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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

Alexander Hotel

Gerakári, Municipality of Amari, 74 061
Rethymno
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
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  • 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 between the Venue and Heraklion or Chania 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 choose the Accommodation Package you will be hosted at Alexander Hotel in Gerakári village (take a look at the venue), in shared en-suite twin rooms, although you will only share rooms with other course participants. There is a possibility that the rooms will be mixed. If this is an inconvenience for you, and you would prefer to stay in an all-female or all-male room, please indicate so in the “Comments” field of the Registration form (below).

If you prefer to stay in a single en-suite room, you can do so with a supplementary charge.

The Accommodation Package includes transportation from the centre of both Heraklion and Chania (the two main cities of Crete with airports) to the venue and back, at the start and end of the course, respectively. The trip takes around 1 hour 50 minutes each way. Once you have booked your flights, please let the course coordinator know which airport you are flying in and out of, in order to arrange your transportation.

If you do not wish to take the Accommodation Package, you can find a few other options in the surrounding area. However, please be aware that access to and travelling around the area requires a private vehicle as public transport is scarce. Therefore, course participants will find choosing the Accommodation Package more convenient.

Alexander Hotel, Gerakári

Alexander Hotel 1

Alexander Hotel twin room

Alexander Hotel, Gerakári

Alexander Hotel 2

Alexander Hotel, Gerakári

Alexander Hotel 3

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:
    • 18:30 Meeting in Heraklion (Archaeological Museum) or Chania (Coach Station) to take the bus to Gerakári.
    • 20:15 Check-in at Alexander Hotel.
    • 20:45 Dinner.
  • Tuesday to Thursday:
    • 8:30 to 9:00 Breakfast.
    • 20:30 Dinner.
  •  Friday:
    • 8:30 to 9:00 Breakfast.
    • 18:30 Meeting at Alexander Hotel to take the bus to Heraklion or Chania.
    • 20:15 Arrival in Heraklion (Archaeological Museum) or Chania (Coach Station).

    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