# episheet - My first CRAN package!

My first R package (or rather function..) is on CRAN.

At ICPE, a recent pharmacoepidemiology conference I attended in Dublin, I went to a talk by Ken Rothman, one of the leading epidemiologists in the field of pharmacoepi. He talked about the p-value, it’s frequent mis-use, and a method of plotting the p-value function that visualises the relationship of your data to a range of potential hypotheses. Essentially, this lets you see the confidence interval.

As Rothman has stated on twitter… I’ve turned it into an R package!

P-value function plot from episheet https://t.co/gJ3aiElQh0 is now an app https://t.co/K0uILXcrCT & R CRAN package (https://t.co/klzLf2JHFX)

— Ken Rothman (@ken_rothman) September 7, 2016

## The package

Rothman already made an excel sheet to plot the function. I simply ported the equations in this function to R. Rothman was kind enough to provide feedback on the package, and I framed it as a campanion to the the original excel file. Below is a table of the current status of the package.

Status | Badge |
---|---|

Link to CRAN entry | http://cran.r-project.org/package=episheet |

Unix build status of last commit | |

Current version on CRAN | |

Total downloads from CRAN |

## A p-value

For the p-value plot to make sense, the only important thing to remember is that a p-value is simply a quantitive expression of the fit of a particular set of data to a specified hypothesis. So, rather than just testing the null, we could also produce a p-value for a range of hypothesised effect sizes.

## What it does

Currently the only function in the package is `pvalueplot`

, to explain how it’s useful, it’s easiest to
give an example Rothman gives in the following comment in the lancet:

Rothman KJ, Johnson ES, Sugano DSIs flutamide effective in patients with bilateral orchiectomy?Lancet(1999) 3;353(9159):1184PMID: 10210003

In summary, *Eisenberger et al* reported an Odds Ratio (OR) of 0·87 (95% CI 0·70, 1·10) in their trial, which
they stated *“does not result in a clinically meaningful improvement in survival”*. An earlier meta-analysis, of the ten
trials that preceded *Eisenberger et al*, found an OR of 0·88 (95% CI 0·76–1·02).

The plot below shows the p-value plot of the two ORs.

This figure makes it painfully obvious that the conclusion reached was probably due to a low power and small effect size. Of course in this case the meta-analysis will be the best source of evidence, but it’s still interesting to see the p-value functions of the current study, and the previous literature. I assume that properly thinking about the effect estimate and CI’s will lead to the same conclusion as plotting the p-value function, but the plot is still a great tool for putting what you are doing in your head down on paper.

## How

```
# Install and load package from CRAN
install.packages("episheet")
load(episheet)
# Make the plot
episheet::pvalueplot(
est1.ll = 0.70,
est1.ul = 1.10,
est2.ll = 0.76,
est2.ul = 1.02,
label1 = "Eisenberger et al",
label2 = "Previous studies",
xlabel = "Odds Ratio"
)
```