Author: Scott Chamberlain
Date: 2020-08-25

# traits introduction

#### Scott Chamberlain

#### 2020-08-25

    library("traits")

## BetyDB

Get trait data for Willow (Salix spp.)

    (salix <- betydb_search("Salix Vcmax"))
    #> # A tibble: 14 x 36
    #>    checked result_type    id citation_id site_id treatment_id sitename city
    #>      <int> <chr>       <int>       <int>   <int>        <int> <chr>    <chr>
    #>  1       1 traits      39217         430     645         1342 ""       Saare
    #>  2       1 traits      39218         430     645         1343 ""       Saare
    #>  3       1 traits      39219         430     645         1344 ""       Saare
    #>  4       1 traits      39220         430     645         1345 ""       Saare
    #>  5       1 traits      25405          51      NA            1  <NA>    <NA>
    #>  6       1 traits      39213         430     645         1342 ""       Saare
    #>  7       1 traits      39214         430     645         1343 ""       Saare
    #>  8       1 traits      39215         430     645         1344 ""       Saare
    #>  9       1 traits      39216         430     645         1345 ""       Saare
    #> 10       1 traits      39221         430     645         1342 ""       Saare
    #> 11       1 traits      39222         430     645         1343 ""       Saare
    #> 12       1 traits      39223         430     645         1344 ""       Saare
    #> 13       1 traits      39224         430     645         1345 ""       Saare
    #> 14       1 traits      37519         381     602         1220  <NA>    <NA>
    #> # … with 28 more variables: lat <dbl>, lon <dbl>, scientificname <chr>,
    #> #   commonname <chr>, genus <chr>, species_id <int>, cultivar_id <int>,
    #> #   author <chr>, citation_year <int>, treatment <chr>, date <chr>, time <chr>,
    #> #   raw_date <chr>, month <int>, year <int>, dateloc <chr>, trait <chr>,
    #> #   trait_description <chr>, mean <dbl>, units <chr>, n <int>, statname <chr>,
    #> #   stat <dbl>, notes <chr>, access_level <int>, cultivar <chr>, entity <lgl>,
    #> #   method_name <lgl>
    # equivalent:
    # (out <- betydb_search("willow"))

Summarise data from the output `data.frame`

    library("dplyr")
    salix %>%
      group_by(scientificname, trait) %>%
      mutate(.mean = as.numeric(mean)) %>%
      summarise(mean = round(mean(.mean, na.rm = TRUE), 2),
                min = round(min(.mean, na.rm = TRUE), 2),
                max = round(max(.mean, na.rm = TRUE), 2),
                n = length(n))
    #> # A tibble: 4 x 6
    #> # Groups:   scientificname [4]
    #>   scientificname                  trait  mean   min   max     n
    #>   <chr>                           <chr> <dbl> <dbl> <dbl> <int>
    #> 1 Salix                           Vcmax  65    65    65       1
    #> 2 Salix dasyclados                Vcmax  46.1  34.3  56.7     4
    #> 3 Salix sachalinensis × miyabeana Vcmax  79.3  79.3  79.3     1
    #> 4 Salix viminalis                 Vcmax  43.0  20.0  61.3     8

## NCBI sequence data

Get sequences by id

    ncbi_byid(ids = "360040093")
    #>                  taxon
    #> 1 Eristalis transversa
    #>                                                                                                                                                                                       taxonomy
    #> 1 Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Holometabola; Diptera; Brachycera; Muscomorpha; Syrphoidea; Syrphidae; Eristalinae; Eristalini; Eristalis
    #>                                                                                                             gene_desc
    #> 1 Eristalis transversa voucher CNC:Diptera:102013 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial
    #>       organelle     gi_no     acc_no keyword   specimen_voucher
    #> 1 mitochondrion 360040093 JN991986.1 BARCODE CNC:Diptera:102013
    #>               lat_lon
    #> 1 38.4623 N 79.2417 W
    #>                                                       country
    #> 1 USA: Virginia, Reddish Knob Lookout, 14.5km W Briery Branch
    #>                                                              paper_title
    #> 1 The evolution of imperfect mimicry in hover flies (Diptera: Syrphidae)
    #>       journal first_author uploaded_date length
    #> 1 Unpublished   Penny,H.D.   03-NOV-2012    658
    #>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             sequence
    #> 1 tactttatattttgtatttggaacatgagcgggtatagtaggaacttcattaagaattttaattcgagctgaattaggtcatccaggtgcattaattggtgatgatcaaatttataatgttattgtaacagctcatgcttttgttataattttttttatagtaatacctattataattggaggatttggaaattgattagtaccacttatattaggagctccagatatagcattccctcgaataaataatataagtttctgattattacctccttctttaactctattattagtaagaagtatagtagaaaatggggctggaacaggatgaacagtttatcctccattatcaagtaatattgcacatggaggagcctcagttgatttagcaattttttcacttcacttatcaggaatatcatctattttaggtgcagtaaattttattacaacagttattaatatacgatcaacaggaattacttatgatcgtatacctttatttgtttgatctgttgctattacagctttattattattattatcattaccagtactagcaggagctattacaatattattaactgatcgaaatttaaatacatcattctttgatccagcaggaggaggagaccctatcctgtaccaacacttattc

Get sequences searching by taxonomic name

    out <- ncbi_searcher(taxa = "Umbra limi", seqrange = "1:2000")
    #> using sleep: 0
    #> ══  1 queries  ═══════════════
    #> ✔  Found:  Umbra+limi
    #> ══  Results  ═════════════════
    #>
    #> ● Total: 1
    #> ● Found: 1
    #> ● Not Found: 0
    head(out)
    #>        taxon length
    #> 1 Umbra limi    298
    #> 2 Umbra limi    761
    #> 3 Umbra limi    765
    #> 4 Umbra limi    764
    #> 5 Umbra limi    743
    #> 6 Umbra limi    758
    #>                                                                                                gene_desc
    #> 1 Umbra limi voucher Umbra_limi_GLF16S large subunit ribosomal RNA gene, partial sequence; mitochondrial
    #> 2                                        Umbra limi voucher NXG2012264 rhodopsin (Rho) gene, partial cds
    #> 3                                         Umbra limi voucher NXG201250 rhodopsin (Rho) gene, partial cds
    #> 4                                        Umbra limi voucher NXG2012183 rhodopsin (Rho) gene, partial cds
    #> 5                                         Umbra limi voucher NXG201252 rhodopsin (Rho) gene, partial cds
    #> 6                                        Umbra limi voucher NXG2012231 rhodopsin (Rho) gene, partial cds
    #>     acc_no      gi_no
    #> 1 MT549086 1847697133
    #> 2 KX146134 1049488959
    #> 3 KX146015 1049488721
    #> 4 KX145969 1049488629
    #> 5 KX145777 1049488245
    #> 6 KX145759 1049488209

## EOL’s traitbank trait data

    traitbank(query = "MATCH (n:Trait) RETURN n LIMIT 1;")
    #> $columns
    #> [1] "n"
    #>
    #> $data
    #> $data[[1]]
    #>   metadata.id metadata.labels    data.eol_pk data.object_page_id
    #> 1    22529388           Trait R20-PK20910350            46581789
    #>                                                    data.resource_pk
    #> 1 ReverseOf_globi:assoc:7296029-FBC:FB:SpecCode:4755-ATE-EOL_V2:281
    #>   data.scientific_name
    #> 1              Plantae
    #>                                                                                                                                                                                                                                                             data.source
    #> 1 Froese, R. and D. Pauly. Editors. 2019. FishBase. World Wide Web electronic publication. www.fishbase.org, version (08/2019). Accessed at <https://github.com/globalbioticinteractions/fishbase/archive/6ebceaacea18c6ff6c247182f9af8ad6fc05cc82.zip> on 25 May 2020.

## Birdlife International

Habitat data

    birdlife_habitat(22721692)
    #>         id Habitat (level 1)                  Habitat (level 2) Importance
    #> 1 22721692            Forest           Subtropical/Tropical Dry      major
    #> 2 22721692            Forest Subtropical/Tropical Moist Montane      major
    #> 3 22721692            Forest                          Temperate   suitable
    #> 4 22721692         Shrubland Subtropical/Tropical High Altitude   suitable
    #>     Occurrence
    #> 1     breeding
    #> 2 non-breeding
    #> 3     breeding
    #> 4     breeding

Threats data

    birdlife_threats(22721692)
    #>          id                                                  threat1
    #> 1  22721692                                Agriculture & aquaculture
    #> 2  22721692                                Agriculture & aquaculture
    #> 3  22721692                                  Biological resource use
    #> 4  22721692                          Climate change & severe weather
    #> 5  22721692                          Climate change & severe weather
    #> 6  22721692                          Climate change & severe weather
    #> 7  22721692 Invasive and other problematic species, genes & diseases
    #> 8  22721692 Invasive and other problematic species, genes & diseases
    #> 9  22721692 Invasive and other problematic species, genes & diseases
    #> 10 22721692 Invasive and other problematic species, genes & diseases
    #> 11 22721692 Invasive and other problematic species, genes & diseases
    #> 12 22721692 Invasive and other problematic species, genes & diseases
    #> 13 22721692                             Natural system modifications
    #> 14 22721692                             Natural system modifications
    #> 15 22721692                     Residential & commercial development
    #> 16 22721692                       Transportation & service corridors
    #>                                                                                   threat2
    #> 1                             Annual & perennial non-timber crops - Agro-industry farming
    #> 2                              Annual & perennial non-timber crops - Small-holder farming
    #> 3  Logging & wood harvesting - Unintentional effects: (subsistence/small scale) [harvest]
    #> 4                                                                                Droughts
    #> 5                                                           Habitat shifting & alteration
    #> 6                                                                       Storms & flooding
    #> 7                                 Invasive non-native/alien species/diseases - Sus scrofa
    #> 8                        Invasive non-native/alien species/diseases - Unspecified species
    #> 9                            Problematic native species/diseases - Dendroctonus frontalis
    #> 10                           Problematic native species/diseases - Odocoileus virginianus
    #> 11                              Problematic native species/diseases - Unspecified species
    #> 12                    Problematic species/disease of unknown origin - Unspecified species
    #> 13                                     Fire & fire suppression - Trend Unknown/Unrecorded
    #> 14                                                          Other ecosystem modifications
    #> 15                                                                  Housing & urban areas
    #> 16                                                                      Roads & railroads
    #>                                                                 stresses
    #> 1                     Ecosystem degradation, Ecosystem conversion, Other
    #> 2                     Ecosystem degradation, Ecosystem conversion, Other
    #> 3                                                  Ecosystem degradation
    #> 4                                                  Ecosystem degradation
    #> 5                            Ecosystem degradation, Ecosystem conversion
    #> 6                                                  Ecosystem degradation
    #> 7                            Ecosystem degradation, Ecosystem conversion
    #> 8                                                      Species mortality
    #> 9                                                  Ecosystem degradation
    #> 10                                                 Ecosystem degradation
    #> 11                   Ecosystem degradation, Reduced reproductive success
    #> 12                                                     Species mortality
    #> 13                           Ecosystem degradation, Ecosystem conversion
    #> 14                           Ecosystem degradation, Ecosystem conversion
    #> 15 Ecosystem degradation, Ecosystem conversion, Species mortality, Other
    #> 16                                                     Species mortality
    #>                                                      timing
    #> 1                                 Agriculture & aquaculture
    #> 2                                 Agriculture & aquaculture
    #> 3                                   Biological resource use
    #> 4                           Climate change & severe weather
    #> 5                           Climate change & severe weather
    #> 6                           Climate change & severe weather
    #> 7  Invasive and other problematic species, genes & diseases
    #> 8  Invasive and other problematic species, genes & diseases
    #> 9  Invasive and other problematic species, genes & diseases
    #> 10 Invasive and other problematic species, genes & diseases
    #> 11 Invasive and other problematic species, genes & diseases
    #> 12 Invasive and other problematic species, genes & diseases
    #> 13                             Natural system modifications
    #> 14                             Natural system modifications
    #> 15                     Residential & commercial development
    #> 16                       Transportation & service corridors
    #>                                                                                     scope
    #> 1                             Annual & perennial non-timber crops - Agro-industry farming
    #> 2                              Annual & perennial non-timber crops - Small-holder farming
    #> 3  Logging & wood harvesting - Unintentional effects: (subsistence/small scale) [harvest]
    #> 4                                                                                Droughts
    #> 5                                                           Habitat shifting & alteration
    #> 6                                                                       Storms & flooding
    #> 7                                 Invasive non-native/alien species/diseases - Sus scrofa
    #> 8                        Invasive non-native/alien species/diseases - Unspecified species
    #> 9                            Problematic native species/diseases - Dendroctonus frontalis
    #> 10                           Problematic native species/diseases - Odocoileus virginianus
    #> 11                              Problematic native species/diseases - Unspecified species
    #> 12                    Problematic species/disease of unknown origin - Unspecified species
    #> 13                                     Fire & fire suppression - Trend Unknown/Unrecorded
    #> 14                                                          Other ecosystem modifications
    #> 15                                                                  Housing & urban areas
    #> 16                                                                      Roads & railroads
    #>    severity  impact
    #> 1   Ongoing Ongoing
    #> 2   Ongoing Ongoing
    #> 3   Ongoing Ongoing
    #> 4   Ongoing Ongoing
    #> 5    Future  Future
    #> 6   Ongoing Ongoing
    #> 7   Ongoing Ongoing
    #> 8   Ongoing Ongoing
    #> 9   Ongoing Ongoing
    #> 10  Ongoing Ongoing
    #> 11  Ongoing Ongoing
    #> 12  Ongoing Ongoing
    #> 13  Ongoing Ongoing
    #> 14   Future  Future
    #> 15  Ongoing Ongoing
    #> 16  Ongoing Ongoing