                    7                  31
#> 6 Helichrysum_stoechas 29.0700                    9                  62
#>   effective_canopy_service recruitment_niche_width recruit_bank_abundance
#> 1                 3.851794                       7                     90
#> 2                 1.000000                       3                      6
#> 3                 6.107480                       7                     25
#> 4                 2.381102                      11                     53
#> 5                 4.992495                       9                     82
#> 6                 6.827787                      12                   1055
#>   effective_recruitment_niche
#> 1                    3.152785
#> 2                    2.749459
#> 3                    5.910236
#> 4                    7.855732
#> 5                    5.461981
#> 6                    2.754019