[R-sig-ME] Course "Introduction to Mixed (Hierarchical) models for biologists using R"
Oliver Hooker
oliverhooker at prstatistics.com
Mon Nov 6 13:04:28 CET 2017
Introduction to Mixed (Hierarchical) models for biologists using R
(IMBR01)
https://www.prstatistics.com/course/introduction-to-mixed-hierarchical-models-for-biologists-using-r-imbr01/
14th May 2018 - 18th May 2018
Prof. Subhash Lele
Course overview:
Mixed models, also known as hierarchical models and multilevel models,
is a useful class of models for many applied sciences, including
biology, ecology and evolution. The goal of this course is to give a
thorough introduction to the logic, theory and most importantly
implementation of these models to solve practical problems in ecology.
Participants are not expected to know mathematics beyond the basic
algebra and calculus. Participants are expected to know some R
programming and to be familiar with the linear and generalized linear
regression. We will be using JAGS (Just Another Gibbs Sampler) for
Markov Chain Monte Carlo (MCMC) simulations for analyzing mixed models.
The course will be conducted so that participants have substantial
hands-on experience.
Monday 14th
Linear and Generalized linear models
To understand mixed models, the most important first step is to
thoroughly understand the linear and generalized linear models. Also,
when conducting the data analysis, it is useful to fit a simpler fixed
effects model before trying to fit a more complex mixed effects
model. Hence, we will start with a very detailed review of these models.
We are assuming that the participants are familiar with these models and
hence we will emphasize some important, but not commonly covered,
topics. This will also give us an opportunity to unify the notation,
review the basic R commands and fill out any gaps in knowledge and
understanding of these topics.
1. We will show the use of non-parametric exploratory techniques such as
classification and regression trees (CART) for learning about important
covariates and possible non-linearities in the relationships.
2. We will emphasize graphical and simulation based methods (e.g. Gelman
and Hill, 2006) to understand and explore the implications of the
fitted model.
3. We will discuss graphical tools such as marginal and conditional
plots that are useful for conveying the results of a multiple regression
model to a lay person.
4. We will emphasize the use of graphical tools to conduct regression
diagnostics and appropriateness of the model.
5. We will discuss the important concepts of confounding, effect
modification and interaction. These are particularly important to
conduct causal, not just correlational, inference using observational
studies.
Tuesday 15th
Computational inference
Many of the topics that will be covered involve the use of matrix
algebra and calculus. While these mathematical techniques are essential
tools for a mathematical statistician who is trying to understand the
theory behind the methods, they can be avoided in practice by using
simulation based techniques. The built-in functions such as the ’lm’
and ’glm’ to fit the regression models use the method of maximum
likelihood to estimate the parameters and conduct statistical inference.
We will discuss the use of JAGS (Just Another Gibbs Sampler) and the R
package ’dclone’ to fit the same models. We will use a different
statistical philosophy, namely the Bayesian inference, to fit these
models. We will show how the Bayesian approach can be tricked into
giving frequentist answers using data cloning (Lele et al. 2007, Ecology
Letters). We will also discuss the rudiments of frequentist and Bayesian
inference although we will not go into the pros and cons of them at this
time. That will be covered during sessions 3 and 4 of the fifth day
(and, over beer afterwards).
1. What makes an inference statistical inference?
2. What do we mean by probability of an event?
3. How do we quantify uncertainty in an inferential statement in the
frequentist framework?
4. How do we quantify uncertainty in an inferential statement in the
Bayesian framework?
We will then discuss the simulation based methods to quantify
uncertainty.
1. Parametric bootstrap to quantify frequentist uncertainty
2. Markov Chain Monte Carlo to quantify Bayesian uncertainty
3. Fitting LM and GLM using JAGS and Bayesian approach
Wednesday 16th
Linear Mixed Models
Historically, linear mixed models arose in the study of quantitative
genetics and heritability issues. They were successfully applied in
animal breeding and led to the ’white’ revolution with abundance of
milk supply for the developing world. They were, also, used in horse
racing and other such fun areas. The other situation where linear mixed
effects models were developed were in the context of growth curves. We
will follow this historical trajectory of mixed models, paying tribute
to the great statisticians R. A. Fisher, C. R. Rao and Jerzy Neyman, and
study linear mixed models first. The questions they tried to solve
were: Deciding the genetic value of a sire and/or a dam, studying
heritability of traits, studying co-evolution of traits etc. These can
be answered provided we assume that the sires and dams in our experiment
or sample are merely a sample from a super-population of sires and dams.
In growth curve analysis, we need to take into account that each
individual is unique in its own way but is also a part of a population.
How do we discuss both individual level and population inferences? In
modern times, linear mixed effects models have arisen in the context of
small area estimation in survey sampling where one is interested in
inferring about a census tract based on county or state level data.
These models arise also in the context of combining remote sensed data
from different resolutions and types. The main issues that we will be
discussing are:
1. What is a random effect? What is a fixed effect? How do we decide
if an effect is random or fixed?
2. How do we modify a linear regression model to accommodate random
effects?
3. Why bother fitting a mixed effects models? What do we gain?
4. How to modify the JAGS linear models program to fit a linear mixed
effects model using JAGS?
5. What is the difference between a Bayesian and a frequentist
inference?
6. What is a prior? What is a non-informative prior?
7. How do we interpret the results of a linear mixed effects model
fit? Graphical and simulation based methods
8. How do we do model selection with mixed effects models?
9. How do we do model diagnostics in mixed effects models?
10. Parameter identifiabilty issues in linear mixed models
As we discuss these applications, we will discuss some subtle
computational issues involved in using MCMC. In my recollection (which
may be biased as it has been about 25 years since the quote), Daryl
Pregibon said: MCMC is the crack cocaine of modern statistics; it is
addictive, seductive and destructive. Hence, it is important for a
practitioner to understand these issues in order not to misuse the MCMC
technique.
1. What is a Markov Chain Monte Carlo method? Why is it necessary for
mixed models?
2. What are the subtleties in implementing MCMC?: Convergence of the
algorithm, Mixing of the chains.
3. Pros and cons of using MCMC
Thursday 17th
Generalised Linear Mixed Models
We will again start the discussion of GLMM in its historical context.
One of the initial uses of mixed models were in the context of over
dispersion in count data. Zero inflated count data was another
important example. The example that drove the current revolution in the
use of GLMM was in the context of spatial epidemiology. Clayton and
Caldor (1989, Biometrics) showed that one can use spatial correlation to
improve the prediction in mapping disease rates. This was also an
example of the application of Empirical Bayes methods that allow one to
pool information from different spatial areas (or, studies, or, scales,
and so on).
1. Zero inflated data In many practical situations, we observe that
there are many locations where there are zero counts, far in excess of
what would be expected under the Poisson regression model. This can be
effectively modelled using a mixed model framework. The mixed models
framework allows us to use much more complex and realistic models.
2. Over dispersion in GLM, Spatial GLM, Spatio-temporal GLM The Poisson
regression model assumes that the mean and variance are equal. This is,
often, not true in practice. Generally the variance in the data exceeds
the mean. One can show that such over-dispersion can be modelled using a
mixed effects model. These models also arise in the context of
capturerecapture sampling where capture probabilities vary across space
or time or individuals.
3. Longitudinal or panel data with discrete response variable Many times
we have data on different individuals where within the individual there
is temporal dependence but individuals are independent of each other.
Cluster sampling is another situation where we have dependence within a
cluster but independence between clusters. Such data needs to take into
account the innate variation between individuals before one can discuss
the effect of interesting covariates or risk factors. Such data are
effectively modelled as GLMM.
4. Measurement error, missing data Missing data and measurement error
are ubiquitous in ecological studies. Mixed models provide a convenient
way to take into account these difficulties and infer about the
underlying processes of interest. We will discuss these issues in the
context of Population Viability Analysis, Spatial population dynamics
and source-sink analysis, Occupancy and abundance surveys. These also
arise while doing usual linear and generalized linear models if the
covariates are measured with error.
5. Additional topics depending on the interest of the participants.
These may include, for example, discussion of Species Distribution
Models, Resource Selection Functions and Animal movement models.
6 Computational issues: Advanced topics
Friday 18th
Mixed Models in a Bayesian Framework
MCMC is not the only approach to analyse mixed models. We will briefly
discuss Laplace approximation based techniques (INLA, in particular)
along with approximate techniques such as Composite likelihood and
Approximate Bayesian Computation. Because of the mathematical nature,
this discussion will be somewhat limited, only giving the basics and
hinting at the important issues.
7 Philosophical issues: Sophie’s choice
1. What are the philosophical problems with using the frequentist
quantification of uncertainty?
2. What are the philosophical problems with using the Bayesian
quantification of uncertainty?
3. Sophie’s choice?
Other upcoming courses
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4. December 4th - 8th 2017
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5. January 29t – February 2nd 2018
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7. February 19th – 23rd 2018
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Dr. Antigoni Kaliontzopoulou
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Glasgow, Scotland, Dr. Neftali Sillero
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11. March 19th – 23rd 2018
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Myuna Bay sport and recreation, Australia, TBC
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--
Oliver Hooker PhD.
PR statistics
2017 publications -
Ecosystem size predicts eco-morphological variability in post-glacial
diversification. Ecology and Evolution. In press.
The physiological costs of prey switching reinforce foraging
specialization. Journal of animal ecology.
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