Aspirin: Effects of Aspirin on Cancer Rates

In abd: The Analysis of Biological Data

Description

Frequency of cancer in 39,876 women taking and not taking aspirin.

Usage

data(Aspirin)

Format

A data frame with 4 observations on the following 3 variables.

treatment

a factor with levels Aspirin and Placebo

cancer

a factor with levels no and yes

count

a numeric vector

Source

Cook, N.R., I. Lee, J.M. Gaziano, D. Gordon, P.M. Ridker, J.E. Manson, C.H. Hennekens, and J.E. Buring. 2005. Low-dose aspirin in the primary prevention of cancer. Journal of the American Medical Association 294: 47-55.

References

http://jama.ama-assn.org/cgi/content/abstract/294/1/47

Examples

demo(sec9.2)

Example output

Loading required package: nlme
Loading required package: lattice
Loading required package: grid
Loading required package: mosaic
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:nlme':

    collapse

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: ggformula
Loading required package: ggplot2
Loading required package: ggstance

Attaching package: 'ggstance'

The following objects are masked from 'package:ggplot2':

    GeomErrorbarh, geom_errorbarh


New to ggformula?  Try the tutorials: 
	learnr::run_tutorial("introduction", package = "ggformula")
	learnr::run_tutorial("refining", package = "ggformula")
Loading required package: mosaicData
Loading required package: Matrix

The 'mosaic' package masks several functions from core packages in order to add 
additional features.  The original behavior of these functions should not be affected by this.

Note: If you use the Matrix package, be sure to load it BEFORE loading mosaic.

Attaching package: 'mosaic'

The following object is masked from 'package:Matrix':

    mean

The following object is masked from 'package:ggplot2':

    stat

The following objects are masked from 'package:dplyr':

    count, do, tally

The following objects are masked from 'package:stats':

    IQR, binom.test, cor, cor.test, cov, fivenum, median, prop.test,
    quantile, sd, t.test, var

The following objects are masked from 'package:base':

    max, mean, min, prod, range, sample, sum



	demo(sec9.2)
	---- ~~~~~~

> str(Aspirin)
'data.frame':	39876 obs. of  2 variables:
 $ treatment: Factor w/ 2 levels "Aspirin","Placebo": 1 1 1 1 1 1 1 1 1 1 ...
 $ cancer   : Factor w/ 2 levels "no","yes": 2 2 2 2 2 2 2 2 2 2 ...

> # Plot 2 X 2 Contingency tables
> plot( ~ treatment + cancer, data = Aspirin)

> plot(table(Aspirin), main = "")

> # Calculate odds
> (Pr.asp <- 18496 / (18496 + 1438))
[1] 0.9278619

> (Odds.asp <- Pr.asp / (1 - Pr.asp))
[1] 12.86231

> (Pr.no.asp <- 18515 / (18515 + 1427))
[1] 0.9284425

> (Odds.no.asp <- Pr.no.asp / (1 - Pr.no.asp))
[1] 12.97477

> (Odds <- Odds.asp / Odds.no.asp)
[1] 0.9913321

> ln.Odds <- log(Odds)

> (SE.Odds <- sqrt(sum(1/table(Aspirin))))
[1] 0.03878475

> Z <- 1.96

> (CI.low <- ln.Odds - Z * SE.Odds)
[1] -0.08472376

> (CI.high <- ln.Odds + Z * SE.Odds)
[1] 0.06731248

> exp(CI.low)
[1] 0.918766

> exp(CI.high)
[1] 1.06963

> # Using oddsRatio() from the mosaic package
> # First reformat the data so that "No cancer" is in column 1
> # and "Aspirin" is in row 2.
> x <- matrix(c(18515, 18496, 1427, 1438), nrow = 2)

> x
      [,1] [,2]
[1,] 18515 1427
[2,] 18496 1438

> oddsRatio(x)
[1] 0.9913321

abd documentation built on May 2, 2019, 4:46 p.m.