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A Python library for p-curve estimation

Project description

pypcurve: A Python Implementation of Simonsohn, Simmons and Nelson's 'p-curve'

Installation

You can install pypcurve with pip:

pip install pypcurve

Using pypcurve

1. Compulsory Reading

First and foremost, read the user guide to the p-curve. It is crucial that users understand what p-curve can and cannot do, that they know which statistical results to select, and that they properly prepare the disclosure table.

2. Formatting the statistical results

pypcurve only requires a list of statistical results, stored in a list (or an array). Similar to the p-curve app, pypcurve accepts the following formats of statistical tests:

  • F(1, 302)=3.273
  • t(103)=4.23
  • r(76)=.42
  • z=1.98
  • chi2(1)=7.1

In addition, pypcurve will accept raw p-values:

  • p = .0023

This is not recommended though: p-values are often weirdly rounded, so enter the statistical result instead if it is reported in the paper.

3. Using pypcurve

A. Initialization

For this example, I will assume that your tests have been properly formatted, and stored in a column called "Tests" of a .csv file.

from pypcurve import PCurve
import pandas as pd
df = pd.read_csv("mydata.csv")
pc = PCurve(df.Tests)

If all your tests are properly formatted, there will be no error, and pcurve will be initialized properly.

B. Printing the p-curve output

Next, you can print the summary of the p-curve, as you would see it using the web-app:

pc.summary()

This will output the p-curve plot, as well as the table summarizing the binomial and Stouffer tests of the p-curve analysis. You can get the plot alone, or the table alone, using the methods pc.plot_pcurve() and pc.pcurve_analysis_summary().

C. Power Estimation

You can use pycurve to estimate the power of the design that generated the statistical tests:

  • pc.estimate_power() will return the power estimate, and the (lower, upper) bounds of 90% confidence interval.
  • pc.plot_power_estimate() will plot the power estimate (as the webapp does).

D. Accessing the results of the p-curve analysis

You can directly access the results of the p-curve analysis using three methods:

  • pc.get_stouffer_tests() will recover the Z and p-values of the Stouffer tests
  • pc.get_binomial_tests() will recover the p-values of the binomial tests
  • pc.get_results_entered() will recover the statistical results entered in the p-curve, and the pp-values and z scores associated with the different alternatives to which they are compared.

You can also directly check if the p-curve passes the cutoff for evidential value, and the cutoff for inadequate evidence (as defined in Better P-Curve), using the properties pc.has_evidential_value and pc.has_inadequate_evidence

Version History

The app is still in beta, so please take care when interpreting the results. I have tested pypcurve against the p-curve app using multiple examples: There are occasional minor deviations between the two, because of the way R (vs. Python) compute the non-central F distribution.

Beta

0.1.0

First beta release.

Project details


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