Calculate the euclidean distance between a set of environmental predictor variables and mutliple taxa
Source:R/calc_distance.R
calc_distance.RdCalculate the euclidean distance between a set of environmental predictor variables and mutliple taxa
Usage
calc_distance(
predictors,
taxa = elements::TaxonomicBackbone$taxon_code,
vars = elements::VariableNames,
method = "median",
append = "ids"
)Arguments
- predictors
A data frame of predictors. Must include the following columns: L, M, N, R, S, SD, GP, bio05, bio06, bio16, bio17, and optionally taxon
- taxa
A vector of strings containing one or more taxa to calculate distances for. See
elements::TaxonomicBackbone.- vars
A vector of variable names, one or more of
elements::VariableNames.- method
One of "median" or "mean" indicating whether to measure the euclidean distance from the predictor variables to the median or mean values.
- append
A string, one of "all", "predictors", or "ids" representing which columns from the predictors data frame to return with the results.
Examples
elements::calc_distance(predictors = elements::ExampleScenarios)
#> scenario timeslice scenario_code taxon_code distance
#> 1.1 Baseline 2007 a abies_alba 3.636952
#> 1.2 Baseline 2007 a abies_borisii-regis 3.406591
#> 1.3 Baseline 2007 a abies_cephalonica 3.123997
#> 1.4 Baseline 2007 a abies_cilicica_subsp._isaurica 2.899396
#> 1.5 Baseline 2007 a abies_grandis 3.219113
#> 1.6 Baseline 2007 a abies_nordmanniana_subsp._equi-trojani 3.387160
#> 1.7 Baseline 2007 a abies_nordmanniana_subsp._nordmanniana 3.683923
#> 1.8 Baseline 2007 a abietinella_abietina 2.860623
#> 1.9 Baseline 2007 a abutilon_theophrasti 2.913475
#> 1.10 Baseline 2007 a acantholimon_acerosum 2.833773
#> 1.11 Baseline 2007 a acantholimon_puberulum_var._puberulum 2.809365
#> 1.12 Baseline 2007 a acantholimon_ulicinum 2.937199
#> 1.13 Baseline 2007 a acantholimon_ulicinum_subsp._ulicinum 2.802648
#> 1.14 Baseline 2007 a acantholimon_venustum_var._venustum 2.850136
#> 1.15 Baseline 2007 a acanthus_hungaricus 3.068189
#> 1.16 Baseline 2007 a acanthus_mollis 3.251038
#> 1.17 Baseline 2007 a acanthus_mollis_subsp._mollis 3.257391
#> 1.18 Baseline 2007 a acanthus_spinosus 3.277638
#> 1.19 Baseline 2007 a acer_campestre 3.316213
#> 1.20 Baseline 2007 a acer_campestre_subsp._campestre 3.126469
#> 1.21 Baseline 2007 a acer_granatense 3.012411
#> 1.22 Baseline 2007 a acer_heldreichii 3.591992
#> 1.23 Baseline 2007 a acer_hyrcanum 3.231464
#> 1.24 Baseline 2007 a acer_monspessulanum 3.140927
#> 1.25 Baseline 2007 a acer_monspessulanum_subsp._monspessulanum 3.287096
#> 1.26 Baseline 2007 a acer_negundo 3.007178
#> 1.27 Baseline 2007 a acer_obtusatum 3.444014
#> 1.28 Baseline 2007 a acer_opalus 3.297285
#> 1.29 Baseline 2007 a acer_platanoides 3.406773
#> 1.30 Baseline 2007 a acer_pseudoplatanus 3.413035
#> 1.31 Baseline 2007 a acer_sempervirens 3.212860
#> 1.32 Baseline 2007 a acer_tataricum 3.182642
#> 1.33 Baseline 2007 a acer_trautvetteri 3.599463
#> 1.34 Baseline 2007 a achillea_arabica 2.830811
#> 1.35 Baseline 2007 a achillea_aspleniifolia 2.830588
#> 1.36 Baseline 2007 a achillea_atrata 3.653152
#> 1.37 Baseline 2007 a achillea_clavennae 3.598935
#> 1.38 Baseline 2007 a achillea_clusiana 3.314449
#> 1.39 Baseline 2007 a achillea_clypeolata 2.927989
#> 1.40 Baseline 2007 a achillea_coarctata 2.901220
#> 1.41 Baseline 2007 a achillea_collina 2.868363
#> 1.42 Baseline 2007 a achillea_crithmifolia 2.878634
#> 1.43 Baseline 2007 a achillea_distans 3.238368
#> 1.44 Baseline 2007 a achillea_distans_subsp._stricta 3.191846
#> 1.45 Baseline 2007 a achillea_erba-rotta_subsp._moschata 3.681318
#> 1.46 Baseline 2007 a achillea_grandifolia 3.079541
#> 1.47 Baseline 2007 a achillea_holosericea 3.103055
#> 1.48 Baseline 2007 a achillea_ligustica 2.942638
#> 1.49 Baseline 2007 a achillea_macrophylla 3.971991
#> 1.50 Baseline 2007 a achillea_maritima 3.234618
#> 1.51 Baseline 2007 a achillea_maritima_subsp._maritima 3.259122
#> 1.52 Baseline 2007 a achillea_micrantha 2.801288
#> 1.53 Baseline 2007 a achillea_micranthoides 2.819302
#> 1.54 Baseline 2007 a achillea_millefolium 2.842956
#> 1.55 Baseline 2007 a achillea_millefolium_aggr. 2.889183
#> 1.56 Baseline 2007 a achillea_millefolium_subsp._millefolium 2.797223
#> 1.57 Baseline 2007 a achillea_millefolium_subsp._sudetica 3.297393
#> 1.58 Baseline 2007 a achillea_nana 3.586640
#> 1.59 Baseline 2007 a achillea_nobilis 2.849483
#> 1.60 Baseline 2007 a achillea_nobilis_subsp._neilreichii 2.851591
#> 1.61 Baseline 2007 a achillea_nobilis_subsp._nobilis 2.854779
#> 1.62 Baseline 2007 a achillea_odorata 2.916762
#> 1.63 Baseline 2007 a achillea_oxyloba 3.569481
#> 1.64 Baseline 2007 a achillea_oxyloba_subsp._schurii 3.336302
#> 1.65 Baseline 2007 a achillea_pannonica 2.851478
#> 1.66 Baseline 2007 a achillea_ptarmica 2.858622
#> 1.67 Baseline 2007 a achillea_pyrenaica 3.039153
#> 1.68 Baseline 2007 a achillea_salicifolia 2.838002
#> 1.69 Baseline 2007 a achillea_santolinoides_subsp._wilhelmsii 2.832791
#> 1.70 Baseline 2007 a achillea_setacea 2.868584
#> 1.71 Baseline 2007 a achillea_tomentosa 2.985516
#> 1.72 Baseline 2007 a achillea_virescens 3.094862
#> 1.73 Baseline 2007 a achnatherum_bromoides 3.189521
#> 1.74 Baseline 2007 a achnatherum_calamagrostis 3.067461
#> 1.75 Baseline 2007 a aconitum_angustifolium 3.640520
#> 1.76 Baseline 2007 a aconitum_anthora 3.046668
#> 1.77 Baseline 2007 a aconitum_degenii 3.904280
#> 1.78 Baseline 2007 a aconitum_firmum 3.365457
#> 1.79 Baseline 2007 a aconitum_lycoctonum 3.800489
#> 1.80 Baseline 2007 a aconitum_lycoctonum_subsp._lycoctonum 3.588196
#> 1.81 Baseline 2007 a aconitum_lycoctonum_subsp._neapolitanum 3.562313
#> 1.82 Baseline 2007 a aconitum_lycoctonum_subsp._vulparia 3.808958
#> 1.83 Baseline 2007 a aconitum_moldavicum 3.520008
#> 1.84 Baseline 2007 a aconitum_napellus 3.365612
#> 1.85 Baseline 2007 a aconitum_napellus_aggr. 3.831748
#> 1.86 Baseline 2007 a aconitum_napellus_subsp._vulgare 3.509561
#> 1.87 Baseline 2007 a aconitum_plicatum 3.312191
#> 1.88 Baseline 2007 a aconitum_tauricum 3.522273
#> 1.89 Baseline 2007 a aconitum_variegatum 3.374926
#> 1.90 Baseline 2007 a aconogonon_alpinum 3.168574
#> 1.91 Baseline 2007 a acorus_calamus 2.883851
#> 1.92 Baseline 2007 a actaea_europaea 3.311772
#> 1.93 Baseline 2007 a actaea_spicata 3.610888
#> 1.94 Baseline 2007 a adenocarpus_complicatus 2.997037
#> 1.95 Baseline 2007 a adenocarpus_telonensis 3.065979
#> 1.96 Baseline 2007 a adenostyles_alliariae 3.744186
#> 1.97 Baseline 2007 a adenostyles_alliariae_subsp._alliariae 3.886905
#> 1.98 Baseline 2007 a adenostyles_alpina 3.881803
#> 1.99 Baseline 2007 a adenostyles_alpina_subsp._alpina 3.547925
#> 1.100 Baseline 2007 a adenostyles_alpina_subsp._pyrenaica 3.555039
#> 1.101 Baseline 2007 a adenostyles_glabra_subsp._glabra 3.797002
#> 1.102 Baseline 2007 a adenostyles_leucophylla 3.338009
#> 1.103 Baseline 2007 a adiantum_capillus-veneris 3.240927
#> 1.104 Baseline 2007 a adonis_aestivalis 2.865460
#> 1.105 Baseline 2007 a adonis_annua 3.046768
#> 1.106 Baseline 2007 a adonis_flammea 2.869221
#> 1.107 Baseline 2007 a adonis_microcarpa 3.013274
#> 1.108 Baseline 2007 a adonis_vernalis 2.902688
#> 1.109 Baseline 2007 a adoxa_moschatellina 3.442337
#> 1.110 Baseline 2007 a aegilops_biuncialis 3.122875
#> 1.111 Baseline 2007 a aegilops_caudata 3.250102
#> 1.112 Baseline 2007 a aegilops_cylindrica 2.892887
#> 1.113 Baseline 2007 a aegilops_geniculata 3.021595
#> 1.114 Baseline 2007 a aegilops_neglecta 2.933335
#> 1.115 Baseline 2007 a aegilops_triuncialis 2.947133
#> 1.116 Baseline 2007 a aegilops_triuncialis_subsp._triuncialis 2.963894
#> 1.117 Baseline 2007 a aegilops_umbellulata 2.932909
#> 1.118 Baseline 2007 a aegonychon_purpurocaeruleum 3.178334
#> 1.119 Baseline 2007 a aegopodium_podagraria 3.225339
#> 1.120 Baseline 2007 a aeluropus_littoralis 2.967920
#> 1.121 Baseline 2007 a aesculus_hippocastanum 3.280604
#> 1.122 Baseline 2007 a aethionema_arabicum 2.843364
#> 1.123 Baseline 2007 a aethionema_saxatile 3.028566
#> 1.124 Baseline 2007 a aethionema_saxatile_subsp._graecum 3.058361
#> 1.125 Baseline 2007 a aethusa_cynapium 2.883293
#> 1.126 Baseline 2007 a aethusa_cynapium_subsp._cynapium 2.826450
#> 1.127 Baseline 2007 a agrimonia_eupatoria 2.887922
#> 1.128 Baseline 2007 a agrimonia_eupatoria_subsp._eupatoria 2.825901
#> 1.129 Baseline 2007 a agrimonia_procera 2.949042
#> 1.130 Baseline 2007 a agropyron_cristatum 2.888303
#> 1.131 Baseline 2007 a agropyron_cristatum_subsp._brandzae 2.904341
#> 1.132 Baseline 2007 a agropyron_cristatum_subsp._pectinatum 2.865567
#> 1.133 Baseline 2007 a agropyron_dasyanthum 2.788287
#> 1.134 Baseline 2007 a agrostemma_githago 2.844972
#> 1.135 Baseline 2007 a agrostis_alpina 3.529333
#> 1.136 Baseline 2007 a agrostis_canina 2.829460
#> 1.137 Baseline 2007 a agrostis_canina_aggr. 2.847522
#> 1.138 Baseline 2007 a agrostis_canina_s.l. 3.058093
#> 1.139 Baseline 2007 a agrostis_capillaris 2.836853
#> 1.140 Baseline 2007 a agrostis_castellana 2.885383
#> 1.141 Baseline 2007 a agrostis_curtisii 2.855063
#> 1.142 Baseline 2007 a agrostis_gigantea 2.828203
#> 1.143 Baseline 2007 a agrostis_gigantea_subsp._maeotica 2.774186
#> 1.144 Baseline 2007 a agrostis_hesperica 2.771401
#> 1.145 Baseline 2007 a agrostis_mertensii 3.144778
#> 1.146 Baseline 2007 a agrostis_rupestris 3.313447
#> 1.147 Baseline 2007 a agrostis_schleicheri 3.046642
#> 1.148 Baseline 2007 a agrostis_schraderiana 3.467704
#> 1.149 Baseline 2007 a agrostis_stolonifera 2.846342
#> 1.150 Baseline 2007 a agrostis_stolonifera_aggr. 2.883735
#> 1.151 Baseline 2007 a agrostis_stolonifera_subsp._maritima 3.002495
#> 1.152 Baseline 2007 a agrostis_vinealis 2.810356
#> 1.153 Baseline 2007 a agrostis_x_fouilladeana 2.924155
#> 1.154 Baseline 2007 a ailanthus_altissima 2.985830
#> 1.155 Baseline 2007 a aira_caryophyllea 2.837323
#> 1.156 Baseline 2007 a aira_caryophyllea_subsp._caryophyllea 2.825524
#> 1.157 Baseline 2007 a aira_cupaniana 3.103830
#> 1.158 Baseline 2007 a aira_elegantissima 3.006436
#> 1.159 Baseline 2007 a aira_praecox 2.800826
#> 1.160 Baseline 2007 a aira_tenorei 3.078650
#> 1.161 Baseline 2007 a aira_uniaristata 3.064657
#> 1.162 Baseline 2007 a ajuga_chamaepitys 2.922216
#> 1.163 Baseline 2007 a ajuga_chamaepitys_subsp._chia 2.871643
#> 1.164 Baseline 2007 a ajuga_genevensis 2.890729
#> 1.165 Baseline 2007 a ajuga_iva 3.114191
#> 1.166 Baseline 2007 a ajuga_laxmannii 2.919480
#> 1.167 Baseline 2007 a ajuga_orientalis 2.885406
#> 1.168 Baseline 2007 a ajuga_pyramidalis 3.193739
#> 1.169 Baseline 2007 a ajuga_reptans 3.203512
#> 1.170 Baseline 2007 a alcea_biennis 3.695590
#> 1.171 Baseline 2007 a alchemilla_acutiloba 2.965728
#> 1.172 Baseline 2007 a alchemilla_alpigena 3.122777
#> 1.173 Baseline 2007 a alchemilla_alpina 3.346503
#> 1.174 Baseline 2007 a alchemilla_anisiaca 3.621825
#> 1.175 Baseline 2007 a alchemilla_catalaunica 3.250545
#> 1.176 Baseline 2007 a alchemilla_caucasica 3.351831
#> 1.177 Baseline 2007 a alchemilla_colorata 3.183223
#> 1.178 Baseline 2007 a alchemilla_conjuncta 3.739237
#> 1.179 Baseline 2007 a alchemilla_conjuncta_aggr. 3.629804
#> 1.180 Baseline 2007 a alchemilla_coriacea 3.287342
#> 1.181 Baseline 2007 a alchemilla_coriacea_aggr. 3.451742
#> 1.182 Baseline 2007 a alchemilla_crinita 3.101606
#> 1.183 Baseline 2007 a alchemilla_filicaulis 3.077561
#> 1.184 Baseline 2007 a alchemilla_fissa 3.398253
#> 1.185 Baseline 2007 a alchemilla_flabellata 3.170051
#> 1.186 Baseline 2007 a alchemilla_glabra 3.114937
#> 1.187 Baseline 2007 a alchemilla_glabra_aggr. 3.511190
#> 1.188 Baseline 2007 a alchemilla_glaucescens 2.895560
#> 1.189 Baseline 2007 a alchemilla_hoppeana 3.364724
#> 1.190 Baseline 2007 a alchemilla_hybrida 3.126706
#> 1.191 Baseline 2007 a alchemilla_hybrida_aggr. 3.412525
#> 1.192 Baseline 2007 a alchemilla_micans 2.966234
#> 1.193 Baseline 2007 a alchemilla_monticola 2.971383
#> 1.194 Baseline 2007 a alchemilla_pentaphyllea 3.579574
#> 1.195 Baseline 2007 a alchemilla_plicatula_var._plicatula 3.366188
#> 1.196 Baseline 2007 a alchemilla_saxatilis 3.119380
#> 1.197 Baseline 2007 a alchemilla_subcrenata 2.999995
#> 1.198 Baseline 2007 a alchemilla_vulgaris 3.050119
#> 1.199 Baseline 2007 a alchemilla_vulgaris_aggr. 3.031662
#> 1.200 Baseline 2007 a alchemilla_xanthochlora 3.029799
#> [ reached 'max' / getOption("max.print") -- omitted 172206 rows ]