Read a csv file that contains the data that defines a taxonomic hierarchy and return it as a graph.
Details
The file must contain column names in the first row. Each row defines a taxon with the following attributes:
- parent
The name of the parent taxon. This column must be empty for the root taxon.
- name
The name of the taxon that should be used to label the nodes, e.g., the common name. These names must be unique.
- scientific
The scientific name of the taxon.
- rank
The rank of the taxon, e.g., "Familie", "Art", or similar (only German ranks are supported so far). These will be used to colour the nodes.
The function checks that the file satisfies the following conditions:
The required columns are all present.
There is exactly one root taxon, which is a taxon without parent.
There are no duplicated names.
Each parent taxon is defined by its own row in the table.
The rank is always defined.
In addition, the function also warns if an unknown rank is used. This will still lead to a graph that can be plotted, but the nodes with unknown rank will not be coloured.
The common names (column "name") of the taxa must be unique, because they are used to create the graph. Sometimes, there are taxa that have identical common names, e.g. the family Equidae and the genus Equus are both called "Pferde" in German. In theses cases, one can use an additional identifier in parenthesis to make the names unique, e.g., "Pferde (F)" and "Pferde" for the family and the genus, respectively. The identifier "(F)" will be removed and not be shown in the visualisation.
Examples
file <- get_example_taxonomy_file()
taxonomy <- read_taxonomy(file)
class(taxonomy)
#> [1] "taxonomy_graph" "igraph"
as_tibble(taxonomy)
#> # A tibble: 98 × 8
#> parent name scientific rank extinct local observed image_url
#> <chr> <chr> <chr> <chr> <lgl> <lgl> <lgl> <chr>
#> 1 NA Raubtiere Carnivora Ordn… NA NA NA https://…
#> 2 Raubtiere Hundeartige Caniformia Unte… NA NA NA https://…
#> 3 Hundeartige Hunde Canidae Fami… NA NA NA https://…
#> 4 Hunde Echte Füchse Vulpini Trib… NA NA NA https://…
#> 5 Echte Füchse Vulpes Vulpes Gatt… NA NA NA https://…
#> 6 Vulpes Polarfuchs Vulpes lago… Art NA NA NA https://…
#> 7 Vulpes Rotfuchs Vulpes vulp… Art NA TRUE TRUE https://…
#> 8 Vulpes Wüstenfuchs Vulpes zerda Art NA NA NA https://…
#> 9 Echte Füchse Marderhund Nyctereutes… Art NA TRUE NA https://…
#> 10 Hunde Echte Hunde Canini Trib… NA NA NA https://…
#> # ℹ 88 more rows