Brachiopods in OBIS

Instructions

Calculate descriptive stats from the Ocean Biodiversity Information System (OBIS) (subset of brachiopod records).

1. Download this file: obis_brachiopoda.csv

2. Read it into R with read.csv()! Check its structure and familiarize yourself with the columns. Every row represents one occurrence of a taxon. These usually belong to a species, but sometimes they are higher-level entries.

3. List the unique genera in the table (column genus). How many genera are there? Do all names make sense? Omit all data rows where the genus column is empty quotes ""

4. We will be working with species-level information. Omit all data rows where the species column is empty quotes ""!

5. Subset your data to the genus "Lingula". List out the species names and count them.

6. Plot a world map with the occurrences of Lingula! First, plot a world map with this chunk of code

# plot a world map with this chunk
library(chronosphere)
ne <- fetch("NaturalEarth")
plot(ne$geometry, col="gray")

To make this work you have to install the chronosphere and sf R extension packages from the CRAN. Which you can do with

install.packages(c("sf", "chronosphere"))

Then you can plot the occurrences using the points() function, with the decimallongitude and decimallatitude columns as x and y coordinates, respectively. Set the arguments of points() so it draws red plus signs!

7. Make sure that the unique list of genera (from step 3.) do not contain the entries that you omitted! Using a for loop count the number of species in every genus!

8. Make a histogram from the number of species in genera!

Expected outputs

1. Species names in the genus Lingula.

2. A world map with the occurrences of Lingula.

3. A named numeric vector with the number of species/genus:

names: names of genera values: the number of species in genera

4. A histogram

Extra questions

Step 7 can be written without a for loop. Do you know how to do it?