Produce a data.frame containing the structure and associated attributes
Source: R/graphdf.R
graphdf.RdProduce a data.frame containing the node (vertex) and link (edge)
structure as well as the associated attributes for these.
This provides an easy way to create data tables describing graphs, particularly
helpful for users unfamiliar with the structure of igraph objects.
Usage
graphdf(x, ...)
# S4 method for list
graphdf(x, ...)
# S4 method for goc
graphdf(x, ...)
# S4 method for grain
graphdf(x, ...)
# S4 method for mpg
graphdf(x, ...)
# S4 method for igraph
graphdf(x, ...)Value
A list object containing:
vnode (vertex) names and associated attributes;
elink (edge) lists and associated attributes.
Please see MPG() and GOC() for details about the attributes.
For GOC() objects which typically contain multiple thresholds,
an enumerated list of the same length as the number of thresholds is returned
each containing v and e elements.
Examples
## Load raster landscape
tiny <- raster::raster(system.file("extdata/tiny.asc", package = "grainscape"))
## Create a resistance surface from a raster using an is-becomes reclassification
tinyCost <- raster::reclassify(tiny, rcl = cbind(c(1, 2, 3, 4), c(1, 5, 10, 12)))
## Produce a patch-based MPG where patches are resistance features=1
tinyPatchMPG <- MPG(cost = tinyCost, patch = tinyCost == 1)
## Extract a representative subset of 5 grains of connectivity
tinyPatchGOC <- GOC(tinyPatchMPG, nThresh = 5)
## Create a data.frame with the structure and attributes of a MPG object
tinyPatchMPG_df <- graphdf(tinyPatchMPG) # nolint
## Create a data.frame with the structure and attributes of a GOC object
tinyPatchGOC_df <- graphdf(tinyPatchGOC) # nolint
## Create a data.frame with the structure and attributes of any igraph object
graphdf(tinyPatchGOC@th[[1]]$goc)
#> [[1]]
#> [[1]]$v
#> name polygonId centroidX centroidY polygonArea totalPatchArea
#> 1 25 25 21.164804 45.946927 179 14
#> 2 11 11 35.528302 76.175472 530 100
#> 3 2 2 24.097561 94.603659 164 30
#> 4 1 1 7.790323 93.129032 186 38
#> 5 33 33 76.029644 30.851779 253 21
#> 6 29 29 97.166667 41.371795 39 1
#> 7 10 10 96.060000 88.340000 25 2
#> 8 7 7 96.933333 94.683333 60 9
#> 9 27 27 39.861345 38.697479 476 76
#> 10 16 16 14.952381 70.563492 252 72
#> 11 15 15 22.877358 79.537736 53 7
#> 12 14 14 12.304688 81.367188 128 11
#> 13 3 3 42.166667 94.927083 192 46
#> 14 4 4 64.107143 90.910714 336 61
#> 15 5 5 72.312500 98.250000 16 1
#> 16 18 18 26.395522 57.385572 201 32
#> 17 38 38 56.521176 13.867059 425 31
#> 18 13 13 3.009804 80.705882 102 4
#> 19 30 30 18.108000 33.252000 250 32
#> 20 21 21 47.242424 58.886364 132 4
#> 21 28 28 83.831361 48.272189 338 4
#> 22 6 6 82.088123 85.595785 522 65
#> 23 20 20 37.360656 54.877049 122 5
#> 24 26 26 6.444134 43.768156 179 4
#> 25 36 36 85.342205 19.600760 526 55
#> 26 39 39 91.982587 6.067164 201 26
#> 27 22 22 60.739336 53.007109 422 39
#> 28 40 40 51.824675 3.058442 77 1
#> 29 9 9 52.510638 84.574468 188 14
#> 30 37 37 22.657810 12.435588 621 42
#> 31 34 34 5.820000 19.433333 375 18
#> 32 35 35 42.981481 23.084362 243 12
#> 33 8 8 19.357143 91.325397 63 7
#> 34 23 23 92.944795 58.755521 317 6
#> 35 31 31 60.324561 33.085965 285 15
#> 36 19 19 8.658451 58.595070 284 9
#> 37 41 41 64.756757 3.216216 74 2
#> 38 24 24 73.349741 51.795337 193 4
#> 39 17 17 60.669856 71.672249 418 2
#> 40 12 12 93.478070 77.478070 228 4
#> 41 32 32 96.159091 33.090909 88 2
#> 42 43 43 76.169643 4.223214 112 2
#> 43 42 42 36.820000 3.692000 125 2
#> totalPatchEdgeArea totalCoreArea patchId
#> 1 14 0 62
#> 2 95 5 30
#> 3 28 2 7
#> 4 37 1 5
#> 5 21 0 80
#> 6 1 0 73
#> 7 2 0 29
#> 8 9 0 19
#> 9 72 4 67
#> 10 67 5 41
#> 11 7 0 40
#> 12 11 0 37
#> 13 45 1 8
#> 14 58 3 9
#> 15 1 0 12
#> 16 32 0 48
#> 17 31 0 95
#> 18 4 0 32
#> 19 32 0 74
#> 20 4 0 55
#> 21 4 0 68
#> 22 64 1 14
#> 23 5 0 54
#> 24 4 0 64
#> 25 55 0 86
#> 26 26 0 100
#> 27 39 0 56
#> 28 1 0 103
#> 29 14 0 28
#> 30 39 3 93
#> 31 18 0 84
#> 32 12 0 85
#> 33 7 0 22
#> 34 6 0 60
#> 35 15 0 76
#> 36 9 0 50
#> 37 2 0 105
#> 38 4 0 61
#> 39 2 0 46
#> 40 4 0 31
#> 41 2 0 78
#> 42 2 0 107
#> 43 2 0 106
#>
#> [[1]]$e
#> e1 e2 maxWeight linkIdMaxWeight minWeight linkIdMinWeight medianWeight
#> 1 25 30 12 1 12 1 12
#> 2 11 16 12 2 12 2 12
#> 3 11 15 10 3 10 3 10
#> 4 2 8 10 4 10 4 10
#> 5 2 1 5 5 5 5 5
#> 6 33 36 10 6 10 6 10
#> 7 29 32 15 7 15 7 15
#> 8 10 12 10 8 10 8 10
#> 9 10 7 10 9 10 9 10
#> 10 27 35 20 10 20 10 20
#> 11 16 18 20 11 20 11 20
#> 12 16 15 20 12 20 12 20
#> 13 16 14 20 13 20 13 20
#> 14 3 9 25 14 25 14 25
#> 15 4 5 20 15 20 15 20
#> 16 5 6 30 16 30 16 30
#> 17 11 18 40 17 40 17 40
#> 18 3 4 32 18 32 18 32
#> 19 18 20 35 19 35 19 35
#> 20 38 40 40 20 40 20 40
#> 21 25 26 44 21 44 21 44
#> 22 1 8 40 22 40 22 40
#> 23 14 13 50 23 50 23 50
#> 24 30 34 40 24 40 24 40
#> 25 21 22 45 25 45 25 45
#> 26 1 13 45 26 45 26 45
#> 27 4 9 40 27 40 27 40
#> 28 33 28 45 28 45 28 45
#> 29 7 6 45 29 45 29 45
#> 30 11 20 50 30 50 30 50
#> 31 1 14 45 31 45 31 45
#> 32 21 20 50 32 50 32 50
#> 33 30 26 52 33 52 33 52
#> 34 36 39 55 34 55 34 55
#> 35 39 43 54 35 54 35 54
#> 36 16 19 55 36 55 36 55
#> 37 22 31 64 37 64 37 64
#> 38 22 24 59 38 59 38 59
#> 39 40 41 65 39 65 39 65
#> 40 4 6 60 40 60 40 60
#> 41 38 41 75 41 75 41 75
#> 42 27 31 75 42 75 42 75
#> 43 27 21 75 43 75 43 75
#> 44 27 22 75 44 75 44 75
#> 45 11 3 76 45 76 45 76
#> 46 10 6 75 46 75 46 75
#> 47 30 37 80 47 80 47 80
#> 48 2 3 70 48 70 48 70
#> 49 9 17 81 49 81 49 81
#> 50 15 14 80 50 80 50 80
#> 51 36 43 85 51 85 51 85
#> 52 37 42 85 52 85 52 85
#> 53 37 34 80 53 80 53 80
#> 54 11 21 85 54 85 54 85
#> 55 38 35 85 55 85 55 85
#> 56 6 12 85 56 85 56 85
#> 57 14 8 85 57 85 57 85
#> 58 29 23 88 58 88 58 88
#> 59 27 20 95 59 95 59 95
#> 60 35 31 95 60 95 60 95
#> 61 26 19 105 61 105 61 105
#> 62 11 9 107 62 107 62 107
#> 63 41 43 105 63 105 63 105
#> 64 16 13 100 64 100 64 100
#> 65 37 35 105 65 105 65 105
#> 66 11 17 100 66 100 66 100
#> 67 28 32 114 67 114 67 114
#> 68 40 42 115 68 115 68 115
#> 69 38 37 115 69 115 69 115
#> 70 28 23 130 70 130 70 130
#> 71 38 31 123 71 123 71 123
#> 72 29 28 129 72 129 72 129
#> 73 28 24 123 73 123 73 123
#> 74 18 19 135 74 135 74 135
#> 75 26 34 125 75 125 75 125
#> 76 38 42 125 76 125 76 125
#> 77 21 17 127 77 127 77 127
#> 78 22 17 132 78 132 78 132
#> 79 25 19 133 79 133 79 133
#> 80 33 31 144 80 144 80 144
#> 81 27 37 146 81 146 81 146
#> 82 4 17 140 82 140 82 140
#> 83 23 12 162 83 162 83 162
#> 84 31 24 200 84 200 84 200
#> 85 38 43 195 85 195 85 195
#> 86 33 38 208 86 208 86 208
#> 87 38 36 208 87 208 87 208
#> 88 33 24 210 88 210 88 210
#> 89 6 17 220 89 220 89 220
#> 90 6 23 290 90 290 90 290
#> 91 24 17 365 91 365 91 365
#> 92 28 6 358 92 358 92 358
#> 93 6 24 432 93 432 93 432
#> meanWeight numEdgesWeight linkIdAll eucCentroidWeight
#> 1 12 1 1 13.057765
#> 2 12 1 2 21.327514
#> 3 10 1 3 13.090118
#> 4 10 1 4 5.763555
#> 5 5 1 5 16.373776
#> 6 10 1 6 14.605109
#> 7 15 1 7 8.341959
#> 8 10 1 8 11.164582
#> 9 10 1 9 6.403170
#> 10 20 1 10 15.921830
#> 11 20 1 11 17.452881
#> 12 20 1 12 11.972565
#> 13 20 1 13 11.123404
#> 14 25 1 14 14.634698
#> 15 20 1 15 11.008769
#> 16 30 1 16 15.990370
#> 17 40 1 17 20.891816
#> 18 32 1 18 22.305060
#> 19 35 1 19 11.248415
#> 20 40 1 20 11.784877
#> 21 44 1 21 14.881034
#> 22 40 1 22 11.706598
#> 23 50 1 23 9.318379
#> 24 40 1 24 18.491903
#> 25 45 1 25 14.721830
#> 26 45 1 26 13.311199
#> 27 40 1 27 13.214648
#> 28 45 1 28 19.087627
#> 29 45 1 29 17.405856
#> 30 50 1 30 21.377098
#> 31 45 1 31 12.598432
#> 32 50 1 32 10.664143
#> 33 52 1 33 15.704627
#> 34 55 1 34 15.074910
#> 35 54 1 35 15.920093
#> 36 55 1 36 13.522451
#> 37 64 1 37 19.925462
#> 38 59 1 38 12.668492
#> 39 65 1 39 12.933044
#> 40 60 1 40 18.750043
#> 41 75 1 41 13.463478
#> 42 75 1 42 21.218679
#> 43 75 1 43 21.495846
#> 44 75 1 44 25.311184
#> 45 76 1 45 19.891979
#> 46 75 1 46 14.238823
#> 47 80 1 47 21.307834
#> 48 70 1 48 18.072000
#> 49 81 1 49 15.265651
#> 50 80 1 50 10.729784
#> 51 85 1 51 17.905441
#> 52 85 1 52 16.643856
#> 53 80 1 53 18.234042
#> 54 85 1 54 20.883820
#> 55 85 1 55 16.379317
#> 56 85 1 56 13.986715
#> 57 85 1 57 12.202584
#> 58 88 1 58 17.889050
#> 59 95 1 59 16.371681
#> 60 95 1 60 20.020352
#> 61 105 1 61 14.991350
#> 62 107 1 62 18.945788
#> 63 105 1 63 11.457225
#> 64 100 1 64 15.668223
#> 65 105 1 65 22.944455
#> 66 100 1 66 25.541668
#> 67 114 1 67 19.556181
#> 68 115 1 68 15.018045
#> 69 115 1 69 33.893609
#> 70 130 1 70 13.890821
#> 71 123 1 71 19.591633
#> 72 129 1 72 15.014853
#> 73 123 1 73 11.057890
#> 74 135 1 74 17.778262
#> 75 125 1 75 24.342826
#> 76 125 1 76 22.173592
#> 77 127 1 77 18.541165
#> 78 132 1 78 18.665269
#> 79 133 1 79 17.787198
#> 80 144 1 80 15.863203
#> 81 146 1 81 31.395040
#> 82 140 1 82 19.543119
#> 83 162 1 83 18.730143
#> 84 200 1 84 22.796840
#> 85 195 1 85 21.887576
#> 86 208 1 86 25.866214
#> 87 208 1 87 29.385831
#> 88 210 1 88 21.114320
#> 89 220 1 89 25.546174
#> 90 290 1 90 28.952844
#> 91 365 1 91 23.576919
#> 92 358 1 92 37.364284
#> 93 432 1 93 34.911741
#>
#>