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Stats Book
Online Statistics Book
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Authors
Authors
Dedication
Introduction
Conventions
Abbreviations
Citation
Software
Installation
RJAH statistics course
Jupyter Notebook
Packages
Transferring Packages to New R Installation (Mac OSX)
JGR on Mac OSX from R 3.4
Data Sets
Functions
Data and Graphics
Data into R
Enter Manually
Copy and Paste
Import Spreadsheet
Open RDA Files
Importing Data from SPSS
Data out of R
Graphics
Plot builder
Export Plots to MS PowerPoint and Word
Citating R, JGR and Packages
Help
Data and Plots
Data Types
Descriptive Statistics
Distribution of Data
Normal Distribution
Other Distributions
Confidence Intervals
Fonts, Themes and Colours
Grammar of Graphics
Plots
Bar Chart
Pie Chart
Strip Plot
Swarm Plot
Box Plot
Violin Plot
Histogram
Scatter Plot
Line Plot
Sunflower Plot
Bag Plot
Regression Plot
Bland-Altman Plot
Funnel Plot
Forest Plot
Radar Plot
Mosaic Plot
ROC Plot
Survival Plot
Time Series
Correlation Plot
Hierarchical Edge Bundling Plot
Circos Plots
Circos Plots – RCircos
Circos Plots – circlize
Circos Plots – BioCircos
Decision Tree Plot
Exploratory Plot
Interactive Plot
Epidemiology
Screening
Prevalence & Incidence
Risks and Odds Ratio
Risk Example
Exposure No Effect on Incidence
Exposure Increases Incidence
Exposure Decreases Incidence
Probability
Probability and Chance
Growth Curves
Percentiles and Quantiles
Z and T scores
Statistical Tests
Hypothesis
P value
Tests for Normality
Parametric Tests
Non Parametric Tests
Which Statistical Test?
Power Analysis
Transformation of Data
Sensitivity / Specificity
Errors
Repeatability and Reproducibility
Bias and Accuracy
Multiple Observers
Interclass Correlation Coefficient
Kappa Test
Curve Fitting
Regression Coefficient
Correlation Coefficient
Interpolation
Other Models
Linear Transformation
Principle Component Analysis
Linear Discriminant Analysis
One-Hot Encoding of Categorical Variables
Studies and Trials
Observational Studies
Randomised Controlled Trial
Meta-Analysis
Hierarchy of Evidence
Survival Analysis
Life Table Survival Analysis
Kaplan-Meier Survival Analysis
Survival Analysis in R / JGR
Cox Proportional Hazards
DNA Analysis
Lady’s Slipper Orchid
IDH2 gene
Genomics – Circos Plot
Selected Papers
P values & Confidence Intervals, Their Use and Abuse
Friday 13th
Easter
Equation of Time
Bird Migration
Advanced Concepts
Questions & Answers
References
Questions Probability
Questions Epidemiology
Questions Statistical Tests
Dedication
To Karen & Oliver – PC
To Elizabeth & Jonathan – MO
September 2015