DataForIrina

The goal of DataForIrina is to document the steps taken for the Dataset provided to Irina

load needed packages

library(dplyr)
library(data.table)
library(readxl)

we will start by reading the dataset delivered to us from from the biodiversiy council, this dataset was generated on the 21st of September of 2022.

ToClean <- readxl::read_xlsx("2022-09-21.xlsx") 

Filter data

We then filter the dataset to include only plants

OnlyPlants <- ToClean |> 
  # make all names machine readable
  janitor::clean_names() |>
  # Filter to Kingdom Plantae
  dplyr::filter(rige == "Plantae")

Bot not all this have been resolved to species level, in the table bellow we see the number of taxa that have been resolved to which level

taxonrang	n
Art	5333
Slægt	1562
Hybrid	612
Underart	460
Familie	358
Varietet	303
Orden	126
Form	70
Klasse	32
Sektion	25
Række	10
Superart	8

We want to keep only some of this, so we only include the ones that are to the level of Species, Form, Subspecies, and Variety (Art, Form, Underart, Varietet).

OnlyPlants <- OnlyPlants |> 
  # Filter only some resolutions
  dplyr::filter(taxonrang %in% c("Art", "Form", "Underart", "Varietet")) |> 
# Ensure no duplecates
  dplyr::distinct()

This leaves us with 6,166 valid taxa. this dataset can be downloaded here

Remove introduced species

Another dataset was made where we removed introduced species

OnlyNatives <- OnlyPlants |> 
  dplyr::filter(herkomst != "Introduceret" | is.na(herkomst)) 

This leaves us with 4,891 valid taxa. this dataset can be downloaded here

Download Datasets

• OnlyPlants Dataset: Filtered dataset including only plant taxa.

• OnlyNatives Dataset: Dataset with introduced species removed.