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kaz_yos

Kazuki Yoshida

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Bayesian Causal Inference 1
Piecewise constant hazard model in Stan
Demystifying Stan, transformed parameters {}, and Jacobians
BUGS Book Measurement Error Example in Stan
Beta Regression in Stan
Count Outcome Models with Stan
Finite Mixture Model with Stan
BIDA: Density Estimation (Finite Mixture Model)
Dirichlet Process Prior
rstanarm feature/survival branch
BIDA in Stan: Piecewise constant hazard Cox
Bayesian Survival Analysis 1: Weibull Model with Stan
rstanarm jm
Bayesian Additive Regression Trees
STEPP
Count data analysis with Stan
Bayesian Thinking Lecture by Jim Albert: Gaussian Model of Height
Ligtning talk at Partners R User Group Meeting
Adaptive LASSO Examples
RStan
R Bootcamp Day 1
R Bootcamp Day 2
Carlisle Anaesthesia. 2017
R Bootcamp (2017 EPI/FACETS Summer Program)
05 regression modeling
04 statistical tools
03 ggplot2: grammar of graphics
tidyverse
01 R and RStudio: getting around
Presentation
LOESS
Residual diagnostics in Cox PH model
Logistic regression and linearity
BST249 Optimizing a Payoff Game by Dynamic Programming
Excluding variables from mice
Dirichlet Process Prior for a Random Probability Measure G
Methods 2011
Coupling from the Past
Sampling Methods (Rejection, MH, and Gibbs)
Bayesian Interpretation of Linear Splines
Transition Matrix
Bayesian Interpretation of LASSO and Ridge Regression
Metropolis-Hasting for Bank data
Metropolis-Hasting sampler exercise
Matching Weights Tutorial
A tutorial accompanying a manuscript and simulation program (https://github.com/kaz-yos/mw).
VarForGmat
GLMM with various R packages
Python in Rmd
Nondifferential misclassification of binary exposure under the null
MI examples
EPI2002Lab2
Very crude interrupted time series
CRAN tableone download log
Multinomial standardized mean difference
Mahalanobis distance
Fisher exact test explained
GoogleScholar
Self-controlled case series examples
Epi Qual 2007 Q1
Poisson Regression in Stan
KU-R3
KU-R2
Splines
Classroom 3-level data analysis in Stan
Three-level nested random intercept model in Stan
KU-R1
Two-level linear model in Stan
marginal.conditional.OLS
Confounder Generation
Multiple logistic regression in Stan
Multiple linear regression with Stan
BIO233 Birth weight example
Hernan Book G-methods examples
Non-collapsibility of logit link
Non-collapsibility of odds ratio
Number of observations
Box-Tidwell Transformation/Test
Poisson regression rate ratio plot
pi calculation
Introduction to tableone
exact_table
20141130a_InteractionExperiment
Hack Ebola
2014-11-21 Model with vaccines
SIR model
BIO 232 Permutation test
Confidence intervals when p-values are bordeline
Formatting data for ggplot2
Different parametrization
More functional approach to R LED
Data structures: RDBMS-like, Long format, Wide format
Data generation for ROC demo
Limit of Agreement (Bland-Altman method)
Titanic
Binomial Confidence Interval
ROC
Fraction of missing information in multiple imputation
group summaries
Plotting group mean responses
igraph demonstration
ggplot2 overlying piece-wise linear model
d3Network demonstration
igraph demonstration
More ggplot2
Handling time data
Mixed effect Cox models using coxme package
lubridate package for date and time management in R
MANOVA etc
Tests for paired proportions
Propensity score using right heart cath dataset
Basic graphics
Accelerated failure time models
Functions used in CRAN packages
rms 4.2 survplot.survfit workaround
glm for generalized linear model
Propensity score using right heart cath dataset (balance check)
Extensive test code for tableone package
CRAN download log for tableone
Use of formula
Anscombe dataset
Converting data
Title
cramVars feature test
tableone: 医学研究で必要な"表1"を作成するRパッケージ
Introduction to tableone, an R package to facilitate creation of Table 1
Extensive test code for tableone package
2014-02-13 useR@HSPH
Test TableOne (merging suggestion from Justin)
開発中のtableoneパッケージの最新版を試す。
開発中のtableoneパッケージの最新版を試す。
tableone CreateCatTable() test (raw code)
tableone CreateCatTable() test
tableone CreateContTable() test (raw code)
tableone CreateContTable() test
Event-free survival, cause-specific hazard, cumulative incidence function in survival analysis
tableone CreateContTable() test
cox.zph to Test the Proportional Hazards Assumption of a Cox Regression
Proportional odds model
Log-linear models for contingency tables
Multiple Imputation Examples
Case-control studies in R
Linear discriminant analysis.
Models for excess zeros using pscl package (Hurdle and zero-inflated regression models) and their interpretations
Critical Data Marathon: Team SAPS Cohort assembly
S3 method version of epiR::epi.tests()
S3 method version of epiR::epi.2by2()
S3 Class and Methods in R
Polynomials and Splines: Head acceleration in motorcycle accidents
Polynomials and Splines: Fractional polynomials example data set
Polynomials and Splines
Generalized Additive Model test run
EPI247 Group Session
Comparison of continuous measurement methods: Bland-Altman plot
ROC after logistic regression
scholar package for GoogleScholar
Models for excess zeros using pscl package
Simple 3D plots in R
Means of distributions (Standard normal vs standard Cauchy)
Propensity score using right heart cath dataset
Applied Longitudinal Analysis: Multilevel Models
SIR models in R
Age-Period-Cohort analysis using Epi package
Competing risk analysisのデモ
Venn diagrams
Faraway Linear Models with R: Collinearity
Modern Epidemiology Chapter 10: Demonstration of p-value functions
Epidemiology: Beyond the Basics: Analysis of Age, Birth Cohort, and Period Effects
Age, Cohort, and Period Effects using Cancer Mortality data in Japan
EPI 288 Lecture 4: Prediction Modeling and Validation (work in progress)
Clinical Prediction Models Chapter 13: Modern Estimation Methods
Cubit spline test run
Use of propensity scores illustrated
Residual plots in linear regression
Principles of Biostatistics Chap 13: Nonparametric Methods
Strange variance covariance matrix Cov(Yi) behavior in nlme
Emulating SAS BY statement in R
survival::survSplit problem with Surv object
Cox regression in R
EPI204 Lab 4 in R
EPI204 Lab 5 in R
95% Confidence interval demonstration
BIO226 Applied Longitudinal Analysis: Marginal Model using Generalized Estimating Equations
Modeling skewed continuous outcome using Gamma family in glm()
Adjustment for multiple testing
EPI204 Lab 2 in R
EPI204 Lab 1 in R
Drawing survival curves in R
BIO 223 Applied Survival Analysis Chapter 8: Parametric Survival Analysis
Overplotting Non-parametric vs Parametric survival models
生存曲線: Non-parametric vs Parametric models
BIO 226: Homework Assignment 3 in R
EPI 204 Homework 3 in R
kaz_yos RPubs もくじ
kaz_yos RPubs Table of Contents
Unified Approach to Ordinal (cumulative) and Polytomous (multinomial) Logistic Regressions using VGAM::vglm
Conditional logistic regression
ggplot2: coloring under empiric density curve using geom_area
regexp test in R
EPI 204 Homework 2 in R
Creating tables, accessing elements of tables, and accessing elements of other objects
coxphにおけるtime-dependent covariatesの使い方
BIO 223 Applied Survival Analysis Chapter 7: Time-varying covariates
pROC test run
BIO 226: Homework 5 in R (Computation parts only)
pROC::roc.test DeLong method possible improvement
pROC and large dataset
Summarizing data by groups in R
Re-installing the same packages in R 3.0.0
Handling of NA in == and is.element()
Basic graphics in R
Kleinbaum: Stratified Cox regression
Kleinbaum: Checking poroportional hazard assupmtion
ggplot2: stat_summary() version 0.9.3.1
BIO 223 Applied Survival Analysis: Checking model fit and poroportional hazard assupmtion
John Snow’s Cholera Map
Preparing data for modeling in R
BIO 226 AUC-MB contrast
Data Manipulation with actual examples
R in Action: Chapter 15 Advanced methods for missing data
BIO 223: Applied Survival Analysis HOMEWORK I in R
cox.zph to Test the Proportional Hazards Assumption of a Cox Regression
Creating permutations and combinations with replacement
Strange variance-covariance matrix in nlme
Reading data in and basic data manipulation in R
Meta-analyses using meta package
BIO 226 Applied Longitudinal Analysis: Introduction to Data Sets
Installing all R Commander plugins
EPI 288 Lecture 5: Classification and Regression Trees (CART)
Assessment of Discrimination in Survival Analysis (C-statistics, etc)
Bayesian Computation with R: Chosing a Beta Prior (page 23)
EPI 288 Lecture 3: Principal Component Analysis
R Color Chart
EPI 288 Lecture 2: Cluster analysis
EPI 271 Propensity Score Lab 3: Use of propensity scores
EPI 271 Propensity Score Lab 2
EPI 271 Lab 1
EPI 288 Lecture 1: Multiple testing
複数のboxplotを一度に作成する
car::recode solution
useR@HSPH
Doing Bayesian Data Analysis: Figure 5.2
Doing Bayesian Data Analysis: Figure 5.1
Doing Bayesian Data Analysis: Figure 3.1
Doing Bayesian Data Analysis: Figures 4.1, 4.2, and 4.3
ggplot2でグラフを部品から組み上げる
A Happy New Year with ggplot2
データ解析のための統計モデリング入門 Chapter 2
ggplot2: Plotting functions
ggplot2: axis manipulation and themes
ggplot2: stat_summary
ggplot2: Toolbox examples in ggplot2 book
ggplot2: layer by layer plotting
Bootstrap (test)
LaplacesDemon package
Dobson An Introduction to GLM: Chapter 12 Bayesian Analysis
Bayesian updating
survey package
Group Sequential Methods
Linearity in logistic regression
Run-length encoding
Epidemiology 202: Homework 3
Polytomous Logistic Regression
Ordinal logistic regression
effects package does not work with logical variables
Function to get odds ratios or rate ratios
Rで臨床研究1: Table 1の検定をする
Logistic regression 1: Prepare data/specify model/read results
Linear regression 2: Model selection
Assessment of performance of prediction models with PredictABEL
Biostatistics 213: Homework 8
Linear regression 1: Prepare data/specify model/read results
Post-test probabilities
My knitr configuration
Repeating univariate logistic regression using R/SAS
Epidemiology 202: Homework 3 Template
BIO 213 Homework 7
Expand tables back to individual-level data
Quantile regression, including median regression
Stepwise model selection
All subset regression with leaps, bestglm, glmulti, and meifly
slidify
Installing slidify
Two-dimentional gaussian surface
Residual analysis in linear regression (abbreviated BIO213 version)
Happy Thanksgiving!!
Residual analysis in linear regression (BIO213 version)
boxplot with arbitrary design with ggplot2
Summary statistics using rpsychi package
dagR: Directed Acyclic Graph with R
Cluster analysis (k-means)
Cross tabulating subgroup means
BIO 213 Regression: Interaction between two categorical variables
PH207x Week 3
PH207x Week 2
Negative Binomial Regression vs Poisson Regression
Poisson regression for rates
EPI 202 HW1
BIO 213 Regression: Interaction between a continuous and categorical variables (effect package)
Code IQ: ログ解析
Code IQ: Rではじめる統計解析 by Tokyo.R
Epidemiology 202: Problem Set 1 Measures of Disease Occurrence and Association
Epidemiology 202: Problem Set 2 Non-Differential Misclassification
PH207x Week 1
Rgraphviz test
BIO 213 Regression: Interaction between a continuous and categorical variables
Categorical Data with R
Using Deducer without GUI
Positive/Negative Predictive Values from Sensitivity, Sepcificity, Prevalence
SAScii test: Import .dat files for SAS using .sas scripts from R
EPI 221 Sep 26
Residual analysis in linear regression
Goodness fit assessment and model comparison
Basic graphing with R
BIO 213 Homework 6
BIO 509 Homework 5
Groupwise comparison for continuous variables
homework5
Exhaustive model selection (test)
BIO 208 Final Exam
Adding smooth curves to scatter plots (test)
Descriptive statistics with R
Merging data
Any idea for creating a new variable from multiple-variable conditions?
BIO 213 Homework 4
BIO 201 Homework 5
BIO 509 Homework 3
BIO 509 Homework 1
BIO 201 Homework 4
BIO 201 Homework 3
Probability functions in R
Reading data into R
BIO232 Homework 1
BIO232 Lab 1
BIO 213 Homework 3
20120921 Introduction to R
ROC曲線とその比較 (in Japanese)
Biostatistics 201: Lab 1
BIO 201: Homework 2
BIO 509 Examples
Links to other pages of mine
EPI 201 Homework 1
Biostatistics 213: Homework 2
BIO 201: Homework 1
Data structures in R (Japanese ver)
Constructing tables with R (Japanese ver)
Kaplan-Meier plot (Japanese ver)
EPI 208 homework2
Homework 1 for EPI 208
BIO 213 homework1
geom_dotplot()
Plotting OR (experimental)
HSPH Materials Translated
subset for a given ggplot2 layer
Getting data from GapMinder.org Revised
USA drug sales data extraction
Getting data from GapMinder.org
Creating multiple xtabs for different row variables with the same row variable
Categorical counterpart of the previous post.
Performing multiple t-tests on different variables between the same two groups
BIO 206 SAS codes translated to R
BIO 208 SAS codes translated to R
HSPH Summer PCE SAS code translated to R
Data manipulation using transform(), within(), or plyr::mutate()
My solution to "My no loops in R hair shirt"
My solution to: http://shape-of-code.coding-guidelines.com/2012/07/27/my-no-loops-in-r-hair-shirt/
metaanalysis (comments in Japanese)
Mantel-Haenszel method OR for stratified data
RDS 286: Case #6 Resource Allocation
RDS 286: Case #5A Utility Assessment
RDS 286: Case #5B Kidney Dialysis and Transplantation
Standard error of mean decreases as sample size gets bigger
BIO 206: Demonstration of central limit theorem
Demonstration of survival curves with different hazard function
EPI 208: Comparison of proportions and odds
RDS 286: Case #3 The Lung Nodule
RDS 286: Case #4 HIV Screening
RDS 286: Chapter 7 of Hunink et all 2001.
RDS 286: Excercise 3.1
RDS 286: Case #2 Giant Cell Arteritis
RDS 286: Case 1: Clinical Case: Young man with Hodgkin’s disease
EPI 208: Rate and Risk
Another demo from Rothman's
Effect measures
Demonstration of equations in Epidemiology: An Introduction