CASIdata

CASIdata provides the datasets from Efron & Hastie, Computer Age Statistical Inference in an accessible R format for those who want to use them for teaching, study or to try to reproduce or extend analyses from the book. They were downloaded from Trevor Hastie’s web site, http://hastie.su.domains/CASI_files/DATA/, but quite a few files were messy and required some processing to make into R datasets.

Even so, some of the datasets may require data cleaning, renaming of variables, re-shaping or other tidying steps to be useful for analysis. But that’s part of learning.

Installation

This package is not yet on CRAN. You can install it from this GitHub repo:

remotes::install.github("friendly/CASIdata")

Datasets included here

Loading package: CASIdata

Dataset	Title
DTI	DTI Brain Imaging Data
als	ALS Data
baseball	Baseball Batting Averages
bivnorm	Bivariate Normal Data
butterfly	Butterfly Species Data
cellinfusion	Cell Infusion Data
cholesterol	Cholesterol Data
diabetes	Diabetes Data
doseresponse	Dose Response Data
galaxy	Galaxy Data
haplotype	Human Ancestry Haplotype Data
insurance	Insurance Life Table Data
leukemia_small	Leukemia Gene Expression Data (Small)
ncog	NCOG Head and Neck Cancer Data
nodes	Lymph Nodes Cancer Data
pediatric	Pediatric Cancer Survival Data
police	Police Racial Bias Data
prostz	Prostate Cancer Z-values
student_score	Student Score Data
supernova	Type Ia Supernova Data
vasoconstriction	Vasoconstriction Data

Missing Datasets

The following dataset appears in data-raw/CASI-save.R but is not (yet) included in the package:

Dataset	Reason
SPAM	Variable names need cleanup; requires mapping from UCI Spambase documentation

See data-raw/missing-datasets.md for details on resolving this.

External Datasets (Not Included)

These large datasets are referenced in the book but not included in the package due to size constraints. They can be downloaded directly from the sources listed below.

CASI datasets (too large for CRAN)

• protein_kernel: 1708 x 1708 inner-product (kernel) matrix for human proteins (Section 19.6). Computed using a string kernel on bag-of-4-grams amino acid representations.
  • Source: https://hastie.su.domains/CASI_files/DATA/protein_kernel.txt
  • Load in R: protein_kernel <- matrix(scan("http://hastie.su.domains/CASI_files/DATA/protein_kernel.txt", what=0), 1708, 1708)
• protein_label: Response labels (-1/+1) for the 1708 proteins (45 positives, 1663 negatives).
  • Source: https://hastie.su.domains/CASI_files/DATA/protein_label.txt
  • Load in R: protein_label <- scan("http://hastie.su.domains/CASI_files/DATA/protein_label.txt", what=0)
• prostmat: 6033 x 102 gene expression matrix comparing 50 controls vs 52 prostate cancer patients (Section 3.3).
  • Source: https://hastie.su.domains/CASI_files/DATA/prostmat.csv
  • Load in R: prostmat <- read.csv("http://hastie.su.domains/CASI_files/DATA/prostmat.csv")
  • Note: Column names need cleanup (see data-raw/missing-datasets.md for renaming code)
• leukemia_big: 7128 x 72 gene expression matrix (10MB). A larger version of leukemia_small.
  • Source: https://hastie.su.domains/CASI_files/DATA/leukemia_big.csv
  • Load in R: leukemia_big <- read.csv("http://hastie.su.domains/CASI_files/DATA/leukemia_big.csv")

Image datasets (hosted externally)

• CIFAR-100: 100 image classes, 600 images each (32x32x3 color). Used in Chapter 18.
  • Source: https://www.cs.toronto.edu/~kriz/cifar.html
• MNIST: Handwritten digit database, 60K training + 10K test images (28x28 grayscale). Used in Chapter 18.
  • Source: http://yann.lecun.com/exdb/mnist/

Variable Renaming

Some datasets had variables renamed for clarity:

Dataset	Original	Renamed
butterfly	x, y	k, count
police	X2.411	z
prostz	X1.47236666651029	z
galaxy	Reshaped from wide to long format with mag, red, freq

Example

No examples yet.

library(CASIdata)
## basic example code