Exploring Edinburgh Biodiversity

Let’s explore my first R Markdown file together. I am following a tutorial from Coding Club, linked here: https://ourcodingclub.github.io/tutorials/rmarkdown/. Coding Club provided a practice script in RStudio. I am taking that script and using it to make this page. Pretty neat!

Packages

library(dplyr) # for data manipulation
library(pander) # to create pretty tables

Data Exploration

This is a preliminary investigation into the biodiversity of Edinburgh, using data from the National Biodiversity Network Gateway https://data.nbn.org.uk/.

What is the species richness across taxonomic groups?

A table of species richness:

richness <- 
  edidiv %>%
  group_by(taxonGroup) %>%
  summarise(Species_richness = n_distinct(taxonName)) 

pander(richness)
taxonGroup Species_richness
Beetle 37
Bird 86
Butterfly 25
Dragonfly 11
Flowering.Plants 521
Fungus 219
Hymenopteran 112
Lichen 94
Liverwort 40
Mammal 33
Mollusc 97

A barplot of the table above:

barplot(richness$Species_richness, 
        names.arg = richness$taxonGroup, 
        xlab="Taxa", ylab="Number of species", 
        ylim=c(0,600)
        )

What is the most common species in each taxonomic group?

A table of the most common species:

#Create a vector of most abundant species per taxa
max_abund <-
  edidiv %>%
    group_by(taxonGroup) %>%
    summarise(taxonName = names(which.max(table(taxonName))))

#Add the vector to the data frame
richness_abund <-
inner_join(richness, max_abund, by = "taxonGroup")
richness_abund <- rename(richness_abund, Most_abundant =  taxonName, Taxon = taxonGroup)
richness_abund <- rename(richness_abund, 
                        "Most Abundant" = Most_abundant,
                        "Species Richness" = Species_richness) #Change the column names
emphasize.italics.cols(3) #Make the 3rd column italics
pander(richness_abund) #Create a table
Taxon Species Richness Most Abundant
Beetle 37 Coccinella septempunctata
Bird 86 Turdus merula
Butterfly 25 Maniola jurtina
Dragonfly 11 Ischnura elegans
Flowering.Plants 521 Urtica dioica
Fungus 219 Auricularia auricula-judae
Hymenopteran 112 Bombus (Bombus) terrestris
Lichen 94 Xanthoria parietina
Liverwort 40 Lophocolea bidentata
Mammal 33 Sciurus carolinensis
Mollusc 97 Cornu aspersum