Epi-Gala

Great references

• Jekel's: Epidemiology, Biostatistics, Preventive Medicine, and Public Health, 5th Edition
• Epidemiology: Beyond the Basics, 4th Edition
• Dr. Martin Bland's "An Introduction to Medical Statistics"
• "Data from: The reproducibility of research and the misinterpretation of p-values", Colquhoun (DRYAD 2017)
• "Applied Survival Analysis using R"
• Epidemics: Models and Data Using R Links to an external site
• "Maximum Likelihood, Profile Likelihood, and Penalized Likelihood: A Primer", Cole et al. J of Epidemiology 2013
• Basic Models for Disease Occurrence in Epidemiology, Flanders et al. 1995

Topics

Click on white arrow to view a table of key terms, related chapter readings (above list), demo notebooks, and supplemental readings.

Epi tooklits

Topic	Relevant chapters	Supp. readings	Colab demos	Key terms / R functions
Describing trends & variations in data	Jekel:9	"Too many digits"		mean(), sd(), median(), IQR(); stem(); hist()
Bivariate regression & correlation	Bland:11; Jekel:11		Bivariate regression vs correlation	data.frame; t(); matrix()
Sample size; Type I & II errors	Jekel:12
Linear regression	Bland:15 (multiple regression)		Simulate funnel plot, LR recapped
GLM	Jekel:13
Logistic regression	Bland:15.10	Harris’ primer		QQ VIF logit
Frequency measures	Jekel:2; Szklo:2; Szklo:3
Probability; PDFs	Jekel:7-8; Bland:6		Distributions
Bayesian approach	Bland:22			P(D;T)∝P(T;D)xP(D)
Hypothesis testing	Jekel:10-11; "Analysis of cross-tabulations" Bland:13	Chi-square test of independence		Confidence interval; standard error; variance
Clinical Epi	Jekel:7-8; Bland:20.6
Survival data analysis w/ CPH	Bland:16.3 (logrank test)	R package survivalmodels	CPH	survfit()

Study designs

Topic	Relevant chapters	Supp. readings	Colab demos	Key terms / R functions
Experimental	Bland:2; Jekel:4,12-13	Series #11: Data Analysis of Epidemiological Studies		Review on applications of poisson regression logistic regresssion relative risk (vs difference), prevalence, cumulative incidence estimate effect modifications
Observational	Bland:3; Szklo:1; Jekel:5	Series #11		Nested case-control; RCT sample()
Cross-over		Series #18 Crossover	demo
Biases	Jekel:4

Advanced topics

Topic	Relevant chapters	Supp. readings	Colab demos	Key terms
Replication		Harris et al. "Reproducibility of 6 Published Studies in Public Health Services and Systems Research"
Reproducibility	Szklo:9	Coding style guide; Writing functions to prevent errors	forloop
Maximum likelihood	Bland:22.7		Likelihood; AIC; BIC; source()
Predictive models			LDA/ Bone mineral density

R: importing function definitions

ncvTest

source('https://raw.githubusercontent.com/cran/car/master/R/durbinWatsonTest.R');
durbinWatsonTest( fit2 )

source('https://raw.githubusercontent.com/cran/AICcmodavg/master/R/useBIC.R');
message( 'BIC of fit1: ', useBIC( fit1 ) )

source('https://raw.githubusercontent.com/cran/car/master/R/ncvTest.R' ); 
ncvTest( fit2)

epi.2by2

source('https://raw.githubusercontent.com/cran/epiR/master/R/epi.2by2.R')
source('https://raw.githubusercontent.com/cran/epiR/master/R/zexact.R')
source('https://raw.githubusercontent.com/cran/epiR/master/R/zincrate.R')
source('https://raw.githubusercontent.com/cran/epiR/master/R/zRRwald.R')
source('https://raw.githubusercontent.com/cran/epiR/master/R/zRRtaylor.R')
source('https://raw.githubusercontent.com/cran/epiR/master/R/zRRscore.R')
source('https://raw.githubusercontent.com/cran/epiR/master/R/zORwald.R')
source('https://raw.githubusercontent.com/cran/epiR/master/R/zORscore.R')
source('https://raw.githubusercontent.com/cran/epiR/master/R/zlimit.R')
source('https://raw.githubusercontent.com/cran/epiR/master/R/zORml.R')
source('https://raw.githubusercontent.com/cran/epiR/master/R/zARwald.R')
source('https://raw.githubusercontent.com/cran/epiR/master/R/zARscore.R')
source('https://raw.githubusercontent.com/cran/epiR/master/R/zz2stat.R')
source('https://raw.githubusercontent.com/cran/epiR/master/R/zlimit.R')
source('https://raw.githubusercontent.com/cran/epiR/master/R/zMHRD.Sato.R')
source('https://raw.githubusercontent.com/cran/epiR/master/R/zMHRD.GR.R')

epi.2by2( c(13,2163,5,3349) )

riskratio.wald

if (0 & (!exists('riskratio')) )
{
  install.packages("epitools")
  library( epitools )  
  
} else
{
  source( 'https://raw.githubusercontent.com/cran/epitools/master/R/ormidp.test.R' )
  source( 'https://raw.githubusercontent.com/cran/epitools/master/R/tab2by2.test.R' )
  source( 'https://raw.githubusercontent.com/cran/epitools/master/R/table.margins.R' )
  source( 'https://raw.githubusercontent.com/cran/epitools/master/R/riskratio.wald.R' )
  source( 'https://raw.githubusercontent.com/cran/epitools/master/R/epitable.R' )

  riskratio.wald( matrix( c(11,23,11,22), 2) )
}