Course – 2nd Edition
Introduction to generalized linear modeling and mixed models using R
October 14th-18th, 2019, Crete (Greece)
Statistics and Bioinformatics
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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.
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)
Contact
LOCATION
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. If the course fills up there will be an assistant instructor to help during the practise time.
Participants who have completed the course will receive a certificate at the end of it.
Program
Daily Program
Monday
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
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
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
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
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
- Early bird (until June 30th, 2019):
- 520 € *
(416 € for Ambassador Institutions) - Regular (after June 30th, 2019):
- 640 € *
(512 € for Ambassador Institutions) - 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
- Early bird (until June 30th, 2019):
- 870 €*
(776 € for Ambassador Institutions)
- Regular (after June 30th, 2019):
- 990 €*
(862 € for Ambassador Institutions) - This includes course material, coffee breaks, transportation between the Venue and Heraklion, accommodation from Sunday to Friday, breakfasts, lunches and dinners (VAT included).
* Participants from companies/industry will have an extra charge of 100 €.
You can check the list of Ambassador Institutions. If you want your institution to become a Transmitting Science Ambassador please contact us at communication@transmittingscience.com
Schedule
Course Schedule
Participants will make their own way
- Monday to Friday:
- 9:30 to 13:30 Lessons.
- 13:30 to 15:00 Lunch (included).
- 15:00 to 18:00 Lessons.
The class 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.
Course + Accommodation Package Schedule
- Sunday:
- 18:30 Meeting at Heraklion Archaeological Museum to take the bus to Gerakári.
- 20:15 Check-in at Alexander Hotel.
- 20:45 Dinner.
- Monday to Thursday:
- 08:00 to 09:00 Breakfast
- 9:30 to 13:30 Lessons
- 13:30 to 15:00 Lunch (included)
- 15:00 to 18:00 Lessons
- 20:30 Dinner
- Friday:
- 8:00 to 9:00 Breakfast.
- 9:30 to 13:30 Lessons
- 13:30 to 15:00 Lunch (included)
- 15:00 to 17:30 Lessons
- 18:30 Meeting at Alexander Hotel to take the bus to Heraklion.
- 20:15 Arrival at Heraklion Archaeological Museum
The class 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.
Accommodation
If you choose the Accommodation Package you will be hosted at Alexander Hotel in Gerakári village, in shared en-suite rooms, although you will only share rooms with other course participants (male or female only).
If you prefer to stay in a single en-suite room, you can do so with a supplementary charge.
More information
The Accommodation Package includes transportation from the centre of Heraklion to the venue and back, at the start and end of the course, respectively. The trip takes around 1 hour 50 minutes each way. If you require transportation from or to Chania (the other city of Crete with an airport), please contact the course coordinator who can arrange it at an additional cost.
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.
Funding
Discounts are not cumulative and apply only on the Course Fee. We offer the possibility of paying in two instalments (contact courses@transmittingscience.com).
5 % Discount
Former participants will have a 5 % discount on the Course Fee.
20 % Discount
20 % discount on the Course Fee is offered for members of some organizations (Ambassador Institutions). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).
40 % Discount
Unemployed scientists living in the country were the course will be held, as well as PhD students based in that country 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.
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