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Statistics for biologists using R

carlo pecoraro, June 14, 2017
 

Course: STATISTICS FOR BIOLOGISTS USING R https://www.physalia-courses.org/courses-workshops/course13/

Dates

18-23 September 2017

Course overview

This course will demonstrate the extensive capabilities of the R environment, and seek to develop/broaden the competency of participants in the use of R statistical applications. The course will have two components presented in morning and afternoon sessions over five days. Component one (Monday Sept. 18, Tuesday Sept. 19) will emphasize R programming characteristics including data management, use of existing package functions, graphics, customized function writing, calling routines from compiled languages, and documentation. The second component (Wednesday Sept. 20 – Friday Sept. 22) will address implementation of statistical analyses with R, particularly linear models. The materials will be presented using biological examples, making frequent use of the library asbio (Applied Statistics and Statistical Pedagogy for Biologists). Intended audience

This course is aimed at scientists, particularly biologists. While no previous experience with R is required, participants should have at least a basic familiarity with statistical terms and concepts.

Curriculum

Monday 18th – Classes from 09:30 to 17:30

Session 1 – R basics

In this session we will briefly consider the history of R, including trends in usage and package development, the relationship of R to other languages and platforms, and the reliability of R base and user-contributed packages. We will then learn and conduct basic command line operations, including defining R programming options, saving work, mathematical functions, simple descriptive statistics functions, utilization of expressions and assignments, R-objects and classes, auxiliary R-packages, accessing and exploring internal R datasets, and getting help.

Session 2 –R graphics

In this session we consider the properties, capabilities, and extensions of R graphics. Session topics will include discussion of the R graphical devices, learning how to alter parameters to make simple plots and multilayer complex plots (e.g., those containing multiple distinct graphs, multiple y and x-axes, unusual fonts, 3d graphics, etc.), lattice graphics, graphical packages (especially ggplot) and the creation of publication-ready high resolution figures.

Tuesday 19th – Classes from 09:30 to 17:30

Session 3 – Handling data in R

The session will address handling data in R. Topics will include properties of R data structures (i.e., vectors, matrices, dataframes, and arrays), command line data entry, importing/exporting delimited spreadsheets and other data, subsetting and querying data, testing and coercing objects, pattern matching, and functions for matrix/dataframe/array management and manipulation.

Session 4 – Writing functions

The session will consider user-defined functions using several extended examples. Topics will include looping, graphical animation, the utilization and development of GUI, and calling routines from compiled languages.

Wednesday 20th – Classes from 09:30 to 17:30

Session 5 –Documentation of work in R and basic applications in statistics

This session will conclude topics in function writing by considering approaches for documenting workflow and function characteristics in R. The session will then turn to the topic of statistical analysis in earnest. Topics will include probability density functions, point estimation (including least squares, maximum likelihood and MOM approaches), and intervallic estimators, including conventional confidence intervals on a priori sampling distribution assumptions, along with bootstrapping approaches and Bayesian credible intervals.

Session 6 –General linear models I

We will begin this session by considering simple methods for making inferences concerning the difference in measures of population location parameters, e.g., t-tests and their non-parametric analogues. We will then introduce general linear models with simple and multiple regression. Emphasis will be given to model selection approaches.

Thursday 21st – Classes from 09:30 to 17:30

Session 7 –General linear models II

This session will continue exploration of general linear models by considering ANOVA approaches including one way ANOVAs with fixed and random effects, two way designs including factorial designs and blocked designs as fixed and mixed effect models. We will also consider methods for simultaneous inference for factor level comparisons.

Session 8 – Generalized linear models, locally fitted models, and associated topics

This session will briefly consider R applications for specialized response variables and locally fitted models. Topics will include logistic and Poisson generalized linear models (GLMs) and definitions of model efficacy in these contexts. Also explored will be locally fitted models, including splines, and their use in generalized additive models (GAMs).

Friday 22nd – Classes from 09:30 to 17:30

Session 9 –Multivariate approaches

This session will briefly consider R applications for the analysis of multivariate data. Topics will include resemblance indices, multivariate hypothesis testing with MANOVA, and permutational MANOVA, ordination, and cluster analysis.

Session 10- Unfinished materials, student data

This session will be devoted to completing unfinished topics and the analysis of student data using methods discussed during the course.