getTaxonInfo gets trait information for a taxon getTaxonomy gets taxonomic information for a taxon metadata gets the description of the content of a database.
utilities.RdgetTaxonInfo extracts trait information for a certain taxon from a trait database.
metadata returns a description of an object, i.e the meaning of the columns, units, etc...
Usage
getTaxonInfo(taxon, trait = Traits_nioz, taxonomy = Taxonomy)
getTaxonomy(taxon, taxonomy=Taxonomy)
metadata(object)Arguments
- taxon
name of the taxon (or vector with names) for which the traits need to be listed.
- trait
a trait database in wide format; it should have taxon as first column, and it should contain a description of the trait database in its attribute ("description"). See Traits_nioz for a suitable structure.
- taxonomy
taxonomic information; first column will be matched with
taxonfrom the trait database, regardless of its name.- object
any object that has a data.frame
descriptionin itsattributes.
Value
getTaxonInfo returns a data.frame with the traits of the species whose modalities are not Null, NULL or None.
getTaxonomy returns the occurrences of taxon within taxonomy.
metadata returns a data.frame with a description of the contents of the database.
See also
. MWTL for the data sets
mapBtrait for simple plotting functions.
getDensity for functions working with density data.
getTraitDensity for functions combining density and traits.
getDbIndex for extracting bioturbation and bioirrigation indices.
extendTrait for functions working with traits.
Examples
## ====================================================
## Description of the Traits_nioz database
## ====================================================
metadata(Traits_nioz)
#> colname trait modality indic
#> 1 ET1.M1 Substratum depth distribution 0 1
#> 2 ET1.M2 Substratum depth distribution 0-5 1
#> 3 ET1.M3 Substratum depth distribution 5-15 1
#> 4 ET1.M4 Substratum depth distribution 15-30 1
#> 5 ET1.M5 Substratum depth distribution >30 1
#> 6 ET2.M1 Biodiffusion Null 2
#> 7 ET2.M2 Biodiffusion Low 2
#> 8 ET2.M3 Biodiffusion High 2
#> 9 ET3.M1 Downward conveying Null 3
#> 10 ET3.M2 Downward conveying Low 3
#> 11 ET3.M3 Downward conveying High 3
#> 12 ET4.M1 Upward conveying Null 4
#> 13 ET4.M2 Upward conveying Low 4
#> 14 ET4.M3 Upward conveying High 4
#> 15 ET5.M1 Regeneration Null 5
#> 16 ET5.M2 Regeneration Low 5
#> 17 ET5.M3 Regeneration High 5
#> 18 ET6.M1 Biodeposition Null 6
#> 19 ET6.M2 Biodeposition Low 6
#> 20 ET6.M3 Biodeposition High 6
#> 21 ET7.M1 Bioerosion Null 7
#> 22 ET7.M2 Bioerosion Low 7
#> 23 ET7.M3 Bioerosion High 7
#> 24 ET8.M1 Biostabilisation Null 8
#> 25 ET8.M2 Biostabilisation Low 8
#> 26 ET8.M3 Biostabilisation High 8
#> 27 ET9.M1 Ventilation/Pumping Null 9
#> 28 ET9.M2 Ventilation/Pumping Low 9
#> 29 ET9.M3 Ventilation/Pumping High 9
#> 30 ET10.M1 Burrow width None 10
#> 31 ET10.M2 Burrow width Narrow 10
#> 32 ET10.M3 Burrow width Intermediate 10
#> 33 ET10.M4 Burrow width Wide 10
#> 34 ET11.M1 Endo-3D structure type None 11
#> 35 ET11.M2 Endo-3D structure type Chimney/Funnel 11
#> 36 ET11.M3 Endo-3D structure type Tube 11
#> 37 ET11.M4 Endo-3D structure type IJ-shaped burrow 11
#> 38 ET11.M5 Endo-3D structure type UY-shaped burrow 11
#> 39 ET11.M6 Endo-3D structure type Branched burrow 11
#> 40 ET11.M7 Endo-3D structure type Anastomosed burrow 11
#> 41 ET12.M1 Endo-3D structure depth None 12
#> 42 ET12.M2 Endo-3D structure depth 0-5 12
#> 43 ET12.M3 Endo-3D structure depth 5-15 12
#> 44 ET12.M4 Endo-3D structure depth 15-30 12
#> 45 ET12.M5 Endo-3D structure depth >30 12
#> 46 ET13.M1 Epi-3D structure type None 13
#> 47 ET13.M2 Epi-3D structure type Mat 13
#> 48 ET13.M3 Epi-3D structure type Mound 13
#> 49 ET13.M4 Epi-3D structure type Tube/Tubular protrusion 13
#> 50 ET13.M5 Epi-3D structure type Shell 13
#> 51 ET13.M6 Epi-3D structure type Stalk/Feather 13
#> 52 ET13.M7 Epi-3D structure type Protuberance 13
#> 53 ET14.M1 Epi-3D structure extension None 14
#> 54 ET14.M2 Epi-3D structure extension Isolated/Clumped 14
#> 55 ET14.M3 Epi-3D structure extension Mat/Lawn 14
#> 56 ET14.M4 Epi-3D structure extension Simple reef 14
#> 57 ET14.M5 Epi-3D structure extension Complex reef 14
#> 58 ET15.M1 Epi-3D structure size None 15
#> 59 ET15.M2 Epi-3D structure size <1 15
#> 60 ET15.M3 Epi-3D structure size 1-3 15
#> 61 ET15.M4 Epi-3D structure size 3-10 15
#> 62 ET15.M5 Epi-3D structure size 10-20 15
#> 63 ET15.M6 Epi-3D structure size 20-50 15
#> 64 ET15.M7 Epi-3D structure size >50 15
#> 65 RT1.M1 Body mass <0.001 1
#> 66 RT1.M2 Body mass 0.001-0.010 1
#> 67 RT1.M3 Body mass 0.010-0.100 1
#> 68 RT1.M4 Body mass 0.100-1.000 1
#> 69 RT1.M5 Body mass >1.000 1
#> 70 RT2.M1 Body length <1 2
#> 71 RT2.M2 Body length 1-3 2
#> 72 RT2.M3 Body length 3-10 2
#> 73 RT2.M4 Body length 10-20 2
#> 74 RT2.M5 Body length 20-50 2
#> 75 RT3.M1 Body resistance Very low 3
#> 76 RT3.M2 Body resistance Low 3
#> 77 RT3.M3 Body resistance Intermediate 3
#> 78 RT3.M4 Body resistance High 3
#> 79 RT3.M5 Body resistance Very high 3
#> 80 RT4.M1 Motility Sessile 4
#> 81 RT4.M2 Motility Tubicolous 4
#> 82 RT4.M3 Motility Crawler 4
#> 83 RT4.M4 Motility Swimmer 4
#> 84 RT5.M1 Burrowing/Sheltering depth 0 5
#> 85 RT5.M2 Burrowing/Sheltering depth 0-5 5
#> 86 RT5.M3 Burrowing/Sheltering depth 5-15 5
#> 87 RT5.M4 Burrowing/Sheltering depth >15 5
#> 88 RT6.M1 Feeding type Deposit feeder 6
#> 89 RT6.M2 Feeding type Suspension feeder 6
#> 90 RT6.M3 Feeding type Herbivore/Grazer 6
#> 91 RT6.M4 Feeding type Carnivore/Scavenger 6
#> 92 RT7.M1 Life span <1 7
#> 93 RT7.M2 Life span 1-3 7
#> 94 RT7.M3 Life span 3-10 7
#> 95 RT7.M4 Life span 10-20 7
#> 96 RT7.M5 Life span >20 7
#> 97 RT8.M1 Age at maturity <1 8
#> 98 RT8.M2 Age at maturity 1-3 8
#> 99 RT8.M3 Age at maturity 3-5 8
#> 100 RT9.M1 Reproductive frequency Sexual seasonal 9
#> 101 RT9.M2 Reproductive frequency Sexual continuous 9
#> 102 RT10.M1 Fertilisation Broadcasting 10
#> 103 RT10.M2 Fertilisation Spermcasting 10
#> 104 RT10.M3 Fertilisation Pairing 10
#> 105 RT11.M1 Annual fecundity <10e2 11
#> 106 RT11.M2 Annual fecundity 10e2-10e3 11
#> 107 RT11.M3 Annual fecundity 10e3-10e4 11
#> 108 RT11.M4 Annual fecundity 10e4-10e5 11
#> 109 RT11.M5 Annual fecundity 10e5-10e6 11
#> 110 RT11.M6 Annual fecundity >10e6 11
#> 111 RT12.M1 Offspring type Egg 12
#> 112 RT12.M2 Offspring type Larva 12
#> 113 RT12.M3 Offspring type Juvenile 12
#> 114 RT13.M1 Offspring size <0.1 13
#> 115 RT13.M2 Offspring size 0.1-0.5 13
#> 116 RT13.M3 Offspring size 0.5-1.5 13
#> 117 RT13.M4 Offspring size 1.5-5 13
#> 118 RT14.M1 Offspring protection None 14
#> 119 RT14.M2 Offspring protection Gel 14
#> 120 RT14.M3 Offspring protection Capsule 14
#> 121 RT14.M4 Offspring protection Burrying 14
#> 122 RT14.M5 Offspring protection Bearing/Brooding 14
#> 123 RT15.M1 Offspring development Planktotrophic 15
#> 124 RT15.M2 Offspring development Lecithotrophic 15
#> 125 RT15.M3 Offspring development Mixed planktotrophic 15
#> 126 RT15.M4 Offspring development Mixed lecithotrophic 15
#> 127 RT15.M5 Offspring development Internal 15
#> 128 RT16.M1 Offspring benthic stage duration Null 16
#> 129 RT16.M2 Offspring benthic stage duration <15 16
#> 130 RT16.M3 Offspring benthic stage duration 15-30 16
#> 131 RT16.M4 Offspring benthic stage duration 30-60 16
#> 132 RT16.M5 Offspring benthic stage duration >60 16
#> 133 RT17.M1 Offspring pelagic stage duration Null 17
#> 134 RT17.M2 Offspring pelagic stage duration <15 17
#> 135 RT17.M3 Offspring pelagic stage duration 15-30 17
#> 136 RT17.M4 Offspring pelagic stage duration 30-60 17
#> 137 RT17.M5 Offspring pelagic stage duration >60 17
#> value score units
#> 1 0.000000e+00 1.0000000 cm
#> 2 2.500000e+00 0.7500000 cm
#> 3 1.000000e+01 0.5000000 cm
#> 4 2.250000e+01 0.2500000 cm
#> 5 3.000000e+01 0.0000000 cm
#> 6 0.000000e+00 0.0000000 -
#> 7 5.000000e-01 0.5000000 -
#> 8 1.000000e+00 1.0000000 -
#> 9 0.000000e+00 0.0000000 -
#> 10 5.000000e-01 0.5000000 -
#> 11 1.000000e+00 1.0000000 -
#> 12 0.000000e+00 0.0000000 -
#> 13 5.000000e-01 0.5000000 -
#> 14 1.000000e+00 1.0000000 -
#> 15 0.000000e+00 0.0000000 -
#> 16 5.000000e-01 0.5000000 -
#> 17 1.000000e+00 1.0000000 -
#> 18 0.000000e+00 0.0000000 -
#> 19 5.000000e-01 0.5000000 -
#> 20 1.000000e+00 1.0000000 -
#> 21 0.000000e+00 0.0000000 -
#> 22 5.000000e-01 0.5000000 -
#> 23 1.000000e+00 1.0000000 -
#> 24 0.000000e+00 0.0000000 -
#> 25 5.000000e-01 0.5000000 -
#> 26 1.000000e+00 1.0000000 -
#> 27 0.000000e+00 0.0000000 -
#> 28 5.000000e-01 0.5000000 -
#> 29 1.000000e+00 1.0000000 -
#> 30 0.000000e+00 0.0000000 mm
#> 31 5.000000e+00 0.3333333 mm
#> 32 7.500000e+00 0.6666667 mm
#> 33 1.250000e+01 1.0000000 mm
#> 34 0.000000e+00 0.0000000 -
#> 35 1.666667e-01 0.1666667 -
#> 36 3.333333e-01 0.3333333 -
#> 37 5.000000e-01 0.5000000 -
#> 38 6.666667e-01 0.6666667 -
#> 39 8.333333e-01 0.8333333 -
#> 40 1.000000e+00 1.0000000 -
#> 41 0.000000e+00 0.0000000 cm
#> 42 2.500000e+00 0.2500000 cm
#> 43 1.000000e+01 0.5000000 cm
#> 44 2.250000e+01 0.7500000 cm
#> 45 3.000000e+01 1.0000000 cm
#> 46 0.000000e+00 0.0000000 -
#> 47 1.666667e-01 0.1666667 -
#> 48 3.333333e-01 0.3333333 -
#> 49 5.000000e-01 0.5000000 -
#> 50 6.666667e-01 0.6666667 -
#> 51 8.333333e-01 0.8333333 -
#> 52 1.000000e+00 1.0000000 -
#> 53 0.000000e+00 0.0000000 -
#> 54 2.500000e-01 0.2500000 -
#> 55 5.000000e-01 0.5000000 -
#> 56 7.500000e-01 0.7500000 -
#> 57 1.000000e+00 1.0000000 -
#> 58 0.000000e+00 0.0000000 mm
#> 59 1.000000e+00 0.1666667 mm
#> 60 2.000000e+00 0.3333333 mm
#> 61 6.500000e+00 0.5000000 mm
#> 62 1.500000e+01 0.6666667 mm
#> 63 3.500000e+01 0.8333333 mm
#> 64 5.000000e+01 1.0000000 mm
#> 65 5.000000e-04 0.0000000 gADWt
#> 66 5.000000e-03 0.2500000 gADWt
#> 67 5.000000e-02 0.5000000 gADWt
#> 68 5.000000e-01 0.7500000 gADWt
#> 69 5.000000e+00 1.0000000 gADWt
#> 70 5.000000e-01 0.0000000 mm
#> 71 2.000000e+00 0.2500000 mm
#> 72 6.500000e+00 0.5000000 mm
#> 73 1.500000e+01 0.7500000 mm
#> 74 3.500000e+01 1.0000000 mm
#> 75 0.000000e+00 1.0000000 -
#> 76 2.500000e-01 0.7500000 -
#> 77 5.000000e-01 0.5000000 -
#> 78 7.500000e-01 0.2500000 -
#> 79 1.000000e+00 0.0000000 -
#> 80 0.000000e+00 1.0000000 -
#> 81 3.333333e-01 0.6666667 -
#> 82 6.666667e-01 0.3333333 -
#> 83 1.000000e+00 0.0000000 -
#> 84 0.000000e+00 1.0000000 cm
#> 85 2.500000e+00 0.7500000 cm
#> 86 1.000000e+01 0.5000000 cm
#> 87 2.000000e+01 0.2500000 cm
#> 88 0.000000e+00 0.0000000 -
#> 89 3.333333e-01 0.3333333 -
#> 90 6.666667e-01 0.6666667 -
#> 91 1.000000e+00 1.0000000 -
#> 92 5.000000e-01 0.0000000 year
#> 93 2.000000e+00 0.2500000 year
#> 94 6.500000e+00 0.5000000 year
#> 95 1.500000e+01 0.7500000 year
#> 96 3.000000e+01 1.0000000 year
#> 97 5.000000e-01 0.0000000 year
#> 98 2.000000e+00 0.5000000 year
#> 99 4.000000e+00 1.0000000 year
#> 100 0.000000e+00 0.0000000 -
#> 101 1.000000e+00 1.0000000 -
#> 102 0.000000e+00 0.0000000 -
#> 103 5.000000e-01 0.5000000 -
#> 104 1.000000e+00 1.0000000 -
#> 105 5.000000e+01 0.0000000 -
#> 106 4.500000e+02 0.2000000 -
#> 107 4.500000e+03 0.4000000 -
#> 108 4.500000e+04 0.6000000 -
#> 109 4.500000e+05 0.8000000 -
#> 110 1.000000e+06 1.0000000 -
#> 111 0.000000e+00 0.0000000 -
#> 112 5.000000e-01 0.5000000 -
#> 113 1.000000e+00 1.0000000 -
#> 114 5.000000e-02 0.0000000 mm
#> 115 3.000000e-01 0.3333333 mm
#> 116 1.000000e+00 0.6666667 mm
#> 117 3.250000e+00 1.0000000 mm
#> 118 0.000000e+00 0.0000000 -
#> 119 2.500000e-01 0.2500000 -
#> 120 5.000000e-01 0.5000000 -
#> 121 7.500000e-01 0.7500000 -
#> 122 1.000000e+00 1.0000000 -
#> 123 0.000000e+00 0.0000000 -
#> 124 2.500000e-01 0.2500000 -
#> 125 5.000000e-01 0.5000000 -
#> 126 7.500000e-01 0.7500000 -
#> 127 1.000000e+00 1.0000000 -
#> 128 0.000000e+00 0.0000000 days
#> 129 7.500000e+00 0.2500000 days
#> 130 2.250000e+01 0.5000000 days
#> 131 4.500000e+01 0.7500000 days
#> 132 6.000000e+01 1.0000000 days
#> 133 0.000000e+00 0.0000000 days
#> 134 7.500000e+00 0.2500000 days
#> 135 2.250000e+01 0.5000000 days
#> 136 4.500000e+01 0.7500000 days
#> 137 6.000000e+01 1.0000000 days
## ====================================================
## Traits for certain taxa
## ====================================================
# Taxonomy of amphiura and related species in the databases.
getTaxonomy("Amphiura filiformis")
#> [[1]]
#> taxon genus family order class
#> 112 Amphiura filiformis Amphiura Amphiuridae Amphilepidida Ophiuroidea
#> phylum AphiaID
#> 112 Echinodermata 125080
#>
getTaxonomy("Amphiura")
#> [[1]]
#> taxon genus family order
#> 109 Amphiura Amphiura Amphiuridae Amphilepidida
#> 110 Amphiura (Ophiopeltis) securigera Amphiura Amphiuridae Amphilepidida
#> 111 Amphiura chiajei Amphiura Amphiuridae Amphilepidida
#> 112 Amphiura filiformis Amphiura Amphiuridae Amphilepidida
#> class phylum AphiaID
#> 109 Ophiuroidea Echinodermata 123613
#> 110 Ophiuroidea Echinodermata 125195
#> 111 Ophiuroidea Echinodermata 125073
#> 112 Ophiuroidea Echinodermata 125080
#>
getTaxonInfo("Amphiura filiformis")
#> taxon trait modality units
#> 1 Amphiura filiformis Substratum depth distribution 0-5 cm
#> 2 Amphiura filiformis Substratum depth distribution 5-15 cm
#> 3 Amphiura filiformis Biodiffusion Low -
#> 7 Amphiura filiformis Biodeposition Low -
#> 10 Amphiura filiformis Ventilation/Pumping High -
#> 11 Amphiura filiformis Burrow width Narrow mm
#> 12 Amphiura filiformis Burrow width Intermediate mm
#> 13 Amphiura filiformis Endo-3D structure type Chimney/Funnel -
#> 14 Amphiura filiformis Endo-3D structure type UY-shaped burrow -
#> 15 Amphiura filiformis Endo-3D structure depth 0-5 cm
#> 16 Amphiura filiformis Endo-3D structure depth 5-15 cm
#> 17 Amphiura filiformis Epi-3D structure type Mound -
#> 18 Amphiura filiformis Epi-3D structure extension Isolated/Clumped -
#> 19 Amphiura filiformis Epi-3D structure size <1 mm
#> 20 Amphiura filiformis Epi-3D structure size 1-3 mm
#> 21 Amphiura filiformis Body mass 0.001-0.010 gADWt
#> 22 Amphiura filiformis Body length 20-50 mm
#> 23 Amphiura filiformis Body resistance Low -
#> 24 Amphiura filiformis Motility Crawler -
#> 25 Amphiura filiformis Burrowing/Sheltering depth 5-15 cm
#> 26 Amphiura filiformis Feeding type Deposit feeder -
#> 27 Amphiura filiformis Feeding type Suspension feeder -
#> 28 Amphiura filiformis Life span 10-20 year
#> 29 Amphiura filiformis Age at maturity 3-5 year
#> 30 Amphiura filiformis Reproductive frequency Sexual seasonal -
#> 31 Amphiura filiformis Fertilisation Pairing -
#> 32 Amphiura filiformis Annual fecundity 10e4-10e5 -
#> 33 Amphiura filiformis Offspring type Egg -
#> 34 Amphiura filiformis Offspring size <0.1 mm
#> 36 Amphiura filiformis Offspring development Planktotrophic -
#> 38 Amphiura filiformis Offspring pelagic stage duration 30-60 days
#> proportion
#> 1 0.75
#> 2 0.25
#> 3 1.00
#> 7 1.00
#> 10 1.00
#> 11 0.50
#> 12 0.50
#> 13 0.50
#> 14 0.50
#> 15 0.50
#> 16 0.50
#> 17 1.00
#> 18 1.00
#> 19 0.50
#> 20 0.50
#> 21 1.00
#> 22 1.00
#> 23 1.00
#> 24 1.00
#> 25 1.00
#> 26 0.50
#> 27 0.50
#> 28 1.00
#> 29 1.00
#> 30 1.00
#> 31 1.00
#> 32 1.00
#> 33 1.00
#> 34 1.00
#> 36 1.00
#> 38 1.00
getTaxonInfo("Amphiura filiformis", trait=Traits_cefas)
#> taxon trait modality
#> 1 Amphiura filiformis Maximum size 101-200
#> 2 Amphiura filiformis Morphology Exoskeleton
#> 3 Amphiura filiformis Lifespan >10
#> 4 Amphiura filiformis Egg development location Sexual_pelagic
#> 5 Amphiura filiformis Larva development location Pelagic_planktotrophic
#> 6 Amphiura filiformis Living habit Free_living
#> 7 Amphiura filiformis Living habit Crevice_hole_under_stones
#> 8 Amphiura filiformis Sediment position Shallow_infauna_0_to_5cm
#> 9 Amphiura filiformis Feeding mode Suspension
#> 10 Amphiura filiformis Feeding mode Surface_deposit
#> 11 Amphiura filiformis Mobility Crawl_creep_climb
#> 12 Amphiura filiformis Mobility Burrower
#> 13 Amphiura filiformis Bioturbation mode Diffusive_mixing
#> 14 Amphiura filiformis Bioturbation mode Surface_deposition
#> units proportion
#> 1 mm 1.00
#> 2 - 1.00
#> 3 years 1.00
#> 4 - 1.00
#> 5 - 1.00
#> 6 - 0.75
#> 7 - 0.25
#> 8 cm 1.00
#> 9 - 0.50
#> 10 - 0.50
#> 11 - 0.50
#> 12 - 0.50
#> 13 - 0.50
#> 14 - 0.50
# there is no direct information on the traits of this species in Traits_cefas
getTaxonInfo("Amphiura filiformis", trait=Traits_cefas, NULL)
#> [1] taxon trait modality units proportion
#> <0 rows> (or 0-length row.names)
## ====================================================
## Northsea dataset
## ====================================================
# show its contents
metadata(MWTL)
#> $title
#> [1] "The MWTL Northsea macrobenthos data (1995 - 2018)"
#>
#> $originator
#> [1] "Ministerie van Infrastructuur en Milieu, Rijkswaterstaat Centrale Informatievoorziening (RWS, CIV)"
#>
#> $implemented
#> [1] "Karline Soetaert, in the frame of the EMODnet biology project"
#>
metadata(MWTL$density)
#> name description units
#> 1 station station name
#> 2 date sampling date, a string
#> 3 taxon taxon name, checked by worms, and adjusted
#> 4 density species total density individuals/m2
#> 5 biomass species total ash-free dry weight gAFDW/m2
#> 6 taxon.original original taxon name