• Header of Geometric Morphometrics at Transmitting Science

Advanced Courses in Life Sciences

2nd Edition

Introduction to generalized linear modeling and mixed models using R

October 14th-18th, 2019, Crete (Greece)

Statistics and Bioinformatics

Statistics and Bioinformatics Logo

Introduction to generalized linear modeling and mixed models using R

Course overview

This course will teach some basic skills to help students get the most out of the R statistical programming language and provide an accessible introduction to generalized linear models, generalized additive models, and mixed models.  We will cover the basic R skills necessary to conduct most of the common analyses in the sciences, and then will focus on giving students a working understanding of ANOVA, GLM, GAM, and GLMM.  The course is intended to give students a conceptual understanding of these methods, not just a set of recipes to follow.

By the end of this course, students will understand:

  • How to perform basic actions in R, like reading, writing, and manipulating data.
  • How to design workflows for efficient and reproducible scientific computing.
  • How to make attractive and informative colour graphics from R.
  • The importance of likelihood in statistics.
  • How regression works and what it means.
  • How to choose the appropriate link function and why it is important.
  • How to model fixed vs. random effects.
  • How to construct, validate, and visualize complex models (GLM, GAM, GLMM).

The course is intended primarily for participants who have some experience in R and wish to develop their skills.

 

LOCATION

Arolithos

Servili Tilissos
715 00 Heraklion, Crete (Greece)

Date

October 14th-18th, 2019

LANGUAGE

English

COURSE LENGTH & ECTS

35 hours on-site.

This course is equivalent to 2 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.

The recognition of ECTS by other institutions depends on each university or school.

PLACES

Places are limited to 16 participants and will be occupied by strict registration order.

Participants who have completed the course will receive a certificate at the end of it.

Instructor

Dan Warren instructor for Transmitting Science

Dr. Dan Warren
Senckenberg Biodiversity and Climate Research Center
Germany

Coordinator

Haris Saslis coordinator for Transmitting Science

Dr. Haris Saslis
Transmitting Science
Greece

Requirements

Graduate or postgraduate degree in Life Sciences and basic knowledge of Statistics. The course is intended primarily for participants who have some experience in R and wish to develop their skills.

All participants must bring their own personal laptop (Windows, Macintosh, Linux)

Program

Monday, October 14th, 2019.

Introduction to R and RStudio:

  • The R statistical programming environment.
  • R Studio.
  • Interacting with the console.
  • Reading in data.

Basic R programming:

  • Objects and types.
  • Working with data frames.
  • Functions.
  • Control flow.

Writing and reading scripts.

What to do when things go wrong:

  • Troubleshooting and debugging.
  • Reading R help files.
  • Vignettes.
  • The internet.

Workflows for efficient and reproducible science:

  • R Markdown.
  • Design of a sample analysis.

Tuesday, October 15th, 2019.

Plotting data and models:

  • Data exploration.
  • Base graphics.
  • Intro to ggplot2 and qplot.
  • Exporting publication-quality graphics.

Viridis: making colour plots accessible to everyone.

Likelihood.

ANOVA.

AIC and deviance.

Wednesday, October 16th, 2019.

Simple linear regression:

  • Model diagnostics for linear models.

Multiple regression:

  • Multiple regression vs. multivariate regression.
  • Collinearity.

Variance inflation factors.

GLM – extending linear regression to different types of data:

  • Logistic.
  • Poisson.
  • Negative binomial.

Model diagnostics for complex models.

Thursday, October 17th, 2019.

Mixed models and applied mixed model exercises:

  • Fixed vs. random effects.
  • Nested effects vs. crossed effects.
  • Model selection for mixed models.
  • Visualizing and validating mixed models.

Simulation.

Friday, October 18th, 2019.

Generalized additive models (GAM and GAMM):

  • Model complexity: inference vs. interpretability.
  • Choosing basis functions for smoothers.
  • Visualizing and validating GAMs.

Wrap-up.

Fees

  • Course Fee
  • {{content-1}}
  • Early bird (until June 30th, 2019):
  • 520 *
  • Regular (after June 30th, 2019):
  • 640 *
  • This includes course material, coffee breaks and lunches (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.
  • Course Fee + Accommodation Package
  • {{content-1}}
  • Early bird (until June 30th, 2019):
  • 520 * + 350 = 870
  • Regular (after June 30th, 2019):
  • 640 * + 350 = 990
  • This includes course material, coffee breaks, transportation from and to Barcelona city, accommodation from Sunday to Friday, breakfasts, lunches and dinners (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.

20 % discount will be applied to your fee If you belong to any of the Institutions listed HERE. Discounts (see Funding below) are not cumulative and apply only on the fee.

We offer the possibility of paying in two instalments (contact the course coordinator).

Accommodation

If you take the Accommodation Package option you will be hosted in Arolithos (take a look at the venue), in shared en-suite twin or triple rooms, although you will only share rooms with other classmates. The possibility exists that rooms will be mixed. Therefore, if this is an inconvenience for you, and you require staying in a room with only women or only men, please indicate so in the “Comments” field of the Registration form (see below).

A supplemental charge will be added if you prefer to stay in a single room with private bathroom. The number of single rooms is limited and if you prefer to have one please let us know as soon as possible. If you require more information on accommodation issues please contact the course coordinator.

If you do not want the Accommodation Package, there are several accommodation options in Heraklion. However please be aware that it takes about 25 minutes by car from Heraklion to Arolithos and there is no public transport between both. Therefore course participants will find that staying in Arolithos is more convenient.

How to get to Arolithos from Heraklion, Chania or Rethimnon.

Arolithos street

Arolithos street (Heraklion, Crete, Greece)

Arolithos twin room

Arolithos twin room (Heraklion, Crete, Greece)

Arolithos twin room

Arolithos twin room (Heraklion, Crete, Greece)

Schedule

Course Schedule
  • Monday to Friday:
    • 9:30 to 13:30 Lessons.
    • 13:30 to 15:00 Lunch (included).
    • 15:00 to 18:00 Lessons.
Accommodation Package Schedule
  • Sunday:
    • 17:00 Registration at hotel in central Heraklion.
    • 20:30 Dinner in Heraklion.
  • Monday:
    • 7:30 to 8:30 Breakfast and check-out.
    • 8:30 Transfer from central Heraklion to Arolithos, where the group will stay the rest of the week, and check-in.
    • 20:30 Dinner.
  • Tuesday to Thursday:
    • 8:30 to 9:00 Breakfast.
    • 20:30 Dinner.
  •  Friday:
    • 8:30 to 9:00 Breakfast.
    • 18:00 Meeting at the Venue to take the bus to Heraklion Archaeological Museum (Heraklion).
    • 18:45 Arrival at Heraklion.

    The schedule is approximate; it is possible that the content of one day may run into the next and a working day may be longer than advertised.

Funding

Discounts

Former participants will have a 5 % discount on the Course Fee.

Furthermore, a 20 % discount on the Course Fee is offered for members of some organizations (Organizations with discount). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).

Unemployed scientists living in Greece, as well as PhD students based in Greece without any grant or scholarship to develop their PhD, could benefit from a 40 % discount on the Course Fee. If you want to ask for this discount, please contact the course coordinator. That would apply for a maximum of 2 places and they will be covered by strict inscription order.

Discounts are not cumulative and apply only on the fee, not to Accommodation Package or other options.

Organizers

Transmitting Science Logo

Collaborators

Colegio Oficial de Biólogos de Castilla y León Logo
Colegio Oficial de Biólogos de Euskadi Logo
Colexio Oficial de Biólogos de Galicia Logo
Col·legi Oficial de Biòlegs de la Comunitat Valenciana Logo

Sponsor

Registration