RMarkdown_Tutorial_Demo_Rmd.Rmd

---
title: "R Markdown Tutorial Demo"
author: "John Doe"
date: "21/11/2016"
output: html_document
---

##Preamble
###Packages
```{r, message=FALSE, warning=FALSE}
library(dplyr) #for data manipulation
library(pander) #to create pretty tables
```

```{r, include=FALSE}
setwd("~/Desktop")
edidiv <- read.csv("edidiv.csv")
```


##Data Exploration
A preliminary investigation into the biodiversity of Edinburgh, using data from the NBN Gateway https://data.nbn.org.uk/.

###What is the species richness across taxonomic groups?
A table of species richness:
```{r, results='asis'}
richness <- 
  edidiv %>%
    group_by(taxonGroup) %>%
    summarise(Species_richness = n_distinct(taxonName))

richness
```


A barplot of the table above:
```{r, fig.align="center", fig.width=15, fig.height=8}
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:
```{r}
#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)
```

```{r}
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
```