PyMinim
A simple minimisation algorithm for 1:1 randomisation in trials
Usage
It uses a single class and the only dependency outside of the standard library is Pandas.
First, decide what variables you want to minimise by by creating a dictionary, where the keys are the variable names, and the values are tuples of the categories. For example:
minimisation_vars = {
'sex': ('male', 'female'),
'age': ('<=50', '>50'),
'ethnicity': ('white', 'black', 'asian'),
'smoker': ('no', 'yes')
}
Then you can instantiate the minimiser:
minimiser = Minimiser(minimisation_vars)
From here on, it's easy to randomise patients with:
minimiser.randomise_patient(id, characteristics)
Where id
is a unique ID for the patient and characteristics
is a dict of key:value pairs for the minimisation variables.
For example, if we wanted to simulate randomising 160 patients using the above values, we could do something like this:
for i in range(160):
pt = {}
pt['id'] = i
pt['sex'] = random.choice(('male', 'male', 'male', 'female', 'female')) # 60% male
pt['age'] = random.choice(('>50', '<=50')) # Equal proportions
pt['ethnicity'] = random.choice( # 70% white, 20% asian, 10% black
('white', 'white', 'white', 'white', 'white', 'white', 'white', 'asian', 'asian', 'black'))
pt['smoker'] = random.choice(('no', 'no', 'no', 'yes')) # 75% non-smokers
patients.append(pt)
for patient in patients:
id = patient.pop('id')
minimiser.randomise_patient(id, patient)
We can see the table of patients and their allocated arms:
>>> minimiser.df_patients
sex age ethnicity smoker arm
0 male >50 white no B
1 male >50 white no A
2 female <=50 white no B
3 male >50 white no B
4 female >50 asian yes A
.. ... ... ... ... ..
155 male >50 asian no B
156 male <=50 asian no A
157 female <=50 asian no B
158 female >50 asian no A
159 female <=50 asian yes A
[160 rows x 5 columns]
And we can see how well the system balanced the 2 arms:
>>> minimiser.characteristics_by_arm())
sex age ethnicity smoker
arm
A {'male': 49, 'female': 31} {'>50': 43, '<=50': 37} {'white': 53, 'asian': 18, 'black': 9} {'no': 58, 'yes': 22}
B {'male': 49, 'female': 31} {'>50': 42, '<=50': 38} {'white': 54, 'asian': 17, 'black': 9} {'no': 59, 'yes': 21}
Details
- THIS SYSTEM IS NOT YET FULLY TESTED
- Currently only works for 1:1 randomisation.
- 20% of the time (by default) a patient will be 'truly randomised' rather than minimised.
- First patient will be truly randomised, by default using their ID as a seed to make reproducibility easier (can be disabled)
- When arms are equally balanaced, allocation is random