kaz_yos RPubs Table of Contents

Overview

Top page http://rpubs.com/kaz_yos

useR at HSPH http://rpubs.com/kaz_yos/useR_at_HSPH

Loading and manipulating data

Functions for loading data http://rpubs.com/kaz_yos/reading-data-into-R

SAScii package for old SAS dataset http://rpubs.com/kaz_yos/SAScii

Table to raw data http://rpubs.com/kaz_yos/expand-table

Indexing using variables that contain NA http://rpubs.com/kaz_yos/is-element

Missing data handling (R in Action) http://rpubs.com/kaz_yos/mice-amelia

Basics

Adjustment for multiple testing (Bonferroni, Holm, Hochberg, FDR q-value) http://rpubs.com/kaz_yos/multiple-testing

95% confidence interval with different sample sizes http://rpubs.com/kaz_yos/confint95

Linear Regression

Model formula, effect graphs, interaction graphs http://rpubs.com/kaz_yos/lm1

Model selection http://rpubs.com/kaz_yos/lm2

Interaction plots http://rpubs.com/kaz_yos/effects

car package plotting function for residual analysis http://rpubs.com/kaz_yos/car-residuals

Residual analysis BIO213 version http://rpubs.com/kaz_yos/residuals-bio213

Simplified residual analysis with car package http://rpubs.com/kaz_yos/residuals-bio213-abbr

Collinearity http://rpubs.com/kaz_yos/lm-collinear

Logistic Regression

Model formula, effect graphs, interaction graphs http://rpubs.com/kaz_yos/logit1

Extracting 95% CI and p-value http://rpubs.com/kaz_yos/glm-ratio

Conditional logistic regression http://rpubs.com/kaz_yos/clogit

Ordinal logistic regression http://rpubs.com/kaz_yos/polr

Polytomous logistic regression http://rpubs.com/kaz_yos/polytomous

Unified approach to ordinal and polytomous logistic regression using VGAM http://rpubs.com/kaz_yos/VGAM

Propensity scores

Use of propensity scores (Adjustment, Stratification, Matching, and Weighting) http://rpubs.com/kaz_yos/epi271-lab3

Use of propensity scores illustrated http://rpubs.com/kaz_yos/use-ps

Propensity score using right heart cath dataset http://rpubs.com/kaz_yos/ps-rhc

Generalized linear models (Poisson regression, etc)

Poisson regression for rates http://rpubs.com/kaz_yos/poisson

Negative binomial regression http://rpubs.com/kaz_yos/nb

Modeling skewed continuous outcome using Gamma family in glm() http://rpubs.com/kaz_yos/glm-Gamma

Relative risk regression for common outcome http://rpubs.com/kaz_yos/epi204-lab4

Prediction modeling

Prediction model assessment (including Net reclassification improvement) http://rpubs.com/kaz_yos/performance

EPI288 Prediction modeling and validation http://rpubs.com/kaz_yos/epi288-validation3

Clinical Prediction Models: Shrinkage, Penalized ML, and Lasso http://rpubs.com/kaz_yos/predict-chap13

Automated model selection

All-subset for linear, logistic, and Cox regressions http://rpubs.com/kaz_yos/all-subset

DIY all-subset for coxph http://rpubs.com/kaz_yos/exhaustive

drop1/add1 manual stepwise http://rpubs.com/kaz_yos/stepwise

Repeat univariable regression for different predictors http://rpubs.com/kaz_yos/repeat-univariate-rsas

Survival analysis

Different hazard functions and corresponding survival curves http://rpubs.com/kaz_yos/hazard-functions

Kaplan-Meier plots Japanese http://rpubs.com/kaz_yos/1547

Kaplan-Meir plots using rms::survplot http://rpubs.com/kaz_yos/km-curves

Time-dependent AUC and integrated AUC http://rpubs.com/kaz_yos/survival-auc

Checking model fit and PH assumption of Cox PH model http://rpubs.com/kaz_yos/coxph-residuals

Checking PH assumption with cox.zph function http://rpubs.com/kaz_yos/cox-zph

Kleinbaum: Different ways to check proportional hazards assumption http://rpubs.com/kaz_yos/kleinbaum-ph-assumption

Kleinbaum: stratified Cox regression http://rpubs.com/kaz_yos/kleinbaum-stratified

Time-dependent covariates Japanese http://rpubs.com/kaz_yos/coxph-time-dep-j

Time-dependent covariates considering clustering http://rpubs.com/kaz_yos/bio223-recidivism

Non-parametric vs Parametric models http://rpubs.com/kaz_yos/survival-parametric

Non-parametric vs Parametric models Japanese http://rpubs.com/kaz_yos/survival-parametric-j

BIO223 Exponential and Weibull model http://rpubs.com/kaz_yos/bio223-survreg

Quantile regression

quantreg for Quantile regression http://rpubs.com/kaz_yos/quantreg

Graphics

ggplot2 for dotplot http://rpubs.com/kaz_yos/1406

GapMinder with ggplot2 http://rpubs.com/kaz_yos/1285

Color chart http://rpubs.com/kaz_yos/color-chart

Venn diagrams http://rpubs.com/kaz_yos/venn

ggplot2

Create a graph from multiple layers Japanese http://rpubs.com/kaz_yos/ggplot2-layers-j

Create a graph from multiple layers http://rpubs.com/kaz_yos/ggplot2-layers

ggplot2 book examples http://rpubs.com/kaz_yos/ggplot2-toolbox

stat_summary() for summarizing data within ggplot2 http://rpubs.com/kaz_yos/ggplot2-summary2

legend http://rpubs.com/kaz_yos/ggplot2-legend

axis http://rpubs.com/kaz_yos/ggplot2-axis

stat_function() to plot functions without data http://rpubs.com/kaz_yos/ggplot2-stat-function

Epidemiology

Epidemiology: Beyond the Basics: Analysis of Age, Birth Cohort, and Period Effects http://rpubs.com/kaz_yos/epi-cross-long

Modern Epidemiology Chapter 10: Demonstration of p-value functions http://rpubs.com/kaz_yos/p-val-fun

SIR models in R http://rpubs.com/kaz_yos/sir

Causal inference methods

IPW and marginal structural model using ipw package and geepack/survey packages http://rpubs.com/kaz_yos/epi289-4-ipw-msm

Use of both IPTW and IPCW to adjust for both confounding and selection bias http://rpubs.com/kaz_yos/epi289-4-iptcw

Clinical epidemiology

ROC and comparison Japanese http://rpubs.com/kaz_yos/1713

Sensitivity and specificity from ROC http://rpubs.com/kaz_yos/pROC-coords

pROC in moderately large data http://rpubs.com/kaz_yos/pROC-large

Sensitivity and specificity and posterior probability http://rpubs.com/kaz_yos/pre-post-prob

meta package for meta-analysis http://rpubs.com/kaz_yos/meta

Bayesian

Dobson An Introduction to GLM: Chapter 12 Bayesian Analysis http://rpubs.com/kaz_yos/dobson-bayesian

Doing Bayesian Data Analysis

Coin toss http://rpubs.com/kaz_yos/doing-bayes-F3-1

Model comparison http://rpubs.com/kaz_yos/doing-bayes-F4-1

Different beta distributions http://rpubs.com/kaz_yos/doing-bayes-F5-1

Prior distribution and their influences http://rpubs.com/kaz_yos/doing-bayes-F5-2

etc

Deducer for baseline comparison Japanese http://rpubs.com/kaz_yos/deducer

knitr configuration for RPubs http://rpubs.com/kaz_yos/knitr-config

Restoring packages at major update http://rpubs.com/kaz_yos/same-pkgs

HSPH 2012-

BIO201 HW1 http://rpubs.com/kaz_yos/1574

BIO201 HW2 http://rpubs.com/kaz_yos/1692

BIO201 HW3 http://rpubs.com/kaz_yos/bio201hw3

BIO201 HW4 http://rpubs.com/kaz_yos/bio201hw4

BIO213 HW3 http://rpubs.com/kaz_yos/bio213hw3

BIO213 HW4 http://rpubs.com/kaz_yos/bio213hw4

BIO213 HW5 http://rpubs.com/kaz_yos/bio213hw5

BIO213 HW6 http://rpubs.com/kaz_yos/bio213hw6

BIO213 HW7 http://rpubs.com/kaz_yos/bio213hw7

BIO213 HW8 http://rpubs.com/kaz_yos/bio213hw8

BIO223 HW1 http://rpubs.com/kaz_yos/bio223hw1

BIO226 GEE http://rpubs.com/kaz_yos/bio226-gee

BIO226 HW2 http://rpubs.com/kaz_yos/bio226hw2

BIO226 HW3 http://rpubs.com/kaz_yos/bio226hw3

BIO226 HW5 http://rpubs.com/kaz_yos/bio226hw5

BIO509 HW1 http://rpubs.com/kaz_yos/bio509hw1

BIO509 HW3 http://rpubs.com/kaz_yos/bio509hw3

EPI204 Lab1 http://rpubs.com/kaz_yos/epi204-lab1

EPI204 Lab2 http://rpubs.com/kaz_yos/epi204-lab2

EPI204 Lab4 http://rpubs.com/kaz_yos/epi204-lab4

EPI204 Lab5 http://rpubs.com/kaz_yos/epi204-lab5

EPI204 HW2 http://rpubs.com/kaz_yos/epi204-hw2

EPI204 HW3 http://rpubs.com/kaz_yos/epi204-hw3

EPI271 Propensity score analysis Lab1 http://rpubs.com/kaz_yos/epi271-lab1

EPI271 Propensity score analysis Lab2 http://rpubs.com/kaz_yos/epi271-lab2

EPI271 Propensity score analysis Lab3 http://rpubs.com/kaz_yos/epi271-lab3

EPI288 Multiple testing http://rpubs.com/kaz_yos/epi288-multiple

EPI288 Cluster analysis http://rpubs.com/kaz_yos/epi288-cluster

EPI288 Principal component analysis http://rpubs.com/kaz_yos/epi288-pca

EPI288 Prediction modeling and validation http://rpubs.com/kaz_yos/epi288-validation3

EPI288 CART http://rpubs.com/kaz_yos/epi288-cart

EPI289 HW1 http://rpubs.com/kaz_yos/epi289hw1

EPI289 HW2 http://rpubs.com/kaz_yos/epi289-hw2

EPI289 HW3 http://rpubs.com/kaz_yos/epi289-hw3

EPI289 HW4 http://rpubs.com/kaz_yos/epi289-hw4

EPI289 Conventional regression http://rpubs.com/kaz_yos/epi289-2-1-conventionalreg

EPI289 PS-adjustment http://rpubs.com/kaz_yos/epi289-2-2-ps

EPI289 Standardization and bootstrap http://rpubs.com/kaz_yos/epi289-3-standard

EPI289 IPW http://rpubs.com/kaz_yos/epi289-4-ipw

EPI289 IPW and MSM http://rpubs.com/kaz_yos/epi289-4-ipw-msm

EPI289 IPTCW http://rpubs.com/kaz_yos/epi289-4-iptcw

EPI289 G-estimation http://rpubs.com/kaz_yos/epi289-gest