A fct that return blocks attribution or probabilities for each nodes in a Sbm fit from the sbm package.
Arguments
- x
Sbm model of class `BipartiteSBM_fit`, `SimpleSBM_fit`.
- labels
labels for nodes. If it's simple sbm it should be a single character ("default" -> c("nodes")). If sbm is bipartite a named character (names are row and col) ("default" -> c(row = 'row', col = 'col')).
- node_names
"bipartite case": named list ("row","col"), row is a character vector containing names of nodes in rows, and respectively for columns
"unipartite case": character: node names
- attribution
Boolean indicating whether or not the produced tables should contain a block attribution column. This column shows the block in which each nodes is the most likely to be.
- proportion
Boolean indicating whether or not the produced tables should contain the probabilities to belong in each blocks. These columns shows for every nodes and every blocks the probabilities that the node belong to the block.
Value
"bipartite case": A list containing two data.frames with block attributions and/or proportions one for the row blocks and one for the column blocks
"unipartite case": A data.frame with block attributions and/or proportions
Examples
# my_sbm_bi <- sbm::estimateBipartiteSBM(sbm::fungusTreeNetwork$fungus_tree,
# model = 'bernoulli')
my_sbm_bi <- FungusTreeNetwork$sbmResults$fungus_tree
node_names_bi <- list(
row = FungusTreeNetwork$networks$fungus_names,
col = FungusTreeNetwork$networks$tree_names
)
my_blocks_bi <- get_block(my_sbm_bi,
labels = c(row = "Fungus", col = "Tree"),
node_names = node_names_bi
)
my_blocks_bi$row
#> Nodes_names
#> 1 Amphiporthe leiphaemia
#> 2 Apiognomonia errabunda
#> 3 Apiognomonia veneta
#> 4 Armillaria cepistipes
#> 5 Armillaria gallica
#> 6 Armillaria mellea
#> 7 Armillaria ostoyae
#> 8 Asteroma tiliae
#> 9 Biscogniauxia mediterranea var. mediterranea
#> 10 Bjerkandera adusta
#> 11 Blumeriella jaapii
#> 12 Botrytis cinerea (grouped with Botryotinia fuckeliana (anamorphic type))
#> 13 Botryosphaeria dothidea
#> 14 Botryosphaeria stevensii
#> 15 Caliciopsis pinea
#> 16 Cenangium ferruginosum
#> 17 Ceratocystis ips
#> 18 Ceratocystis minor
#> 19 Ceratocystis platani
#> 20 Chondrostereum purpureum
#> 21 Chrysomyxa abietis
#> 22 Chrysomyxa ledi var. rhododendri
#> 23 Coleosporium tussilaginis f.sp. senecionis-silvatici
#> 24 Colpoma quercinum
#> 25 Cristulariella depraedans
#> 26 Cronartium flaccidum
#> 27 Cronartium quercuum
#> 28 Cronartium ribicola
#> 29 Crumenulopsis sororia
#> 30 Cryptodiaporthe castanea
#> 31 Cryptostroma corticale
#> 32 Cryptodiaporthe hystrix
#> 33 Cryphonectria parasitica
#> 34 Cryptodiaporthe populea
#> 35 Cyclaneusma minus
#> 36 Cyclaneusma niveum
#> 37 Cylindrocarpon didymum
#> 38 Daedaleopsis confragosa
#> 39 Delphinella abietis
#> 40 Dicarpella dryina
#> 41 Discella castanea
#> 42 Drepanopeziza punctiformis
#> 43 Entoleuca mammata
#> 44 Eutypa lata
#> 45 Fistulina hepatica
#> 46 Fomes fomentarius
#> 47 Fomitopsis cytisina
#> 48 Fomitopsis pinicola
#> 49 Fusarium oxysporum
#> 50 Fusicoccum quercus
#> 51 Ganoderma adspersum
#> 52 Ganoderma applanatum
#> 53 Ganoderma resinaceum
#> 54 Gnomonia leptostyla
#> 55 Gremmeniella abietina
#> 56 Gymnopus fusipes
#> 57 Haematonectria haematococca
#> 58 Herpotrichia juniperi
#> 59 Heterobasidion annosum
#> 60 Hypoxylon fragiforme
#> 61 Lachnellula willkommii
#> 62 Laetiporus sulphureus
#> 63 Leptographium lundbergii
#> 64 Leptographium procerum
#> 65 Leucostoma persoonii
#> 66 Lirula macrospora
#> 67 Lirula nervisequia var. nervisequia
#> 68 Lophodermium conigenum
#> 69 Lophodermium piceae
#> 70 Lophodermium pinastri
#> 71 Lophodermium seditiosum
#> 72 Melampsora allii-populina
#> 73 Melampsorella caryophyllacearum
#> 74 Melampsora laricis-populina
#> 75 Melanconis modonia
#> 76 Melampsora populnea
#> 77 Meripilus giganteus
#> 78 Microsphaera alphitoides
#> 79 Microstroma juglandis
#> 80 Monochaetia monochaeta
#> 81 Mycosphaerella castaneicola
#> 82 Mycosphaerella dearnessii
#> 83 Mycosphaerella microsora
#> 84 Mycosphaerella pini
#> 85 Nectria cinnabarina
#> 86 Nectria coccinea (grouped with Cylindocarpon candidum (teleomorphic type))
#> 87 Nectria ditissima
#> 88 Nectria fuckeliana
#> 89 Nectria veuillotiana
#> 90 Neonectria galligena
#> 91 Ophiostoma piceae
#> 92 Ophiostoma serpens
#> 93 Ophiostoma ulmi (grouped with Ophiostoma novo-ulmi)
#> 94 Oudemansiella mucida
#> 95 Oxyporus populinus
#> 96 Pestalotiopsis funerea
#> 97 Pezicula cinnamomea
#> 98 Phacidium coniferarum
#> 99 Phaeocryptopus gaeumannii
#> 100 Phaeolus schweinitzii
#> 101 Phellinus chrysoloma
#> 102 Phellinus hartigii
#> 103 Phellinus igniarius
#> 104 Phellinus pini
#> 105 Phellinus robustus
#> 106 Phloeospora aceris
#> 107 Phomopsis juniperivora
#> 108 Phomopsis quercella
#> 109 Phyllosticta aceris
#> 110 Phyllactinia guttata
#> 111 Pleurotus ostreatus
#> 112 Pleuroceras pseudoplatani
#> 113 Podosphaera clandestina var. aucupariae
#> 114 Pollaccia radiosa
#> 115 Polyporus squamosus
#> 116 Pseudoinonotus dryadeus
#> 117 Pucciniastrum epilobii
#> 118 Rhabdocline pseudotsugae
#> 119 Rhizosphaera kalkhoffii
#> 120 Rhizosphaera macrospora
#> 121 Rhizosphaera oudemansii
#> 122 Rhizina undulata
#> 123 Rhytisma acerinum
#> 124 Rosellinia necatrix
#> 125 Sarea resinae
#> 126 Sawadaea tulasnei
#> 127 Schizophyllum commune
#> 128 Seiridium cardinale
#> 129 Septotis podophyllina
#> 130 Septoria quercicola
#> 131 Sirococcus strobilinus
#> 132 Sparassis crispa
#> 133 Sphaeropsis sapinea
#> 134 Stegonsporium pyriforme
#> 135 Stereum hirsutum
#> 136 Stereum sanguinolentum
#> 137 Stigmina carpophila
#> 138 Sydowia polyspora
#> 139 Taphrina betulina
#> 140 Taphrina caerulescens
#> 141 Taphrina cerasi
#> 142 Taphrina populina
#> 143 Titaeosporina tremulae
#> 144 Trametes gibbosa
#> 145 Trametes versicolor
#> 146 Truncatella hartigii
#> 147 Valsa ambiens
#> 148 Valsa kunzei
#> 149 Valsa nivea
#> 150 Valsa sordida
#> 151 Venturia fraxini
#> 152 Venturia inaequalis
#> 153 Verticillium dahliae
#> 154 Zythiostroma pinastri
#> Blocks
#> 1 Fungus_B
#> 2 Fungus_B
#> 3 Fungus_B
#> 4 Fungus_B
#> 5 Fungus_B
#> 6 Fungus_B
#> 7 Fungus_B
#> 8 Fungus_B
#> 9 Fungus_B
#> 10 Fungus_B
#> 11 Fungus_B
#> 12 Fungus_B
#> 13 Fungus_B
#> 14 Fungus_B
#> 15 Fungus_B
#> 16 Fungus_B
#> 17 Fungus_B
#> 18 Fungus_B
#> 19 Fungus_B
#> 20 Fungus_B
#> 21 Fungus_B
#> 22 Fungus_B
#> 23 Fungus_B
#> 24 Fungus_B
#> 25 Fungus_B
#> 26 Fungus_B
#> 27 Fungus_B
#> 28 Fungus_B
#> 29 Fungus_B
#> 30 Fungus_B
#> 31 Fungus_B
#> 32 Fungus_B
#> 33 Fungus_B
#> 34 Fungus_B
#> 35 Fungus_B
#> 36 Fungus_B
#> 37 Fungus_B
#> 38 Fungus_B
#> 39 Fungus_B
#> 40 Fungus_B
#> 41 Fungus_B
#> 42 Fungus_B
#> 43 Fungus_B
#> 44 Fungus_B
#> 45 Fungus_B
#> 46 Fungus_B
#> 47 Fungus_B
#> 48 Fungus_B
#> 49 Fungus_B
#> 50 Fungus_B
#> 51 Fungus_B
#> 52 Fungus_B
#> 53 Fungus_B
#> 54 Fungus_B
#> 55 Fungus_B
#> 56 Fungus_B
#> 57 Fungus_B
#> 58 Fungus_B
#> 59 Fungus_B
#> 60 Fungus_B
#> 61 Fungus_B
#> 62 Fungus_B
#> 63 Fungus_B
#> 64 Fungus_B
#> 65 Fungus_B
#> 66 Fungus_B
#> 67 Fungus_B
#> 68 Fungus_B
#> 69 Fungus_B
#> 70 Fungus_B
#> 71 Fungus_B
#> 72 Fungus_B
#> 73 Fungus_B
#> 74 Fungus_B
#> 75 Fungus_B
#> 76 Fungus_B
#> 77 Fungus_B
#> 78 Fungus_B
#> 79 Fungus_B
#> 80 Fungus_B
#> 81 Fungus_B
#> 82 Fungus_B
#> 83 Fungus_B
#> 84 Fungus_B
#> 85 Fungus_B
#> 86 Fungus_B
#> 87 Fungus_B
#> 88 Fungus_B
#> 89 Fungus_B
#> 90 Fungus_B
#> 91 Fungus_B
#> 92 Fungus_B
#> 93 Fungus_B
#> 94 Fungus_B
#> 95 Fungus_B
#> 96 Fungus_B
#> 97 Fungus_B
#> 98 Fungus_B
#> 99 Fungus_B
#> 100 Fungus_B
#> 101 Fungus_B
#> 102 Fungus_B
#> 103 Fungus_B
#> 104 Fungus_B
#> 105 Fungus_B
#> 106 Fungus_B
#> 107 Fungus_B
#> 108 Fungus_B
#> 109 Fungus_B
#> 110 Fungus_B
#> 111 Fungus_B
#> 112 Fungus_B
#> 113 Fungus_B
#> 114 Fungus_B
#> 115 Fungus_B
#> 116 Fungus_B
#> 117 Fungus_B
#> 118 Fungus_B
#> 119 Fungus_B
#> 120 Fungus_B
#> 121 Fungus_B
#> 122 Fungus_B
#> 123 Fungus_B
#> 124 Fungus_B
#> 125 Fungus_B
#> 126 Fungus_B
#> 127 Fungus_B
#> 128 Fungus_B
#> 129 Fungus_B
#> 130 Fungus_B
#> 131 Fungus_B
#> 132 Fungus_B
#> 133 Fungus_B
#> 134 Fungus_B
#> 135 Fungus_B
#> 136 Fungus_B
#> 137 Fungus_B
#> 138 Fungus_B
#> 139 Fungus_B
#> 140 Fungus_B
#> 141 Fungus_B
#> 142 Fungus_B
#> 143 Fungus_B
#> 144 Fungus_B
#> 145 Fungus_B
#> 146 Fungus_B
#> 147 Fungus_B
#> 148 Fungus_B
#> 149 Fungus_B
#> 150 Fungus_B
#> 151 Fungus_B
#> 152 Fungus_B
#> 153 Fungus_B
#> 154 Fungus_B
my_blocks_bi$col
#> Nodes_names
#> 1 Abies alba
#> 2 Abies grandis
#> 3 Abies nordmanniana
#> 4 Large Maples (Acer platanoides, Acer pseudoplatanus)
#> 5 Small Maples (Acer campestre, Acer monspessulanum, Acer negundo, Acer opalus)
#> 6 Alnus glutinosa
#> 7 Betulus spp (Betula pendula, Betula pubescens)
#> 8 Carpinus betulus
#> 9 Castanea sativa
#> 10 Cedrus spp (Cedrus atlantica, Cedrus libani)
#> 11 Cupressus sempervirens
#> 12 Fagus silvatica
#> 13 Fraxinus spp (Fraxinus angustifolia, Fraxinus excelsior)
#> 14 Juglans spp (Juglans nigra, Juglans regia)
#> 15 Larix decidua
#> 16 Larix kaempferi
#> 17 Picea excelsa
#> 18 Picea sitchensis
#> 19 Pinus brutia (Pinus brutia, Pinus brutia eldarica)
#> 20 Pinus cembra
#> 21 Pinus halepensis
#> 22 Pinus nigra laricio
#> 23 Pinus nigra nigra
#> 24 Pinus pinaster
#> 25 Pinus pinea
#> 26 Pinus radiata
#> 27 Pinus strobus
#> 28 Pinus sylvestris
#> 29 Pinus taeda
#> 30 Pinus uncinata
#> 31 Platanus hybrida
#> 32 Cultivated Poplars (Populus trichocarpa, P. canescens, P.alba, P.nigra and their cultivated hybrids)
#> 33 Populus tremula
#> 34 Prunus avium
#> 35 Pseudotsuga menziesii
#> 36 Quercus ilex
#> 37 Quercus petraea
#> 38 Quercus pubescens
#> 39 Quercus pyrenaica
#> 40 Quercus robur
#> 41 Quercus rubra
#> 42 Quercus suber
#> 43 Sorbus aria
#> 44 Sorbus aucuparia
#> 45 Sorbus domestica
#> 46 Sorbus torminalis
#> 47 Taxus baccata
#> 48 Thuja plicata
#> 49 Tilia spp (Tilia platiphyllos, Tilia cordata)
#> 50 Tsuga heterophylla
#> 51 Ulmus spp (Ulmus minor, Ulmus laevis, Ulmus glabra)
#> Blocks
#> 1 Tree_B
#> 2 Tree_B
#> 3 Tree_B
#> 4 Tree_B
#> 5 Tree_B
#> 6 Tree_B
#> 7 Tree_B
#> 8 Tree_B
#> 9 Tree_B
#> 10 Tree_B
#> 11 Tree_B
#> 12 Tree_B
#> 13 Tree_B
#> 14 Tree_B
#> 15 Tree_B
#> 16 Tree_B
#> 17 Tree_B
#> 18 Tree_B
#> 19 Tree_B
#> 20 Tree_B
#> 21 Tree_B
#> 22 Tree_B
#> 23 Tree_B
#> 24 Tree_B
#> 25 Tree_B
#> 26 Tree_B
#> 27 Tree_B
#> 28 Tree_B
#> 29 Tree_B
#> 30 Tree_B
#> 31 Tree_B
#> 32 Tree_B
#> 33 Tree_B
#> 34 Tree_B
#> 35 Tree_B
#> 36 Tree_B
#> 37 Tree_B
#> 38 Tree_B
#> 39 Tree_B
#> 40 Tree_B
#> 41 Tree_B
#> 42 Tree_B
#> 43 Tree_B
#> 44 Tree_B
#> 45 Tree_B
#> 46 Tree_B
#> 47 Tree_B
#> 48 Tree_B
#> 49 Tree_B
#> 50 Tree_B
#> 51 Tree_B
# my_sbm_uni <- sbm::estimateSimpleSBM(sbm::fungusTreeNetwork$tree_tree,
# model = "poisson")
my_sbm_uni <- FungusTreeNetwork$sbmResults$tree_tree
node_names_uni <- list(FungusTreeNetwork$networks$tree_names)
my_blocks_uni <- get_block(my_sbm_uni,
labels = c("Tree"),
node_names = node_names_uni
)
my_blocks_uni
#> Nodes_names
#> 1 Abies alba
#> 2 Abies grandis
#> 3 Abies nordmanniana
#> 4 Large Maples (Acer platanoides, Acer pseudoplatanus)
#> 5 Small Maples (Acer campestre, Acer monspessulanum, Acer negundo, Acer opalus)
#> 6 Alnus glutinosa
#> 7 Betulus spp (Betula pendula, Betula pubescens)
#> 8 Carpinus betulus
#> 9 Castanea sativa
#> 10 Cedrus spp (Cedrus atlantica, Cedrus libani)
#> 11 Cupressus sempervirens
#> 12 Fagus silvatica
#> 13 Fraxinus spp (Fraxinus angustifolia, Fraxinus excelsior)
#> 14 Juglans spp (Juglans nigra, Juglans regia)
#> 15 Larix decidua
#> 16 Larix kaempferi
#> 17 Picea excelsa
#> 18 Picea sitchensis
#> 19 Pinus brutia (Pinus brutia, Pinus brutia eldarica)
#> 20 Pinus cembra
#> 21 Pinus halepensis
#> 22 Pinus nigra laricio
#> 23 Pinus nigra nigra
#> 24 Pinus pinaster
#> 25 Pinus pinea
#> 26 Pinus radiata
#> 27 Pinus strobus
#> 28 Pinus sylvestris
#> 29 Pinus taeda
#> 30 Pinus uncinata
#> 31 Platanus hybrida
#> 32 Cultivated Poplars (Populus trichocarpa, P. canescens, P.alba, P.nigra and their cultivated hybrids)
#> 33 Populus tremula
#> 34 Prunus avium
#> 35 Pseudotsuga menziesii
#> 36 Quercus ilex
#> 37 Quercus petraea
#> 38 Quercus pubescens
#> 39 Quercus pyrenaica
#> 40 Quercus robur
#> 41 Quercus rubra
#> 42 Quercus suber
#> 43 Sorbus aria
#> 44 Sorbus aucuparia
#> 45 Sorbus domestica
#> 46 Sorbus torminalis
#> 47 Taxus baccata
#> 48 Thuja plicata
#> 49 Tilia spp (Tilia platiphyllos, Tilia cordata)
#> 50 Tsuga heterophylla
#> 51 Ulmus spp (Ulmus minor, Ulmus laevis, Ulmus glabra)
#> Blocks
#> 1 Tree_B1
#> 2 Tree_B1
#> 3 Tree_B3
#> 4 Tree_B2
#> 5 Tree_B4
#> 6 Tree_B4
#> 7 Tree_B6
#> 8 Tree_B6
#> 9 Tree_B4
#> 10 Tree_B1
#> 11 Tree_B5
#> 12 Tree_B2
#> 13 Tree_B2
#> 14 Tree_B2
#> 15 Tree_B1
#> 16 Tree_B3
#> 17 Tree_B1
#> 18 Tree_B3
#> 19 Tree_B5
#> 20 Tree_B5
#> 21 Tree_B3
#> 22 Tree_B1
#> 23 Tree_B3
#> 24 Tree_B1
#> 25 Tree_B5
#> 26 Tree_B5
#> 27 Tree_B3
#> 28 Tree_B1
#> 29 Tree_B5
#> 30 Tree_B3
#> 31 Tree_B5
#> 32 Tree_B2
#> 33 Tree_B6
#> 34 Tree_B2
#> 35 Tree_B1
#> 36 Tree_B4
#> 37 Tree_B2
#> 38 Tree_B4
#> 39 Tree_B6
#> 40 Tree_B2
#> 41 Tree_B2
#> 42 Tree_B4
#> 43 Tree_B4
#> 44 Tree_B6
#> 45 Tree_B6
#> 46 Tree_B2
#> 47 Tree_B6
#> 48 Tree_B6
#> 49 Tree_B4
#> 50 Tree_B5
#> 51 Tree_B6