Introduction to BASV53

with R

Aurélien Ginolhac, DLSM

University of Luxembourg

Tuesday, the 25^th of February, 2025

Hello!

What you can do now:

• Check for material at the main site

https://basv53.uni.lu

• Install R, RStudio and packages

setup

Check your install

library(tidyverse)
read_csv("https://biostat2.uni.lu/practicals/data/swiss.csv",
         show_col_types = FALSE) |>
  pivot_longer(cols = c(Fertility, Agriculture),
               names_to = "measurement", 
               values_to = "value") |>
  ggplot(aes(x = value, y = Education, colour = measurement)) +
  geom_point() +
  geom_smooth(method = "loess", formula = "y ~ x") +
  theme_bw(14)

Overview

This course provides an introduction to and the tidyverse, one of its dialect.

• Brief computer history, programming and hardware notions
• Biology track: data analysis is mandatory
• Focusing on loading and cleaning data for exploratory visualizations

Lectures

• Slides, formal lecture
• Quick exercises inserted
• Unprepared live demo

Practicals

• Detailed exercises
• Solutions hidden/revealed

Projects

• Different projects, team up by (2, 3)
• Due date: June
• 10 min defense
• No slides to prepare: Quarto HTML

This course is composed of ~ 30 hours (2 ECTS)

1 ECTS

• Written and practical exam, qmd file
• 2 hours
• All document allowed
• Internet allowed
• AI allowed if tool specified and prompt included

1 ECTS

• Home work project in a group
• AI allowed if tool specified and prompt included
• Wide range of subjects:
  • Gene expression in yeast cells
  • Spotify song characteristics
  • Temperatures from ice records
  • Voyager Golden Record images
  • CO₂ worldwide emissions
  • Human genome gene structures
  • Colon rectal cancer microarray

Internet access allowed. Watch out for time!

Why allowed ?

Hello my name is Joby, I have a PhD in Physics and I work for NASA and I just had to look up the equation for the volume of a sphere

— Joby Hollis 🏳️ 🌈🇪🇺 (@Jobium) 3 September 2018

Downside!

• Time vanishes fast if you aren’t prepared
• AI is NOT running code

Teacher

Aurélien Ginolhac

• Bioinformatician
• : Work at the Department of Life Sciences and Medecine
  University of Luxembourg
  Campus Belval - 6 avenue du Swing
  KT4 – Office 403 L-4367 Belvaux
• +352 46 66 44 6560
• : aurelien.ginolhac@uni.lu

This website

Entirely built with Quarto, and hosted on the LCSB Gitlab

Highlights, more data science than pure computing

• Computer parts
• Programming basics, exemplified in
  • Data types
  • Data structures
  • Sub-setting
  • Control flow for and if
• Data wrangling
  • Import data
  • Manipulating
  • Visualizing
• Literate programming
  • Quarto

Literate programming, separate content from formatting

HTML

PDF

Demo live: French first names over 120 years

Dataset was gathered by a French company Thinkr, compiling babies names in France over 120 years (data from the French statistic institute INSEE)

Dataset

remotes is itself a package that is not part of base, you can install it with:

install.packages("remotes")
remotes::install_github("ThinkR-open/prenoms")

Loading a package is a call to library():

library(prenoms)

prenoms_france

# A tibble: 648,370 × 5
    year sex   name          n      prop
   <dbl> <chr> <chr>     <int>     <dbl>
 1  1900 F     Abeline       3 0.0000127
 2  1900 F     Abelle        3 0.0000127
 3  1900 F     Ada           4 0.0000170
 4  1900 F     Adelaide    194 0.000822 
 5  1900 F     Adelheid      3 0.0000127
 6  1900 F     Adelia       12 0.0000509
 7  1900 F     Adelie        3 0.0000127
 8  1900 F     Adelina      50 0.000212 
 9  1900 F     Adeline     224 0.000949 
10  1900 F     Adelphine    19 0.0000805
# ℹ 648,360 more rows
# ℹ Use `print(n = ...)` to see more rows

Data analysis

Questions?

• Number of babies born per year
• Births per month across recent years
• Ratio Male / Female
• Evolution of your first names
• Dynamic of novelty
• Novelty versus Saints
• Double gender first names
• …