converts the community data collected in the field, where each row represents a single canopy-recruit interaction, into a matrix format, with recruit species as rows and canopy species as columns. For general recruitment networks, the matrix should be square including all species observed at the study site. This means that the same set of species appears in both rows and columns, with "Open" areas treated as an additional category in both the Canopy and Recruit variables. In contrast, for recruitment enhancement (i.e. facilitation) or depression (i.e. competition), the matrix can be non-square. In this case, rows represent the species whose recruitment is enhanced or suppressed, while columns represent the canopy species that influence this recruitment. These two groups may not include the same species.
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 analyzed: general recruitment, recruitment enhancement (i.e. facilitation) or recruitment depression (i.e. competition). Explanation of its options:
rec: All the pairwise interactions observed will be in the output. Focuses on canopy-recruit interactions considering that every recruit growing under the canopy of another plant may occupy that space in the future, thus having a potentially positive effect on the recruit species population. Therefore, even a single observation is considered an interaction. This type of networks considers every species present in the study system, whether as a canopy or as a recruit, as a node in the network. It also includes "Open" as a particular node since some species may recruit away from established plants. Non-detected interactions are also considered since zero frequency can provide evidence of a very negative interaction if the expected frequency under the canopy species is large.
fac: Only those pairwise interactions that resulted in recruitment enhancement will be in the output. Focuses on interactions with a significantly higher recruitment density under canopy than in "Open" (i.e. facilitation). Non-detected interactions are not considered and "Open" is not included as a node, although its relative cover is considered as part of the sampling area.
comp: Only those pairwise interactions that resulted in a recruitment depression will be in the output. Focuses on interactions with a significantly lower recruitment density under canopy than "Open" (i.e. competition). Non-detected interactions are considered (i.e. expanding with 0 all possible interactions in the study system), as the absence of recruitment of a species under a given canopy can reflect a particularly strong depression of recruitment under that canopy species. "Open" is not included as a node, although its relative cover is considered as part of the sampling area.
- weight
Specifies the metric used to represent interaction strength (i.e., the weight) assigned to each pair of species in the matrix. Explanation of its options (more mathematical information in the description of the function
associndex():Fcr: frequency of recruitment, in number of recruits by canopy-recruit pair.
Dcr: density of recruitment, as number of recruits per unit area of canopy species cover.
Dro: density of recruitment in open interspaces, as number of recruits per unit area of open interspaces.
Ns: The Normalized Neighbour Suitability index; suitable for comparisons of interaction strength between pairs of species within a local community.
NIntA: The Additive symmetry intensity index.
NIntC: The Commutative symmetry intensity index.
RII: The Relative Interaction Index.
Value
A matrix with recruit species in rows and canopy species in columns, with cells describing the measure selected to describe the interaction strength (i.e. weight) between each pair of species.
Examples
RN_to_matrix(Amoladeras_int, Amoladeras_cover, int_type="rec", weight="Dcr")
#> Based on Weibull distribution fitted to the observed values, the threshold density has been set to: 1.12346719046902.
#> Artemisia_barrelieri Artemisia_campestris Asparagus_albus
#> Artemisia_barrelieri 3 0 0.00000000
#> Artemisia_campestris 0 0 0.00000000
#> Asparagus_albus 0 0 0.00000000
#> Asparagus_horridus 0 0 0.00000000
#> Ballota_hirsuta 0 0 0.00000000
#> Helichrysum_stoechas 3 0 0.00000000
#> Hyparrhenia_hirta 0 0 0.00000000
#> Launaea_arborescens 0 0 0.00000000
#> Launaea_lanifera 0 0 0.00000000
#> Lycium_intrincatum 0 0 0.07213706
#> Lygeum_spartum 0 0 0.03606853
#> Maytenus_senegalensis 0 0 0.03606853
#> Ononis_natrix 0 0 0.03606853
#> Open 0 0 0.00000000
#> Phagnalon_saxatile 9 0 0.14427412
#> Piptatherum_miliaceum 0 0 0.00000000
#> Salsola_oppositifolia 0 0 0.00000000
#> Stipa_tenacissima 0 0 0.00000000
#> Teucrium_lusitanicum 0 0 0.00000000
#> Teucrium_polium 2 0 0.00000000
#> Thymelaea_hirsuta 0 0 0.07213706
#> Thymus_hyemalis 1 0 0.00000000
#> Whitania_frutescens 0 0 0.10820559
#> Ziziphus_lotus 0 0 0.00000000
#> Asparagus_horridus Ballota_hirsuta Helichrysum_stoechas
#> Artemisia_barrelieri 0.00000 0.00000000 0.00000000
#> Artemisia_campestris 0.00000 0.00000000 0.00000000
#> Asparagus_albus 0.00000 0.00000000 0.00000000
#> Asparagus_horridus 0.00000 0.05200884 0.06879945
#> Ballota_hirsuta 0.63593 0.00000000 0.10319917
#> Helichrysum_stoechas 0.00000 0.10401768 0.00000000
#> Hyparrhenia_hirta 0.00000 0.00000000 0.00000000
#> Launaea_arborescens 0.00000 0.00000000 0.03439972
#> Launaea_lanifera 0.00000 0.00000000 0.00000000
#> Lycium_intrincatum 0.00000 0.00000000 0.00000000
#> Lygeum_spartum 0.00000 0.00000000 0.00000000
#> Maytenus_senegalensis 0.00000 0.00000000 0.00000000
#> Ononis_natrix 0.00000 0.05200884 0.51599587
#> Open 0.00000 0.00000000 0.00000000
#> Phagnalon_saxatile 2.54372 0.36406189 0.13759890
#> Piptatherum_miliaceum 0.00000 0.00000000 0.00000000
#> Salsola_oppositifolia 0.00000 0.13002210 0.24079807
#> Stipa_tenacissima 0.00000 0.00000000 0.00000000
#> Teucrium_lusitanicum 0.00000 0.00000000 0.00000000
#> Teucrium_polium 0.00000 0.02600442 0.41279670
#> Thymelaea_hirsuta 0.00000 0.07801326 0.48159615
#> Thymus_hyemalis 0.63593 0.00000000 0.13759890
#> Whitania_frutescens 0.00000 0.00000000 0.00000000
#> Ziziphus_lotus 0.00000 0.00000000 0.00000000
#> Hyparrhenia_hirta Launaea_arborescens Launaea_lanifera
#> Artemisia_barrelieri 0.00000000 0.000000000 0
#> Artemisia_campestris 0.00000000 0.000000000 0
#> Asparagus_albus 0.00000000 0.010551528 0
#> Asparagus_horridus 0.00000000 0.014772140 0
#> Ballota_hirsuta 0.00000000 0.010551528 0
#> Helichrysum_stoechas 0.00000000 0.073860699 0
#> Hyparrhenia_hirta 0.00000000 0.008441223 0
#> Launaea_arborescens 0.07544323 0.018992751 0
#> Launaea_lanifera 0.00000000 0.000000000 0
#> Lycium_intrincatum 0.07544323 0.012661834 0
#> Lygeum_spartum 0.00000000 0.002110306 0
#> Maytenus_senegalensis 0.00000000 0.002110306 0
#> Ononis_natrix 0.07544323 0.238464542 0
#> Open 0.00000000 0.000000000 0
#> Phagnalon_saxatile 0.60354583 0.354531354 0
#> Piptatherum_miliaceum 0.00000000 0.004220611 0
#> Salsola_oppositifolia 0.00000000 0.016882445 0
#> Stipa_tenacissima 0.00000000 0.000000000 0
#> Teucrium_lusitanicum 0.37721614 0.008441223 0
#> Teucrium_polium 0.15088646 0.029544279 0
#> Thymelaea_hirsuta 0.15088646 0.042206114 0
#> Thymus_hyemalis 0.07544323 0.029544279 0
#> Whitania_frutescens 0.07544323 0.075971004 0
#> Ziziphus_lotus 0.00000000 0.000000000 0
#> Lycium_intrincatum Lygeum_spartum Maytenus_senegalensis
#> Artemisia_barrelieri 0.00000000 0.035730098 0.000000000
#> Artemisia_campestris 0.00000000 0.004660448 0.000000000
#> Asparagus_albus 0.00618047 0.006213930 0.008587377
#> Asparagus_horridus 0.01236094 0.010874378 0.000000000
#> Ballota_hirsuta 0.12360939 0.000000000 0.000000000
#> Helichrysum_stoechas 0.10506799 0.006213930 0.000000000
#> Hyparrhenia_hirta 0.00000000 0.000000000 0.000000000
#> Launaea_arborescens 0.01854141 0.009320895 0.008587377
#> Launaea_lanifera 0.00000000 0.000000000 0.000000000
#> Lycium_intrincatum 0.02472188 0.003106965 0.008587377
#> Lygeum_spartum 0.00000000 0.015534825 0.000000000
#> Maytenus_senegalensis 0.00000000 0.001553483 0.000000000
#> Ononis_natrix 0.05562423 0.015534825 0.025762130
#> Open 0.00000000 0.000000000 0.000000000
#> Phagnalon_saxatile 0.25957973 0.063692783 0.060111636
#> Piptatherum_miliaceum 0.00000000 0.000000000 0.000000000
#> Salsola_oppositifolia 0.07416564 0.026409203 0.000000000
#> Stipa_tenacissima 0.00000000 0.000000000 0.000000000
#> Teucrium_lusitanicum 0.00000000 0.009320895 0.000000000
#> Teucrium_polium 0.04326329 0.026409203 0.000000000
#> Thymelaea_hirsuta 0.02472188 0.020195273 0.000000000
#> Thymus_hyemalis 0.00000000 0.018641790 0.017174753
#> Whitania_frutescens 0.00000000 0.000000000 0.008587377
#> Ziziphus_lotus 0.00000000 0.000000000 0.000000000
#> Ononis_natrix Open Phagnalon_saxatile
#> Artemisia_barrelieri 0.004082216 0.0077955915 0.00000000
#> Artemisia_campestris 0.000000000 0.0001443628 0.00000000
#> Asparagus_albus 0.000000000 0.0010105396 0.00000000
#> Asparagus_horridus 0.000000000 0.0025985305 0.05895357
#> Ballota_hirsuta 0.000000000 0.0015879909 0.00000000
#> Helichrysum_stoechas 0.008164432 0.1149127933 0.00000000
#> Hyparrhenia_hirta 0.008164432 0.0049083354 0.00000000
#> Launaea_arborescens 0.077562101 0.0128482897 0.08843036
#> Launaea_lanifera 0.000000000 0.0008661768 0.00000000
#> Lycium_intrincatum 0.008164432 0.0028872561 0.02947679
#> Lygeum_spartum 0.000000000 0.0115490245 0.00000000
#> Maytenus_senegalensis 0.000000000 0.0000000000 0.00000000
#> Ononis_natrix 0.146959770 0.2654831996 0.14738394
#> Open 0.000000000 0.0000000000 0.00000000
#> Phagnalon_saxatile 0.012246647 0.0762235614 0.08843036
#> Piptatherum_miliaceum 0.000000000 0.0027428933 0.00000000
#> Salsola_oppositifolia 0.012246647 0.0086617683 0.14738394
#> Stipa_tenacissima 0.000000000 0.0001443628 0.00000000
#> Teucrium_lusitanicum 0.000000000 0.0023098049 0.00000000
#> Teucrium_polium 0.016328863 0.0444637441 0.23581430
#> Thymelaea_hirsuta 0.004082216 0.0245416770 0.26529108
#> Thymus_hyemalis 0.000000000 0.1486936898 0.11790715
#> Whitania_frutescens 0.000000000 0.0007218140 0.00000000
#> Ziziphus_lotus 0.000000000 0.0005774512 0.00000000
#> Piptatherum_miliaceum Salsola_oppositifolia
#> Artemisia_barrelieri 0.00000000 0.03246226
#> Artemisia_campestris 0.00000000 0.00000000
#> Asparagus_albus 0.00000000 0.00000000
#> Asparagus_horridus 0.00000000 0.03246226
#> Ballota_hirsuta 0.00000000 0.06492453
#> Helichrysum_stoechas 0.00000000 0.51939620
#> Hyparrhenia_hirta 0.00000000 0.01623113
#> Launaea_arborescens 0.32293483 0.14608018
#> Launaea_lanifera 0.00000000 0.00000000
#> Lycium_intrincatum 0.06458697 0.08115566
#> Lygeum_spartum 0.00000000 0.01623113
#> Maytenus_senegalensis 0.00000000 0.00000000
#> Ononis_natrix 0.00000000 0.09738679
#> Open 0.00000000 0.00000000
#> Phagnalon_saxatile 0.25834787 0.74663204
#> Piptatherum_miliaceum 0.00000000 0.00000000
#> Salsola_oppositifolia 0.00000000 0.00000000
#> Stipa_tenacissima 0.00000000 0.00000000
#> Teucrium_lusitanicum 0.00000000 0.00000000
#> Teucrium_polium 0.25834787 0.27592923
#> Thymelaea_hirsuta 0.00000000 0.08115566
#> Thymus_hyemalis 0.00000000 0.22723584
#> Whitania_frutescens 0.00000000 0.00000000
#> Ziziphus_lotus 0.00000000 0.00000000
#> Stipa_tenacissima Teucrium_lusitanicum Teucrium_polium
#> Artemisia_barrelieri 0 0.0000000 0.0000000
#> Artemisia_campestris 0 0.0000000 0.0000000
#> Asparagus_albus 0 0.0000000 0.0000000
#> Asparagus_horridus 0 0.0000000 0.0000000
#> Ballota_hirsuta 0 0.0000000 0.0000000
#> Helichrysum_stoechas 0 0.0000000 0.3520094
#> Hyparrhenia_hirta 0 0.0000000 0.1760047
#> Launaea_arborescens 0 0.0000000 0.0000000
#> Launaea_lanifera 0 0.0000000 0.0000000
#> Lycium_intrincatum 0 0.0000000 0.0000000
#> Lygeum_spartum 0 0.0000000 0.0000000
#> Maytenus_senegalensis 0 0.0000000 0.0000000
#> Ononis_natrix 0 0.1893043 0.4693458
#> Open 0 0.0000000 0.0000000
#> Phagnalon_saxatile 0 0.0000000 0.4106776
#> Piptatherum_miliaceum 0 0.0000000 0.1173365
#> Salsola_oppositifolia 0 0.0000000 0.1760047
#> Stipa_tenacissima 0 0.0000000 0.0000000
#> Teucrium_lusitanicum 0 0.0000000 0.0000000
#> Teucrium_polium 0 0.0000000 0.0000000
#> Thymelaea_hirsuta 0 0.1893043 0.7040188
#> Thymus_hyemalis 0 0.1893043 0.1760047
#> Whitania_frutescens 0 0.0000000 0.0000000
#> Ziziphus_lotus 0 0.0000000 0.0000000
#> Thymelaea_hirsuta Thymus_hyemalis Whitania_frutescens
#> Artemisia_barrelieri 0.035478606 0.003827165 0.00000000
#> Artemisia_campestris 0.000000000 0.003827165 0.00000000
#> Asparagus_albus 0.000000000 0.005740748 0.00000000
#> Asparagus_horridus 0.035478606 0.003827165 0.07040394
#> Ballota_hirsuta 0.035478606 0.001913583 0.00000000
#> Helichrysum_stoechas 0.411551834 0.164568104 0.00000000
#> Hyparrhenia_hirta 0.014191443 0.005740748 0.00000000
#> Launaea_arborescens 0.049670049 0.007654330 0.14080789
#> Launaea_lanifera 0.007095721 0.001913583 0.00000000
#> Lycium_intrincatum 0.007095721 0.003827165 0.05280296
#> Lygeum_spartum 0.014191443 0.011481496 0.00000000
#> Maytenus_senegalensis 0.000000000 0.000000000 0.01760099
#> Ononis_natrix 0.305116015 0.013395078 0.07040394
#> Open 0.000000000 0.000000000 0.00000000
#> Phagnalon_saxatile 0.979209537 0.254506487 0.17600986
#> Piptatherum_miliaceum 0.000000000 0.007654330 0.00000000
#> Salsola_oppositifolia 0.078052934 0.051666730 0.00000000
#> Stipa_tenacissima 0.000000000 0.000000000 0.00000000
#> Teucrium_lusitanicum 0.035478606 0.000000000 0.00000000
#> Teucrium_polium 0.383168949 0.166481687 0.05280296
#> Thymelaea_hirsuta 0.134818704 0.124382870 0.03520197
#> Thymus_hyemalis 0.241254524 0.017222243 0.08800493
#> Whitania_frutescens 0.007095721 0.000000000 0.01760099
#> Ziziphus_lotus 0.000000000 0.000000000 0.00000000
#> Ziziphus_lotus
#> Artemisia_barrelieri 0.000000000
#> Artemisia_campestris 0.000000000
#> Asparagus_albus 0.008598545
#> Asparagus_horridus 0.000000000
#> Ballota_hirsuta 0.068788358
#> Helichrysum_stoechas 0.025795634
#> Hyparrhenia_hirta 0.008598545
#> Launaea_arborescens 0.008598545
#> Launaea_lanifera 0.000000000
#> Lycium_intrincatum 0.027945270
#> Lygeum_spartum 0.004299272
#> Maytenus_senegalensis 0.000000000
#> Ononis_natrix 0.019346726
#> Open 0.000000000
#> Phagnalon_saxatile 0.085985447
#> Piptatherum_miliaceum 0.000000000
#> Salsola_oppositifolia 0.030094906
#> Stipa_tenacissima 0.000000000
#> Teucrium_lusitanicum 0.015047453
#> Teucrium_polium 0.019346726
#> Thymelaea_hirsuta 0.006448909
#> Thymus_hyemalis 0.019346726
#> Whitania_frutescens 0.004299272
#> Ziziphus_lotus 0.000000000