import pandas as pd
import dabest
from palmerpenguins import load_penguins04. DABEST Introduction
DABEST is a package that performs estimation statistics available on Python and R. With Jupyter Notebook you can try DABEST-Python.
penguins = load_penguins()
# if you had trouble installing the package, you can also read in the data from the csv file by uncommenting the line below.
# penguins = pd.read_csv("penguins.csv")penguins.head()| species | island | bill_length_mm | bill_depth_mm | flipper_length_mm | body_mass_g | sex | year | |
|---|---|---|---|---|---|---|---|---|
| 0 | Adelie | Torgersen | 39.1 | 18.7 | 181.0 | 3750.0 | male | 2007 |
| 1 | Adelie | Torgersen | 39.5 | 17.4 | 186.0 | 3800.0 | female | 2007 |
| 2 | Adelie | Torgersen | 40.3 | 18.0 | 195.0 | 3250.0 | female | 2007 |
| 3 | Adelie | Torgersen | NaN | NaN | NaN | NaN | NaN | 2007 |
| 4 | Adelie | Torgersen | 36.7 | 19.3 | 193.0 | 3450.0 | female | 2007 |
penguins_analyse = dabest.load(data=penguins,
x="species", y="bill_length_mm",
idx=("Adelie", "Chinstrap", "Gentoo")
)penguins_analyse.mean_diffDABEST v2023.02.14
==================
Good evening!
The current time is Thu Oct 19 12:57:27 2023.
The unpaired mean difference between Adelie and Chinstrap is 10.0 [95%CI 9.14, 10.9].
The p-value of the two-sided permutation t-test is 0.0, calculated for legacy purposes only.
The unpaired mean difference between Adelie and Gentoo is 8.71 [95%CI 8.03, 9.41].
The p-value of the two-sided permutation t-test is 0.0, calculated for legacy purposes only.
5000 bootstrap samples were taken; the confidence interval is bias-corrected and accelerated.
Any p-value reported is the probability of observing theeffect size (or greater),
assuming the null hypothesis ofzero difference is true.
For each p-value, 5000 reshuffles of the control and test labels were performed.
To get the results of all valid statistical tests, use `.mean_diff.statistical_tests`penguins_analyse.mean_diff.plot(raw_marker_size = 4, fig_size=(6, 6), swarm_label="Bill length (mm)")/Applications/anaconda3/envs/dabest/lib/python3.9/site-packages/dabest/plotter.py:473: FutureWarning: Passing `palette` without assigning `hue` is deprecated.
rawdata_plot = sns.swarmplot(data=plot_data, x=xvar, y=yvar,
/Applications/anaconda3/envs/dabest/lib/python3.9/site-packages/dabest/plotter.py:563: UserWarning: FixedFormatter should only be used together with FixedLocator
rawdata_axes.set_xticklabels(ticks_with_counts)
penguins.dropna().melt(id_vars="species", value_vars="metric").head()| species | variable | value | |
|---|---|---|---|
| 0 | Adelie | year | 2007 |
| 1 | Adelie | year | 2007 |
| 2 | Adelie | year | 2007 |
| 3 | Adelie | year | 2007 |
| 4 | Adelie | year | 2007 |