Difference between revisions of "CRG PhD & Masters Course 2016 Introduction to Statistics in R"

Revision as of 16:18, 7 September 2016

Course Description

This introductory course to statistics and R is offered in 3 consecutive modules (please see Course Syllabus below), each consisting of A two-hour practicum in a computer class, using R Studio.

Course Objectives

To introduce the basic concepts of statistics and how they can be applied to real-life datasets using R. Knowledge of statistics or R is not required for taking this course. However, familiarity with the material in the previous modules is recommended if the modules are not taken in a sequence.

Course Instructors

• Sarah Bonnin (Module I) sarah.bonnin@crg.eu
• Julia Ponomarenko (organizer, Module II) julia.ponomarenko@crg.eu
• German Demidov (Module III) german.demidov@crg.eu

Time and Location

• Oct 5, 10, 11, 2016. 11:00 - 13:00. PRBB Building. Boinformatics classroom. 468. 4th floor. The hotel wing.

Course Syllabus, Schedule, and Materials

MODULE I. Descriptive statistics. Oct 5, 2016.

• Introduction to R programming language and R Studio: Data types, variables, packages, functions, handling files/scripts/projects.
• Exploratory data analysis: bar-plot, histogram, box-plot, scatter-plot, pie charts. Outliers.
• Basic plots in R. The ggplot2 package.
• TO CHANGE TO A NEW ONE. SCRIPT.View pdf-file in this browser window.
• TO CHANGE TO A NEW ONE. SLIDES.View pdf-file in this browser window.

TO MAKE UP THE OTHER TWO MODULES

MODULE II. Introduction to Probability. May 9, 2016. CRG.

• LECTURE. View slides in this browser window. Independence, conditional probability, Bayes formula. Distributions, population mean and population variance, Binomial, Poisson, and Normal distribution. Central Limit theorem and the Law of large numbers. Continuity correction. Sampling with and without replacement. Correction for finite population size.
• PRACTICUM. Download the zip-file. Elementary probability problems in R, pdf and cdf functions, simulation explicating the law of large numbers.
• STATISTICAL TABLES
• QUIZ 2

MODULE III. Statistical Inference, part I. May 13, 2016. CRG.

• LECTURE. View slides in this browser window. Statistical Inference, part I. The concept of hypothesis testing, type I and type II error, false discovery rate. Significance and confidence level, p-value. Confidence intervals. One-sided and two-sided tests and confidence intervals. Sampling distribution, estimators, standard error. Normal probabilities in application to p-value. One-sample and two-sample tests for independent and matched samples with known variance. The case of unknown variance and Student t-distribution, assumption of normality. Pooled variance and equal variances assumption.
• PRACTICUM. Download the zip-file. One- and two-sample tests with known and unknown variance, test for proportions, simulation involving confidence intervals and t-distribution.
• QUIZ 3

MODULE IV. Statistical Inference, part II. May 18, 2016. CRG.

• LECTURE. View slides in this browser window. Statistical Inference, part II. Estimation of variance. Fisher test for variance equality. Non-parametric tests. Sign test, Wilcoxon sum of ranks test (Mann-Whitney U-test), Wilcoxon signed rank test. Chi-square test for goodness of fit, chi-square test for independence. Kolmogorov-Smirnov (KS) test. Shapiro test for normality. Sample size estimation. Correction for multiple testing, family-wise error rate.
• PRACTICUM. Download the zip-file. Tests with unknown variance, non-parametric tests, simulations explicating non-parametric tests, FDR.
• QUIZ 4

MODULE V. Statistical modeling, Regression. May 20, 2016. CRG.

• LECTURE. View slides in this browser window. Simple linear regression model, residuals, degrees of freedom, least squares method, correlation coefficient, variance decomposition, determination coefficient. Interpretation of the slope, correlation, and determination coefficients. Standard error and statistical inference in simple linear regression model. Analysis of variance (ANOVA). One-way and two-way ANOVA.
• PRACTICUM. Download the zip-file. Problems on linear regression, ANOVA, data transformation.
• QUIZ 5

External Resources

• Nature Web-collection "Statistics for Biologists"
• 100 Statistical Tests.pdf - ResearchGate - just search Google to get a link
• Book "Basics of Statistics" by Jarko Isotalo
• "Introduction to Probability and Statistics using R" by G. Jay Kerns
• R Tutorials by William B. King
• Tutorials "R for basic statistics"
• Blog "R-bloggers"
• StatsBlogs
• Blog "Learning R"
• Blog "R you ready?"
• "R-statistics blog"
• Self-paced online courses from UC Berkeley: Descriptive Statistics. Probability. Inference.
• Online book recommended for the UC Berkeley courses
• Self-paced online course "Explore Statistics with R"
• Online course from Stanford "An Introduction to Statistical Learning with Applications in R"
• Self-paced online course from Microsoft "Intro to R programming"
• Self-paced online course from Harvard "Statistics and R"
• Self-paced online course from Harvard "Statistical Inference and Modeling for High-throughput Experiments"
• VIB "Basic statistics theory" course slides.
• VIB "Basic statistics in R" course. Tutorial, excercises, cheat sheets.