README.md
In bioatlas/dyntaxa: Dyntaxa - Swedish Taxonomic Database Of Organisms in Sweden
dyntaxa
The goal of the dyntaxa R package is to provide a read-only R package
to interface with Dyntaxa - the taxonomic database of organisms in
Sweden.
Dyntaxa contains information about 61,500 species occurring in Sweden.
This includes about 95% of known multicellular species – remaining gaps
mainly found among the fungi. The scope of organisms include
multicellular species documented in Sweden and such unicellular species
that are included in environmental monitoring by the Swedish EPA. In
addition to these species there are many names at other taxonomic
levels, scientific synonyms, Swedish vernaculars.
Credits and acknowledgements
The Dyntaxa database is published by
Artdatabanken
at
GBIF.org
by Johan Liljeblad.
Citation to use for refering to Dyntaxa
Liljeblad J (2019). Dyntaxa. Svensk taxonomisk databas. ArtDatabanken.
Checklist dataset https://doi.org/10.15468/j43wfc.
Installation
You can install the dyntaxa R package from
GitHub with:
library(devtools)
install_github("bioatlas/dyntaxa", build_opts = c("--no-resave-data", "--no-manual"))
Example usage
This package can be used to automate the following tasks:
- Taxonomic identifier from a taxonomic name and vice versa
- Taxonomic name from a vernacular (common) name and vice versa
- Taxonomic hierarchy/classification from identifier or name
- Taxonomic children of an identifier or name
- All taxa downstream to a certain rank from identifier or name
- Taxonomic synonyms from identifier or name
Here are some short and simple usage examples which shows you how to
download and access data from Dyntaxa for those tasks.
# we use dplyr for data manipulation (pipe, filtering etc)
suppressPackageStartupMessages(library(dplyr))
library(dyntaxa)
__ __
.--| .--.--.-----| |_.---.-.--.--.---.-.
| _ | | | | _| _ |_ _| _ |
|_____|___ |__|__|____|___._|__.__|___._|
|_____|
# looking up identifiers/keys from taxon names and vice versa
# taxonomic name from taxonomic identifier
dyntaxa_name_from_id(5000001)
[1] "Animalia"
# taxonomic identifier from taxonomic name
key <- dyntaxa_id_from_name("Alces alces")
key
[1] "206046"
# the taxon key or identifier is often needed to retrieve taxonomic data
# taxonomic hierarchy/classification from identifier or name
dyntaxa_classification(key)
# A tibble: 13 x 5
taxonId scientificName parentNameUsageID taxonRank rankDistance
<chr> <chr> <chr> <chr> <dbl>
1 206046 Alces alces 1001660 species 0
2 1001660 Alces 6007818 genus 1
3 6007818 Capreolinae 2002172 subfamily 2
4 2002172 Cervidae 2002171 family 3
5 2002171 Ruminantia 3000305 suborder 4
6 3000305 Artiodactyla 6034822 order 5
7 6034822 Laurasiatheria 6034827 superorder 6
8 6034824 Placentalia 4000107 infraclass 7
9 4000107 Mammalia 6034835 class 8
10 6000993 Vertebrata 4000099 infraphylum 9
11 4000099 Craniata 5000034 subphylum 10
12 5000034 Chordata 5000001 phylum 11
13 5000001 Animalia <NA> kingdom 12
# taxa downstream from identifier or name
dyntaxa_downstream(dyntaxa_id_from_name("Cervidae"))
# A tibble: 26 x 5
taxonId scientificName parentNameUsageID taxonRank rankDistance
<chr> <chr> <chr> <chr> <dbl>
1 2002172 Cervidae 2002171 family 0
2 6007818 Capreolinae 2002172 subfamily 1
3 6007819 Cervinae 2002172 subfamily 1
4 6011558 Hydropotinae 2002172 subfamily 1
5 1001659 Capreolus 6007818 genus 2
6 1001660 Alces 6007818 genus 2
7 1001661 Rangifer 6007818 genus 2
8 1015254 Odocoileus 6007818 genus 2
9 1001657 Cervus 6007819 genus 2
10 1001658 Dama 6007819 genus 2
# … with 16 more rows
# taxonomic immediate children of an identifier or name
dyntaxa_children(dyntaxa_id_from_name("Carnivora"))
# A tibble: 2 x 5
taxonId scientificName parentNameUsageID taxonRank rankDistance
<chr> <chr> <chr> <chr> <dbl>
1 2002151 Feliformia 3000303 suborder 1
2 2002153 Caniformia 3000303 suborder 1
# taxa downstream of a specific taxon identifier
# can be filtered at species level (or at other ranks)
dyntaxa_downstream(dyntaxa_id_from_name("Carnivora")) %>%
filter(taxonRank == "species")
# A tibble: 26 x 5
taxonId scientificName parentNameUsage… taxonRank rankDistance
<chr> <chr> <chr> <chr> <dbl>
1 100057 Lynx lynx 1001652 species 4
2 233620 Felis catus 1009403 species 4
3 6007816 Urva javanica 6037429 species 4
4 267320 Canis lupus 1001643 species 4
5 6011549 Canis aureus 1001643 species 4
6 100005 Vulpes lagopus 1001644 species 4
7 206026 Vulpes vulpes 1001644 species 4
8 206028 Nyctereutes procyonoides 1001646 species 4
9 100145 Ursus arctos 1001642 species 4
10 206029 Mustela erminea 1001647 species 4
# … with 16 more rows
# search a fulltext index of Dyntaxa a vernacular name
dyntaxa_search_all("blåklocka") %>%
select(taxonId, scientificName, vernacularName, title, creator)
# A tibble: 6 x 5
taxonId scientificName vernacularName title creator
<chr> <chr> <chr> <chr> <chr>
1 220018 Campanula persicifol… stor blåklocka Thomas Karlsso… Aronsson,…
2 220023 Campanula rotundifol… liten blåklocka Thomas Karlsso… Aronsson,…
3 235014 Campanula americana amerikansk blåk… Databas levere… Svenska k…
4 223657 Campanula rotundifol… Blåklocka Thomas Karlsso… Aronsson,…
5 223657 Campanula rotundifol… liten blåklocka Thomas Karlsso… Aronsson,…
6 265920 Campanula persicifol… vanlig stor blå… Databas levere… Svenska k…
# another example of a full text search
dyntaxa_search_all("Thomas Karlssons Kärlväxtlista") %>%
filter(taxonRank == "family")
# A tibble: 15 x 10
taxonId scientificName taxonRank scientificNameA… taxonomicStatus
<chr> <chr> <chr> <chr> <chr>
1 2002896 Menispermaceae family Juss. accepted
2 2002886 Ixioliriaceae family Nakai accepted
3 2002887 Acoraceae family Martinov accepted
4 2002889 Bignoniaceae family Juss. accepted
5 2002890 Cercidiphylla… family Engl. accepted
6 2002892 Hymenophyllac… family Mart. accepted
7 2002895 Tofieldiaceae family Takht. accepted
8 2002897 Myrtaceae family Juss. accepted
9 2002898 Piperaceae family Giseke accepted
10 2002899 Ruppiaceae family Horan. accepted
11 2002921 Cannaceae family Juss. accepted
12 2002922 Musaceae family Juss. accepted
13 2002900 Styracaceae family DC. & Spreng. accepted
14 2002923 Platanaceae family T. Lestib. accepted
15 2002894 Nartheciaceae family Fr. ex Bjurzon accepted
# … with 5 more variables: nomenclaturalStatus <chr>,
# vernacularName <chr>, language <chr>, title <chr>, creator <chr>
# what are synonyms for Sagedia zonata?
dyntaxa_synonyms(dyntaxa_id_from_name("Sagedia zonata"))
# A tibble: 32 x 3
scientificName taxonomicStatus nomenclaturalStatus
<chr> <chr> <chr>
1 Aspicilia curvabilis synonym valid
2 Aspicilia haerjedalica synonym valid
3 Aspicilia inconspicua synonym valid
4 Aspicilia litorea synonym valid
5 Aspicilia malmeana synonym valid
6 Aspicilia obscurascens synonym valid
7 Aspicilia obscurata synonym valid
8 Aspicilia pleiocarpa synonym valid
9 Aspicilia rolleana synonym valid
10 Aspicilia subarctica synonym valid
# … with 22 more rows
# more examples for synonyms
dyntaxa_search_all("scientificName:Phyllachora graminis")
# A tibble: 3 x 10
taxonId scientificName taxonRank scientificNameA… taxonomicStatus
<chr> <chr> <chr> <chr> <chr>
1 5509 Phyllachora g… species (Pers.:Fr.) Fuc… accepted
2 urn:ls… Phyllachora g… species Rehm synonym
3 urn:ls… Phyllachora g… species (Fr.) Sacc. synonym
# … with 5 more variables: nomenclaturalStatus <chr>,
# vernacularName <chr>, language <chr>, title <chr>, creator <chr>
dyntaxa_synonyms(dyntaxa_id_from_name("Phyllachora graminis"))
# A tibble: 21 x 3
scientificName taxonomicStatus nomenclaturalStatus
<chr> <chr> <chr>
1 Sphaeria graminis synonym valid
2 Sphaeria graminis var. elymorum synonym valid
3 Sphaeria graminis var. poarum synonym valid
4 Scirrhia poae synonym valid
5 Polystigma graminis synonym valid
6 Phyllachora poae-pratensis synonym valid
7 Phyllachora poae synonym valid
8 Phyllachora poae f. alpina synonym valid
9 Phyllachora melicae synonym valid
10 Phyllachora hordei synonym valid
# … with 11 more rows
# does "Citronfjäril" / "Gonepteryx rhamni" have synonyms?
key <- dyntaxa_search_vernacular("citronfjäril")$taxonId
dyntaxa_name_from_id(key)
[1] "Gonepteryx rhamni"
dyntaxa_synonyms(key)
# A tibble: 1 x 3
scientificName taxonomicStatus nomenclaturalStatus
<chr> <chr> <chr>
1 Papilio rhamni synonym valid
Other use cases
The vignette provides more usage information on other common use cases,
such as:
- Using the above functions with vectors of several keys/identifiers
or names
- Resolving potentially misspelled scientific names
- Exporting data
- Looking at counts / aggregates
bioatlas/dyntaxa documentation built on May 15, 2019, 10:37 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
dyntaxa
The goal of the dyntaxa R package is to provide a read-only R package
to interface with Dyntaxa - the taxonomic database of organisms in
Sweden.
Dyntaxa contains information about 61,500 species occurring in Sweden. This includes about 95% of known multicellular species – remaining gaps mainly found among the fungi. The scope of organisms include multicellular species documented in Sweden and such unicellular species that are included in environmental monitoring by the Swedish EPA. In addition to these species there are many names at other taxonomic levels, scientific synonyms, Swedish vernaculars.
Credits and acknowledgements
The Dyntaxa database is published by Artdatabanken at GBIF.org by Johan Liljeblad.
Citation to use for refering to Dyntaxa
Liljeblad J (2019). Dyntaxa. Svensk taxonomisk databas. ArtDatabanken. Checklist dataset https://doi.org/10.15468/j43wfc.
Installation
You can install the dyntaxa R package from
GitHub with:
library(devtools)
install_github("bioatlas/dyntaxa", build_opts = c("--no-resave-data", "--no-manual"))
Example usage
This package can be used to automate the following tasks:
- Taxonomic identifier from a taxonomic name and vice versa
- Taxonomic name from a vernacular (common) name and vice versa
- Taxonomic hierarchy/classification from identifier or name
- Taxonomic children of an identifier or name
- All taxa downstream to a certain rank from identifier or name
- Taxonomic synonyms from identifier or name
Here are some short and simple usage examples which shows you how to download and access data from Dyntaxa for those tasks.
# we use dplyr for data manipulation (pipe, filtering etc)
suppressPackageStartupMessages(library(dplyr))
library(dyntaxa)
__ __
.--| .--.--.-----| |_.---.-.--.--.---.-.
| _ | | | | _| _ |_ _| _ |
|_____|___ |__|__|____|___._|__.__|___._|
|_____|
# looking up identifiers/keys from taxon names and vice versa
# taxonomic name from taxonomic identifier
dyntaxa_name_from_id(5000001)
[1] "Animalia"
# taxonomic identifier from taxonomic name
key <- dyntaxa_id_from_name("Alces alces")
key
[1] "206046"
# the taxon key or identifier is often needed to retrieve taxonomic data
# taxonomic hierarchy/classification from identifier or name
dyntaxa_classification(key)
# A tibble: 13 x 5
taxonId scientificName parentNameUsageID taxonRank rankDistance
<chr> <chr> <chr> <chr> <dbl>
1 206046 Alces alces 1001660 species 0
2 1001660 Alces 6007818 genus 1
3 6007818 Capreolinae 2002172 subfamily 2
4 2002172 Cervidae 2002171 family 3
5 2002171 Ruminantia 3000305 suborder 4
6 3000305 Artiodactyla 6034822 order 5
7 6034822 Laurasiatheria 6034827 superorder 6
8 6034824 Placentalia 4000107 infraclass 7
9 4000107 Mammalia 6034835 class 8
10 6000993 Vertebrata 4000099 infraphylum 9
11 4000099 Craniata 5000034 subphylum 10
12 5000034 Chordata 5000001 phylum 11
13 5000001 Animalia <NA> kingdom 12
# taxa downstream from identifier or name
dyntaxa_downstream(dyntaxa_id_from_name("Cervidae"))
# A tibble: 26 x 5
taxonId scientificName parentNameUsageID taxonRank rankDistance
<chr> <chr> <chr> <chr> <dbl>
1 2002172 Cervidae 2002171 family 0
2 6007818 Capreolinae 2002172 subfamily 1
3 6007819 Cervinae 2002172 subfamily 1
4 6011558 Hydropotinae 2002172 subfamily 1
5 1001659 Capreolus 6007818 genus 2
6 1001660 Alces 6007818 genus 2
7 1001661 Rangifer 6007818 genus 2
8 1015254 Odocoileus 6007818 genus 2
9 1001657 Cervus 6007819 genus 2
10 1001658 Dama 6007819 genus 2
# … with 16 more rows
# taxonomic immediate children of an identifier or name
dyntaxa_children(dyntaxa_id_from_name("Carnivora"))
# A tibble: 2 x 5
taxonId scientificName parentNameUsageID taxonRank rankDistance
<chr> <chr> <chr> <chr> <dbl>
1 2002151 Feliformia 3000303 suborder 1
2 2002153 Caniformia 3000303 suborder 1
# taxa downstream of a specific taxon identifier
# can be filtered at species level (or at other ranks)
dyntaxa_downstream(dyntaxa_id_from_name("Carnivora")) %>%
filter(taxonRank == "species")
# A tibble: 26 x 5
taxonId scientificName parentNameUsage… taxonRank rankDistance
<chr> <chr> <chr> <chr> <dbl>
1 100057 Lynx lynx 1001652 species 4
2 233620 Felis catus 1009403 species 4
3 6007816 Urva javanica 6037429 species 4
4 267320 Canis lupus 1001643 species 4
5 6011549 Canis aureus 1001643 species 4
6 100005 Vulpes lagopus 1001644 species 4
7 206026 Vulpes vulpes 1001644 species 4
8 206028 Nyctereutes procyonoides 1001646 species 4
9 100145 Ursus arctos 1001642 species 4
10 206029 Mustela erminea 1001647 species 4
# … with 16 more rows
# search a fulltext index of Dyntaxa a vernacular name
dyntaxa_search_all("blåklocka") %>%
select(taxonId, scientificName, vernacularName, title, creator)
# A tibble: 6 x 5
taxonId scientificName vernacularName title creator
<chr> <chr> <chr> <chr> <chr>
1 220018 Campanula persicifol… stor blåklocka Thomas Karlsso… Aronsson,…
2 220023 Campanula rotundifol… liten blåklocka Thomas Karlsso… Aronsson,…
3 235014 Campanula americana amerikansk blåk… Databas levere… Svenska k…
4 223657 Campanula rotundifol… Blåklocka Thomas Karlsso… Aronsson,…
5 223657 Campanula rotundifol… liten blåklocka Thomas Karlsso… Aronsson,…
6 265920 Campanula persicifol… vanlig stor blå… Databas levere… Svenska k…
# another example of a full text search
dyntaxa_search_all("Thomas Karlssons Kärlväxtlista") %>%
filter(taxonRank == "family")
# A tibble: 15 x 10
taxonId scientificName taxonRank scientificNameA… taxonomicStatus
<chr> <chr> <chr> <chr> <chr>
1 2002896 Menispermaceae family Juss. accepted
2 2002886 Ixioliriaceae family Nakai accepted
3 2002887 Acoraceae family Martinov accepted
4 2002889 Bignoniaceae family Juss. accepted
5 2002890 Cercidiphylla… family Engl. accepted
6 2002892 Hymenophyllac… family Mart. accepted
7 2002895 Tofieldiaceae family Takht. accepted
8 2002897 Myrtaceae family Juss. accepted
9 2002898 Piperaceae family Giseke accepted
10 2002899 Ruppiaceae family Horan. accepted
11 2002921 Cannaceae family Juss. accepted
12 2002922 Musaceae family Juss. accepted
13 2002900 Styracaceae family DC. & Spreng. accepted
14 2002923 Platanaceae family T. Lestib. accepted
15 2002894 Nartheciaceae family Fr. ex Bjurzon accepted
# … with 5 more variables: nomenclaturalStatus <chr>,
# vernacularName <chr>, language <chr>, title <chr>, creator <chr>
# what are synonyms for Sagedia zonata?
dyntaxa_synonyms(dyntaxa_id_from_name("Sagedia zonata"))
# A tibble: 32 x 3
scientificName taxonomicStatus nomenclaturalStatus
<chr> <chr> <chr>
1 Aspicilia curvabilis synonym valid
2 Aspicilia haerjedalica synonym valid
3 Aspicilia inconspicua synonym valid
4 Aspicilia litorea synonym valid
5 Aspicilia malmeana synonym valid
6 Aspicilia obscurascens synonym valid
7 Aspicilia obscurata synonym valid
8 Aspicilia pleiocarpa synonym valid
9 Aspicilia rolleana synonym valid
10 Aspicilia subarctica synonym valid
# … with 22 more rows
# more examples for synonyms
dyntaxa_search_all("scientificName:Phyllachora graminis")
# A tibble: 3 x 10
taxonId scientificName taxonRank scientificNameA… taxonomicStatus
<chr> <chr> <chr> <chr> <chr>
1 5509 Phyllachora g… species (Pers.:Fr.) Fuc… accepted
2 urn:ls… Phyllachora g… species Rehm synonym
3 urn:ls… Phyllachora g… species (Fr.) Sacc. synonym
# … with 5 more variables: nomenclaturalStatus <chr>,
# vernacularName <chr>, language <chr>, title <chr>, creator <chr>
dyntaxa_synonyms(dyntaxa_id_from_name("Phyllachora graminis"))
# A tibble: 21 x 3
scientificName taxonomicStatus nomenclaturalStatus
<chr> <chr> <chr>
1 Sphaeria graminis synonym valid
2 Sphaeria graminis var. elymorum synonym valid
3 Sphaeria graminis var. poarum synonym valid
4 Scirrhia poae synonym valid
5 Polystigma graminis synonym valid
6 Phyllachora poae-pratensis synonym valid
7 Phyllachora poae synonym valid
8 Phyllachora poae f. alpina synonym valid
9 Phyllachora melicae synonym valid
10 Phyllachora hordei synonym valid
# … with 11 more rows
# does "Citronfjäril" / "Gonepteryx rhamni" have synonyms?
key <- dyntaxa_search_vernacular("citronfjäril")$taxonId
dyntaxa_name_from_id(key)
[1] "Gonepteryx rhamni"
dyntaxa_synonyms(key)
# A tibble: 1 x 3
scientificName taxonomicStatus nomenclaturalStatus
<chr> <chr> <chr>
1 Papilio rhamni synonym valid
Other use cases
The vignette provides more usage information on other common use cases, such as:
- Using the above functions with vectors of several keys/identifiers or names
- Resolving potentially misspelled scientific names
- Exporting data
- Looking at counts / aggregates
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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